JASPAR 2024: 20th anniversary of the open-access database of transcription factor binding profiles.
paper
Cited
Public
- Authors
- Rauluseviciute, Ieva; Riudavets-Puig, Rafael; Blanc-Mathieu, Romain; Castro-Mondragon, Jaime A; Ferenc, Katalin; Kumar, Vipin; Lemma, Roza Berhanu; Lucas, Jérémy; Chèneby, Jeanne; Baranasic, Damir; Khan, Aziz; Fornes, Oriol; Gundersen, Sveinung; Johansen, Morten; Hovig, Eivind; Lenhard, Boris; Sandelin, Albin; Wasserman, Wyeth W; Parcy, François; Mathelier, Anthony
- Year
- 2024
- Journal
- Nucleic acids research
- PMID
- 37962376
- DOI
- 10.1093/nar/gkad1059
- PMCID
- PMC10767809
JASPAR (https://jaspar.elixir.no/) is a widely-used open-access database presenting manually curated high-quality and non-redundant DNA-binding profiles for transcription factors (TFs) across taxa. In this 10th release and 20th-anniversary update, the CORE collection has expanded with 329 new profiles. We updated three existing profiles and provided orthogonal support for 72 profiles from the previous release's UNVALIDATED collection. Altogether, the JASPAR 2024 update provides a 20% increase in CORE profiles from the previous release. A trimming algorithm enhanced profiles by removing low information content flanking base pairs, which were likely uninformative (within the capacity of the PFM models) for TFBS predictions and modelling TF-DNA interactions. This release includes enhanced metadata, featuring a refined classification for plant TFs' structural DNA-binding domains. The new JASPAR collections prompt updates to the genomic tracks of predicted TFΒ binding sites (TFBSs) in 8 organisms, with human and mouse tracks available as native tracks in the UCSC Genome browser. All data are available through the JASPAR web interface and programmatically through its API and the updated Bioconductor and pyJASPAR packages. Finally, a new TFBS extraction tool enables users to retrieve predicted JASPAR TFBSs intersecting their genomic regions of interest.
Overview of the growth of the number of profiles in JASPAR CORE collection across releases and taxons.
LLM interpretation
This is a stacked bar chart showing the growth of the number of profiles in the JASPAR CORE collection from 2004 to 2024. The x-axis represents the year of release, and the y-axis represents the number of profiles, which increases steadily over time to nearly 2,500. The bars are color-coded by taxon, with "Vertebrates" (purple) and "Plants" (green) constituting the largest proportions of the growth.
TF binding profile trimming. (A, B) Examples of trimmed PFMs for FOXA1 (A) and Atoh7 (B) TFs with the logos of the original PFMs at the top and the logos of the trimmed PFMs at the bottom. (C) The number of trimmed positions varied from 1 to 19 for PFMs originating from JASPAR 2022. (D) The distribution of Gini coefficients computed on the IC of each position in the original (green) and trimmed (purple) PFMs from JASPAR 2022 exhibits a concentration of informative positions in the updated PFMs.
LLM interpretation
This figure illustrates the process and results of TF binding profile trimming. Panels A and B show sequence logos comparing original and trimmed Position Frequency Matrices (PFMs) for FOXA1 and Atoh7, where the trimmed versions remove low-information flanking positions. Panel C is a histogram showing the number of trimmed positions for JASPAR 2022 motifs, ranging from 1 to 19. Panel D is a density plot comparing Gini coefficients of information content, showing a shift toward lower values for trimmed PFMs (purple) compared to original PFMs (green).
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| Citation | PMID | DOI | Status |
|---|---|---|---|
| Auslander N. , GussowA.B., KooninE.V. Incorporating machine learning into established bioinformatics frameworks. Int. J. Mol. Sci.2021; 22:2903.33809353 10.3390/ijms22062903PMC8000113 | β | β | β |
| Avsec Ε½. , WeilertM., ShrikumarA., KruegerS., AlexandariA., DalalK., FropfR., McAnanyC., GagneurJ., KundajeA.et al. Base-resolution models of transcription-factor binding reveal soft motif syntax. Nat. Genet.2021; 53:354β366.33603233 10.1038/s41588-021-00782-6PMC8812996 | β | β | β |
| Bartlett A. , OβMalleyR.C., HuangS.-S.C., GalliM., NeryJ.R., GallavottiA., EckerJ.R. Mapping genome-wide transcription-factor binding sites using DAP-seq. Nat. Protoc.2017; 12:1659β1672.28726847 10.1038/nprot.2017.055PMC5576341 | β | β | β |
| Berger M.F. , BulykM.L. Universal protein-binding microarrays for the comprehensive characterization of the DNA-binding specificities of transcription factors. Nat. Protoc.2009; 4:393β411.19265799 10.1038/nprot.2008.195PMC2908410 | β | β | β |
| Blanc-Mathieu R. , DumasR., TurchiL., LucasJ., ParcyF. Plant-TFClass: a structural classification for plant transcription factors. Trends Plant Sci.2023; 10.1016/j.tplants.2023.06.023.37482504 | β | β | β |
| Brand A. , AllenL., AltmanM., HlavaM., ScottJ. Beyond authorship: attribution, contribution, collaboration, and credit. Learn. Publ.2015; 28:151β155. | β | β | β |
| Brennan K.J. , WeilertM., KruegerS., PampariA., LiuH.-Y., YangA.W.H., MorrisonJ.A., HughesT.R., RushlowC.A., KundajeA.et al. Chromatin accessibility in the Drosophila embryo is determined by transcription factor pioneering and enhancer activation. Dev. Cell. 2023; 58:1898β1916.37557175 10.1016/j.devcel.2023.07.007PMC10592203 | β | β | β |
| Castro-Mondragon J.A. , JaegerS., ThieffryD., Thomas-ChollierM., van HeldenJ. RSAT matrix-clustering: dynamic exploration and redundancy reduction of transcription factor binding motif collections. Nucleic Acids Res.2017; 45:e119.28591841 10.1093/nar/gkx314PMC5737723 | β | β | β |
| Castro-Mondragon J.A. , Riudavets-PuigR., RauluseviciuteI., LemmaR.B., TurchiL., Blanc-MathieuR., LucasJ., BoddieP., KhanA., Manosalva PΓ©rezN.et al. JASPAR 2022: the 9th release of the open-access database of transcription factor binding profiles. Nucleic Acids Res.2022; 50:D165βD173.34850907 10.1093/nar/gkab1113PMC8728201 | β | β | β |
| Fornes O. , Castro-MondragonJ.A., KhanA., van der LeeR., ZhangX., RichmondP.A., ModiB.P., CorreardS., GheorgheM., BaranaΕ‘iΔD.et al. JASPAR 2020: update of the open-access database of transcription factor binding profiles. Nucleic Acids Res.2020; 48:D87βD92.31701148 10.1093/nar/gkz1001PMC7145627 | β | β | β |
| Fornes O. , GheorgheM., RichmondP.A., ArenillasD.J., WassermanW.W., MathelierA. MANTA2, update of the Mongo database for the analysis of transcription factor binding site alterations. Sci. Data. 2018; 5:180141.30040077 10.1038/sdata.2018.141PMC6057437 | β | β | β |
| Fu Y. , LiuZ., LouS., BedfordJ., MuX.J., YipK.Y., KhuranaE., GersteinM. FunSeq2: a framework for prioritizing noncoding regulatory variants in cancer. Genome Biol.2014; 15:480.25273974 10.1186/s13059-014-0480-5PMC4203974 | β | β | β |
| Fuxman Bass J.I. , PonsC., KozlowskiL., Reece-HoyesJ.S., ShresthaS., HoldorfA.D., MoriA., MyersC.L., WalhoutA.J. A gene-centered C. elegans protein-DNA interaction network provides a framework for functional predictions. Mol. Syst. Biol.2016; 12:884.27777270 10.15252/msb.20167131PMC5081483 | β | β | β |
| Gramates L.S. , AgapiteJ., AttrillH., CalviB.R., CrosbyM.A., Dos SantosG., GoodmanJ.L., Goutte-GattatD., JenkinsV.K., KaufmanT.et al. FlyBase: a guided tour of highlighted features. Genetics. 2022; 220:iyac035.35266522 10.1093/genetics/iyac035PMC8982030 | β | β | β |
| Grau J. , SchmidtF., SchulzM.H. Widespread effects of DNA methylation and intra-motif dependencies revealed by novel transcription factor binding models. Nucleic Acids Res.2023; 51:e95.37650641 10.1093/nar/gkad693PMC10570048 | β | β | β |
| Hammal F. , de LangenP., BergonA., LopezF., BallesterB. ReMap 2022: a database of Human, Mouse, Drosophila and Arabidopsis regulatory regions from an integrative analysis of DNA-binding sequencing experiments. Nucleic Acids Res.2022; 50:D316βD325.34751401 10.1093/nar/gkab996PMC8728178 | β | β | β |
| Isakova A. , GrouxR., ImbeaultM., RainerP., AlpernD., DaineseR., AmbrosiniG., TronoD., BucherP., DeplanckeB. SMiLE-seq identifies binding motifs of single and dimeric transcription factors. Nat. Methods. 2017; 14:316β322.28092692 10.1038/nmeth.4143 | β | β | β |
| Johnson D.S. , MortazaviA., MyersR.M., WoldB. Genome-wide mapping of in vivo protein-DNA interactions. Science. 2007; 316:1497β1502.17540862 10.1126/science.1141319 | β | β | β |
| Khan A. , FornesO., StiglianiA., GheorgheM., Castro-MondragonJ.A., van der LeeR., BessyA., ChΓ¨nebyJ., KulkarniS.R., TanG.et al. JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework. Nucleic Acids Res.2018; 46:D260βD266.29140473 10.1093/nar/gkx1126PMC5753243 | β | β | β |
| Khan A. , MathelierA. JASPAR RESTful API: accessing JASPAR data from any programming language. Bioinformatics. 2018; 34:1612β1614.29253085 10.1093/bioinformatics/btx804 | β | β | β |
| Khan A. pyJASPAR: a Pythonic interface to JASPAR transcription factor motifs. 2021; https://github.com/asntech/pyjaspar/tree/v2.0.0. | β | β | β |
| Kolmykov S. , YevshinI., KulyashovM., SharipovR., KondrakhinY., MakeevV.J., KulakovskiyI.V., KelA., KolpakovF. GTRD: an integrated view of transcription regulation. Nucleic Acids Res.2021; 49:D104βD111.33231677 10.1093/nar/gkaa1057PMC7778956 | β | β | β |
| Kshirsagar M. , YuanH., FerresJ.L., LeslieC. BindVAE: dirichlet variational autoencoders for de novo motif discovery from accessible chromatin. Genome Biol.2022; 23:174.35971180 10.1186/s13059-022-02723-wPMC9380350 | β | β | β |
| Kulakovskiy I.V. , VorontsovI.E., YevshinI.S., SobolevaA.V., KasianovA.S., AshoorH., Ba-AlawiW., BajicV.B., MedvedevaY.A., KolpakovF.A.et al. HOCOMOCO: expansion and enhancement of the collection of transcription factor binding sites models. Nucleic Acids Res.2016; 44:D116βD125.26586801 10.1093/nar/gkv1249PMC4702883 | β | β | β |
| Lai W.K.M. , MarianiL., RothschildG., SmithE.R., VentersB.J., BlandaT.R., KuntalaP.K., BocklundK., MairoseJ., DweikatS.N.et al. A ChIP-exo screen of 887 Protein Capture Reagents Program transcription factor antibodies in human cells. Genome Res.2021; 31:1663β1679.34426512 10.1101/gr.275472.121PMC8415381 | β | β | β |
| Lambert S.A. , JolmaA., CampitelliL.F., DasP.K., YinY., AlbuM., ChenX., TaipaleJ., HughesT.R., WeirauchM.T. The Human Transcription Factors. Cell. 2018; 172:650β665.29425488 10.1016/j.cell.2018.01.029 | β | β | β |
| Lambert S.A. , YangA.W.H., SasseA., CowleyG., AlbuM., CaddickM.X., MorrisQ.D., WeirauchM.T., HughesT.R. Similarity regression predicts evolution of transcription factor sequence specificity. Nat. Genet.2019; 51:981β989.31133749 10.1038/s41588-019-0411-1 | β | β | β |
| Lenhard B. , WassermanW.W. TFBS: computational framework for transcription factor binding site analysis. Bioinformatics. 2002; 18:1135β1136.12176838 10.1093/bioinformatics/18.8.1135 | β | β | β |
| Lobentanzer S. , AloyP., BaumbachJ., BoharB., CareyV.J., CharoentongP., DanhauserK., DoΔanT., DreoJ., DunhamI.et al. Democratizing knowledge representation with BioCypher. Nat. Biotechnol.2023; 41:1056β1059.37337100 10.1038/s41587-023-01848-y | β | β | β |
| Longo D.L. , DrazenJ.M. Data sharing. N. Engl. J. Med.2016; 374:276β277.26789876 10.1056/NEJMe1516564 | β | β | β |
| Lovering R.C. , GaudetP., AcencioM.L., IgnatchenkoA., JolmaA., FornesO., KuiperM., KulakovskiyI.V., LΓ¦greidA., MartinM.J.et al. A GO catalogue of human DNA-binding transcription factors. Biochim. Biophys. Acta Gene Regul. Mech.2021; 1864:194765.34673265 10.1016/j.bbagrm.2021.194765 | β | β | β |
| Maslova A. , RamirezR.N., MaK., SchmutzH., WangC., FoxC., NgB., BenoistC., MostafaviS.Immunological Genome Project Deep learning of immune cell differentiation. Proc. Natl. Acad. Sci. U.S.A.2020; 117:25655β25666.32978299 10.1073/pnas.2011795117PMC7568267 | β | β | β |
| Mathelier A. , FornesO., ArenillasD.J., ChenC.-Y., DenayG., LeeJ., ShiW., ShyrC., TanG., Worsley-HuntR.et al. JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles. Nucleic Acids Res.2016; 44:D110βD115.26531826 10.1093/nar/gkv1176PMC4702842 | β | β | β |
| Mathelier A. , WassermanW.W. The next generation of transcription factor binding site prediction. PLoS Comput. Biol.2013; 9:e1003214.24039567 10.1371/journal.pcbi.1003214PMC3764009 | β | β | β |
| Mathelier A. , ZhaoX., ZhangA.W., ParcyF., Worsley-HuntR., ArenillasD.J., BuchmanS., ChenC.-Y., ChouA., IenasescuH.et al. JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles. Nucleic Acids Res.2014; 42:D142βD147.24194598 10.1093/nar/gkt997PMC3965086 | β | β | β |
| Muir P. , LiS., LouS., WangD., SpakowiczD.J., SalichosL., ZhangJ., WeinstockG.M., IsaacsF., RozowskyJ.et al. The real cost of sequencing: scaling computation to keep pace with data generation. Genome Biol.2016; 17:53.27009100 10.1186/s13059-016-0917-0PMC4806511 | β | β | β |
| Navarro Gonzalez J. , ZweigA.S., SpeirM.L., SchmelterD., RosenbloomK.R., RaneyB.J., PowellC.C., NassarL.R., MauldingN.D., LeeC.M.et al. The UCSC Genome Browser database: 2021 update. Nucleic Acids Res.2021; 49:D1046βD1057.33221922 10.1093/nar/gkaa1070PMC7779060 | β | β | β |
| Novakovsky G. , DexterN., LibbrechtM.W., WassermanW.W., MostafaviS. Obtaining genetics insights from deep learning via explainable artificial intelligence. Nat. Rev. Genet.2023; 24:125β137.36192604 10.1038/s41576-022-00532-2 | β | β | β |
| Novakovsky G. , FornesO., SaraswatM., MostafaviS., WassermanW.W. ExplaiNN: interpretable and transparent neural networks for genomics. Genome Biol.2023; 24:154.37370113 10.1186/s13059-023-02985-yPMC10303849 | β | β | β |
| Pepke S. , WoldB., MortazaviA. Computation for ChIP-seq and RNA-seq studies. Nat. Methods. 2009; 6:S22βS32.19844228 10.1038/nmeth.1371PMC4121056 | β | β | β |
