ECR Browser: a tool for visualizing and accessing data from comparisons of multiple vertebrate genomes

Basic local alignment search tool

Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990) · Journal of Molecular Biology · doi:10.1006/jmbi.1990.9999 · Cited by 98,669 · see citing works

<tt>BLAT</tt> —The <tt>BLAST</tt> -Like Alignment Tool

Kent, W. J. (2002) · Genome Research · doi:10.1101/gr.229202 · Cited by 8,480 · see citing works

Initial sequencing and comparative analysis of the mouse genome

Mouse Genome Sequencing Consortium (2002) · Nature · doi:10.1038/nature01262 · Cited by 7,187 · see citing works

The UCSC Genome Browser Database

Karolchik, D. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg129 · Cited by 1,887 · see citing works

The Ensembl genome database project

Hubbard, T. (2002) · Nucleic Acids Research · doi:10.1093/nar/30.1.38 · Cited by 1,610 · see citing works

Whole-Genome Shotgun Assembly and Analysis of the Genome of <i>Fugu rubripes</i>

Aparicio, S., Chapman, J., Stupka, E., Putnam, N., Chia, J.-M., Dehal, P., Christoffels, A., Rash, S., Hoon, S., Smit, A., et al. (2002) · Science · doi:10.1126/science.1072104 · Cited by 1,591 · see citing works

Human–Mouse Alignments with BLASTZPreprint

Schwartz, S., Kent, W. J., Miller, W., Zhang, Z., Baertsch, R., Hardison, R. C., Haussler, D. H., & Miller, W. (2002) · Genome Research · doi:10.1101/gr.809403 · Cited by 1,231 · see citing works

PipMaker—A Web Server for Aligning Two Genomic DNA SequencesPreprint

Schwartz, S., Zhang, Z., Frazer, K. A., Smit, A. F. A., Riemer, C., Bouck, J. B., Gibbs, R. A., Hardison, R. C., & Miller, W. (2000) · Genome Research · doi:10.1101/gr.10.4.577 · Cited by 1,165 · see citing works

A long-range Shh enhancer regulates expression in the developing limb and fin and is associated with preaxial polydactyly

Lettice, L. A. (2003) · Human Molecular Genetics · doi:10.1093/hmg/ddg180 · Cited by 1,164 · see citing works

TRANSFAC: a database on transcription factors and their DNA binding sites

Wingender, E. (1996) · Nucleic Acids Research · doi:10.1093/nar/24.1.238 · Cited by 1,064 · see citing works

Fast algorithms for large-scale genome alignment and comparison

Delcher, A. L. (2002) · Nucleic Acids Research · doi:10.1093/nar/30.11.2478 · Cited by 1,036 · see citing works

VISTA : visualizing global DNA sequence alignments of arbitrary length

Mayor, C., Brudno, M., Schwartz, J. R., Poliakov, A., Rubin, E. M., Frazer, K. A., Pachter, L. S., & Dubchak, I. L. (2000) · Bioinformatics · doi:10.1093/bioinformatics/16.11.1046 · Cited by 1,017 · see citing works

An Apolipoprotein Influencing Triglycerides in Humans and Mice Revealed by Comparative Sequencing

Pennacchio, L. A., Olivier, M., Hubacek, J. A., Cohen, J. C., Cox, D. R., Fruchart, J.-C., Krauss, R. M., & Rubin, E. M. (2001) · Science · doi:10.1126/science.1064852 · Cited by 921 · see citing works

Identification of a Coordinate Regulator of Interleukins 4, 13, and 5 by Cross-Species Sequence Comparisons

Loots, G. G., Locksley, R. M., Blankespoor, C. M., Wang, Z., Miller, W., Rubin, E. M., & Frazer, K. A. (2000) · Science · doi:10.1126/science.288.5463.136 · Cited by 783 · see citing works

Comparative analyses of multi-species sequences from targeted genomic regions

Thomas, J. W., Touchman, J., Blakesley, R. W., Bouffard, G. G., Beckstrom‐Sternberg, S. M., Margulies, E. H., Blanchette, M., Siepel, A. C., Thomas, P. J., McDowell, J. C., et al. (2003) · Nature · doi:10.1038/nature01858 · Cited by 638 · see citing works

Scanning Human Gene Deserts for Long-Range Enhancers

Nobrega, M. A., Ovcharenko, I., Afzal, V., & Rubin, E. M. (2003) · Science · doi:10.1126/science.1088328 · Cited by 608 · see citing works

Phylogenetic Shadowing of Primate Sequences to Find Functional Regions of the Human Genome

Boffelli, D., McAuliffe, J., Ovcharenko, D., Lewis, K. D., Ovcharenko, I., Pachter, L., & Rubin, E. M. (2003) · Science · doi:10.1126/science.1081331 · Cited by 516 · see citing works

rVista for Comparative Sequence-Based Discovery of Functional Transcription Factor Binding SitesPreprint

Loots, G. G., Ovcharenko, I., Pachter, L. S., Dubchak, I. L., & Rubin, E. M. (2002) · Genome Research · doi:10.1101/gr.225502 · Cited by 439 · see citing works

Identification and Characterization of Multi-Species Conserved SequencesPreprint

Margulies, E. H. (2003) · Genome Research · doi:10.1101/gr.1602203 · Cited by 336 · see citing works

Covariation in Frequencies of Substitution, Deletion, Transposition, and Recombination During Eutherian EvolutionPreprint

Hardison, R. C., Roskin, K. M., Yang, S., Diekhans, M., Kent, W. J., Weber, R. J., Elnitski, L. L., Li, J., O’Connor, M. J., Kolbe, D. L., et al. (2003) · Genome Research · doi:10.1101/gr.844103 · Cited by 282 · see citing works

