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+"Date.Added","Manual.Tags","Title"
+"2024-10-01 17:20:16","Arabidopsis; DAP-seq; DL; Model; Plant; TF; TFBS","TSPTFBS: a Docker image for trans-species prediction of transcription factor binding sites in plants"
+"2024-10-01 14:18:26","DL; Model; Plant; TF; TFBS; ChIP-seq; SeqConv","Deep learning-based prediction of TFBSs in plants"
+"2024-10-01 14:59:26","DL; Model; TF; ExplaiNN","ExplaiNN: interpretable and transparent neural networks for genomics"
+"2024-10-01 12:54:33","Atlas","Atlas to do list"
+"2024-10-01 12:38:28","","How Perfect Can Protein Interactomes Be?"
+"2024-10-03 08:18:20","DL; TF; TFBS","PTFSpot: deep co-learning on transcription factors and their binding regions attains impeccable universality in plants"
+"2024-10-03 08:19:25","Arabidopsis; DAP-seq; DL; Model; Plant; TF; TFBS","TSPTFBS 2.0: trans-species prediction of transcription factor binding sites and identification of their core motifs in plants"
+"2024-10-03 08:21:05","Arabidopsis; DL; Model; Plant; TF; TFBS; ChIP-seq","PlantBind: an attention-based multi-label neural network for predicting plant transcription factor binding sites"
+"2025-02-12 10:25:50","","Functional Analysis of the Homeodomain Transcription Factors KNAT2 and KNAT6 in Arabidopsis Thaliana"
+"2025-02-03 07:43:59","Model; TFBS; Review","Comprehensive analysis of computational approaches in plant transcription factors binding regions discovery"
+"2025-01-22 16:08:05","Arabidopsis; TFBS; Cistrome; Methylation; WUS14","Cytosine Methylation Changes the Preferred Cis-Regulatory Configuration of Arabidopsis WUSCHEL-Related Homeobox 14"
+"2025-01-20 15:30:19","TFBS; Conservation; Network; Soy; Transinet","Transcriptional regulatory network reveals key transcription factors for regulating agronomic traits in soybean"
+"2025-01-20 14:11:13","TFBS; Conservation; Transinet; Complex; Module; Syntax","Leveraging Cross-Species Transcription Factor Binding Site Patterns: From Diabetes Risk Loci to Disease Mechanisms"
+"2025-01-06 09:05:05","TF; TFBS; Models","The evaluation of transcription factor binding site prediction tools in human and Arabidopsis genomes"
+"2024-12-17 08:29:56","Transinet; Complex; FAC; FD; FT","FT Modulates Genome-Wide DNA-Binding of the bZIP Transcription Factor FD"
+"2024-12-06 09:47:49","TF; Atlas; Jaspar; Matrix; Tool","RSAT matrix-clustering: dynamic exploration and redundancy reduction of transcription factor binding motif collections"
+"2024-11-28 14:09:52","C2H2; Classif","Conservation, diversification and expansion of C2H2 zinc finger proteins in the Arabidopsis thaliana genome"
+"2024-11-28 14:08:13","C2H2; Classif","Genome-wide characterization of C2H2 zinc-finger gene family provides insight into the mechanisms and evolution of the dehydration–rehydration responses in Physcomitrium and Arabidopsis"
+"2024-11-28 14:05:15","C2H2; Classif; Phylogeny; Plant-TFClass","Phylogenetic Study of Plant Q-type C2H2 Zinc Finger Proteins and Expression Analysis of Poplar Genes in Response to Osmotic, Cold and Mechanical Stresses"
+"2024-11-22 15:16:38","TF; Classif; Phylogeny; Trihelix","Large‐scale analysis of trihelix transcription factors reveals their expansion and evolutionary footprint in plants"
+"2024-11-22 15:15:42","TF; Classif; Phylogeny; Trihelix","Identification and Characterization of Trihelix Transcription Factors and Expression Changes during Flower Development in Pineapple"