| Phuycharoen M. , ZarrinehP., BridouxL., AminS., LosaM., ChenK., BobolaN., RattrayM. Uncovering tissue-specific binding features from differential deep learning. Nucleic Acids Res.2020; 48:e27.31974574 10.1093/nar/gkaa009PMC7049686 | β | β | β |
| Quang D. , XieX. DanQ: a hybrid convolutional and recurrent deep neural network for quantifying the function of DNA sequences. Nucleic Acids Res.2016; 44:e107.27084946 10.1093/nar/gkw226PMC4914104 | β | β | β |
| Reid J.E. , EvansK.J., DyerN., WernischL., OttS. Variable structure motifs for transcription factor binding sites. BMC Genomics. 2010; 11:30.20074339 10.1186/1471-2164-11-30PMC2824720 | β | β | β |
| Reuter J.A. , SpacekD.V., SnyderM.P. High-throughput sequencing technologies. Mol. Cell. 2015; 58:586β597.26000844 10.1016/j.molcel.2015.05.004PMC4494749 | β | β | β |
| Roulet E. , BussoS., CamargoA.A., SimpsonA.J.G., MermodN., BucherP. High-throughput SELEX SAGE method for quantitative modeling of transcription-factor binding sites. Nat. Biotechnol.2002; 20:831β835.12101405 10.1038/nbt718 | β | β | β |
| Sandelin A. , WassermanW.W. Constrained binding site diversity within families of transcription factors enhances pattern discovery bioinformatics. J. Mol. Biol.2004; 338:207β215.15066426 10.1016/j.jmb.2004.02.048 | β | β | β |
| Sapoval N. , AghazadehA., NuteM.G., AntunesD.A., BalajiA., BaraniukR., BarberanC.J., DannenfelserR., DunC., EdrisiM.et al. Current progress and open challenges for applying deep learning across the biosciences. Nat. Commun.2022; 13:1728.35365602 10.1038/s41467-022-29268-7PMC8976012 | β | β | β |
| Sheffield N.C. , BockC. LOLA: enrichment analysis for genomic region sets and regulatory elements in R and Bioconductor. Bioinformatics. 2016; 32:587β589.26508757 10.1093/bioinformatics/btv612PMC4743627 | β | β | β |
| Stormo G.D. Modeling the specificity of protein-DNA interactions. Quant Biol. 2013; 1:115β130.25045190 10.1007/s40484-013-0012-4PMC4101922 | β | β | β |
| Tan G. , LenhardB. TFBSTools: an R/bioconductor package for transcription factor binding site analysis. Bioinformatics. 2016; 32:1555β1556.26794315 10.1093/bioinformatics/btw024PMC4866524 | β | β | β |
| Thomas-Chollier M. , HerrmannC., DefranceM., SandO., ThieffryD., van HeldenJ. RSAT peak-motifs: motif analysis in full-size ChIP-seq datasets. Nucleic Acids Res.2012; 40:e31.22156162 10.1093/nar/gkr1104PMC3287167 | β | β | β |
| Tian F. , YangD.-C., MengY.-Q., JinJ., GaoG. PlantRegMap: charting functional regulatory maps in plants. Nucleic Acids Res.2020; 48:D1104βD1113.31701126 10.1093/nar/gkz1020PMC7145545 | β | β | β |
| Ullah F. , Ben-HurA. A self-attention model for inferring cooperativity between regulatory features. Nucleic Acids Res.2021; 49:e77.33950192 10.1093/nar/gkab349PMC8287919 | β | β | β |
| Viner C. , IshakC.A., JohnsonJ., WalkerN.J., ShiH., SjΓΆberg-HerreraM.K., ShenS.Y., LardoS.M., AdamsD.J., Ferguson-SmithA.C.et al. Modeling methyl-sensitive transcription factor motifs with an expanded epigenetic alphabet. 2023; bioRxiv doi:28 February 2023, preprint: not peer reviewed10.1101/043794.PMC1077311138191487 | β | β | β |
| Weirauch M.T. , HughesT.R. A catalogue of eukaryotic transcription factor types, their evolutionary origin, and species distribution. Subcell. Biochem.2011; 52:25β73.21557078 10.1007/978-90-481-9069-0_3 | β | β | β |
| Weirauch M.T. , YangA., AlbuM., CoteA.G., Montenegro-MonteroA., DreweP., NajafabadiH.S., LambertS.A., MannI., CookK.et al. Determination and inference of eukaryotic transcription factor sequence specificity. Cell. 2014; 158:1431β1443.25215497 10.1016/j.cell.2014.08.009PMC4163041 | β | β | β |
| Wilkinson M.D. , DumontierM., AalbersbergI.J.J., AppletonG., AxtonM., BaakA., BlombergN., BoitenJ.-W., da Silva SantosL.B., BourneP.E.et al. The FAIR Guiding Principles for scientific data management and stewardship. Sci. Data. 2016; 3:160018.26978244 10.1038/sdata.2016.18PMC4792175 | β | β | β |
| Wingender E. , SchoepsT., HaubrockM., DΓΆnitzJ. TFClass: a classification of human transcription factors and their rodent orthologs. Nucleic Acids Res.2015; 43:D97βD102.25361979 10.1093/nar/gku1064PMC4383905 | β | β | β |
| Wingender E. , SchoepsT., HaubrockM., KrullM., DΓΆnitzJ. TFClass: expanding the classification of human transcription factors to their mammalian orthologs. Nucleic Acids Res.2018; 46:D343βD347.29087517 10.1093/nar/gkx987PMC5753292 | β | β | β |
| Wu Y.-H. , HuangY.-A., LiJ.-Q., YouZ.-H., HuP.-W., HuL., LeungV.C.M., DuZ.-H. Knowledge graph embedding for profiling the interaction between transcription factors and their target genes. PLoS Comput. Biol.2023; 19:e1011207.37339154 10.1371/journal.pcbi.1011207PMC10313080 | β | β | β |
| Xuan Lin Q.X. , SianS., AnO., ThieffryD., JhaS., BenoukrafT MethMotif: an integrative cell specific database of transcription factor binding motifs coupled with DNA methylation profiles. Nucleic Acids Res.2019; 47:D145βD154.30380113 10.1093/nar/gky1005PMC6323897 | β | β | β |
| Yang J. , MaA., HoppeA.D., WangC., LiY., ZhangC., WangY., LiuB., MaQ. Prediction of regulatory motifs from human Chip-sequencing data using a deep learning framework. Nucleic Acids Res.2019; 47:7809β7824.31372637 10.1093/nar/gkz672PMC6735894 | β | β | β |
| Yuan H. , KelleyD.R. scBasset: sequence-based modeling of single-cell ATAC-seq using convolutional neural networks. Nat. Methods. 2023; 19:1088β1096.10.1038/s41592-022-01562-835941239 | β | β | β |
| Zabardast A. , TamerE.G., SonY.A., YΔ±lmazA. An automated framework for evaluation of deep learning models for splice site predictions. Sci. Rep.2023; 13:10221.37353532 10.1038/s41598-023-34795-4PMC10290104 | β | β | β |
| Zhang S. , MaA., ZhaoJ., XuD., MaQ., WangY. Assessing deep learning methods in cis-regulatory motif finding based on genomic sequencing data. Brief. Bioinform.2022; 23:bbab374.34607350 10.1093/bib/bbab374PMC8769700 | β | β | β |
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| A structure-guided approach to noncoding variant evaluation for transcription factor binding using AlphaFoldΒ 3. | Gerasimavicius L et al. | β | 2026 | β |
| A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest. | Bates AD et al. | β | 2026 | β |
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| Bisphosphate nucleotidase 1 promotes progression and docetaxel resistance in triple-negative breast cancer via STUB1-mediated destabilization of LIMA1. | Ling YX et al. | β | 2026 | β |
| Bridging the variant-to-function gap in type 2 diabetes: advances and challenges. | Maynard AG et al. | β | 2026 | β |
| C9orf72 hexanucleotide repeat RNA drives transcriptional dysregulation through genome-wide DNA:RNA hybrid G-quadruplexes. | Liu H et al. | β | 2026 | β |
| Cardiomyocytes FGFBP1 induction by STAT3 drives pathological cardiac remodeling. | Shen Y et al. | β | 2026 | β |
| C/EBPΞ²-induced alternative splicing of RCAN1 generates a potent TCR-T target in mesenchymal glioblastoma. | Xiong Z et al. | β | 2026 | β |
| CellSNVReg: a multidimensional resource for SNV-mediated regulatory perturbations in single-cell and spatial omics. | Shi J et al. | β | 2026 | β |
| Chicken Shank Color Determined by Inhibition of Dermal Melanin (ID) is Mediated by a Structural Variation Regulating CDKN2A Expression. | Li J et al. | β | 2026 | β |
| Circadian disruption increases sperm DNA damage through impaired CREB1-mediated of homologous recombination repairβ . | Zhu W et al. | β | 2026 | β |
| c-MYC enhances transcription of the type 1 diabetes mellitus associated gene BATF3 via promoter binding. | Zhao Y et al. | β | 2026 | β |
| Comparative genome-wide analysis in Setaria italica and Arabidopsis thaliana revealed functional conservation of specific FtsH proteases under high light and heat stress. | Ghosh D et al. | β | 2026 | β |
| Computational modelling of cell identity. | Shim WJ et al. | β | 2026 | β |
| Controlling gene expression using AI designed Cis-regulatory elements. | Xia Y et al. | β | 2026 | β |
| Convergent evolution through independent rearrangements in the primate amylase locus. | Karageorgiou C et al. | β | 2026 | β |
| CRISPR tiling deletion screens reveal functional enhancers and allelic compensation effects (ACE) on SIN3A transcription. | Ren X et al. | β | 2026 | β |
| C-X-C chemokine receptor CXCR4 mediates diurnal changes in the aggregation and dispersion of CD8<sup>+</sup> T cells within the tumor microenvironment. | Tsuruta A et al. | β | 2026 | β |
| Dbert2_LR: A deep learning-based model for predicting cis-regulatory elements in crops. | Liu H et al. | β | 2026 | β |
| Deciphering the 3D genome organization across species from Hi-C data. | Shkolikov A et al. | β | 2026 | β |
| Deciphering the regulatory landscape of venom gene expression in a parasitoid wasp at single-cell resolution. | Wang S et al. | β | 2026 | β |
| Decode and rewire: programming Komagataella phaffii for bioproduction with synthetic transcriptional tools. | Wei X et al. | β | 2026 | β |
| De novo formation of cis-regulatory contacts in the absence of NIPBL-driven chromatin loop extrusion. | Aboreden NG et al. | β | 2026 | β |
| Designing synthetic regulatory elements using the generative AI framework DNA-Diffusion. | DaSilva LF et al. | β | 2026 | β |
| Dexmedetomidine potentiates cisplatin chemosensitivity in esophageal carcinoma cells via the SREBF1/miR-185-5p/Caspase-1 axis through pyroptosis. | Xu J et al. | β | 2026 | β |
| Diet and temperature interactively impact brown adipose tissue gene regulation controlled by DNA methylation. | Hagemann T et al. | β | 2026 | β |
| Differential gene expression analysis reveals signaling pathways of proliferation, angiogenesis and metastasis is associated with interferon suppression in advanced hypopharyngeal cancer cells. | Kao CW et al. | β | 2026 | β |
| DNA methylation profiles aid to identify putative genome activation histories along lymphomagenesis. | Albinati L et al. | β | 2026 | β |
| Dual Nurr1/RXR agonism of valerenic acid and synthetic mimetics enables dimer-selective Nurr1 modulation. | Scholz K et al. | β | 2026 | β |
| Duck lncRNA lnc455 enhances RIG-I/MAVS type I interferon signaling by modulating hnRNPAB-mediated regulation of MAVS signaling. | Legaspi RJ et al. | β | 2026 | β |
| Early-life inflammation increases aggressive behavior in adult male mice through an astrocyte-neuron signaling. | Wang J et al. | β | 2026 | β |
| Endothelial stem cells of the retinal vasculature reside in the optic nerve. | Sakimoto S et al. | β | 2026 | β |
| Environmental PFOS and 6:2 Cl-PFESA Reshape Ferroptosis Vulnerability in Liver Cancer. | Hong J et al. | β | 2026 | β |
| EPInformer: scalable and integrative prediction of gene expression from promoter-enhancer sequences with multimodal epigenomic profiles. | Lin J et al. | β | 2026 | β |
| Epitranscriptomic Control of Vascular Smooth Muscle Cell Ferroptosis by WTAP in the Pathogenesis of Vascular Restenosis. | Yin Y et al. | β | 2026 | β |
| Escherichia coli promotes colorectal cancer metastasis by maintaining enhancer-promoter loops through releasing neutrophil extracellular traps. | Pan B et al. | β | 2026 | β |
| Evolutionary Transitions in Social Behavior are Associated With Convergent and Partially Reversible Expansions of Transcription Factor Binding Sites. | Ploessl SG et al. | β | 2026 | β |
| Expanding the fly eye gene regulatory network: From Drosophila to the hoverfly Episyrphus balteatus. | Navarro T et al. | β | 2026 | β |
| Exploring potential transcription factors and their regulatory relationships based on asymmetric covariance natural vector encoding method and machine learning algorithms. | Hu G et al. | β | 2026 | β |
| Extensive enhancer crosstalk controls PPARG2 activation during adipogenesis. | Cetnarowska A et al. | β | 2026 | β |
| Fortilin binds and stabilizes MEF2C, activates it through phosphorylation, and drives transcription of the cell structural and survival protein CTNNA3. | Nakashima M et al. | β | 2026 | β |
| FOXP1 deficiency exacerbates cellular senescence in PM<sub>2.5</sub>-induced renal injury. | Chen H et al. | β | 2026 | β |
| FOXP1 is differentially active during development of murine vasopressin and oxytocin magnocellular neurons. | Berkhout JB et al. | β | 2026 | β |
| Functional variants at 1p36.23 confer risk of schizophrenia through modulating RERE. | Liu Y et al. | β | 2026 | β |
| GAMMA: gap-aware motif mining under incomplete labeling with applications to MHC motifs. | Tang X et al. | β | 2026 | β |
| Genome-wide association study of HBV-related hepatocellular carcinoma identifies a functional variant at the FAM114A1 locus. | Yu HP et al. | β | 2026 | β |
| Global reorganization of genome architecture at the transition to gametogenesis. | Huang TC et al. | β | 2026 | β |
| Glucosamine suppresses hepatocellular carcinoma progression through dual inhibition of cell cycle progression and nucleotide metabolism. | Zhang YL et al. | β | 2026 | β |
| HDAC8 inhibition targets STAT3-MYC axis and synergizes with Venetoclax in KMT2A-rearranged acute myeloid leukemia. | Zhang L et al. | β | 2026 | β |
| HLTF cooperates with GATA1 to activate transcriptional programs and chromatin remodeling during erythroid development. | Gong H et al. | β | 2026 | β |
| HMBOX1 inhibits hepatocellular carcinoma progression via PTPN1 mediated AKT1 phosphorylation. | Zhang C et al. | β | 2026 | β |
| HOXB4 Promotes Bladder Cancer Progression in Part Through Transcriptional Activation of Smoothened. | Jin Z et al. | β | 2026 | β |
| Human hippocampal neurogenesis in adulthood, ageing and Alzheimer's disease. | Disouky A et al. | β | 2026 | β |