Strategies and tools for whole-genome alignments

Couronne, O., Poliakov, A., Bray, N., Ishkhanov, T., Ryaboy, D., Rubin, E., Pachter, L., & Dubchak, I. (2003) · Genome Research · doi:10.1101/gr.762503 · Cited by 224 · see citing works

Mouse models of Down syndrome: how useful can they be? Comparison of the gene content of human chromosome 21 with orthologous mouse genomic regions

Gardiner, K., Fortna, A., Bechtel, L. J., & Davisson, M. T. (2003) · Gene · doi:10.1016/s0378-1119(03)00769-8 · Cited by 207 · see citing works

Regulatory Roles of Conserved Intergenic Domains in Vertebrate Dlx Bigene ClustersPreprint

Ghanem, N., Jarinova, O., Amores, A., Long, Q., Hatch, G., Park, B. K., Rubenstein, J. L. R., & Ekker, M. (2003) · Genome Research · doi:10.1101/gr.716103 · Cited by 177 · see citing works

Evolutionary Conservation of Regulatory Elements in Vertebrate Hox Gene ClustersPreprint

Santini, S., Boore, J. L., & Meyer, A. (2003) · Genome Research · doi:10.1101/gr.700503 · Cited by 161 · see citing works

Ensembl 2004

Birney, E. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkh038 · Cited by 143 · see citing works

zPicture: Dynamic Alignment and Visualization Tool for Analyzing Conservation ProfilesPreprint

Ovcharenko, I., Loots, G. G., Hardison, R. C., Miller, W., & Stubbs, L. J. (2004) · Genome Research · doi:10.1101/gr.2129504 · Cited by 142 · see citing works

Distinguishing Regulatory DNA From Neutral SitesPreprint

Elnitski, L. L., Hardison, R. C., Li, J., Yang, S., Kolbe, D. L., Eswara, P., O’Connor, M. J., Schwartz, S., Miller, W., & Chiaromonte, F. (2003) · Genome Research · doi:10.1101/gr.817703 · Cited by 135 · see citing works

Quantitative Estimates of Sequence Divergence for Comparative Analyses of Mammalian GenomesPreprint

Cooper, G. M., Brudno, M., Program, N. C. S., Green, E. D., Batzoglou, S., & Sidow, A. (2003) · Genome Research · doi:10.1101/gr.1064503 · Cited by 119 · see citing works

Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes

(2002) · Nature · doi:10.1038/news020722-10 · Cited by 106 · see citing works

Complex β-Satellite Repeat Structures and the Expansion of the Zinc Finger Gene Cluster in 19p12Preprint

Eichler, E. E., Hoffman, S. M. G., Adamson, A. A., Gordon, L. A., McCready, P., Lamerdin, J. E., & Mohrenweiser, H. W. (1998) · Genome Research · doi:10.1101/gr.8.8.791 · Cited by 72 · see citing works

GALA, a Database for Genomic Sequence Alignments and AnnotationsPreprint

Giardine, B. M., Elnitski, L. L., Riemer, C., Makałowska, I., Schwartz, S., Miller, W., & Hardison, R. C. (2003) · Genome Research · doi:10.1101/gr.603103 · Cited by 47 · see citing works

A Negative Cis-element Regulates the Level of Enhancement by Hypersensitive Site 2 of the β-Globin Locus Control Region

Elnitski, L. L., Li, J., Noguchi, C. T., Miller, W., & Hardison, R. C. (2001) · Journal of Biological Chemistry · doi:10.1074/jbc.m009624200 · Cited by 18 · see citing works

The DNA damage response induces inflammation and senescence by inhibiting autophagy of GATA4.

Kang, C., Xu, Q., Martin, T. D., Li, M. Z., Demaria, M., Aron, L., Lu, T., Yankner, B. A., Campisi, J., & Elledge, S. J. (2015) · Science · doi:10.1126/science.aaa5612 · Cited by 982 · see citing works

Regulation of the expression of inducible nitric oxide synthase

Pautz, A., Art, J., Hahn, S., Nowag, S., Voss, C., & Kleinert, H. (2010) · Nitric Oxide · doi:10.1016/j.niox.2010.04.007 · Cited by 549 · see citing works

Paracrine TGF-β Signaling Counterbalances BMP-Mediated Repression in Hair Follicle Stem Cell Activation

Oshimori, N., & Fuchs, E. V. (2012) · Cell stem cell · doi:10.1016/j.stem.2011.11.005 · Cited by 397 · see citing works

Oct4 and LIF/Stat3 Additively Induce Krüppel Factors to Sustain Embryonic Stem Cell Self-Renewal

Hall, J., Guo, G., Wray, J. P., Eyres, I., Nichols, J., Grotewold, L., Morfopoulou, S., Humphreys, P. D., Mansfield, W. M., Walker, R. V., et al. (2009) · Cell stem cell · doi:10.1016/j.stem.2009.11.003 · Cited by 380 · see citing works

Genome-wide scans for footprints of natural selection

Oleksyk, T. K., Smith, M. W., & O'Brien, S. J. (2010) · Philosophical Transactions of the Royal Society B: Biological Sciences · doi:10.1098/rstb.2009.0219 · Cited by 340 · see citing works

The making of a melanocyte: the specification of melanoblasts from the neural crest

Thomas, A. J., & Erickson, C. A. (2008) · Pigment Cell & Melanoma Research · doi:10.1111/j.1755-148x.2008.00506.x · Cited by 253 · see citing works

Homotypic clusters of transcription factor binding sites are a key component of human promoters and enhancers