+"2024-11-22 15:14:35","TF; Classif; Phylogeny; Trihelix","GENOME-WIDE ANALYSIS OF TRIHELIX TRANSCRIPTION FACTOR GENE FAMILY IN Arabidopsis thaliana"
+"2024-11-18 14:53:27","Model; TFBS; Atlas; Transinet; Complex; Syntax; PPI; Spacing; TF-COMB","TF-COMB – Discovering grammar of transcription factor binding sites"
+"2024-11-18 08:30:43","Review; Complex; Development; Evolution; Flower","Evolution and development of complex floral displays"
+"2024-11-18 08:29:35","Review; Transcription","Transcription regulation by biomolecular condensates"
+"2024-11-18 08:23:42","TFBS; Transinet; Syntax; Co-occurrance; COBIND; Mathelier","Identification of transcription factor co-binding patterns with non-negative matrix factorization"
+"2024-11-08 16:30:26","TFBS; Classif; Structure; TCP; Motif","DNA–TCP complex structures reveal a unique recognition mechanism for TCP transcription factor families"
+"2024-11-08 16:28:45","Classif; Animal; TFClass","TFClass: expanding the classification of human transcription factors to their mammalian orthologs"
+"2024-11-08 16:28:14","TF; Review; General","Transcription factors: from enhancer binding to developmental control"
+"2024-11-08 16:27:39","Plant; TF; Evolution","Transcription Factor Families Have Much Higher Expansion Rates in Plants than in Animals"
+"2024-11-08 16:26:39","TF; Evolution; Eucaryote","Origin and evolution of eukaryotic transcription factors"
+"2024-11-08 16:25:35","Development; AG; Algues; AP1; LFY; WUS","A Molecular Link between Stem Cell Regulation and Floral Patterning in Arabidopsis"
+"2024-11-08 16:24:21","ChIP-seq; Method","Genomic location analysis by ChIP‐Seq"
+"2024-11-08 16:23:33","Review; Data; Informatique; ML","Ten quick tips for machine learning in computational biology"
+"2024-11-08 16:20:49","DAP-seq; Method","Mapping genome-wide transcription-factor binding sites using DAP-seq"
+"2024-11-08 16:17:35","Syntax; Spacing; Development; Structure; MADS; SEP; StrucDev","SEPALLATA-driven MADS transcription factor tetramerization is required for inner whorl floral organ development"
+"2024-11-08 16:15:31","DAP-seq; TFBS; Methylation; LFY; Epigénétique; ampDAP-seq; Flo_Re; méthylation ADN","The LEAFY floral regulator displays pioneer transcription factor properties"
+"2024-11-08 16:13:00","TFBS; Syntax; Spacing; ARF","Capturing Auxin Response Factors Syntax Using DNA Binding Models"
+"2024-11-08 16:11:11","Plant; TFBS; Evolution; LFY","A Promiscuous Intermediate Underlies the Evolution of LEAFY DNA Binding Specificity"
+"2024-11-08 16:09:26","Development; AG; AP1; LFY; Flo_Re; AP3","A genetic framework for floral patterning"
+"2024-11-08 14:16:12","Model; TFBS; LFY; Flo_Re; TFFM","Prediction of Regulatory Interactions from Genome Sequences Using a Biophysical Model for the <i>Arabidopsis</i> LEAFY Transcription Factor"
+"2024-11-08 15:57:06","Arabidopsis; Plant; TFBS; Syntax; TSS","Positional distribution of transcription factor binding sites in Arabidopsis thaliana"
+"2024-11-08 15:55:49","TFBS; ChIP-seq; Syntax; KAN1; Orientation","Meta-Analysis of Arabidopsis KANADI1 Direct Target Genes Identifies a Basic Growth-Promoting Module Acting Upstream of Hormonal Signaling Pathways"
+"2024-11-08 15:52:27","Arabidopsis; TFBS; Syntax; TSS; Orientation","The orientation of transcription factor binding site motifs in gene promoter regions: does it matter?"