| Human-specific lncRNAs contributed critically to human evolution by distinctly regulating gene expression. | Lin J et al. | β | 2026 | β |
| Hypoxia promotes progression of cervical cancer by modulating the ATXN3-enhanced P53 stability or STAT5 phosphorylation. | Zhang R et al. | β | 2026 | β |
| Identification and bioinformatic functional analysis of novel and known polymorphisms in the myostatin gene of Ukrainian Carpathian Mountain sheep. | Buslyk T et al. | β | 2026 | β |
| Impact of a naturally occurring hepatitis B virus genotype D-specific core-promoter mutation on viral replication. | Kanai M et al. | β | 2026 | β |
| Impaired retinoic acid signaling mediated Rbm20 downregulation induces aberrant splicing of Ca<sub>V</sub>1.2 calcium channel: implications in myocardial hypertrophy. | Song X et al. | β | 2026 | β |
| Inhibiting Arachidonate-5-lipoxygenase expression ameliorates osteoarthritis progression by suppressing ferroptosis via the JAK2/STAT3 signaling pathway. | Zou F et al. | β | 2026 | β |
| In-silico identification of genetic variants associated with chronic lymphocytic leukemia for diagnostic and therapeutic applications. | Islam MS et al. | β | 2026 | β |
| Integrated multi-omics data to identify the key genes affecting egg-laying performance in late-phase hens. | Yang H et al. | β | 2026 | β |
| Intelectin-2 is a broad-spectrum antimicrobial lectin. | Dugan AE et al. | β | 2026 | β |
| Interferon regulatory factor 1 enhances T cell differentiation in patients with myasthenia gravis. | Luo Y et al. | β | 2026 | β |
| Interphase chromosome conformation is specified by distinct folding programmes inherited through mitotic chromosomes or the cytoplasm. | Schooley A et al. | β | 2026 | β |
| JASPAR 2026: expansion of transcription factor binding profiles and integration of deep learning models. | Ovek Baydar D et al. | β | 2026 | β |
| Kinesin KIF20A Regulated by ATF2 Transcription Promotes Prostate Cancer Proliferation and Invasion. | Yang M et al. | β | 2026 | β |
| KLF5 Activation Promotes Malignant Transformation to Drive Development of Lung Squamous Cell Carcinoma. | Zeng J et al. | β | 2026 | β |
| Laminin Ξ²1 stimulates the Hippo-YAP1 pathway to advance the progression and lenvatinib resistance in hepatocellular carcinoma. | Cai Z et al. | β | 2026 | β |
| Large-scale multi-omic biosequence transformers for modeling protein-nucleic acid interactions. | Chen SF et al. | β | 2026 | β |
| Lipid oxidation reprogramming in cancer-associated fibroblasts enhances CD8<sup>+</sup> T cell cytotoxicity and therapeutic response. | Ma Z et al. | β | 2026 | β |
| Machine learning-driven identification of shared and disease-specific mitochondria-related genes in COPD, NSCLC, and NSCLC with COPD. | Wu S et al. | β | 2026 | β |
| Mapping cis-regulatory mutations at scale in sorghum enables modulation of gene expression. | Groover ED et al. | β | 2026 | β |
| Mapping convergent regulators of melanoma drug resistance by PerturbFate. | Xu Z et al. | β | 2026 | β |
| Mechanism of FOXP2 in the Hepatocellular Carcinoma Progression via Ferroptosis Through RBM15B-Mediated m6A Modification. | Liu W et al. | β | 2026 | β |
| Metalloreductase STEAP4 suppresses TNBC progression via the ROS/NRF2/NOTCH1 signaling axis and is stabilized by lncRNA ENST00000595121. | Chen WJ et al. | β | 2026 | β |
| MLL1-pioneered H3K4me3 modification on KLF7 promoter accelerates the invasion of fibroblast-like synoviocytes in rheumatoid arthritis. | Cen Y et al. | β | 2026 | β |
| m<sup>6</sup>A Modification Genetic Variants Associated with Autism Spectrum Disorder Risks. | Wang H et al. | β | 2026 | β |
| Modulation of the Receptor Tyrosine Kinase TIE2/<i>Tek</i> Pathway by NRF2 Activation in Neurovascular Endothelial Cells. | Cazalla E et al. | β | 2026 | β |
| Molecular and cellular processes disrupted in the early postnatal Down syndrome prefrontal cortex. | Risgaard RD et al. | β | 2026 | β |
| Molecular regulatory mechanisms of schizophrenia-associated functional non-coding variants. | Dai SS et al. | β | 2026 | β |
| Molecular Responses to Temperature Changes Across Timescales in the Madagascar Ground Gecko (Paroedura picta). | Sakamoto F et al. | β | 2026 | β |
| Motif grammar and transcriptional programs decouple CTCF binding from nucleosome phasing to control cell-type-specific chromatin insulation. | Do C et al. | β | 2026 | β |
| Multi-omics analysis Taiwanofungus gaoligongensis fermentation with traditional Chinese medicine. | He T et al. | β | 2026 | β |
| NEDD8 promotes the ferritinophagy and ferroptosis of neurons in ischemic stroke via mediating neddylation of NRF2. | Rao W et al. | β | 2026 | β |
| NIBAN2/FLII/RREB1 Axis Drives Glioma Stem Cell Malignancy via TLR3 Pathway Activation. | Shi LL et al. | β | 2026 | β |
| NSD2 targeting reverses plasticity and drug resistance in prostate cancer. | Li JJ et al. | β | 2026 | β |
| Nuclear factor erythroid 2-related factor 2 induction abrogates mitochondrial stress through parkin regulation. | Safreena N et al. | β | 2026 | β |
| Nucleotide-resolution mapping of regulatory elements via allelic readout of tiled base editing. | Becerra B et al. | β | 2026 | β |
| NUSAP1 Recruits DAXX to Suppress HIF-Driven Triple-Negative Breast Cancer Progression. | Du Y et al. | β | 2026 | β |
| Nutritional and hormonal regulation of mitochondrial biogenesis drives fat body remodeling for reproductive competence. | Li Y et al. | β | 2026 | β |
| OsMYB99 Modulates Grain Wax Biosynthesis and Redox Homeostasis to Control Head Rice Yield and Chalkiness. | Yu T et al. | β | 2026 | β |
| Overcoming EGFR-Mediated Dendritic Cell Dysfunction to Enhance Anti-tumor Immunity in EGFR-Mutant NSCLC by Precisely Targeting CD73 With pH-responsive Nanocarriers. | Shang X et al. | β | 2026 | β |
| Pervasive and programmed nucleosome distortion on single chromatin fibres. | Yang MG et al. | β | 2026 | β |
| Phylogenetic Analysis of NEAT1 and MALAT1 Long Non-Coding RNAs Highlights Structure-Function Relationships in Paraspeckle Biology. | Arkhipova K et al. | β | 2026 | β |
| Pioneer Factor FOXA1 Boosts CHO Cell Productivity. | Butterfield SP et al. | β | 2026 | β |
| Polycomb misregulation in enterocytes drives tissue decline in the aging <i>Drosophila</i> intestine. | Leichter SM et al. | β | 2026 | β |
| POU2F1 drives cholesterol biosynthesis and lipid remodeling through the DHCR24/ELOVL2 axis in endometrial cancer. | Zhang ZH et al. | β | 2026 | β |
| Pre-training genomic language model with variants for better modeling functional genomics. | Liu T et al. | β | 2026 | β |
| Programming Next-Generation Synthetic Biosensors by Genetic Circuit Design. | Gao Y et al. | β | 2026 | β |
| Protein-DNA interactions in disease and drug discovery. | Mishra R et al. | β | 2026 | β |
| Rare Variants in Antisense Long Noncoding RNA-Protein-Coding Gene Overlap Regions Contribute to Obsessive-Compulsive Disorder. | Jung S et al. | β | 2026 | β |
| Receptor-like-kinase-interacting protein TOW stabilizes PIN transporters for auxin canalization. | Li M et al. | β | 2026 | β |
| Regulatory grammar in human promoters uncovered by MPRA-based deep learning. | Barbadilla-MartΓnez L et al. | β | 2026 | β |
| Regulatory risk loci link disrupted androgen response to the pathophysiology of polycystic ovary syndrome. | Srivastava J et al. | β | 2026 | β |
| Rewired gene interactions during evolution of the analia and genitalia in Drosophila. | Ridgway AM et al. | β | 2026 | β |
| RFC4 drives temozolomide resistance in glioblastoma by activating STK38-BECN1-dependent autophagy. | Mao M et al. | β | 2026 | β |
| Role of ZNF652 in Regulating Hepatocellular Carcinoma Cell Proliferation and Apoptosis via the circRHOT1/SLC38A6 Axis. | Chen K et al. | β | 2026 | β |
| S1P-S1PR1 signaling impairs CD8<sup>+</sup> T cell metabolism and effector function in tumors. | Basak D et al. | β | 2026 | β |
| scBrainScope: cross-species multidimensional brain atlas. | Qin S et al. | β | 2026 | β |
| SDC1<sup>+</sup> CAFs secreting CTGF drive tumour metastasis via FGFR3 signalling in cancers. | Gao GF et al. | β | 2026 | β |
| SDC4 is a novel target of the KLF5 transcription factor. | Yokoyama Y et al. | β | 2026 | β |
| SEdb 3.0: a comprehensive super-enhancer database across multiple species. | Song S et al. | β | 2026 | β |
| Sequence and chemical specificity define the functional landscape of intrinsically disordered regions. | Langstein-Skora I et al. | β | 2026 | β |
| ShapeME: A Tool and Web Front-end for De Novo Discovery of Structural Motifs Underpinning Protein-DNA Interactions. | Schroeder JW et al. | β | 2026 | β |
| Single-cell analysis of signalling and transcriptional responses to type I interferons. | Rigby RE et al. | β | 2026 | β |
| Single-cell multi-omic analyses highlight the essential role of NKX2.2-CLEC16A/endosomal pathway for human pancreatic differentiation and function. | Chen G et al. | β | 2026 | β |
| Single Cell Multiomics of Hooked Potato Stolons Reveals Parallels to Shoot Apical Meristems in Arabidopsis. | Martin D et al. | β | 2026 | β |
| SMURF2-Mediated Ubiquitination and Degradation of HOXA5 Augments Endoplasmic Reticulum Stress in Alveolar Epithelial Type II Cells Induced by LPS. | Wang L et al. | β | 2026 | β |
| SPEECHLESS duplication in grasses expands potential for environmental regulation of stomatal development. | Erberich JM et al. | β | 2026 | β |
| Spongy mesophyll cell death is induced by jasmonic acid during leaf senescence in chrysanthemum. | Song J et al. | β | 2026 | β |
| SREBP-1 increases glucose uptake to promote tumor resistance to lysosome inhibition. | Zhong Y et al. | β | 2026 | β |
| SREBP-1 upregulates SOAT1 to promote tumor growth by preventing lipotoxicity. | Zhong Y et al. | β | 2026 | β |
| Subtype-resolved transcriptomic analysis reveals distinct zinc-finger regulatory hubs in breast cancer. | Ali M et al. | β | 2026 | β |
| SUZ12 promotes pancreatic ductal adenocarcinoma progression and chemoresistance by epigenetically silencing NCOA4-induced ferroptosis. | Yin L et al. | β | 2026 | β |
| Targeting CDK12 rescues C/EBPΞ²-mediated platinum and PARP inhibitor resistance in ovarian cancer. | Tan J et al. | β | 2026 | β |
| Targeting DHODH promoter G-quadruplex to induce ferroptosis in melanoma cells. | Zhang W et al. | β | 2026 | β |
| Targeting the 5-HT<sub>1B</sub>-YAP positive feedback loop protects against disturbed flow-induced atherogenesis in mice. | Jiang MC et al. | β | 2026 | β |
| TF2TG: an online resource mining the potential gene targets of transcription factors in Drosophila. | Hu Y et al. | β | 2026 | β |
| The conserved noncoding sequence CNS11 is a master control region for <i>Rorc</i> transcription in type 17 immune cells. | Zhang H et al. | β | 2026 | β |
| The creative mind in the shadow of depressive symptoms: Epigenetic variation in HPA axis genes is associated with the link between depressive symptoms and creative personality. | Feinmesser D et al. | β | 2026 | β |
| The HIF1Ξ±-PUM1-KCNK3 axis drives pulmonary hypertension by destabilizing KCNK3 mRNA in pulmonary artery smooth muscle cells. | Deng X et al. | β | 2026 | β |
| The interaction between virus-bound KLF4 and host-bound PARP1 directs the localization of wild-type adeno-associated virus type 2 (wtAAV2) to cellular sites of DNA damage. | Abrahams RR et al. | β | 2026 | β |
| Therapeutic potential of Cuscutae Semen and Rehmanniae Radix Preparata in age-related central hearing loss associated with Gad1 regulation. | Nam YH et al. | β | 2026 | β |
| The Zeb1/system X<sub>c</sub><sup>-</sup> axis safeguards iron-loaded cancer-associated fibroblasts against ferroptosis and promotes immunosuppression in prostate cancer. | Zhang Y et al. | β | 2026 | β |
| Three-dimensional genome reorganization foreshadows zygotic genome activation in Drosophila. | Maziak N et al. | β | 2026 | β |
| Time-course ATAC-seq and RNA-seq analysis of porcine synovium-derived mesenchymal stem cells under in vitro osteogenic induction. | Li S et al. | β | 2026 | β |
| Tissue-resident exhausted and memory CD8<sup>+</sup> T cells have distinct ontogeny, function and role in disease. | Park SL et al. | β | 2026 | β |
| Tissue signatures of human macrophages during homeostasis and activation. | Caron DP et al. | β | 2026 | β |
| Transcriptional and cellular maturation of the chick spinal cord in the context of distinct neuromuscular circuits. | Sacher F et al. | β | 2026 | β |
| Transcription and potential functions of a novel <i>XIST</i> isoform in male peripheral glia. | O'Leary KS et al. | β | 2026 | β |
| Transcriptomic Analysis and Multiple Machine Learning Approaches Identify ZDHHC20 and Its Highly Correlated Gene AK5 as Biomarkers in Multiple System Atrophy. | Lu Z et al. | β | 2026 | β |
| Transposable Elements Seed Transcription Factor Binding Sites to Sequence-Specific Double-Stranded DNA Binding TF Networks Contributing to Governance of Primate Brain Evolution. | Glinsky GV | β | 2026 | β |
| Tumor-specific lncRNA IGF1R-AS1 trans-regulates chromatin interactions associated with oncogenic MYC signaling. | Yang Y et al. | β | 2026 | β |
| WAT-to-BAT communication facilitates the sustained activation of BAT thermogenesis during cold exposure. | Xue J et al. | β | 2026 | β |
| Web-Based Discovery of Regulatory Motifs in Non-model Plants. | Ksouri N et al. | β | 2026 | β |
| Widespread turnover of a conserved cis-regulatory code across 589 grass species. | Hale CO et al. | β | 2026 | β |
| YamOmics: a comprehensive data resource on yam multi-omics. | Zhao Y et al. | β | 2026 | β |