Gotea, V., Visel, A., Westlund, J. M., Nobrega, M. A., Pennacchio, L. A., & Ovcharenko, I. (2010) · Genome Research · doi:10.1101/gr.104471.109 · Cited by 248 · see citing works

Phosphatidylethanolamine N ‐methyltransferase (PEMT) gene expression is induced by estrogen in human and mouse primary hepatocytes

Resseguie, M., Song, J., Niculescu, M. D., da Costa, K.-A., Randall, T. A., & Zeisel, S. H. (2007) · The FASEB Journal · doi:10.1096/fj.07-8227com · Cited by 246 · see citing works

Evolution and functional classification of vertebrate gene desertsPreprint

Ovcharenko, I., Loots, G. G., Nóbrega, M. A., Hardison, R. C., Miller, W., & Stubbs, L. J. (2004) · Genome Research · doi:10.1101/gr.3015505 · Cited by 237 · see citing works

Contribution of Clinical Correlates and 13 C-Reactive Protein Gene Polymorphisms to Interindividual Variability in Serum C-Reactive Protein Level

Kathiresan, S., Larson, M. G., Vasan, R. S., Guo, C., Gona, P. N., Keaney, J. F., Wilson, P. W. F., Newton‐Cheh, C., Musone, S. L., Camargo, A. L., et al. (2006) · Circulation · doi:10.1161/circulationaha.105.591271 · Cited by 228 · see citing works

NKX2.1 specifies cortical interneuron fate by activatingLhx6

Du, T., Xu, Q., Ocbina, P. J. R., & Anderson, S. A. (2008) · Development · doi:10.1242/dev.015123 · Cited by 220 · see citing works

Elevated and sustained expression of the transcription factors Egr1 and Egr2 controls NKT lineage differentiation in response to TCR signaling

Seiler, M. P., Mathew, R. S., Liszewski, M. K., Spooner, C. J., Barr, K., Meng, F., Singh, H., & Bendelac, A. S. (2012) · Nature Immunology · doi:10.1038/ni.2230 · Cited by 218 · see citing works

Locating mammalian transcription factor binding sites: A survey of computational and experimental techniquesPreprint

Elnitski, L. L., Jin, V. X., Farnham, P., & Jones, S. J. M. (2006) · Genome Research · doi:10.1101/gr.4140006 · Cited by 216 · see citing works

A global role for EKLF in definitive and primitive erythropoiesis

Hodge, D. J., Coghill, E., Keys, J. R., Maguire, T. L., Hartmann, B., McDowall, A. W., Weiss, M. J., Grimmond, S. M., & Perkins, A. C. (2005) · Blood · doi:10.1182/blood-2005-07-2888 · Cited by 209 · see citing works

Regulatory variation in a TBX5 enhancer leads to isolated congenital heart disease

Smemo, S., Campos, L. C. G., Moskowitz, I. P. G., Krieger, J. E., Pereira, A. C., & Nóbrega, M. A. (2012) · Human Molecular Genetics · doi:10.1093/hmg/dds165 · Cited by 204 · see citing works

Interplay between Notch1 and Notch3 promotes EMT and tumor initiation in squamous cell carcinoma

Natsuizaka, M., Whelan, K. A., Kagawa, S., Tanaka, K., Giroux, V., Chandramouleeswaran, P. M., Long, A., Sahu, V., Darling, D. S., Que, J., et al. (2017) · Nature Communications · doi:10.1038/s41467-017-01500-9 · Cited by 203 · see citing works

Neurogenin and NeuroD direct transcriptional targets and their regulatory enhancers

Seo, S., Lim, J.-W., Yellajoshyula, D., Chang, L.-W., & Kroll, K. L. (2007) · The EMBO Journal · doi:10.1038/sj.emboj.7601923 · Cited by 202 · see citing works

Smad3 promotes cancer progression by inhibiting E4BP4-mediated NK cell development

Tang, P. M., Zhou, S., Meng, X., Wang, Q.-M., Li, C., Lian, G., Huang, X.-R., Tang, Y.-J., Guan, X., Yan, B. P.-Y., et al. (2017) · Nature Communications · doi:10.1038/ncomms14677 · Cited by 191 · see citing works

FOXD3 regulates the lineage switch between neural crest-derived glial cells and pigment cells by repressing MITF through a non-canonical mechanism

Thomas, A. J., & Erickson, C. A. (2009) · Development · doi:10.1242/dev.031989 · Cited by 176 · see citing works

Comparative Analysis of Insulin Gene Promoters

Hay, C. W., & Docherty, K. (2006) · Diabetes · doi:10.2337/db06-0788 · Cited by 169 · see citing works

Direct Regulation of CLOCK Expression by REV-ERB

Crumbley, C., & Burris, T. P. (2011) · PLoS ONE · doi:10.1371/journal.pone.0017290 · Cited by 165 · see citing works

TBX5 drives Scn5a expression to regulate cardiac conduction system function

Arnolds, D. E., Liu, F., Fahrenbach, J. P., Kim, G. H., Schillinger, K. J., Smemo, S., McNally, E. M., Nóbrega, M. A., Patel, V. V., & Moskowitz, I. P. G. (2012) · Journal of Clinical Investigation · doi:10.1172/jci62617 · Cited by 164 · see citing works

Genomic Perspectives of Transcriptional Regulation in Forebrain Development

Nord, A. S., Pattabiraman, K., Visel, A., & Rubenstein, J. L. R. (2015) · Neuron · doi:10.1016/j.neuron.2014.11.011 · Cited by 152 · see citing works

EPHA2 Is Associated with Age-Related Cortical Cataract in Mice and Humans

Jun, G., Guo, H., Klein, R., Klein, R., Wang, J. J., Mitchell, P., Miao, H., Lee, K. E., Joshi, T., Buck, M., et al. (2009) · PLoS Genetics · doi:10.1371/journal.pgen.1000584 · Cited by 158 · see citing works

