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Abbreviation : CRMs
Long Form : cis-regulatory modules
No. Year Title Co-occurring Abbreviation
2020 Candidate Cancer Driver Mutations in Distal Regulatory Elements and Long-Range Chromatin Interaction Networks. FMREs
2020 Functional effects of variation in transcription factor binding highlight long-range gene regulation by epromoters. TF
2019 Computational enhancer prediction: evaluation and improvements. ---
2019 ELMER v.2: an R/Bioconductor package to reconstruct gene regulatory networks from DNA methylation and transcriptome profiles. GRNs
2019 Engineering the architecture of erythritol-inducible promoters for regulated and enhanced gene expression in Yarrowia lipolytica. UASs
2019 Exploring a Drosophila Transcription Factor Interaction Network to Identify Cis-Regulatory Modules. TFs
2019 Genome-wide identification of binding sites and gene targets of Alx1, a pivotal regulator of echinoderm skeletogenesis. ---
2019 Next-generation muscle-directed gene therapy by in silico vector design. ---
2019 Shared cis-regulatory architecture identified across defense response genes is associated with broad-spectrum quantitative resistance in rice. BS-DR, DR, QTL
10  2019 The cis-regulatory logic underlying abdominal Hox-mediated repression versus activation of regulatory elements in Drosophila. Abd-A, Exd, Hth, Ubx
11  2019 The regulatory control of Cebpa enhancers and silencers in the myeloid and red-blood cell lineages. TF
12  2018 Analysis of Genetic Variation Indicates DNA Shape Involvement in Purifying Selection. SNPs, TFs
13  2018 Cooperative recruitment of Yan via a high-affinity ETS supersite organizes repression to confer specificity and robustness to cardiac cell fate specification. ETS, eve, Pnt
14  2018 Global analysis of primary mesenchyme cell cis-regulatory modules by chromatin accessibility profiling. GRN, PMCs
15  2018 Organizing combinatorial transcription factor recruitment at cis-regulatory modules. TF, TRMs
16  2018 Towards a map of cis-regulatory sequences in the human genome. CREs, TF
17  2017 A long-range flexible billboard model of gene activation. GC, GR, TF
18  2017 A New Algorithm for Identifying Cis-Regulatory Modules Based on Hidden Markov Model. ---
19  2017 A novel method for predicting activity of cis-regulatory modules, based on a diverse training set. ---
20  2017 Diverse Cis-Regulatory Mechanisms Contribute to Expression Evolution of Tandem Gene Duplicates. ---
21  2017 Foxh1 Occupies cis-Regulatory Modules Prior to Dynamic Transcription Factor Interactions Controlling the Mesendoderm Gene Program. ---
22  2017 Genome-wide discovery of active regulatory elements and transcription factor footprints in Caenorhabditis elegans using DNase-seq. DHSs, TF
23  2017 Identification of Cis-Regulatory Modules that Function in the Male Germline of Flowering Plants. ---
24  2017 Perspectives on Gene Regulatory Network Evolution. DSD, GRNs
25  2017 Sequential Response to Multiple Developmental Network Circuits Encoded in an Intronic cis-Regulatory Module of Sea Urchin hox11/13b. ---
26  2017 Sex combs reduced (Scr) regulatory region of Drosophila revisited. IEs, PREs, Scr
27  2017 Simple Expression Domains Are Regulated by Discrete CRMs During Drosophila Oogenesis. ---
28  2017 Single embryo-resolution quantitative analysis of reporters permits multiplex spatial cis-regulatory analysis. MMOSAIC
29  2017 Synthetic Core Promoters as Universal Parts for Fine-Tuning Expression in Different Yeast Species. UTRs
30  2017 The logic of transcriptional regulator recruitment architecture at cis-regulatory modules controlling liver functions. TRMs, TRs
31  2016 A Hox Transcription Factor Collective Binds a Highly Conserved Distal-less cis-Regulatory Module to Generate Robust Transcriptional Outcomes. Exd, Hth, TFs
32  2016 Characterization of a new Gsx2-cre line in the developing mouse telencephalon. CGE, LGE, MGE
33  2016 INSECT 2.0: a web-server for genome-wide cis-regulatory modules prediction. ---
34  2016 LedPred: an R/bioconductor package to predict regulatory sequences using support vector machines. SVMs