+"2024-11-08 15:39:04","Arabidopsis; TF; TFBS; ChIP-seq; Syntax; Orientation; BBM","An Arabidopsis AT-hook motif nuclear protein mediates somatic embryogenesis and coinciding genome duplication"
+"2024-11-08 15:35:58","Arabidopsis; TF; TFBS; ChIP-seq; Syntax; Orientation; BBM","The BABY BOOM Transcription Factor Activates the LEC1-ABI3-FUS3-LEC2 Network to Induce Somatic Embryogenesis"
+"2024-11-08 15:37:32","ChIP-seq; Syntax; KAN1; Orientation","<i>Arabidopsis</i> KANADI1 Acts as a Transcriptional Repressor by Interacting with a Specific <i>cis</i> -Element and Regulates Auxin Biosynthesis, Transport, and Signaling in Opposition to HD-ZIPIII Factors"
+"2024-11-08 15:33:13","Arabidopsis; Plant; Evolution; Structure; Algues; ARF; Auxins","Evolution of the Auxin Response Factors from charophyte ancestors"
+"2024-11-08 14:20:00","Model; TFBS; Review","Assessing computational tools for the discovery of transcription factor binding sites"
+"2024-11-08 14:19:06","Model; TFBS; Review","A survey on algorithms to characterize transcription factor binding sites"
+"2024-11-08 14:17:52","Model; TFBS; PWM","Use of the 'Perceptron' algorithm to distinguish translational initiation sites in E. coli"
+"2024-11-08 14:15:07","Model; TFBS; TFFM; HMM","The Next Generation of Transcription Factor Binding Site Prediction"
+"2024-11-08 14:13:11","DL; Model; TFBS; TFFM; DNAshape","DNA Shape Features Improve Transcription Factor Binding Site Predictions In Vivo"
+"2024-11-08 14:10:14","Model; TFBS; PWM","Insights gained from a comprehensive all-against-all transcription factor binding motif benchmarking study"
+"2024-11-08 14:08:51","Data; méthylation ADN; Analyses","Methylation interactions in <i>Arabidopsis</i> hybrids require RNA-directed DNA methylation and are influenced by genetic variation"
+"2024-11-08 14:07:42","TF; TFBS; Animal; Epigénétique; méthylation ADN","Impact of cytosine methylation on DNA binding specificities of human transcription factors"
+"2024-11-08 14:06:04","Review; Epigénétique; short","Epigenetics: Core misconcept"
+"2024-11-08 14:04:28","TF; Review; Epigénétique; méthylation ADN","Transcription factors as readers and effectors of DNA methylation"
+"2024-11-08 13:41:17","DAP-seq; Plant; TF; Cistrome; Methylation; Data; Epigénétique; méthylation ADN; ARF","Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape"
+"2024-11-08 13:58:58","Arabidopsis; Plant; Development; WUS; Auxin; Transcriptomic","Transcriptional Control of a Plant Stem Cell Niche"
+"2024-11-08 14:00:26","Arabidopsis; Development; WUS; Auxin; SAM","WUSCHEL acts as an auxin response rheostat to maintain apical stem cells in Arabidopsis"
+"2024-11-08 13:57:48","DL; Model; TFBS; Animal; DeepSea","Predicting effects of noncoding variants with deep learning–based sequence model"
+"2024-11-08 13:56:16","DL; Model; TFBS; Review","A Review About Transcription Factor Binding Sites Prediction Based on Deep Learning"
+"2024-11-08 13:54:34","DL; Plant; TFBS; Cistrome","Deep learning the cis-regulatory code for gene expression in selected model plants"
+"2024-11-08 13:52:09","DL; Model; TF; TFBS; Review; Opinion","Deep learning for inferring transcription factor binding sites"
+"2024-11-08 13:51:22","DL; Model; TF; TFBS; DanQ","DanQ: a hybrid convolutional and recurrent deep neural network for quantifying the function of DNA sequences"
+"2024-11-08 13:50:14","DL; Model; Animal; DeepBind","Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning"
+"2024-11-08 13:49:18","TF; Eucaryote; DataBase","TRANSFAC(R) and its module TRANSCompel(R): transcriptional gene regulation in eukaryotes"
+"2024-11-08 13:48:36","TF; DataBase","ReMap 2022: a database of Human, Mouse, Drosophila and Arabidopsis regulatory regions from an integrative analysis of DNA-binding sequencing experiments"
+"2024-11-08 13:47:36","Plant; TF; DataBase","PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants"
+"2024-11-08 13:46:42","TF; TFBS; Jaspar; DataBase","JASPAR 2024: 20th anniversary of the open-access database of transcription factor binding profiles"
+"2024-11-08 13:45:00","Plant; TF; Classif; MADS","Molecular and Phylogenetic Analyses of the Complete MADS-Box Transcription Factor Family in Arabidopsis"
+"2025-10-31 08:19:53","Development; Early Flower; RNA; Single","The role of FRUITFULL controlling cell cycle during early flower development revealed by time-series snRNA-seq experiments"