Multiple congenital anomalies-hypotonia-seizures syndrome is caused by a mutation in PIGN

Maydan, G., Noyman, I., Har‐Zahav, A., Neriah, Z. B., Pasmanik, M., Yeheskel, A., Albin‐Kaplanski, A., Maya, I., Magal, N., Birk, E., et al. (2011) · Journal of Medical Genetics · doi:10.1136/jmg.2010.087114 · Cited by 148 · see citing works

Identification of Novel Long Noncoding RNAs Associated with TGF-β/Smad3-Mediated Renal Inflammation and Fibrosis by RNA Sequencing

Zhou, Q., Chung, A. C. K., Huang, X. R., Dong, Y., Yu, X., & Lan, H. Y. (2013) · American Journal Of Pathology · doi:10.1016/j.ajpath.2013.10.007 · Cited by 148 · see citing works

Chromosome 9p21.3 Coronary Heart Disease Locus Genotype and Prospective Risk of CHD in Healthy Middle-Aged Men

Talmud, P. J., Cooper, J. A., Palmen, J., Lovering, R. C., Drenos, F., Hingorani, A. D., & Humphries, S. E. (2008) · Clinical Chemistry · doi:10.1373/clinchem.2007.095489 · Cited by 147 · see citing works

Tbr2 Is Essential for Hippocampal Lineage Progression from Neural Stem Cells to Intermediate Progenitors and Neurons

Hodge, R. D., Nelson, B. R., Kahoud, R. J., Yang, R., Mussar, K. E., Reiner, S. L., & Hevner, R. F. (2012) · Journal of Neuroscience · doi:10.1523/jneurosci.0532-12.2012 · Cited by 144 · see citing works

TGF-β Mediates Renal Fibrosis via the Smad3-Erbb4-IR Long Noncoding RNA Axis

Feng, M., Tang, P. M., Huang, X., Sun, S., You, Y., Xiao, J., Lv, L., Xu, A., & Lan, H.-Y. (2017) · Molecular Therapy · doi:10.1016/j.ymthe.2017.09.024 · Cited by 142 · see citing works

Characterization of the Core Mammalian Clock Component, NPAS2, as a REV-ERBα/RORα Target Gene

Crumbley, C., Wang, Y., Kojetin, D. J., & Burris, T. P. (2010) · Journal of Biological Chemistry · doi:10.1074/jbc.m110.129288 · Cited by 136 · see citing works

UCNEbase—a database of ultraconserved non-coding elements and genomic regulatory blocks

Dimitrieva, S., & Bucher, P. (2013) · Nucleic Acids Research · doi:10.1093/nar/gks1092 · Cited by 124 · see citing works

The signaling suppressor CIS controls proallergic T cell development and allergic airway inflammation

Yang, X. O., Zhang, H., Kim, B. S., Niu, X., Peng, J., Chen, Y., Kerketta, R., Lee, Y., Chang, S. H., Corry, D. B., et al. (2013) · Nature Immunology · doi:10.1038/ni.2633 · Cited by 134 · see citing works

Predicting tissue-specific enhancers in the human genomePreprint

Pennacchio, L. A., Loots, G. G., Nóbrega, M. A., & Ovcharenko, I. (2007) · Genome Research · doi:10.1101/gr.5972507 · Cited by 133 · see citing works

Mechanistic Differences in the Transcriptional Interpretation of Local and Long-Range Shh Morphogen Signaling

Oosterveen, T., Kurdija, S., Alekseenko, Z., Uhde, C. W., Bergsland, M., Sandberg, M., Andersson, E., Dias, J. M. M., Muhr, J., & Ericson, J. (2012) · Developmental Cell · doi:10.1016/j.devcel.2012.09.015 · Cited by 132 · see citing works

SETBP1 induces transcription of a network of development genes by acting as an epigenetic hub

Piazza, R., Magistroni, V., Redaelli, S., Mauri, M., Massimino, L., Sessa, A., Peronaci, M., Lalowski, M. M., Soliymani, R., Mezzatesta, C., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-04462-8 · Cited by 132 · see citing works

The proto-oncogene tyrosine protein kinase Src is essential for macrophage-myofibroblast transition during renal scarring

Tang, P. M., Zhou, S., Li, C., Liao, J., Xiao, J., Wang, Q., Lian, G., Li, J., Huang, X., To, K., et al. (2017) · Kidney International · doi:10.1016/j.kint.2017.07.026 · Cited by 130 · see citing works

DiRE: identifying distant regulatory elements of co-expressed genes

Gotea, V., & Ovcharenko, I. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn300 · Cited by 127 · see citing works

PDGFR blockade is a rational and effective therapy for NPM-ALK–driven lymphomas

Laimer, D., Dolznig, H., Kollmann, K., Vesely, P. W., Schlederer, M., Merkel, O., Schiefer, A. I., Hassler, M. R., Heider, S., Amenitsch, L., et al. (2012) · Nature Medicine · doi:10.1038/nm.2966 · Cited by 128 · see citing works

Genome-Wide Association Scan Identifies a Risk Locus for Preeclampsia on 2q14, Near the Inhibin, Beta B Gene

Johnson, M. P., Brennecke, S. P., East, C. E., Göring, H. H. H., Kent, J. W., Dyer, T. D., Said, J. M., Roten, L. T., Iversen, A., Abraham, L. J., et al. (2012) · PLoS ONE · doi:10.1371/journal.pone.0033666 · Cited by 122 · see citing works