35  2016 MyoD reprogramming requires Six1 and Six4 homeoproteins: genome-wide cis-regulatory module analysis. MEFs
36  2016 Nucleotide Interdependency in Transcription Factor Binding Sites in the Drosophila Genome. TFs
37  2016 On the comparison of regulatory sequences with multiple resolution Entropic Profiles. EPs
38  2016 Opening up the blackbox: an interpretable deep neural network-based classifier for cell-type specific enhancer predictions. DNN
39  2016 Sequential construction of a model for modular gene expression control, applied to spatial patterning of the Drosophila gene hunchback. GAs, hb
40  2016 SMCis: An Effective Algorithm for Discovery of Cis-Regulatory Modules. TRSs
41  2016 Streamlined scanning for enhancer elements in Drosophila melanogaster. ---
42  2016 Structure of developmental gene regulatory networks from the perspective of cell fate-determining genes. GRNs, TF
43  2016 The analysis of novel distal Cebpa enhancers and silencers using a transcriptional model reveals the complex regulatory logic of hematopoietic lineage specification. ---
44  2016 The Zebrafish as Model for Deciphering the Regulatory Architecture of Vertebrate Genomes. ---
45  2015 Brachyury, Foxa2 and the cis-Regulatory Origins of the Notochord. ---
46  2015 Conserved Cis-Regulatory Modules Control Robustness in Msx1 Expression at Single-Cell Resolution. ---
47  2015 Establishment of a Developmental Compartment Requires Interactions between Three Synergistic Cis-regulatory Modules. ap
48  2015 Evolution of lineage-specific functions in ancient cis-regulatory modules. ---
49  2015 Evolution of transcription factor function as a mechanism for changing metazoan developmental gene regulatory networks. Evo-Devo, GRNs
50  2015 Functional interplay of SP family members and nuclear factor Y is essential for transcriptional activation of the human Calreticulin gene. CALR, JAK2, NF-Y
51  2015 Identification of Lineage-Specific Cis-Regulatory Modules Associated with Variation in Transcription Factor Binding and Chromatin Activity Using Ornstein-Uhlenbeck Models. OU
52  2015 Identifying transcriptional cis-regulatory modules in animal genomes. TFs
53  2014 Beyond Fixed-Resolution Alignment-Free Measures for Mammalian Enhancers Sequence Comparison. ---
54  2014 BMPs regulate msx gene expression in the dorsal neuroectoderm of Drosophila and vertebrates by distinct mechanisms. BMPs, CNS, Danio rerio
55  2014 cgChIP: a cell type- and gene-specific method for chromatin analysis. Dll
56  2014 cisMEP: an integrated repository of genomic epigenetic profiles and cis-regulatory modules in Drosophila. ---
57  2014 Computationally designed liver-specific transcriptional modules and hyperactive factor IX improve hepatic gene therapy. FIX, scAAV9, vg
58  2014 De novo prediction of cis-regulatory elements and modules through integrative analysis of a large number of ChIP datasets. CREs, TFs
59  2014 Divergent functions of hematopoietic transcription factors in lineage priming and differentiation during erythro-megakaryopoiesis. ERY, Meg
60  2014 HAND2 targets define a network of transcriptional regulators that compartmentalize the early limb bud mesenchyme. ---
61  2014 Imogene: identification of motifs and cis-regulatory modules underlying gene co-regulation. ChIP
62  2014 In silico evolution of the hunchback gene indicates redundancy in cis-regulatory organization and spatial gene expression. hb
63  2014 Induction and dorsal restriction of Paired-box 3 (Pax3) gene expression in the caudal neuroectoderm is mediated by integration of multiple pathways on a short neural crest enhancer. NCE2, PAX3
64  2014 Modular evolution of DNA-binding preference of a Tbrain transcription factor provides a mechanism for modifying gene regulatory networks. GRNs
65  2014 Multi-species, multi-transcription factor binding highlights conserved control of tissue-specific biological pathways. TF
66  2014 Neural precursor-specific expression of multiple Drosophila genes is driven by dual enhancer modules with overlapping function. bHLH, neur, NP, SOP
67  2014 Occupancy of tissue-specific cis-regulatory modules by Otx2 and TLE/Groucho for embryonic head specification. TFs