| ZBTB21 Is a Dual Suppressor of Pyroptosis and MHC-I Antigen Presentation That Promotes Tumor Immune Evasion. | Zhao L et al. | β | 2026 | β |
| ZNF282 Promotes Colorectal Cancer Progression Possibly via E2F1 Activation. | Abe T et al. | β | 2026 | β |
| A cell-state axis underlying colonization in carcinomas with implications for metastasis risk prediction and interception. | Handler JS et al. | β | 2025 | β |
| ACKR1<sup>hi</sup>ECs Promote Aortic Dissection Through Adjusting Macrophage Behavior. | Wang Y et al. | β | 2025 | β |
| Activated TBK1 promotes ACSL1-mediated microglia lipid droplet accumulation and neuroinflammation in Parkinson's disease. | Han C et al. | β | 2025 | β |
| Adaptive protein synthesis in genetic models of copper deficiency and childhood neurodegeneration. | Lane AR et al. | β | 2025 | β |
| A DSSM network for inferring and prioritizing cell-type-specific regulons using single-cell RNA-seq data. | Fan Y et al. | β | 2025 | β |
| A feedback loop at the THERMOSENSITIVE PARTHENOCARPY 4 locus controls tomato fruit set under heat stress. | Lu X et al. | β | 2025 | β |
| A gene regulatory network for specification and morphogenesis of a Mauthner Cell homolog in non-vertebrate chordates. | Kim K et al. | β | 2025 | β |
| Aloin blocks the malignant behavior of lung squamous cell carcinoma cells and M2 macrophage polarization by modulating the NR3C2/MT1M axis. | Chen YN et al. | β | 2025 | β |
| Alternatively spliced isoforms of IRF7 differentially regulate interferon expression to tune response to viral infection. | Panthi A et al. | β | 2025 | β |
| Alternative Promoters Drive Transcriptomic Reprogramming and Prognostic Stratification in TNBC. | Jit S et al. | β | 2025 | β |
| A machine learning-based tool for predicting transcription factor-target gene interactions in soybean. | Zhu X et al. | β | 2025 | β |
| A multi-layered regulatory model uncovers the central role of OsPRR37 in coordinating multiple agronomic traits. | Liu C et al. | β | 2025 | β |
| Analysis of the Transcriptional Control of <i>Bcl11b</i> in Chicken: IRF1 and GATA1 as Negative Regulators. | Qiu L et al. | β | 2025 | β |
| An Attention-Based Deep Neural Network Model to Detect Cis-Regulatory Elements at the Single-Cell Level From Multi-Omics Data. | Murakami K et al. | β | 2025 | β |
| Androgen receptor promotes arachidonic acid metabolism and angiogenic microenvironment in AFP-negative hepatocellular carcinoma. | Lin Z et al. | β | 2025 | β |
| An endogenous retroviral element co-opts an upstream regulatory sequence to achieve somatic expression and mobility. | Rubanova N et al. | β | 2025 | β |
| A novel lncRNA-mediated signaling axis governs cancer stemness and splicing reprogramming in hepatocellular carcinoma with therapeutic potential. | Si K et al. | β | 2025 | β |
| A pan-cancer analysis of small nucleolar RNA host gene 14 (SNHG14) in human tumors. | Feng C et al. | β | 2025 | β |
| APOC1, transcriptionally regulated by FOXM1, promotes M2 macrophage polarization and cervical cancer progression. | Chai Q et al. | β | 2025 | β |
| Arctigenin Prevents Metabolic Dysfunction-associated Steatohepatitis by Inhibiting NLRP3/GSDMD-N Axis in Macrophages. | Xue R et al. | β | 2025 | β |
| ARID3A inhibits colorectal cancer cell stemness and drug-resistance by targeting a multitude of stemness-associated genes. | Gope TK et al. | β | 2025 | β |
| A spatially resolved multi-omic single-cell atlas of soybean development. | Zhang X et al. | β | 2025 | β |
| Association of human-specific expanded short tandem repeats with neuron-specific regulatory features. | Liu Q et al. | β | 2025 | β |
| A stem cell differentiation model reveals two alternative fates in CBFA2T3::GLIS2-driven acute megakaryoblastic leukemia initiation. | Shoeb MR et al. | β | 2025 | β |
| A survey of hypothalamic phenotypes identifies molecular and behavioral consequences of MYT1L haploinsufficiency in male and female mice. | Maloney SE et al. | β | 2025 | β |
| Asymmetry of Motif Conservation Within Their Homotypic Pairs Distinguishes DNA-Binding Domains of Target Transcription Factors in ChIP-Seq Data. | Levitsky VG et al. | β | 2025 | β |
| ATAC-seq in Emerging Model Organisms: Challenges and Strategies. | ErdoΔan DE et al. | β | 2025 | β |
| A transcriptomic atlas at bulk and single-cell levels identifies novel transcriptional and splicing regulators of ECM homeostasis in osteoarthritis. | Ye X et al. | β | 2025 | β |
| Autoimmune disease risk gene ANKRD55 promotes TH17 effector function through metabolic modulation. | Xu J et al. | β | 2025 | β |
| Benchmark of chromatin-protein interaction methods in haploid round spermatids. | Wang R et al. | β | 2025 | β |
| Bexarotene signaling in human B and T lymphocytes induces gut-homing receptor expression. | Kaiser S et al. | β | 2025 | β |
| Beyond Iron: The Roles of CD71 in the Pathophysiology of Cancer-A Comprehensive Review. | Markopoulos GS et al. | β | 2025 | β |
| bHLH35 mediates specificity in plant responses to multiple stress conditions. | Sinha R et al. | β | 2025 | β |
| BHLHA15 promotes cervical cancer cholesterol synthesis and tumor progression. | Ye H et al. | β | 2025 | β |
| Bilateral Synergistic Effects of Phototherapy-Based NIR-II Absorption Photosensitizer for Allergic Rhinitis. | Shao T et al. | β | 2025 | β |
| Blockade of ZMIZ1-GATA4 Axis Regulation Restores Youthfulness to Aged Cartilage. | Nam J et al. | β | 2025 | β |
| Blood-based detection of MMP11 as a marker of prostate cancer progression regulated by the ALDH1A1-TGF-Ξ²1 signaling mechanism. | Gorodetska I et al. | β | 2025 | β |
| Brassinosteroid promotes leaf wrinkling in Brassica campestris by regulating a key transcription factor and its downstream genes. | Chen J et al. | β | 2025 | β |
| BRF110, an Orally Active Nurr1-RXRΞ±-Selective Rexinoid, Enhances BDNF Expression without Elevating Triglycerides. | Asvos X et al. | β | 2025 | β |
| Calpain Proteases and the Evolving Signaling Network in Insect Embryonic Patterning. | Julio A et al. | β | 2025 | β |
| CanASM: a comprehensive database for genome-wide allele-specific DNA methylation identification and annotation in cancer. | Zhao J et al. | β | 2025 | β |
| CD22 exacerbates brain injury in subarachnoid hemorrhage by inhibiting microglial phagocytic function. | Jin E et al. | β | 2025 | β |
| C/EBPΞ± activates <i>Irf8</i> expression in myeloid progenitors at the +56-kb enhancer to initiate cDC1 development. | Chen J et al. | β | 2025 | β |
| C/EBP-Ξ²/MeCP2/Wnt Axis Participates in the Testicular Injury in Rats Under Simulated Microgravity Conditions. | Ge P et al. | β | 2025 | β |
| Cellular Senescence Genes as Cutting-Edge Signatures for Abdominal Aortic Aneurysm Diagnosis: Potential for Innovative Therapeutic Interventions. | Zhang S et al. | β | 2025 | β |
| Characterization of blood group variants in an Omani population by comparison of whole genome sequencing and serology. | Haffener PE et al. | β | 2025 | β |
| Characterization of non-coding variants associated with transcription-factor binding through ATAC-seq-defined footprint QTLs in liver. | Dudek MF et al. | β | 2025 | β |
| CHIP-seq and transcriptomics reveal a new role of circadian-regulated StBBX24 protein in potato reproduction. | GrΔ dzka K et al. | β | 2025 | β |
| Chromatin-dependent motif syntax defines differentiation trajectories. | Durdu S et al. | β | 2025 | β |
| Chromatin dynamics and transcriptional regulation of heat stress in an ectothermic fish. | Huang S et al. | β | 2025 | β |
| CircAKT3 promotes prostate cancer proliferation and metastasis by enhancing the binding of RPS27A and RPL11. | Song X et al. | β | 2025 | β |
| Comparative analysis of tongue cancer organoids among patients identifies the heritable nature of minimal residual disease. | Sase M et al. | β | 2025 | β |
| Comparative Profiling of Regulatory Modules as a Tool for Identifying the Transcription Factor Network Linked to Leukemogenesis. | Subramanian S et al. | β | 2025 | β |
| Complement C4b as a key mediator of synaptic loss and cognitive decline in brain aging. | Zheng Y et al. | β | 2025 | β |
| Comprehensive Analysis of Multi-Omics Data on RNA Polymerase as an Adverse Factor in Head and Neck Squamous Cell Carcinoma. | Gu YJ et al. | β | 2025 | β |
| Comprehensive analysis reveals MCM4 as a biomarker for guiding therapies and immunomodulatory role in skin cutaneous melanoma. | Ou W et al. | β | 2025 | β |
| Comprehensive Identification of <i>HD-Zip</i> Family Genes in <i>Coix lacryma-jobi</i> L. and Their Potential Roles in Response to Abiotic Stress. | Wang Y et al. | β | 2025 | β |
| Computational Analyses Identified Three Diagnostic Biomarkers Associated With Programmed Cell Death for Lung Adenocarcinoma. | Gong T et al. | β | 2025 | β |
| Computational analysis of promoter features associated with contrasting expression patterns of human genes under normal and disease conditions. | Manivelan V et al. | β | 2025 | β |
| Computer-aided unveiling molecular mechanisms of Xylocarpus granatum against colorectal cancer: therapeutic intervention targeting P13K-AKT signaling pathway. | Ahamed MS et al. | β | 2025 | β |
| Control of myeloid lineage fidelity and response to stimuli by ISWI-enforced nucleosome phasing. | Polletti S et al. | β | 2025 | β |
| Coordinated action of multiple active histone modifications shapes the zygotic genome activation in teleost embryos. | Fukushima HS et al. | β | 2025 | β |
| Coordinated epigenetic dysregulation of CNR1 and FAAH genes drives endocannabinoid system dysfunction in anorexia nervosa. | Gilardini F et al. | β | 2025 | β |
| Correlation between variations in promoter region of LvITGΞ² gene and anti-infection trait of shrimp, Litopenaeus vannamei, against a microsporidium, Ecytonucleospora hepatopenaei. | Yin J et al. | β | 2025 | β |
| CREB1-BCL2 drives mitochondrial resilience in RAS GAP-dependent breast cancer chemoresistance. | Man KF et al. | β | 2025 | β |
| CRISPR/Cas9-based editing of NF-YC4 promoters yields high-protein rice and soybean. | Wang L et al. | β | 2025 | β |
| CsMPDB 1.0: An interactive web application for visualizing and exploring the microRNAs and phasiRNAs of tea plant (Camellia sinensis var. sinensis 'Shuchazao'). | Zhao S et al. | β | 2025 | β |
| CTCF couples long-range loop extrusion and diffusion to mediate a diverse IgΞΊ repertoire. | Bush EL et al. | β | 2025 | β |
| DDX55 safeguards naΓ―ve T cell homeostasis by suppressing activation-promoting transposable elements. | Wu M et al. | β | 2025 | β |
| Deciphering genetic susceptibility to clear cell renal cell carcinoma. | Mandelia M et al. | β | 2025 | β |
| Deciphering the sequence basis and application of transcriptional initiation regulation in plant genomes through deep learning. | Gao P et al. | β | 2025 | β |
| Decoding and reengineering the promoter specificity of T7-like RNA polymerases based on phage genome sequences. | Zhu J et al. | β | 2025 | β |
| Decoding cell-class specific roles of non-coding variants in human retina. | VandenBosch LS et al. | β | 2025 | β |
| Decoding sex differences in human immunity through systems immunology. | EscrivΓ -Font J et al. | β | 2025 | β |
| Decoding SFRP2 progenitors in sustaining tooth growth at single-cell resolution. | Zhao T et al. | β | 2025 | β |
| Decoding tissue-specific enhancers in plants using massively parallel assays and deep learning. | Deng ιι 欣 Y et al. | β | 2025 | β |
| Deep learning reveals determinants of transcriptional infidelity at nucleotide resolution in the allopolyploid line by goldfish and common carp hybrids. | Jing K et al. | β | 2025 | β |
| Deep Neural Network-Mining of Rice Drought-Responsive TF-TAG Modules by a Combinatorial Analysis of ATAC-Seq and RNA-Seq. | Liu J et al. | β | 2025 | β |
| Deleting adipose FXR exacerbates metabolic defects and induces endocannabinoid lipid, 2-oleoyl glycerol, in obesity. | Zhou W et al. | β | 2025 | β |
| Depletion of LINC01133 from cancer-associated fibroblasts exacerbates the progression of gastric adenocarcinoma. | Liang X et al. | β | 2025 | β |
| Disease-linked regulatory DNA variants and homeostatic transcription factors in epidermis. | Porter DF et al. | β | 2025 | β |
| Disrupted development of sensory systems and the cerebellum in a zebrafish ebf3a mutant. | Dang NDP et al. | β | 2025 | β |
| Distinct roles of Atf3, Zfp711 and Bcl6b in early embryonic hematopoietic and endothelial lineage specification. | Cetin R et al. | β | 2025 | β |
| DNA probe pulldown screening uncovers O-GlcNAcylation modulation of transcription factor DNA interactions. | Li G et al. | β | 2025 | β |
| DNAproDB: an updated database for the automated and interactive analysis of protein-DNA complexes. | Mitra R et al. | β | 2025 | β |
| Domoic acid biosynthesis and genome expansion in <i>Nitzschia navis-varingica</i>. | Wood-Rocca SM et al. | β | 2025 | β |
| Dora, a key component of target-directed miRNA degradation, is essential for local genomic amplification in Drosophila ovarian follicle cells. | Akulenko N et al. | β | 2025 | β |
| Double and single stranded detection of 5-methylcytosine and 5-hydroxymethylcytosine with nanopore sequencing. | Halliwell DO et al. | β | 2025 | β |
| Dynamic barriers modulate cohesin positioning and genome folding at fixed occupancy. | Rahmaninejad H et al. | β | 2025 | β |
| Dynamic regulation and embryo-endosperm crosstalk revealed by whole transcriptome profiling of wheat seed development. | Guo X et al. | β | 2025 | β |
| E26 transformation-specific transcription factor 3 tips the balance: repressing tropomyosin 2 to fuel Yes-associated protein 1-driven cisplatin resistance in ovarian cancer. | Wang Y et al. | β | 2025 | β |