Genome-wide discovery of human heart enhancersPreprint

Narlikar, L., Sakabe, N. J., Blanski, A. A., Arimura, F. E., Westlund, J. M., Nóbrega, M. A., & Ovcharenko, I. (2010) · Genome Research · doi:10.1101/gr.098657.109 · Cited by 117 · see citing works

TNF-α blockade induces IL-10 expression in human CD4+ T cells

Evans, H. G., Roostalu, U., Walter, G. J., Gullick, N., Frederiksen, K. S., Roberts, C. A., Sumner, J., Baeten, D., Gerwien, J. G., Cope, A. P., et al. (2014) · Nature Communications · doi:10.1038/ncomms4199 · Cited by 116 · see citing works

Transient Infantile Hypertriglyceridemia, Fatty Liver, and Hepatic Fibrosis Caused by Mutated GPD1, Encoding Glycerol-3-Phosphate Dehydrogenase 1

Basel‐Vanagaite, L., Zevit, N., Har‐Zahav, A., Guo, L., Parathath, S., Pasmanik‐Chor, M., McIntyre, A. D., Wang, J., Albin‐Kaplanski, A., Hartman, C., et al. (2012) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2011.11.028 · Cited by 106 · see citing works

Function of microRNA‐375 and microRNA‐124a in pancreas and brain

Baroukh, N., & OBBERGHEN, E. V. (2009) · FEBS Journal · doi:10.1111/j.1742-4658.2009.07353.x · Cited by 105 · see citing works

Fine-tuning of the intracellular canonical Notch signaling pathway

Borggrefe, T., & Liefke, R. (2012) · Cell Cycle · doi:10.4161/cc.11.2.18995 · Cited by 102 · see citing works

RAB26 and RAB3D Are Direct Transcriptional Targets of MIST1 That Regulate Exocrine Granule Maturation

Tian, X., Jin, R. U., Bredemeyer, A. J., Oates, E. J., Błażewska, K. M., McKenna, C. E., & Mills, J. C. (2009) · Molecular and Cellular Biology · doi:10.1128/mcb.01328-09 · Cited by 102 · see citing works

Acheate-scute like 1 (Ascl1) is required for normal delta-like (Dll) gene expression and notch signaling during retinal development

Nelson, B. R., Hartman, B. H., Ray, C. A., Hayashi, T., Bermingham‐McDonogh, O., & Reh, T. A. (2009) · Developmental Dynamics · doi:10.1002/dvdy.21848 · Cited by 94 · see citing works

Genome-wide CTCF distribution in vertebrates defines equivalent sites that aid the identification of disease-associated genes

Martin, D., Pantoja, C., Fernández‐Miñán, A., Valdes‐Quezada, C., Moltó, E., Matesanz, F., Bogdanović, O., de la Calle‐Mustienes, E., Domı́nguez, O., Taher, L., et al. (2011) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2059 · Cited by 91 · see citing works

Ancora: a web resource for exploring highly conserved noncoding elements and their association with developmental regulatory genes

Engström, P. G., Fredman, D., & Lenhard, B. (2008) · Genome biology · doi:10.1186/gb-2008-9-2-r34 · Cited by 91 · see citing works

Mutually repressive interaction between Brn1/2 and Rorb contributes to the establishment of neocortical layer 2/3 and layer 4

Oishi, K., Aramaki, M., & Nakajima, K. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1515949113 · Cited by 83 · see citing works

Regulation of vertebrate corticotropin-releasing factor genes

Yao, M., & Denver, R. J. (2007) · General and Comparative Endocrinology · doi:10.1016/j.ygcen.2007.01.046 · Cited by 87 · see citing works

Imaging Light Responses of Targeted Neuron Populations in the Rodent Retina

Borghuis, B. G., Tian, L., Xu, Y., Nikonov, S. S., Vardi, N., Zemelman, B. V., & Looger, L. L. (2011) · Journal of Neuroscience · doi:10.1523/jneurosci.6064-10.2011 · Cited by 87 · see citing works

Hoxa2 Selectively Enhances Meis Binding to Change a Branchial Arch Ground State

Amin, S., Donaldson, I. J., Zannino, D. A., Hensman, J. J., Rattray, M., Losa, M., Spitz, F., Ladam, F., Sagerström, C. G., & Bobola, N. (2015) · Developmental Cell · doi:10.1016/j.devcel.2014.12.024 · Cited by 86 · see citing works

Human-zebrafish non-coding conserved elements act in vivo to regulate transcription

Shin, J. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki853 · Cited by 86 · see citing works

Regulating Il9 transcription in T helper cells

Perumal, N. B., & Kaplan, M. H. (2011) · Trends in Immunology · doi:10.1016/j.it.2011.01.006 · Cited by 85 · see citing works

Epigenetics and T helper 1 differentiation

Aune, T. M., Collins, P. L., & Chang, S. (2008) · Immunology · doi:10.1111/j.1365-2567.2008.03026.x · Cited by 83 · see citing works

Mitochondrial SOD2 regulates epithelial–mesenchymal transition and cell populations defined by differential CD44 expression

Kinugasa, H., Whelan, K. A., Tanaka, K., Natsuizaka, M., Long, A., Guo, A. J., Chang, S., Kagawa, S., Srinivasan, S., Guha, M., et al. (2015) · Oncogene · doi:10.1038/onc.2014.449 · Cited by 80 · see citing works

cJun integrates calcium activity and tlx3 expression to regulate neurotransmitter specification

Marek, K. W., Kurtz, L. M., & Spitzer, N. C. (2010) · Nature Neuroscience · doi:10.1038/nn.2582 · Cited by 82 · see citing works