68  2014 Subtle changes in motif positioning cause tissue-specific effects on robustness of an enhancer's activity. TFs
69  2013 A statistical thin-tail test of predicting regulatory regions in the Drosophila genome. NCNRs, TFBSs
70  2013 Autoregulatory feedback controls sequential action of cis-regulatory modules at the brinker locus. brk, PPE
71  2013 Flanking sequence context-dependent transcription factor binding in early Drosophila development. PWM, TFs
72  2013 Functional Brachyury binding sites establish a temporal read-out of gene expression in the Ciona notochord. Ci-Bra
73  2013 Functional dissection of the PROPEP2 and PROPEP3 promoters reveals the importance of WRKY factors in mediating microbe-associated molecular pattern-induced expression. AtPeps, DAMPs, MAMPs
74  2013 INSECT: IN-silico SEarch for Co-occurring Transcription factors. ChIP-seq, TFBSs, TFs
75  2013 Org-1 is required for the diversification of circular visceral muscle founder cells and normal midgut morphogenesis. dpp, opa, org-1, tsh, Ubx, wg
76  2013 SoxB1-driven transcriptional network underlies neural-specific interpretation of morphogen signals. Shh
77  2012 A dynamic network of morphogens and transcription factors patterns the fly leg. dac, Dll, Dpp, PD, Wg
78  2012 A graphical modelling approach to the dissection of highly correlated transcription factor binding site profiles. DDGraph, NCPC, TFs
79  2012 A novel mammal-specific three partite enhancer element regulates node and notochord-specific Noto expression. ---
80  2012 A statistical fat-tail test of predicting regulatory regions in the Drosophila genome. ---
81  2012 An ancient genomic regulatory block conserved across bilaterians and its dismantling in tetrapods by retrogene replacement. GRBs
82  2012 An evolutionarily conserved enhancer regulates Bmp4 expression in developing incisor and limb bud. AER, ChIP, EMSA, PBM
83  2012 Barcoded DNA-tag reporters for multiplex cis-regulatory analysis. ---
84  2012 ChIP-enriched in silico targets (ChEST), a ChIP-on-chip approach applied to analyzing skeletal muscle genes. ChEST, ChIP, TF
85  2012 COPS: detecting co-occurrence and spatial arrangement of transcription factor binding motifs in genome-wide datasets. BSs, COPS, TFs
86  2012 CORECLUST: identification of the conserved CRM grammar together with prediction of gene regulation. CORECLUST
87  2012 Disentangling the many layers of eukaryotic transcriptional regulation. TF
88  2012 Dynamic in vivo binding of transcription factors to cis-regulatory modules of cer and gsc in the stepwise formation of the Spemann-Mangold organizer. cer, gsc, Sia
89  2012 Engrailed cooperates directly with Extradenticle and Homothorax on a distinct class of homeodomain binding sites to repress sloppy paired. en, En, Exd, Hth, slp
90  2012 Genomic approaches towards finding cis-regulatory modules in animals. ---
91  2012 Huckebein is part of a combinatorial repression code in the anterior blastoderm. eve, ftz, hkb
92  2012 Integration of an abdominal Hox complex with Pax2 yields cell-specific EGF secretion from Drosophila sensory precursor cells. SOPs
93  2012 Mechanistic differences in the transcriptional interpretation of local and long-range Shh morphogen signaling. ---
94  2012 Novel cis-regulatory modules control expression of the Hairy and Enhancer of Split-1 (HES1) transcription factor in myoblasts. Hes1
95  2012 Org-1, the Drosophila ortholog of Tbx1, is a direct activator of known identity genes during muscle specification. lb, org-1, slou
96  2012 Predicting tissue specific cis-regulatory modules in the human genome using pairs of co-occurring motifs. TF
97  2012 Regulation of gene expression and the transcription factor cycle hypothesis. FDTs, TFC, TFs
98  2012 Thousands of cis-regulatory sequence combinations are shared by Arabidopsis and poplar. TFs
99  2012 Unveiling combinatorial regulation through the combination of ChIP information and in silico cis-regulatory module detection. TF
100  2011 A cluster of non-redundant Ngn1 binding sites is required for regulation of deltaA expression in zebrafish. ---