| E2F1-mediated <i>ESPL1</i> transcriptional activation predicts poor prognosis and promotes the proliferation of leiomyosarcoma. | Yang X et al. | β | 2025 | β |
| E2F1 suppresses Epstein-Barr virus lytic reactivation through cellular and viral transcriptional networks. | Biswas J et al. | β | 2025 | β |
| E2F2 inhibits hippocampal neurogenesis in poststroke depression rats via the miR-1290/CBR1 axis. | Yang X et al. | β | 2025 | β |
| Elucidating the chromatin-driven transcription regulatory networks response to Streptococcus agalactiae infection under low temperature in Nile tilapia. | Huang S et al. | β | 2025 | β |
| EnhancerMatcher: comparing cell-type-specific enhancer activity of DNA sequences using deep convolutional neural networks and explainable AI. | Solis LM et al. | β | 2025 | β |
| Enhancer regulatory networks globally connect non-coding breast cancer loci to cancer genes. | Wang Y et al. | β | 2025 | β |
| Enhancer RNA-mediated transcriptional regulatory programs reveal the malignant progression of glioma. | Ma Y et al. | β | 2025 | β |
| Epigenetic alteration of smooth muscle cells regulates endothelin-dependent blood pressure and hypertensive arterial remodeling. | Mangum KD et al. | β | 2025 | β |
| Epigenetic mechanism of iPSC-MSC-EVs in colonic epithelial cell pyroptosis in ulcerative colitis cell models via modulation of ELF3/miR-342-3p/KDM6B axis and histone methylation. | Li L et al. | β | 2025 | β |
| Ero1a, the most strongly hypoxia-induced protein in PASMCs, promotes the development of hypoxia- and monocrotaline-induced pulmonary hypertension in rats. | Hao X et al. | β | 2025 | β |
| ERΞ²/circAHNAK Axis Inhibits USP10-FMR1 Deubiquitination to Prevent mβΆA-Mediated ADAM17 Decay and Promote Angiogenesis in Clear Cell Renal Cell Carcinoma. | Xu C et al. | β | 2025 | β |
| Escape from X-chromosome inactivation at KDM5C is driven by promoter-proximal DNA elements and enhanced by domain context. | Peeters S et al. | β | 2025 | β |
| ETVs dictate hPSC differentiation by tuning biophysical properties. | ZiojΕa NM et al. | β | 2025 | β |
| Evidence for enhancer activity in intron 1 of TNFRSF1A using CRISPR/Cas9 in human induced pluripotent stem cell-derived macrophages. | Osgood JA et al. | β | 2025 | β |
| Evolution of cetacean-specific conserved non-coding elements suggests their role in the limb changes during secondary aquatic adaptation. | Zhang Z et al. | β | 2025 | β |
| Examination of MGMT as a risk gene for dementia in the Amish. | Main LR et al. | β | 2025 | β |
| Expansion of lysosomal capacity in early adult neurons driven by TFEB/HLH-30 protects dendrite maintenance during aging in Caenorhabditis elegans. | Zhong R et al. | β | 2025 | β |
| Exploring the maize transcriptional regulatory landscape through large-scale profiling of transcription factor binding sites. | Huo Q et al. | β | 2025 | β |
| Feedback regulation of m<sup>6</sup>A modification creates local auxin maxima essential for rice microsporogenesis. | Cheng P et al. | β | 2025 | β |
| Feedback regulation of retinaldehyde reductase DHRS3, a critical determinant of retinoic acid homeostasis. | Varshosaz P et al. | β | 2025 | β |
| FN1 Immunoregulation in Glioblastoma: Insights From Neutrophil-Centric Studies. | Meng X et al. | β | 2025 | β |
| FoxO1-zDHHC4-CD36 S-Acylation Axis Drives Metabolic Dysfunction in Diabetes. | Dennis KMJH et al. | β | 2025 | β |
| FOXP3 inhibits inflammatory activation of conjunctival epithelial cells in allergic conjunctivitis via the KAT5/PDCD4 axis. | Deng Z | β | 2025 | β |
| Frizzled5 controls murine intestinal epithelial cell plasticity through organization of chromatin accessibility. | Deng L et al. | β | 2025 | β |
| From trauma to resilience: psychological and epigenetic adaptations in the third generation of holocaust survivors. | Oren G et al. | β | 2025 | β |
| FTO-mediated m6A demethylation of KLF4 promotes the proliferation and collagen deposition of keloid fibroblasts. | Li Y et al. | β | 2025 | β |
| Functional maps of a genomic locus reveal confinement of an enhancer by its target gene. | Eder M et al. | β | 2025 | β |
| Gastrula-Premarked Posterior Enhancer Primes Posterior Tissue Development Through Cross-Talk with TGF-Ξ² Signaling Pathway. | Chen Y et al. | β | 2025 | β |
| GATA3-Driven ceRNA Network in Lung Adenocarcinoma Bone Metastasis Progression and Therapeutic Implications. | Liu Y et al. | β | 2025 | β |
| Gene expression divergence following gene and genome duplications in spatially resolved plant transcriptomes. | Almeida-Silva F et al. | β | 2025 | β |
| Gene regulatory networks and essential transcription factors for de novo-originated genes. | Peng J et al. | β | 2025 | β |
| Genetic and chromatin regulation of Pvt1 monoallelic expression. | Luong C et al. | β | 2025 | β |
| Genetic influence of a STAU2 frameshift mutation and RELN regulatory elements on performance in Icelandic horses. | SigurΓ°ardΓ³ttir H et al. | β | 2025 | β |
| Genetic regulation of the estrogen receptor and inherited predisposition to breast cancer. | Pierce SB et al. | β | 2025 | β |
| Genetic variation in a tandemly duplicated TPS gene cluster contributes to the diversity of aroma in lychee fruit. | Hu H et al. | β | 2025 | β |
| Genetic variation in the Nr1d1 transcription factor binding site shapes metabolism-related protein networks associated with cognitive resilience in an Alzheimer's disease mouse reference panel. | Chen Y et al. | β | 2025 | β |
| Genome-wide demethylation and targeted remethylation during metamorphosis in the jewel wasp Nasonia vitripennis. | Thomas CL et al. | β | 2025 | β |
| Genome-wide identification and expression analysis of HD-ZIP gene family in sunflower (Helianthus annuus L.) under water deficit stress. | Ahangarani Farahani YH et al. | β | 2025 | β |
| Genome-Wide Identification, Drought-Responsive Expression, and EAR-Mediated Regulatory Network Construction of <i>TOPLESS</i> Genes in <i>Populus ussuriensis Kom.</i> | Li W et al. | β | 2025 | β |
| Genome-wide investigation of transcription factor footprints and dynamics using cFOOT-seq. | Wang H et al. | β | 2025 | β |
| Genotype inference from aggregated chromatin accessibility data reveals genetic regulatory mechanisms. | Wenz BM et al. | β | 2025 | β |
| GnRHR inhibits the malignant progression of triple-negative breast cancer by upregulating FOS and IFI44L. | Chen C et al. | β | 2025 | β |
| H2AJ Is a Direct Androgen Receptor Target Gene That Regulates Androgen-Induced Cellular Senescence and Inhibits Mesenchymal Markers in Prostate Cancer Cells. | Heidari Horestani M et al. | β | 2025 | β |
| H3K4me2 distinguishes a distinct class of enhancers during the maternal-to-zygotic transition. | Hurton MD et al. | β | 2025 | β |
| HBV upregulates TNNT1 expression through PI3K/AKT/mTOR-c-Myc axis, which in turn induces EMT and liver fibrosis in mice. | Qu H et al. | β | 2025 | β |
| HDAC4 Inhibits NMDA Receptor-mediated Stimulation of Neurogranin Expression. | de AndrΓ©s R et al. | β | 2025 | β |
| Hepatic micropeptide modulates mitochondrial RNA processing machinery in hepatocellular carcinoma. | Zhu L et al. | β | 2025 | β |
| Hepatocyte nuclear factor 1 in renal lipid metabolism: molecular mechanisms and therapeutic potentials. | Zhu W et al. | β | 2025 | β |
| Hexosamine biosynthesis dysfunction-induced LIFR N-glycosylation deficiency exacerbates steatotic liver ischemia/reperfusion injury. | Liu R et al. | β | 2025 | β |
| HIF2Ξ± drives ccRCC metastasis through transcriptional activation of methylation-controlled J protein and enhanced prolegumain secretion. | Shen T et al. | β | 2025 | β |
| High expression of <i>THY1</i> is a prognostic marker for gastric Cancer: Deciphering its transcriptional regulation as a component of the Epithelial-mesenchymal transition. | Rohan P et al. | β | 2025 | β |
| Highly Conserved STAT3 Motifs Present in the Neuronal Pomc Enhancer nPE1 are Critical for Maximal Hypothalamic Pomc Expression. | Hael CE et al. | β | 2025 | β |
| High MRPL12 expression drives esophageal cancer proliferation, invasion and migration. | Wang G et al. | β | 2025 | β |
| High-throughput transcriptome analysis reveals a developmental increase in Acvr1c which mediates epigenetic repression of the gene encoding the pubertal brake, Makorin ring finger protein 3. | Shalev D et al. | β | 2025 | β |
| HSF1 and CPSF1 affect milk fat and protein synthesis by regulating the AKT/mTOR signaling pathway. | Chen Z et al. | β | 2025 | β |
| Human-specific genomic evolution of a regulatory network enables fine-tuning of N-cadherin gene expression. | Erdmann Γ et al. | β | 2025 | β |
| Hyperactive 20<i>S</i> proteasome enhances proteostasis and ERAD in <i>C. elegans</i> via degradation of intrinsically disordered proteins. | Salcedo-Tacuma D et al. | β | 2025 | β |
| Hypomethylation of the MEG8:Int2-DMR in patients with pathogenic PLAG1 variants suggests new role of the chr14q32 imprinting cluster in Silver-Russell syndrome. | D'Angelo E et al. | β | 2025 | β |
| Identification of biomarkers associated with programmed cell death in liver ischemia-reperfusion injury: insights from machine learning frameworks and molecular docking in multiple cohorts. | Liu J et al. | β | 2025 | β |
| Identification of candidate transcription factors that regulate Sox9 expression through the testis-specific enhancer in the Amami spiny rat Tokudaia osimensis, an XO/XO mammal. | Mitsukawa S et al. | β | 2025 | β |
| Identification of Indoquinazoline Derivatives as Novel NR4A1 Agonists by Suppressing Adipocyte Lipogenesis for Treatment of Obesity. | Hu YT et al. | β | 2025 | β |
| Identification of transcription factors that regulate placental sFLT1 expression. | Yong Q et al. | β | 2025 | β |
| Identifying deleterious noncoding variation through gain and loss of CTCF binding activity. | Tubbs C et al. | β | 2025 | β |
| Identifying Lactylation-related biomarkers and therapeutic drugs in ulcerative colitis: insights from machine learning and molecular docking. | Yang Y et al. | β | 2025 | β |
| IFNΞ³ regulates MR1 transcription and antigen presentation. | Huber ME et al. | β | 2025 | β |
| Immune evasion from macrophages by NEAT1-induced CD24 in liver cancer. | Tsuchiya H et al. | β | 2025 | β |
| Inference of transcriptional regulation from STARR-seq data. | Safaeesirat A et al. | β | 2025 | β |
| Inflammatory cytokines promote interferon regulatory factor (IRF) transcriptional activity in human pulmonary epithelial cells through the induction of IRF1 by nuclear factor-ΞΊB. | Necker-Brown A et al. | β | 2025 | β |
| INHBA, transcriptionally activated by SPI1, facilitates gastric cancer progression by inducing macrophage recruitment and M2 polarization via activating the TGF-Ξ² signaling to increase CCL2. | Zhang F et al. | β | 2025 | β |
| Inhibition of UBE2C Promotes Parkin-Mediated K63-Linked Ubiquitination of TOP2A to Induce Senescence and Increase Sensitivity of Doxorubicin in Breast Cancer. | Yang Y et al. | β | 2025 | β |
| InsectTFDB: A Comprehensive Database and Analysis Platform for Insect Transcription Factors. | Zhou H et al. | β | 2025 | β |
| Insight into the genetic network governing long-stalked glandular trichome development in Nicotiana tabacum. | Berhin A et al. | β | 2025 | β |
| Insulin levels at 18-20 gestational weeks in pregnant women with obesity are associated with newborn abdominal fat deposition and DNA methylation in cord blood. | Maguolo A et al. | β | 2025 | β |
| Integrated insights into gene expression dynamics and transcription factor roles in diabetic and diabetic-infectious wound healing using rat model. | Sharma V et al. | β | 2025 | β |
| Integrated methylome analysis identifies an epigenetically silenced tumor suppressor RASA4 in small cell lung cancer. | Fu M et al. | β | 2025 | β |
| Integrated screens identify AURKB dependency in advanced gastrointestinal stromal tumors. | Cheng Y et al. | β | 2025 | β |
| Integrated single-cell multiomic profiling of caudate nucleus suggests key mechanisms in alcohol use disorder. | Green NC et al. | β | 2025 | β |
| Integrating bioinformatics and machine learning to identify glomerular injury genes and predict drug targets in diabetic nephropathy. | Zhang L et al. | β | 2025 | β |
| Integrative analysis of senescence-related genes identifies robust prognostic clusters with distinct features in hepatocellular carcinoma. | Liu S et al. | β | 2025 | β |
| Integrative genome and transcriptome analysis identifies smoke-responsive glycosyltransferases in grapevine berries. | Paineau M et al. | β | 2025 | β |
| Integrative Multimodal Profiling of TAp73 and DNp73 Reveals Isoform-Specific Transcriptomic Coregulator Landscapes in Cancer Programs. | MΓΆller S et al. | β | 2025 | β |
| Interaction of neuropilin-1 and hepatocyte growth factor/C-Met pathway in liver fibrosis progression in hepatocyte-specific NRP-1 knockout mice. | Ding H et al. | β | 2025 | β |
| Interferon regulatory factor 4 mediates nonenzymatic IRE1 dependency in multiple myeloma cells. | Oikonomidi I et al. | β | 2025 | β |
| Interpretable and integrative analysis of single-cell multiomics with scMKL. | Kupp SD et al. | β | 2025 | β |
| Interpreting the CTCF-mediated sequence grammar of genome folding with AkitaV2. | Smaruj PN et al. | β | 2025 | β |
| Intratumoral Brevibacillus parabrevis enhances antitumor immunity by inhibiting NK cell ferroptosis in hepatocellular carcinoma. | Pan B et al. | β | 2025 | β |
| Investigating associations between JAK inhibition and venous thromboembolism by systematic mining of large-scale datasets. | Haysen SR et al. | β | 2025 | β |