Functional Access to Neuron Subclasses in Rodent and Primate Forebrain

Mehta, P., Kreeger, L., Wylie, D. C., Pattadkal, J. J., Lusignan, T., Davis, M. J., Turi, G. F., Li, W.-K., Whitmire, M. P., Chen, Y., et al. (2019) · Cell Reports · doi:10.1016/j.celrep.2019.02.011 · Cited by 67 · see citing works

Computational methods to detect conserved non-genic elements in phylogenetically isolated genomes: application to zebrafish

Hiller, M., Agarwal, S., Notwell, J. H., Parikh, R., Guturu, H., Wenger, A. M., & Bejerano, G. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt557 · Cited by 72 · see citing works

Human ribosomal protein S13 regulates expression of its own gene at the splicing step by a feedback mechanism

Malygin, A. A., Parakhnevitch, N. M., Ivanov, A. V., Eperon, I. C., & Karpova, G. G. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm701 · Cited by 79 · see citing works

Foxc1 and Foxc2 deletion causes abnormal lymphangiogenesis and correlates with ERK hyperactivation

Fatima, A., Wang, Y., Uchida, Y., Norden, P. R., Liu, T., Culver, A. E., Dietz, W. H., Culver, F., Millay, M., Mukouyama, Y., et al. (2016) · Journal of Clinical Investigation · doi:10.1172/jci80465 · Cited by 79 · see citing works

Identification of cis-regulatory elements for MECP2 expression

Liu, J., & Francke, U. (2006) · Human Molecular Genetics · doi:10.1093/hmg/ddl099 · Cited by 78 · see citing works

A Recently Evolved Novel Trophoblast-Enriched Secreted Form of fms-Like Tyrosine Kinase-1 Variant Is Up-Regulated in Hypoxia and Preeclampsia

Thomas, C. P., Andrews, J. I., Raikwar, N. S., Kelley, E. A., Herse, F., Dechend, R., Golos, T. G., & Liu, K. Z. (2009) · The Journal of Clinical Endocrinology & Metabolism · doi:10.1210/jc.2009-0017 · Cited by 78 · see citing works

Rapid and widespread suppression of self-renewal by microRNA-203 during epidermal differentiation

Jackson, S. J., Zhang, Z., Feng, D., Flagg, M., O’Loughlin, E., Wang, D., Stokes, N., Fuchs, E. V., & Yi, R. (2013) · Development · doi:10.1242/dev.089649 · Cited by 77 · see citing works

ZEB2 Shapes the Epigenetic Landscape of Atherosclerosis

Cheng, P. P., Wirka, R. C., Clarke, S. L., Zhao, Q., Kundu, R. K., Nguyen, T., Nair, S., Sharma, D., Kim, H.-J., Shi, H., et al. (2022) · Circulation · doi:10.1161/circulationaha.121.057789 · Cited by 75 · see citing works

ETS1 governs pathological tissue-remodeling programs in disease-associated fibroblasts

Yan, M., Komatsu, N., Muro, R., Huynh, N. C., Tomofuji, Y., Okada, Y., Suzuki, H. I., Takaba, H., Kitazawa, R., Kitazawa, S., et al. (2022) · Nature Immunology · doi:10.1038/s41590-022-01285-0 · Cited by 74 · see citing works

Bmp2 Transcription in Osteoblast Progenitors Is Regulated by a Distant 3′ Enhancer Located 156.3 Kilobases from the Promoter

Chandler, R. L., Chandler, K. J., McFarland, K. A., & Mortlock, D. P. (2007) · Molecular and Cellular Biology · doi:10.1128/mcb.01609-06 · Cited by 73 · see citing works

Sex chromosomes drive gene expression and regulatory dimorphisms in mouse embryonic stem cells

Werner, R. J., Schultz, B. M., Huhn, J. M., Jelı́nek, J., Madžo, J., & Engel, N. (2017) · Biology of Sex Differences · doi:10.1186/s13293-017-0150-x · Cited by 73 · see citing works

Oestrogen Receptor-α binds the FOXP3 promoter and modulates regulatory T-cell function in human cervical cancer

Adurthi, S., Kumar, M. M., Vinodkumar, H. S., Mukherjee, G., Krishnamurthy, H., Kshitish, A. K., Bafna, U. D., Uma, D. K., Basavarajegowda, A., Krishna, S., et al. (2017) · Scientific Reports · doi:10.1038/s41598-017-17102-w · Cited by 73 · see citing works

Cellular senescence checkpoint function determines differential Notch1-dependent oncogenic and tumor-suppressor activities

Kagawa, S., Natsuizaka, M., Whelan, K. A., Facompre, N. D., Naganuma, S., Ohashi, S., Kinugasa, H., Egloff, A. M., Basu, D., Gimotty, P. A., et al. (2014) · Oncogene · doi:10.1038/onc.2014.169 · Cited by 71 · see citing works

EKLF/KLF1 Controls Cell Cycle Entry via Direct Regulation of E2f2

Tallack, M. R., Keys, J. R., Humbert, P. O., & Perkins, A. C. (2009) · Journal of Biological Chemistry · doi:10.1074/jbc.m109.006346 · Cited by 71 · see citing works

Evaluating the Association Between Keratoconus and the Corneal Thickness Genes in an Independent Australian Population

Sahebjada, S., Schäche, M., Richardson, A. J., Snibson, G. R., MacGregor, S., Daniell, M. D., & Baird, P. N. (2013) · Investigative Ophthalmology & Visual Science · doi:10.1167/iovs.13-12982 · Cited by 70 · see citing works

Dynamic transcription programs during ES cell differentiation towards mesoderm in serum versus serum-freeBMP4 culture

Bruce, S. J., Gardiner, B., Burke, L. J., Gongora, M., Grimmond, S. M., & Perkins, A. C. (2007) · BMC Genomics · doi:10.1186/1471-2164-8-365 · Cited by 70 · see citing works