+"2025-10-17 09:27:59","Plant; TFBS; AT rich; Motif","DNA-binding specificities of plant transcription factors and their potential to define target genes"
+"2025-10-17 07:53:22","TFBS; Syntax; Motif; Animals; Dynamics; Homotypic Cluster","Homotypic clusters of transcription factor binding sites: A model system for understanding the physical mechanics of gene expression"
+"2025-10-17 07:43:20","TFBS; Review; Syntax; AT rich; Motif; Dynamics; Antenna","How motif environment influences transcription factor search dynamics: Finding a needle in a haystack"
+"2025-10-17 07:41:41","Arabidopsis; Plant; TFBS; Syntax; MADS; AT rich; Dynamics; Antenna; Basic; MYC2","DNA features beyond the transcription factor binding site specify target recognition by plant MYC2-related bHLH proteins"
+"2025-10-17 07:40:36","TFBS; Syntax; PPI; Motif; Homodimere; Human; TF-TF","DNA-guided transcription factor interactions extend human gene regulatory code"
+"2025-10-17 07:38:03","TFBS; Dynamics; Antenna","A widespread role of the motif environment in transcription factor binding across diverse protein families"
+"2025-05-14 15:38:24","TF; Structure; Epigénétique; Dynamics; Physics; Pionneer","The physical size of transcription factors is key to transcriptional regulation in chromatin domains"
+"2025-02-28 08:56:44","TF; Review; Syntax; Structure; Dynamics; Physics; Binding; IDR","Intrinsically disordered regions as facilitators of the transcription factor target search"
+"2025-10-03 09:32:25","TF; TFBS; Review; Phylogeny; Dynamics; Binding","Transcription Factor Dynamics: One Molecule at a Time"
+"2025-10-03 09:23:37","Plant; Review; Syntax; Combinatorial; Complexes; Gene; o; Regulation","Combinatorial control of plant gene expression"
+"2025-10-03 09:26:45","TFBS; Review; Eukaryote; Low Affinity","Low-Affinity Binding Sites and the Transcription Factor Specificity Paradox in Eukaryotes"
+"2025-10-03 09:29:48","TFBS; Review; CRE; Gene Regulation; TRN","Decoding complexity: tackling the challenge of how many transcription factors regulate a plant gene"
+"2025-10-03 09:28:08","TFBS; Binding; Low Affinity","Multiple overlapping binding sites determine transcription factor occupancy"
+"2025-08-13 09:23:29","Review; Syntax; Development; Co-occurrance; Animal; Regulation; Complexe; Enhancer","Enhancer grammar in development, evolution, and disease: dependencies and interplay"
+"2025-08-13 09:23:10","","Enhancer grammar in development, evolution, and disease: dependencies and interplay"
+"2025-07-07 09:40:36","Complex; Binding; Regulation; Levure","Low overlap of transcription factor DNA binding and regulatory targets"
+"2025-06-24 06:49:20","Methylation; Collab; WRKY","Single-cytosine methylation at W-boxes repels binding of WRKY transcription factors through steric hindrance"
+"2025-06-24 06:47:41","TF; Review; Evolution; Functional; Paralog","Mechanisms driving functional divergence of transcription factor paralogs"
+"2025-06-12 14:54:06","TFBS; Syntax; Spacing; Animal; HOMERE2","Position-dependent function of human sequence-specific transcription factors"
+"2025-06-05 09:25:37","TFBS; Models; Bioinformatics tools; Performance evaluation; Transcription factor binding sites","The evaluation of transcription factor binding site prediction tools in human and Arabidopsis genomes"
+"2025-06-05 09:17:59","Arabidopsis; How many TF in A.th","A collection of inducible transcription factor‐glucocorticoid receptor fusion lines for functional analyses in <i>Arabidopsis thaliana</i>"
+"2025-06-05 08:30:52","Arabidopsis; DAP-seq; Cistrome; Cis-regulation; O'Malley","Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape"
+"2025-06-05 08:21:10","ChIP-seq; Method","Genomic location analysis by ChIP‐Seq"
+"2025-06-05 08:04:10","TFBS; Syntax; Animal; Pairs","DNA-guided transcription factor interactions extend human gene regulatory code"
+"2025-06-05 08:01:24","TFBS; Complex; Syntax; ARF; Flo_RE","Auxin response factors are keys to the many auxin doors"
+"2025-06-05 08:00:30","TFBS; Syntax; Animal; Regulation","Transcription factor binding site orientation and order are major drivers of gene regulatory activity"
+"2025-06-05 07:58:55","TF; Review; Complex; Regulation","What do Transcription Factors Interact With?"