| Investigating the Oncogenic and Immunological Implications of YTHDF1 in Ovarian Cancer. | Yin B et al. | β | 2025 | β |
| IPMK depletion influences genome-wide DNA methylation. | Sin Z et al. | β | 2025 | β |
| Isoliquiritigenin Inhibits Triple-Negative Breast Cancer Progression via Targeting the IRF5/SLC7A5/IDO1-Mediated Tryptophan Metabolism Pathway. | Duan S et al. | β | 2025 | β |
| KDM2B promotes chemoresistance in glioma cells by inhibiting ferroptosis via the LINC01018/miR-182-5p axis. | Hu S et al. | β | 2025 | β |
| KLF1 Promotes Non-Small Cell Lung Cancer Cell Proliferation and Invasion by Upregulating the LINC02159/DYNC1H1 Pathway. | Yang H | β | 2025 | β |
| KLF4 mediates the contradictory effects of phenylethyl isothiocyanate in gastric cancer intervention. | Zhang Q et al. | β | 2025 | β |
| Klf5-adjacent super-enhancer functions as a 3D genome structure-dependent transcriptional driver to safeguard ESC identity. | Su G et al. | β | 2025 | β |
| KLF5 facilitates lung adenocarcinoma metastasis by regulating the epithelial-mesenchymal transition pathway through RHPN2. | Zhang T et al. | β | 2025 | β |
| KSHVbook: An Information-Sharing Database for Kaposi's Sarcoma-Associated Herpesvirus. | Jiang Y et al. | β | 2025 | β |
| Kujigamberol Inhibits IFN-Ξ³ and IL-2 mRNA Expression and NFATc2 Binding to Their Promoters in Response to a Phorbol Ester and Ionomycin Stimulation. | Yodweerapong T et al. | β | 2025 | β |
| LCORL and STC2 Variants Increase Body Size and Growth Rate in Cattle and Other Animals. | Bai F et al. | β | 2025 | β |
| Leveraging prior knowledge to infer gene regulatory networks from single-cell RNA-sequencing data. | Stock M et al. | β | 2025 | β |
| Limitations in PPARΞ±-dependent mitochondrial programming restrain the differentiation of human stem cell-derived Ξ² cells. | Lietzke AC et al. | β | 2025 | β |
| LINC01783 Promotes Glioma Tumorigenesis by Enhancing GATA3 Expression Through CBP-Mediated H3K27 Acetylation to Suppress PTEN Expression. | Hao S et al. | β | 2025 | β |
| LINC02878/ZNF282/PYCR2 axis promotes proline synthesis and tumor progression in colorectal cancer. | Lei JP et al. | β | 2025 | β |
| Linkage: an interactive web application for linking of DNA regulatory peaks to genes. | Xu S et al. | β | 2025 | β |
| Loss of Adenosine Deaminase Acting on RNA 1 Induces Panoptosis and Immune Response in Ulcerative Colitis Gut Mucosa. | Iannucci A et al. | β | 2025 | β |
| Loss of negative regulation by HDAC1 and REST contributes to MAD1 overexpression in breast cancer. | Copeland SE et al. | β | 2025 | β |
| Low-Density Lipoprotein Receptor-Related Protein 11 Promotes Proliferation in Lung Adenocarcinoma. | Kiwaki T et al. | β | 2025 | β |
| Low Expression of Selenoprotein S Modulates Osteogenic Differentiation Through Bidirectional Regulation of the <i>SP7</i>-<i>HSP47</i>/<i>COL1A1</i>/<i>SPARC</i> Axis. | Wu H et al. | β | 2025 | β |
| <i>Cis</i>-Regulation of the <i>CFTR</i> Gene in Pancreatic Cells. | Blotas C et al. | β | 2025 | β |
| <i>Cis</i>-regulatory elements: systematic identification and horticultural applications. | Li T et al. | β | 2025 | β |
| <i>In vitro</i> and <i>in silico</i> insights on the regulation by gonadal hormones of pituitary GnRH receptor expression in a basal teleost, the European eel. | Lin CJ et al. | β | 2025 | β |
| Machine learning and WGCNA reveal the PVT1/miR-143-3p/CDK1 ceRNA axis as a key regulator in NSCLC. | Safarzadeh A et al. | β | 2025 | β |
| MAFin: motif detection in multiple alignment files. | Patsakis M et al. | β | 2025 | β |
| MAGIC: A Multimodal Adaptive GRN Inference Constructor. | Yao D et al. | β | 2025 | β |
| Mapping rat lncRNA Bdnf-as. | Shaburova EV et al. | β | 2025 | β |
| Marker Metabolite-Based Multi-Omics Analysis Identifies New Loci Controlling Thousand Seed Weight in Brassica Napus. | Li L et al. | β | 2025 | β |
| Maternal behavior promotes resilience to adolescent stress in mice through a microglia-neuron axis. | Chen H et al. | β | 2025 | β |
| McACO2 gene promotes ethylene-mediated scopoletin biosynthesis in noni (Morinda citrifolia). | Wang Q et al. | β | 2025 | β |
| MCTASmRNA: A deep learning framework for alternative splicing events classification. | Zheng JY et al. | β | 2025 | β |
| Mechanism of EZH2-mediated histone methylation promoting bFGF-induced angiogenesis of human umbilical vein endothelial cells. | Gao M et al. | β | 2025 | β |
| Mechanism of FOXC1 in the invasion and migration of ectopic endometrial stromal cells in endometriosis. | Huang R et al. | β | 2025 | β |
| Mechanism of LncRNA CBR3-AS1 in regulating pyroptosis of intestinal epithelial cells in ulcerative colitis. | Li X et al. | β | 2025 | β |
| Mechanism of RBM15 in the malignant proliferation of colorectal cancer cells through regulating the stability of LncRNA FGD5-AS1 via m6A modification. | Ma L et al. | β | 2025 | β |
| MEIS1βregulated miRβ488β3p suppresses the malignant progression of laryngeal squamous cell carcinoma by targeting ACVR1C. | Zhang C et al. | β | 2025 | β |
| Melanin deposition and key molecular features in Xenopus tropicalis oocytes. | Yi H et al. | β | 2025 | β |
| Modeling and designing enhancers by introducing and harnessing transcription factor binding units. | Li J et al. | β | 2025 | β |
| Molecular determinants of thrombosis recurrence risk across venous thromboembolism subtypes. | Munsch G et al. | β | 2025 | β |
| Molecular mechanism of METTL14-mediated m6A modification regulating microglial function post ischemic stroke. | Zhang X et al. | β | 2025 | β |
| Molecular mechanism of the crosstalk between glucocorticoid receptor (GR) and hypoxia-inducible factor 3Ξ± (HIF-3Ξ±) pathways. | Zhang M et al. | β | 2025 | β |
| Molecular Mechanism of the IRF1/NFE2L1-DT/ALKBH5/Cx43 Axis in Radiation-Induced Injury in Vascular Endothelial Cells Through Pyroptosis. | Li C et al. | β | 2025 | β |
| Molecular Subtypes and Biomarkers of Ulcerative Colitis Revealed by Sphingolipid Metabolism-Related Genes: Insights from Machine Learning and Molecular Dynamics. | Li Q et al. | β | 2025 | β |
| Mouse cortical cellular diversification through lineage progression of radial glia. | Yang L et al. | β | 2025 | β |
| Multimodal single cell analyses reveal gene networks of planarian stem cell differentiation. | PΓ©rez-Posada A et al. | β | 2025 | β |
| Multi-omics analyses identify mannose phosphate isomerase-centered hypoxia-induced angiogenesis signature in colorectal cancer. | Liu S et al. | β | 2025 | β |
| Multi-omics analysis of <i>Taiwanofungus gaoligongensis</i>: effects of different cultivation methods on secondary metabolites. | He T et al. | β | 2025 | β |
| Multi-omics integration analysis of the amino-acid metabolism-related genes identifies putatively causal variants of ACCS associated with hepatitis B virus-related hepatocellular carcinoma survival. | Wei X et al. | β | 2025 | β |
| Mutant THAP11 causes cerebellar neurodegeneration and triggers TREM2-mediated microglial activation in mice. | Ruan E et al. | β | 2025 | β |
| MYC/TET3-Regulated TMEM65 Activates OXPHOS-SERPINB3 Pathway to Promote Progression and Cisplatin Resistance in Triple-Negative Breast Cancer. | Zhang YL et al. | β | 2025 | β |
| MYEOV Is a Novel Marker of Differentiated Corneal Epithelium. | Fukuda Y et al. | β | 2025 | β |
| Native top-down proteomics enables discovery in endocrine-resistant breast cancer. | Gomes FP et al. | β | 2025 | β |
| N-glycosylated LTΞ²R increases the Th17/Treg cell ratio in liver cancer by blocking RORC ubiquitination and FOXP3 transcription. | Pan B et al. | β | 2025 | β |
| Novel environment exposure drives temporally defined and region-specific chromatin accessibility and gene expression changes in the hippocampus. | TraunmΓΌller L et al. | β | 2025 | β |
| Novel Truncated Peptide Derived From circCDYL Exacerbates Cardiac Hypertrophy. | Li M et al. | β | 2025 | β |
| N-terminal basic residues of HOXD9 homeodomain drives its target-site searching along DNA. | Li S et al. | β | 2025 | β |
| Nucleosome binding by TP53, TP63, and TP73 is determined by the composition, accessibility, and helical orientation of their binding sites. | Wilson PD et al. | β | 2025 | β |
| o8G-modified circKIAA1797 promotes lung cancer development by inhibiting cuproptosis. | Xu H et al. | β | 2025 | β |
| Obesity induced transcriptional changes in skeletal muscle across different species. | Wang Y et al. | β | 2025 | β |
| On the analysis of genetic association with long-read sequencing data. | He G et al. | β | 2025 | β |
| Palmitoylation Dynamics in Systemic Lupus Erythematosus: Multi-Omics Insights and Potential Therapeutic Implications. | Liu Z et al. | β | 2025 | β |
| PBK/TOPK mediates Ikaros, Aiolos and CTCF displacement from mitotic chromosomes and alters chromatin accessibility at selected C2H2-zinc finger protein binding sites. | Dimond A et al. | β | 2025 | β |
| Perimenopausal state oestradiol to progesterone imbalance drives Alzheimer's risk via ERRΞ± dysregulation and energy dyshomeostasis. | Sun JK et al. | β | 2025 | β |
| PERP suppresses breast cancer metastasis via the ATF3-HSPA6 signaling pathway. | Chen C et al. | β | 2025 | β |
| Perspective on recent developments and challenges in regulatory and systems genomics. | Zeitlinger J et al. | β | 2025 | β |
| Phytochrome B-mediated light signalling enhances rice resistance to saline-alkaline and sheath blight by regulating multiple downstream transcription factors. | Chen H et al. | β | 2025 | β |
| Plac1<sup>+</sup> Tumor Cell-Treg Interplay Supports Tumorigenesis and Progression of Head and Neck Cancer. | Meng X et al. | β | 2025 | β |
| Polygraph: a software framework for the systematic assessment of synthetic regulatory DNA elements. | Lal A et al. | β | 2025 | β |
| Polyphyllin VII promotes hepatic stellate cell ferroptosis via the HIC1/CX3CL1/GPX4 axis. | Jiang F et al. | β | 2025 | β |
| Pra-GE-ATLAS: Empowering Pinus radiata stress and breeding research through a multi-omics database. | Roces V et al. | β | 2025 | β |
| Predicting rare DNA conformations via dynamical graphical models: a case study of the BβA transition. | De Silva N et al. | β | 2025 | β |
| PRMT1 inhibition enhances the cardioprotective effect of adipose-derived mesenchymal stem cells against myocardial infarction through RUNX1. | Du D et al. | β | 2025 | β |
| Programs, origins and immunomodulatory functions of myeloid cells in glioma. | Miller TE et al. | β | 2025 | β |
| Promoter Motif Profiling and Binding Site Distribution Analysis of Transcription Factors Predict Auto- and Cross-Regulatory Mechanisms in <i>Arabidopsis</i> Flowering Genes. | VirΓ‘g E et al. | β | 2025 | β |
| Proteomic- and metabolomic-based mechanisms of androgen-mediated right ventricular maladaptive remodeling under pressure overload. | Zhang J et al. | β | 2025 | β |
| QTFPred: robust high-performance quantum machine learning modeling that predicts main and cooperative transcription factor bindings with base resolution. | Matsubara T et al. | β | 2025 | β |
| Quantifying transcription factor specificity with advanced DNA universal microarrays featuring long and modified binding sites. | Bayer Y et al. | β | 2025 | β |
| Reactivation of an embryonic cardiac neural crest transcriptional profile during zebrafish heart regeneration. | Dhillon-Richardson RM et al. | β | 2025 | β |
| Receptor tyrosine kinase inhibitor tivozanib regulates cell state plasticity and restores MITF dependency in BRAF wild-type melanoma. | Ma YN et al. | β | 2025 | β |
| Regulatory Mechanisms of SPARC Overexpression in Melanoma Progression. | Vinyals A et al. | β | 2025 | β |
| Regulatory Plasticity of the Human Genome. | Srivastava J et al. | β | 2025 | β |
| RelA Inhibits Embryonic Myogenesis by Coordinately Regulating a Novel Distal Enhancer of Myogenin. | Hossain MN et al. | β | 2025 | β |
| Retinoic acid and ascorbate synergize to suppress myeloid leukemia via TET2 activation. | Leesang TE et al. | β | 2025 | β |
| Rewiring of 3D chromatin topology orchestrates transcriptional reprogramming in muscle fiber-type specification and transformation. | Tan B et al. | β | 2025 | β |
| Rewriting regulatory DNA to dissect and reprogram gene expression. | Martyn GE et al. | β | 2025 | β |
| Rise and SINE: roles of transcription factors and retrotransposons in zygotic genome activation. | Kravchenko P et al. | β | 2025 | β |
| RIT1 Promotes the Proliferation of Gliomas Through the Regulation of the PI3K/AKT/c-Myc Signalling Pathway. | Liu Z et al. | β | 2025 | β |
| Role of Activating Transcription Factor 3 in Hyperosmotic Stress-Induced Human Corneal Epithelial Cell Damage. | Gao M et al. | β | 2025 | β |
| scNucMap: mapping the nucleosome landscapes at single-cell resolution. | Xiang Q et al. | β | 2025 | β |
| ScRDAVis: An R shiny application for single-cell transcriptome data analysis and visualization. | Jagadesan S et al. | β | 2025 | β |
| SCRIPT: Predicting Single-Cell Long-Range Cis-Regulation Based on Pretrained Graph Attention Networks. | Zhang Y et al. | β | 2025 | β |
| Secreted LGALS3BP facilitates distant metastasis of breast cancer. | Kim SS et al. | β | 2025 | β |
| SerpinA3N inhibits mitochondrial complex I activity to prevent neuron ferroptosis following cerebral ischemic stroke. | Liu X et al. | β | 2025 | β |
| Sex differences in DNA methylation in bats. | Rayner JG et al. | β | 2025 | β |
| Short-term starvation inhibits CD36 N-glycosylation and downregulates USP7 UFMylation to alleviate RBPJ-maintained T cell exhaustion in liver cancer. | Pan B et al. | β | 2025 | β |