Recognition of the polycistronic nature of human genes is critical to understanding the genotype-phenotype relationshipPreprint

Brunet, M. A., Levesque, S. A., Hunting, D. J., Cohen, A. A., & Roucou, X. (2018) · Genome Research · doi:10.1101/gr.230938.117 · Cited by 69 · see citing works

MIR-NATs repress MAPT translation and aid proteostasis in neurodegeneration

Simone, R., Javad, F., Emmett, W., Wilkins, O. G., Almeida, F., Barahona‐Torres, N., Zarȩba-Pasławska, J., Ehteramyan, M., Zuccotti, P., Modelska, A., et al. (2021) · Nature · doi:10.1038/s41586-021-03556-6 · Cited by 69 · see citing works

C-Reactive Protein Promotes Diabetic Kidney Disease in db/db Mice via the CD32b-Smad3-mTOR signaling Pathway

You, Y., Huang, X., Chen, H., Lyu, X., Liu, J., & Lan, H. Y. (2016) · Scientific Reports · doi:10.1038/srep26740 · Cited by 69 · see citing works

Local insulin-like growth factor I expression is essential for Purkinje neuron survival at birth

Croci, L., Barili, V., Chia, D. J., Massimino, L., van Vugt, R., Masserdotti, G., Longhi, R., Rotwein, P. S., & Consalez, G. G. (2010) · Cell Death and Differentiation · doi:10.1038/cdd.2010.78 · Cited by 65 · see citing works

Shear stimulation of FOXC1 and FOXC2 differentially regulates cytoskeletal activity during lymphatic valve maturation

Norden, P. R., Sabine, A., Wang, Y., Demir, C. S., Liu, T., Petrova, T. V., & Kume, T. (2020) · eLife · doi:10.7554/elife.53814 · Cited by 65 · see citing works

Differential Activity by Polymorphic Variants of a Remote Enhancer that Supports Galanin Expression in the Hypothalamus and Amygdala: Implications for Obesity, Depression and Alcoholism

Davidson, S., Lear, M., Shanley, L. J., Hing, B. W. Q., Baizan-Edge, A., Herwig, A., Quinn, J. P., Breen, G. D., McGuffin, P., Starkey, A. J., et al. (2011) · Neuropsychopharmacology · doi:10.1038/npp.2011.93 · Cited by 65 · see citing works

Vitamin D Related Genes, CYP24A1 and CYP27B1, and Colon Cancer Risk

Dong, L. M., Ulrich, C. M., Hsu, L., Duggan, D. J., Benitez, D. S., White, E., Slattery, M. L., Farin, F. M., Makar, K. W., Carlson, C. S., et al. (2009) · Cancer Epidemiology Biomarkers & Prevention · doi:10.1158/1055-9965.epi-09-0228 · Cited by 65 · see citing works

Stimulation of Steroid Receptor Coactivator-3 (SRC-3) Gene Overexpression by a Positive Regulatory Loop of E2F1 and SRC-3

Mussi, P., Yu, C., O’Malley, B. W., & Xu, J. (2006) · Molecular Endocrinology · doi:10.1210/me.2005-0522 · Cited by 65 · see citing works

A systematic approach to identify functional motifs within vertebrate developmental enhancers

Li, Q., Ritter, D., Yang, N., Dong, Z., Li, H., Chuang, J. H., & Guo, S. (2009) · Developmental Biology · doi:10.1016/j.ydbio.2009.10.019 · Cited by 65 · see citing works

Functional characterization of tissue-specific enhancers in the DLX5/6 locus

Birnbaum, R. Y., Everman, D. B., Murphy, K. K., Gurrieri, F., Schwartz, C. E., & Ahituv, N. (2012) · Human Molecular Genetics · doi:10.1093/hmg/dds336 · Cited by 63 · see citing works

Upregulation of Ets1 expression by NFATc2 and NFKB1/RELA promotes breast cancer cell invasiveness

Kim, G.-C., Kwon, H., Lee, C., Verma, R. P., Rudra, D., Kim, T., Kang, K., Nam, J. H., Kim, Y., & Im, S. (2018) · Oncogenesis · doi:10.1038/s41389-018-0101-3 · Cited by 64 · see citing works

Meta-analysis of genome-wide association studies in five cohorts reveals common variants in RBFOX1, a regulator of tissue-specific splicing, associated with refractive error

Stambolian, D. E., Wojciechowski, R., Oexle, K., Pirastu, M., Li, X., Raffel, L. J., Cotch, M. F., Chew, E. Y., Klein, B. E. K., Klein, R., et al. (2013) · Human Molecular Genetics · doi:10.1093/hmg/ddt116 · Cited by 64 · see citing works

IL-13Rα2 Membrane and Soluble Isoforms Differ in Humans and Mice

Chen, W., Sivaprasad, U., Tabata, Y., Gibson, A. M., Stier, M. T., Finkelman, F. D., & Hershey, G. K. K. (2009) · The Journal of Immunology · doi:10.4049/jimmunol.0901028 · Cited by 63 · see citing works

Diethylstilbestrol induces vaginal adenosis by disrupting SMAD/RUNX1-mediated cell fate decision in the Müllerian duct epithelium

Laronda, M. M., Unno, K., Ishi, K., Serna, V. A., Butler, L. M., Mills, A. A., Orvis, G. D., Behringer, R. R., Deng, C., Sinha, S., et al. (2013) · Developmental Biology · doi:10.1016/j.ydbio.2013.06.024 · Cited by 63 · see citing works

Gtf2ird1-Dependent Mohawk Expression Regulates Mechanosensing Properties of the Tendon