+"2025-06-05 07:56:22","Plant; Syntax; Co-occurrance; Regulation; Complexe","Combinatorial control of plant gene expression"
+"2025-06-05 07:54:42","Plant; Classif; Plant-TFClass; Structure; Flo_RE","Plant-TFClass: a structural classification for plant transcription factors"
+"2025-06-05 07:53:41","Plant; TF; Structure; DBD","DNA-binding domains of plant-specific transcription factors: structure, function, and evolution"
+"2025-06-05 07:51:44","Arabidopsis; TFBS; Models; Flo_RE","Building Transcription Factor Binding Site Models to Understand Gene Regulation in Plants"
+"2025-05-23 16:29:27","Transinet; Co-occurrance; AP1; Binding; Complexe; bZIP","The Arabidopsis bZIP transcription factor family — an update"
+"2025-05-22 15:58:52","TF; Complex; PPI; TF-TF; Complexe; Pairs","DNA-guided transcription factor interactions extend human gene regulatory code"
+"2025-04-24 09:21:00","HSF; structure; trimere","Structures of heat shock factor trimers bound to DNA"
+"2025-04-24 09:21:13","Complex; Structure; Binding; HSF","Structures of heat shock factor trimers bound to DNA"
+"2025-04-18 12:57:51","TFBS; ML; MEME","The MEME Suite"
+"2025-03-13 09:57:48","TFBS; Conservation; Classif; Evolution; Motif; Binding","Manuscript: Many transcription factor families have evolutionarily conserved binding motifs in plants"
+"2025-03-12 16:07:11","Atlas; Classif; Motif; LBD; LOB","The LOB domain protein, a novel transcription factor with multiple functions: A review"
+"2025-03-07 10:06:02","ChIP-seq; Syntax; Spacing; Co-occurrance; Structure; WUS; Motif; Binding; JASPAR2026","Structural basis for the complex DNA binding behavior of the plant stem cell regulator WUSCHEL"
+"2025-03-06 12:12:36","Classif; Phylogeny; Structure; TCP; Motif","The <i>Arabidopsis thaliana</i> TCP transcription factors: A broadening horizon beyond development"
+"2025-02-19 15:45:04","Methylation; Method; Epigénétique; Binding; Expérimental; QuMFRA","Non-independence of Mnt repressor-operator interaction determined by a new quantitative multiple fluorescence relative affinity (QuMFRA) assay"
+"2025-02-19 15:44:46","","Non-independence of Mnt repressor-operator interaction determined by a new quantitative multiple fluorescence relative affinity (QuMFRA) assay"
+"2025-02-18 16:18:12","JASPAR2026; ATHB-2; HB-HD-ZIP-2A-2","The Athb-1 and −2 HD-Zip domains homodimerize forming complexes of different DNA binding specificities."
+"2025-02-18 15:03:32","JASPAR2026; HB-HD-ZIP-2A-1; Oshox22; TraesCS2A02G389400","Characterization of Rice Homeobox Genes, OsHOX22 and OsHOX24, and Over-expression of OsHOX24 in Transgenic Arabidopsis Suggest Their Role in Abiotic Stress Response"
+"2025-02-18 15:00:36","JASPAR2026; AP2-ERF-4B-2; TraesCS4B02G299700","Knockout of transcription factor <i>OsERF65</i> enhances <span style=""font-variant:small-caps;"">ROS</span> scavenging ability and confers resistance to rice sheath blight"
+"2025-02-18 14:07:03","JASPAR2026; AP2-ERF-4B-2; TraesCS4B02G299700; OsBIERF4","Molecular characterization of four rice genes encoding ethylene-responsive transcriptional factors and their expressions in response to biotic and abiotic stress"
+"2025-02-14 11:51:35","JASPAR2026","Transposable elements orchestrate subgenome-convergent and -divergent transcription in common wheat"
+"2025-11-27 07:52:22","TF; TFBS; PWM; Binding; Enhancer; Cis-regulatory module; Drosophila; Flanking regions; Transcription factor","Flanking sequence context-dependent transcription factor binding in early Drosophila development"
+"2025-11-27 07:50:07","DL; TF; Atlas; Models; PWM; Human; Flanking regions","Benchmarking transcription factor binding site prediction models: a comparative analysis on synthetic and biological data"