| Similar Genetic Routes Are Independently Targeted for Mimetic Color Convergence in Bumble Bees. | Hines HM et al. | β | 2025 | β |
| Simultaneous capture of single cell RNA-seq, ATAC-seq, and CRISPR perturbation enables multiomic screens to identify gene regulatory relationships. | Shevade K et al. | β | 2025 | β |
| Single-cell multi-omics analysis reveals the plasticity of isthmus stem cells in gastric carcinogenesis. | Liu A et al. | β | 2025 | β |
| Single-Cell Transcriptome Profiling Reveals Conserved IFNΞ³-IL8 Signaling-Induced Antibacterial Neutrophil States during Bacterial Infection. | Zhai X et al. | β | 2025 | β |
| Single-cell ultra-high-throughput multiplexed chromatin and RNA profiling reveals gene regulatory dynamics. | Lobato-Moreno S et al. | β | 2025 | β |
| Sociability genetically separable from social hierarchy in amniotes. | Lin X et al. | β | 2025 | β |
| SOX11-mediated CBLN2 Upregulation Contributes to Neuropathic Pain through NF-ΞΊB-Driven Neuroinflammation in Dorsal Root Ganglia of Mice. | Ma LJ et al. | β | 2025 | β |
| SOX12 promotes serine synthesis and tumor progression in endometrial cancer. | Zhang ZH et al. | β | 2025 | β |
| Sox9 regulates Papss2 mRNA expression through derepression of the transcriptional repressor, C/EBPΞ², in chondrogenic cells. | Liu C et al. | β | 2025 | β |
| SPONGE: simple prior omics network GEnerator. | Hovan L et al. | β | 2025 | β |
| SRGN-mediated reactivation of the YAP/CRISPLD2 axis promotes aggressiveness of hepatocellular carcinoma. | Zhang S et al. | β | 2025 | β |
| STAT3 expression is reduced in cardiac pericytes in HFpEF and its loss reduces cellular adhesion and induces pericyte senescence. | Vanicek LR et al. | β | 2025 | β |
| Structural basis for genome-wide site-specific DNA recognition by Nuclear Factor IA. | Zhu C et al. | β | 2025 | β |
| SUMOylation of RAD51 upregulates GOLPH3 expression and promotes cisplatin resistance in colon cancer cells by Sp1 transcriptional activity. | Wu Y et al. | β | 2025 | β |
| Systematic Identification of Mitochondrial Signatures in Alzheimer's Disease and Inflammatory Bowel Disease. | Wang F et al. | β | 2025 | β |
| TACC3 enhances glycolysis in bladder cancer cells through inducing acetylation of c-Myc. | Lin Z et al. | β | 2025 | β |
| Targeting AKR1B1 inhibits metabolic reprogramming to reverse systemic therapy resistance in hepatocellular carcinoma. | Wang Q et al. | β | 2025 | β |
| Targeting MTPN sensitizes pancreatic cancer of wild-type BRCA1/2 to Cisplatin-based chemotherapy. | Wang Z et al. | β | 2025 | β |
| Targeting PIKfyve-driven lipid metabolism in pancreatic cancer. | Cheng C et al. | β | 2025 | β |
| Targeting RAS-mutant cancer cells using a synthetic RAS-activated cancer killing system. | Teng F et al. | β | 2025 | β |
| Targeting RBM39 suppresses tumor growth and sensitizes osteosarcoma cells to cisplatin. | Wang J et al. | β | 2025 | β |
| Targeting Sodium Transport Reveals CHP1 Downregulation as a Novel Molecular Feature of Malignant Progression in Clear Cell Renal Cell Carcinoma: Insights from Integrated Multi-Omics Analyses. | Wu Y et al. | β | 2025 | β |
| Targeting TAZ-TEAD in minimal residual disease enhances the duration of targeted therapy in melanoma models. | Ott CA et al. | β | 2025 | β |
| Targeting the HLA-E-NKG2A axis in combination with MS-275 enhances NK cell-based immunotherapy against DMG. | Deng Y et al. | β | 2025 | β |
| Targets of the transcription factor Six1 identify previously unreported candidate deafness genes. | Ranganathan R et al. | β | 2025 | β |
| TCP19 regulates nitrogen-dependent sheath blight susceptibility by modulating nitrogen uptake and signalling in rice. | Zhou T et al. | β | 2025 | β |
| Temporally discordant chromatin accessibility and DNA demethylation define short- and long-term enhancer regulation during cell fate specification. | Guerin LN et al. | β | 2025 | β |
| TFcomb identifies transcription factor combinations for cellular reprogramming based on single-cell multiomics data. | Li C et al. | β | 2025 | β |
| The cGAS-STING pathway is a master regulator of OCT4 expression in persistent sarcoma cells and enhances cellular immunotherapy with NK and CIK lymphocytes. | Giordano G et al. | β | 2025 | β |
| The contrasting regulatory effects of valproic acid on ferroptosis and disulfidptosis in hepatocellular carcinoma. | Liu R et al. | β | 2025 | β |
| The dual-targeted transcription factor BAI1 orchestrates nuclear and plastid gene transcription in land plants. | Qin J et al. | β | 2025 | β |
| The Dysregulation of Tuning Receptors and Transcription Factors in the Antennae of <i>Orco</i> and <i>Ir8a</i> Mutants in <i>Aedes aegypti</i> Suggests a Chemoreceptor Regulatory Mechanism Involving the MMB/dREAM Complex. | Cooke MM et al. | β | 2025 | β |
| The ELF3-TRIM22-MAVS signaling axis regulates type I interferon and antiviral responses. | Zhao Q et al. | β | 2025 | β |
| The emerging sequence grammar of 3D genome organisation. | Tamon L et al. | β | 2025 | β |
| The feedback loop between miR-222-3p and ZEB1 harnesses metastasis in renal cell carcinoma. | Wang F et al. | β | 2025 | β |
| The Fire Ant Social Chromosome Exerts a Major Influence on Genome Regulation. | Jones BM et al. | β | 2025 | β |
| The gene regulatory landscape driving mouse gonadal supporting cell differentiation. | StΓ©vant I et al. | β | 2025 | β |
| The homeotic gene PhDEF regulates production of volatiles in petunia flowers by activating EOBI and EOBII. | Bednarczyk D et al. | β | 2025 | β |
| The human proteome with direct physical access to DNA. | Trendel J et al. | β | 2025 | β |
| The impact of tokenizer selection in genomic language models. | Lindsey LM et al. | β | 2025 | β |
| The inbred newt genome unveils molecular mechanisms of behavior, development, and regeneration in urodele amphibians. | Kimura Y et al. | β | 2025 | β |
| The long-term associations of childhood parental loss with attachment, creativity, and epigenetic regulation. | Dvilansky AS et al. | β | 2025 | β |
| The myoblast methylome: multiple types of associations with chromatin and transcription. | Sen S et al. | β | 2025 | β |
| The p53-miR17 family-Rankl axis bridges liver-bone communication. | Ma G et al. | β | 2025 | β |
| The proximal enhancer of the snail gene mediates negative autoregulatory feedback in Drosophila melanogaster. | Dunipace L et al. | β | 2025 | β |
| The Relevance of G-Quadruplexes in Gene Promoters and the First Introns Associated with Transcriptional Regulation in Breast Cancer. | Shu H et al. | β | 2025 | β |
| The RSPO2 gene is associated with bilateral anterior amelia in Chihuahuas. | Chevallier L et al. | β | 2025 | β |
| The specificity landscape of WRKY transcription factors reveals the bidirectional influence of non-CG methylation. | Ma N et al. | β | 2025 | β |
| The sweet and the bitter sides of galectin-1 in immunity: its role in immune cell functions, apoptosis, and immunotherapies for cancer with a focus on T cells. | NovΓ‘k J et al. | β | 2025 | β |
| The toggle switch model for gene expression change during duck skeletal muscle development. | Ding D et al. | β | 2025 | β |
| The toll signaling pathway confers resistance of Neoseiulus barkeri to Beauveria bassiana via cascade lysozyme expression. | Niu T et al. | β | 2025 | β |
| The viral proteins of influenza A virus competitively bind to TRIM31 with MAVS to fine-tune the antiviral innate immunity. | Huang J et al. | β | 2025 | β |
| Tie2-expressing monocytes/macrophages promote angiogenesis in chronically ischaemic brain tissue. | Tai C et al. | β | 2025 | β |
| Toll-Interacting Protein Down-Regulation by Cigarette Smoke Exposure Impairs Human Lung Defense against Influenza A Virus Infection. | Agraval H et al. | β | 2025 | β |
| Tomtom-lite: accelerating Tomtom enables large-scale and real-time motif similarity scoring. | Schreiber J | β | 2025 | β |
| Total glucosides of paeony ameliorates lupus nephritis by suppressing ZBP1-mediated PANoptosis in podocytes. | Wang Y et al. | β | 2025 | β |
| Transcriptional control in microalgae: co-regulated fatty acid biosynthesis and carbon dioxide fixation. | Kayani SI et al. | β | 2025 | β |
| Transcriptional regulation of the piRNA pathway by Ovo in animal ovarian germ cells. | Alizada A et al. | β | 2025 | β |
| Transcription factors in Orinus: novel insights into transcription regulation for speciation adaptation on the Qinghai-Xizang (Tibet) Plateau. | Min Q et al. | β | 2025 | β |
| Transcription start sites experience a high influx of heritable variants fueled by early development. | CortΓ©s GuzmΓ‘n M et al. | β | 2025 | β |
| Transcriptomic and lipidomic analysis of aging-associated inflammatory signature in mouse liver. | Ishihara T et al. | β | 2025 | β |
| Transcriptomic profiling in canine B-cell lymphoma supports a synergistic effect of BTK and PI3K inhibitors. | Lainscsek X et al. | β | 2025 | β |
| Transposable elements drive evolution and perturb gene expression in Brassica rapa and B. oleracea. | Zheng PX et al. | β | 2025 | β |
| Transposable elements drive species-specific and tissue-specific transcriptomes in human development. | Zhang Y et al. | β | 2025 | β |
| Trem2+ Macrophages Alleviate Renal Tubule Lipid Accumulation and Ferroptosis in Diabetic Nephropathy by Repressing IL-1Ξ²-Mediated CD36 Expression. | Wang X et al. | β | 2025 | β |
| tRF3a-MetCAT Promotes EGFR-Targeted Therapeutic Resistance through the TRIM21-STAT1-C5a Axis in Lung Adenocarcinoma. | Zhang Y et al. | β | 2025 | β |
| TRIM21-mediated ubiquitination of SIX2 attenuates breast cancer stemness via LGSN suppression. | Chen H et al. | β | 2025 | β |
| Tryptophan metabolism-related gene CYP1B1 serves as a shared biomarker for both Parkinson's disease and insomnia. | Li XY et al. | β | 2025 | β |
| Two Cohorts, One Network: Consensus Master Regulators Orchestrating Papillary Thyroid Carcinoma. | Tapia-Carrillo D et al. | β | 2025 | β |
| Ultrastable and versatile multimeric ensembles of FoxP3 on microsatellites. | Leng F et al. | β | 2025 | β |
| Uncovering the chromatin-mediated transcriptional regulatory network governing cold stress responses in fish immune cells. | Jiao H et al. | β | 2025 | β |
| Understanding the regulatory grammar of sepsis-causing Staphylococcus aureus bacteria using contexualised DNA language models. | Chen T et al. | β | 2025 | β |
| Unraveling the Role of MDK-SDC4 Interaction in Pancreatic Cancer-Associated New-Onset Diabetes by Single-Cell Transcriptomic Analysis. | Feng Z et al. | β | 2025 | β |
| Unveiling a pervasive DNA adenine methylation regulatory network in the early-diverging fungus Rhizopus microsporus. | Lax C et al. | β | 2025 | β |
| Unveiling regulatory variants in the blood transcriptome and their association with immunity traits in pigs. | JovΓ©-JuncΓ T et al. | β | 2025 | β |
| USF1-activated hsa_circ_0076691 induces oxaliplatin resistance via facilitating FGF9 expression in miR-589-3p-dependent manners. | Tang L et al. | β | 2025 | β |
| USP10 Inhibits Ferroptosis via Deubiquinating POLR2A in Head and Neck Squamous Cell Carcinoma. | Zhang D et al. | β | 2025 | β |
| USP18 deubiquitinates and stabilizes SOX9 to promote the stemness and malignant progression of glioblastoma. | Liu Z et al. | β | 2025 | β |
| Variant-specific disruption to notch signalling in PAX6 microphthalmia and aniridia patient-derived hiPSC optic cup-like organoids. | Harding P et al. | β | 2025 | β |
| VEGF-A cis-located SNPs on human chromosome 6 associated with VEGF-A plasma levels and survival in a coronary disease cohort. | Meza-Alvarado JC et al. | β | 2025 | β |
| Viral Appropriation of Specificity Protein 1 (Sp1): The Role of Sp1 in Human Retro- and DNA Viruses in Promoter Activation and Beyond. | Sviderskaia K et al. | β | 2025 | β |
| Virus-Host Interaction: Investigating Novel Transcription Factors Involved in Coupling Human Papillomavirus Life Cycle and Epithelial Differentiation. | Ribeiro AL et al. | β | 2025 | β |
| Whole-genome sequencing reveals complex structural variations at a major locus linked to pigmented spot sizes in Tianfu goats. | Guo J et al. | β | 2025 | β |
| YY1-induced DDX18 modulates EMT via the AKT/mTOR pathway in esophageal cancer: a novel therapeutic target. | Ma X et al. | β | 2025 | β |
| YY1 induced USP13 transcriptional activation drives the malignant progression of hepatocellular carcinoma by deubiquitinating WWP1. | Zhu Q et al. | β | 2025 | β |
| A Bioinformatically Initiated Approach to Evaluate GATA1 Regulatory Regions in Samples with Weak D, Del, or D- Phenotypes Despite Normal <i>RHD</i> Exons. | McGowan EC et al. | β | 2024 | β |
| Agonists of the Nuclear Receptor PPARΞ³ Can Produce Biased Signaling. | Rayl ML et al. | β | 2024 | β |
| A miR-219-5p-bmal1b negative feedback loop contributes to circadian regulation in zebrafish. | Wu L et al. | β | 2024 | β |
| A novel <i>cis</i>-regulatory element regulates Ξ±D and Ξ±A-globin gene expression in chicken erythroid cells. | CortΓ©s-FernΓ‘ndez de Lara J et al. | β | 2024 | β |
| A novel interpretable deep learning-based computational framework designed synthetic enhancers with broad cross-species activity. | Li Z et al. | β | 2024 | β |
| ARID1B controls transcriptional programs of axon projection in an organoid model of the human corpus callosum. | Martins-Costa C et al. | β | 2024 | β |
| A role for TRPC3 in mammalian testis development. | Ming Z et al. | β | 2024 | β |
| Assessing next-generation sequencing-based computational methods for predicting transcriptional regulators with query gene sets. | Lu Z et al. | β | 2024 | β |