Kayama, T., Mori, M., Ito, Y., Matsushima, T., Nakamichi, R., Suzuki, H., Ichinose, S., Saito, M., Marumo, K., & Asahara, H. (2016) · Molecular and Cellular Biology · doi:10.1128/mcb.00950-15 · Cited by 63 · see citing works

ERCC4 Associated with Breast Cancer Risk: A Two-Stage Case-Control Study Using High-throughput Genotyping

Milne, R. L., Ribas, G., González‐Neira, A., Fagerholm, R., Salas, A., González, E., Dopazo, J., Nevanlinna, H. A., Robledo, M., & Benitez, J. J. (2006) · Cancer Research · doi:10.1158/0008-5472.can-06-1418 · Cited by 61 · see citing works

IL-36γ drives skin toxicity induced by EGFR/MEK inhibition and commensal Cutibacterium acnes

Satoh, T. K., Mellett, M., Meier-Schiesser, B., Fenini, G., Otsuka, A., Beer, H., Rordorf, T., Maul, J., Hafner, J., Navarini, A. A., et al. (2019) · Journal of Clinical Investigation · doi:10.1172/jci128678 · Cited by 61 · see citing works

Pitx1 broadly associates with limb enhancers and is enriched on hindlimb cis-regulatory elements

Infante, C. R., Park, S., Mihala, A. G., Kingsley, D. M., & Menke, D. B. (2012) · Developmental Biology · doi:10.1016/j.ydbio.2012.11.017 · Cited by 61 · see citing works

Association of the Hepatocyte Growth Factor Gene with Keratoconus in an Australian Population

Sahebjada, S., Schäche, M., Richardson, A. J., Snibson, G. R., Daniell, M. D., & Baird, P. N. (2014) · PLoS ONE · doi:10.1371/journal.pone.0084067 · Cited by 60 · see citing works

Dispersed Chromosomal Stat5b-binding Elements Mediate Growth Hormone-activated Insulin-like Growth Factor-I Gene Transcription

Chia, D. J., Varco-Merth, B., & Rotwein, P. S. (2010) · Journal of Biological Chemistry · doi:10.1074/jbc.m110.117697 · Cited by 57 · see citing works

PGC-1α Coordinates Mitochondrial Respiratory Capacity and Muscular Fatty Acid Uptake via Regulation of VEGF-B

Mehlem, A., Palombo, I., Wang, X., Hagberg, C. E., Eriksson, U., & Falkevall, A. (2016) · Diabetes · doi:10.2337/db15-1231 · Cited by 60 · see citing works

An Ultraconserved Brain-Specific Enhancer Within ADGRL3 (LPHN3) Underpins Attention-Deficit/Hyperactivity Disorder Susceptibility

Martinez, A. F., Abe, Y., Hong, S., Molyneux, K., Yarnell, D. S., Löhr, H., Driever, W., Acosta, M. T., Arcos‐Burgos, M., & Muenke, M. (2016) · Biological Psychiatry · doi:10.1016/j.biopsych.2016.06.026 · Cited by 59 · see citing works

Etsrp/Etv2 Is Directly Regulated by Foxc1a/b in the Zebrafish Angioblast

Veldman, M. B., & Lin, S. (2011) · Circulation Research · doi:10.1161/circresaha.111.251298 · Cited by 58 · see citing works

SOST/Sclerostin improves posttraumatic osteoarthritis and inhibits MMP2/3 expression after injury

Chang, J. C., Christiansen, B. A., Murugesh, D. K., Sebastian, A., Hum, N. R., Collette, N. M., Hatsell, S., Economides, A. N., Blanchette, C. D., & Loots, G. G. (2018) · Journal of Bone and Mineral Research · doi:10.1002/jbmr.3397 · Cited by 58 · see citing works

ATAC-Seq Reveals an Isl1 Enhancer That Regulates Sinoatrial Node Development and Function

Galang, G., Mandla, R., Ruan, H., Jung, C., Sinha, T., Stone, N. R., Wu, R. S., Mannion, B. J., Allu, P. K. R., Chang, K. C., et al. (2020) · Circulation Research · doi:10.1161/circresaha.120.317145 · Cited by 55 · see citing works

Repeated mutation of a developmental enhancer contributed to human thermoregulatory evolution

Aldea, D., Atsuta, Y., Kokalari, B., Schaffner, S. F., Prasasya, R. D., Aharoni, A., Dingwall, H. L., Warder, B. N., & Kamberov, Y. G. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2021722118 · Cited by 57 · see citing works

Comparative Analysis and Visualization of Genomic Sequences Using VISTA Browser and Associated Computational Tools

Dubchak, I. L. (2007) · Methods in molecular biology · doi:10.1007/978-1-59745-514-5_1 · Cited by 29 · see citing works

Dcode.org anthology of comparative genomic tools. Nucleic Acids Res., 33, W56–W64. Loots,G.G. et al. (2002) rVista for comparative sequence-based discovery of functional transcription factor binding sites

Loots, G. G., & Ovcharenko, I. (2005)

doi:10.1093/nar/gki355 Dcode.org anthology of comparative genomic tools

Loots, G. G., & Ovcharenko, I. (2005)

Dcode.org anthology of comparative genomic tools

Loots, G. G., & Ovcharenko, I. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki355 · Cited by 35 · see citing works

Comparative Genomic Analysis Using the UCSC Genome Browser

Karolchik, D., Bejerano, G., Hinrichs, A. S., Kuhn, R. M., Miller, W., Rosenbloom, K. R., Zweig, A. S., Haussler, D. H., & Kent, W. J. (2007) · Methods in molecular biology · doi:10.1007/978-1-59745-514-5_2 · Cited by 24 · see citing works