| Bmi-1 Epigenetically Orchestrates Osteogenic and Adipogenic Differentiation of Bone Marrow Mesenchymal Stem Cells to Delay Bone Aging. | Zhao J et al. | β | 2024 | β |
| CAF-EVs carry lncRNA MAPKAPK5-AS1 into hepatocellular carcinoma cells and promote malignant cell proliferation. | Sheng L et al. | β | 2024 | β |
| Cell-type-directed design of synthetic enhancers. | Taskiran II et al. | β | 2024 | β |
| CHAC1 blockade suppresses progression of lung adenocarcinoma by interfering with glucose metabolism via hijacking PKM2 nuclear translocation. | Pan J et al. | β | 2024 | β |
| ChIP-Atlas 3.0: a data-mining suite to explore chromosome architecture together with large-scale regulome data. | Zou Z et al. | β | 2024 | β |
| Cis-regulatory polymorphism at fiz ecdysone oxidase contributes to polygenic evolutionary response to malnutrition in Drosophila. | Cavigliasso F et al. | β | 2024 | β |
| Combinatorial targeting of glutamine metabolism and lysosomal-based lipid metabolism effectively suppresses glioblastoma. | Zhong Y et al. | β | 2024 | β |
| Comprehensive network modeling approaches unravel dynamic enhancer-promoter interactions across neural differentiation. | DeGroat W et al. | β | 2024 | β |
| Co-Regulation Mechanism of Host p53 and Fos in Transcriptional Activation of ILTV Immediate-Early Gene <i>ICP4</i>. | Liu Z et al. | β | 2024 | β |
| Correlating gene expression levels with transcription factor binding sites facilitates identification of key transcription factors from transcriptome data. | Huang T et al. | β | 2024 | β |
| CPT1A mediates radiation sensitivity in colorectal cancer. | Chen Z et al. | β | 2024 | β |
| Cross-Omic Transcription Factor Analysis: An Insight on Transcription Factor Accessibility and Expression Correlation. | Martini L et al. | β | 2024 | β |
| Decoding polygenic diseases: advances in noncoding variant prioritization and validation. | Chin IM et al. | β | 2024 | β |
| Deletions in the MAL gene result in loss of Mal protein, defining the rare inherited AnWj-negative blood group phenotype. | Tilley LA et al. | β | 2024 | β |
| Dissecting the functions and regulatory mechanisms of disulfidoptosis-related RPN1 in pan-cancer: modulation of immune microenvironment and cellular senescence. | Qin L et al. | β | 2024 | β |
| Distinct granzyme k expression in immune cells: a single-cell rna-seq meta-analysis. | Kim HY et al. | β | 2024 | β |
| Dual targeting macrophages and microglia is a therapeutic vulnerability in models of PTEN-deficient glioblastoma. | Liu Y et al. | β | 2024 | β |
| Effects of Red Sorghum-Derived Deoxyanthocyanidins and Their O-Ξ²-D-Glucosides on E-Cadherin Promoter Activity in PC-3 Prostate Cancer Cells. | Mora N et al. | β | 2024 | β |
| Engrailed 2 facilitates progression of triple-negative and HER2-enriched breast cancer by binding to enhancer region of Tenascin-C. | Chen D et al. | β | 2024 | β |
| eQTLs identify regulatory networks and drivers of variation in the individual response to sepsis. | Burnham KL et al. | β | 2024 | β |
| Exercise training attenuates cardiac dysfunction induced by excessive sympathetic activation through an AMPK-KLF4-FMO2 axis. | Fan S et al. | β | 2024 | β |
| Exploring the oncogenic potential of circSOD2 in clear cell renal cell carcinoma: a novel positive feedback loop. | Yao GS et al. | β | 2024 | β |
| Expression of Iron Metabolism Genes Is Potentially Regulated by DOF Transcription Factors in <i>Dendrocalamus latiflorus</i> Leaves. | Zhu PK et al. | β | 2024 | β |
| Ferritin-mediated mitochondrial iron homeostasis is essential for the survival of hematopoietic stem cells and leukemic stem cells. | Yi W et al. | β | 2024 | β |
| Functional redundancy of the three insulin receptors of cockroaches. | Pujal D et al. | β | 2024 | β |
| Genome-wide identification and diversity of FAD2, FAD3 and FAE1 genes in terms of biotechnological importance in Camelina species. | Blume RY et al. | β | 2024 | β |
| Genome-Wide Identification and Expression Analysis of Growth-Regulating Factor Family in Sweet Potato and Its Two Relatives. | Huang W et al. | β | 2024 | β |
| Genome-wide identification and expression analysis of the Trihelix transcription factor family in potato (<i>Solanum tuberosum</i> L.) during development. | Mei C et al. | β | 2024 | β |
| Genome-wide identification of TCP transcription factors and their potential roles in hydrolyzable tannin production in <i>Quercus variabilis</i> cupule. | Wang Y et al. | β | 2024 | β |
| Genome-wide single-cell and single-molecule footprinting of transcription factors with deaminase. | He R et al. | β | 2024 | β |
| Genomic background sequences systematically outperform synthetic ones in de novo motif discovery for ChIP-seq data. | Raditsa VV et al. | β | 2024 | β |
| High incidence and geographic distribution of cleft palate in Finland are associated with the IRF6 gene. | Rahimov F et al. | β | 2024 | β |
| Host genetics and microbiota data analysis in colorectal cancer research. | GonzΓ‘lez A et al. | β | 2024 | β |
| Huaier inhibits cholangiocarcinoma cells through the twist1/FBP1/Wnt/Ξ²-catenin axis. | Cong L et al. | β | 2024 | β |
| ID3 is a novel target gene of p53 and modulates lung cancer cell metastasis. | Nagasaka M et al. | β | 2024 | β |
| Identification of a lactylation-related gene signature as the novel biomarkers for early diagnosis of acute myocardial infarction. | Zhu D et al. | β | 2024 | β |
| Identification of Biomarkers Associated with Oxidative Stress in Aortic Dissection Based on Bulk Transcriptome Analyses. | Li Z et al. | β | 2024 | β |
| Identification of transcription factor co-binding patterns with non-negative matrix factorization. | Rauluseviciute I et al. | β | 2024 | β |
| <i>GSTA1</i> gene polymorphisms are associated with cyclophosphamide effectiveness in lupus nephritis patients: A case-control study in Indonesia. | Indrawijaya YY et al. | β | 2024 | β |
| <i>HNF1B</i> Transcription Factor: Key Regulator in Renal Physiology and Pathogenesis. | SΓ‘nchez-Cazorla E et al. | β | 2024 | β |
| Integrated multiplexed assays of variant effect reveal determinants of catechol-O-methyltransferase gene expression. | Hoskins I et al. | β | 2024 | β |
| Integrative Analysis of ATAC-Seq and RNA-Seq through Machine Learning Identifies 10 Signature Genes for Breast Cancer Intrinsic Subtypes. | Park JW et al. | β | 2024 | β |
| Intronic Variants in the <i>MSH2</i> (rs2303426 and rs10179950) and <i>PMS2</i> (rs2286681 and rs62456178) Genes Are Not Associated with Colorectal Cancer in Mexican Patients. | Rico-MΓ©ndez MA et al. | β | 2024 | β |
| Key extracellular proteins and TF-miRNA co-regulatory network in diabetic foot ulcer: Bioinformatics and experimental insights. | Lin G et al. | β | 2024 | β |
| LAIR1-mediated resistance of hepatocellular carcinoma cells to T cells through a GSK-3Ξ²/Ξ²-catenin/MYC/PD-L1 pathway. | Pan B et al. | β | 2024 | β |
| Long-term exposure to BAY2416964 reduces proliferation, migration and recapitulates transcriptional changes induced by AHR loss in PyMT-induced mammary tumor cells. | Olafsen NE et al. | β | 2024 | β |
| Lost in translation? Evidence for a muted proteomic response to thermal stress in a stenothermal Antarctic fish and possible evolutionary mechanisms. | Dowd WW et al. | β | 2024 | β |
| MAZ-mediated up-regulation of BCKDK reprograms glucose metabolism and promotes growth by regulating glucose-6-phosphate dehydrogenase stability in triple-negative breast cancer. | Li Y et al. | β | 2024 | β |
| Mechanism of HOXA10 in nasopharyngeal carcinoma cell proliferation through the PTPRG-AS1/USP1 axis. | Zhou H et al. | β | 2024 | β |
| Mechanism of KLF2 in young mice with pneumonia induced by Streptococcus pneumoniae. | Li X et al. | β | 2024 | β |
| Mechanisms and Physiological Roles of Polymorphisms in Gestational Diabetes Mellitus. | Suthon S et al. | β | 2024 | β |
| Meta-analysis of differential gene expression in lower motor neurons isolated by laser capture microdissection from post-mortem ALS spinal cords. | Swindell WR | β | 2024 | β |
| MetArea: a software package for analysis of the mutually exclusive occurrence in pairs of motifs of transcription factor binding sites based on ChIP-seq data. | Levitsky VG et al. | β | 2024 | β |
| MiR-338-5p, a novel metastasis-related miRNA, inhibits triple-negative breast cancer progression by targeting the ETS1/NOTCH1 axis. | Chen WJ et al. | β | 2024 | β |
| Molecular Landscape of Bladder Cancer: Key Genes, Transcription Factors, and Drug Interactions. | Danishuddin et al. | β | 2024 | β |
| Molecular regulation of PPARΞ³/RXRΞ± signaling by the novel cofactor ZFP407. | Charrier A et al. | β | 2024 | β |
| MpANT regulates meristem development in Marchantia polymorpha. | Liu W et al. | β | 2024 | β |
| Multidimensional profiling of human TΒ cells reveals high CD38 expression, marking recent thymic emigrants and age-related naive TΒ cell remodeling. | Bohacova P et al. | β | 2024 | β |
| Multiscale mapping of transcriptomic signatures for cardiotoxic drugs. | Hansen J et al. | β | 2024 | β |
| NNMT switches the proangiogenic phenotype of cancer-associated fibroblasts via epigenetically regulating ETS2/VEGFA axis. | Wang X et al. | β | 2024 | β |
| Novel regulatory variant in ABO intronic RUNX1 binding site inducing A<sub>3</sub> phenotype. | Thun GA et al. | β | 2024 | β |
| Parkin deficiency promotes liver cancer metastasis by TMEFF1 transcription activation via TGF-Ξ²/Smad2/3 pathway. | Su Q et al. | β | 2024 | β |
| PRDM3/16 regulate chromatin accessibility required for NKX2-1 mediated alveolar epithelial differentiation and function. | He H et al. | β | 2024 | β |
| Recent advances in exploring transcriptional regulatory landscape of crops. | Huo Q et al. | β | 2024 | β |
| Regulation of Myc transcription by an enhancer cluster dedicated to pluripotency and early embryonic expression. | Li-Bao L et al. | β | 2024 | β |
| Repeated Shifts in Sociality Are Associated With Fine-tuning of Highly Conserved and Lineage-Specific Enhancers in a Socially Flexible Bee. | Jones BM et al. | β | 2024 | β |
| RNF122 promotes glioblastoma growth via the JAK2/STAT3/c-Myc signaling Axis. | Xiao Q et al. | β | 2024 | β |
| Role of deubiquitinase USP47 in cardiac function alleviation and anti-inflammatory immunity after myocardial infarction by regulating NLRP3 inflammasome-mediated pyroptotic signal pathways. | Wu Z et al. | β | 2024 | β |
| Selection on synonymous codon usage in soybean (Glycine max) WRKY genes. | Sinha K et al. | β | 2024 | β |
| Se-methylselenocysteine inhibits inflammatory response in an LPS-stimulated chicken HD11 macrophage-like cell model through the NFKB2 pathway. | Yao M et al. | β | 2024 | β |
| Single-Cell Meta-Analysis Uncovers the Pancreatic Endothelial Cell Transcriptomic Signature and Reveals a Key Role for NKX2-3 in PLVAP Expression. | Khan ST et al. | β | 2024 | β |
| Spermidine augments salt stress resilience in rice roots potentially by enhancing OsbZIP73's RNA binding capacity. | Shen X et al. | β | 2024 | β |
| Systems genetic analysis of lignin biosynthesis in Populus tremula. | Luomaranta M et al. | β | 2024 | β |
| Targeting ALDH1A1 to enhance the efficacy of KRAS-targeted therapy through ferroptosis. | Bian Y et al. | β | 2024 | β |
| TF-High-Evolutionary: In Vivo Mutagenesis of Gene Regulatory Networks for the Study of the Genetics and Evolution of the Drosophila Regulatory Genome. | Li XC et al. | β | 2024 | β |
| TFTF: An R-Based Integrative Tool for Decoding Human Transcription Factor-Target Interactions. | Wang J | β | 2024 | β |
| The 2024 Nucleic Acids Research database issue and the online molecular biology database collection. | Rigden DJ et al. | β | 2024 | β |
| The Adhesion GPCR ADGRL2/LPHN2 Can Protect Against Cellular and Organismal Dysfunction. | Jakobs P et al. | β | 2024 | β |
| The evaluation of transcription factor binding site prediction tools in human and Arabidopsis genomes. | Wanniarachchi DV et al. | β | 2024 | β |
| The Human OCTN Sub-Family: Gene and Protein Structure, Expression, and Regulation. | Galluccio M et al. | β | 2024 | β |
| The Regulatory Logic of Planarian Stem Cell Differentiation | PΓ©rez-Posada A et al. | β | 2024 | β |
| The STAT3/SETDB2 axis dictates NF-ΞΊB-mediated inflammation in macrophages during wound repair. | Mangum KD et al. | β | 2024 | β |
| Three-dimensional genome architecture persists in a 52,000-year-old woolly mammoth skin sample. | Sandoval-Velasco M et al. | β | 2024 | β |
| TIANA: transcription factors cooperativity inference analysis with neural attention. | Li RZ et al. | β | 2024 | β |
| TonEBP: A Key Transcription Factor in Microglia Following Intracerebral Hemorrhage Induced-Neuroinflammation. | Palahati A et al. | β | 2024 | β |
| Towards the genomic sequence code of DNA fragility for machine learning. | Pflughaupt P et al. | β | 2024 | β |
| Transcription factor EB reprograms branched-chain amino acid metabolism and promotes pancreatic cancer progression via transcriptional regulation of BCAT1. | Wang T et al. | β | 2024 | β |
| Transposable elements alter gene expression and may impact response to cisplatin therapy in ovarian cancer. | Mombach DM et al. | β | 2024 | β |
| Uncovering the role of the subcommissural organ in early brain development through transcriptomic analysis. | GonzΓ‘lez M et al. | β | 2024 | β |
| ZBP1-mediated apoptosis and inflammation exacerbate steatotic liver ischemia/reperfusion injury. | Liu R et al. | β | 2024 | β |
| ZFP64 drives glycolysis-mediated stem cell-like properties and tumorigenesis in breast cancer. | Sun J et al. | β | 2024 | β |