Bart Deplancke, Ph.D. - Publications

Affiliations: 
2002 University of Illinois, Urbana-Champaign, Urbana-Champaign, IL 
Area:
Molecular Biology, Toxicology, Microbiology Biology, Pathology

61 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2016 Deplancke B, Alpern D, Gardeux V. The Genetics of Transcription Factor DNA Binding Variation. Cell. 166: 538-54. PMID 27471964 DOI: 10.1016/J.Cell.2016.07.012  0.96
2016 Loviglio MN, Leleu M, Männik K, Passeggeri M, Giannuzzi G, van der Werf I, Waszak SM, Zazhytska M, Roberts-Caldeira I, Gheldof N, Migliavacca E, Alfaiz AA, Hippolyte L, Maillard AM, ... ... Deplancke B, et al. Chromosomal contacts connect loci associated with autism, BMI and head circumference phenotypes. Molecular Psychiatry. PMID 27240531 DOI: 10.1038/Mp.2016.84  0.96
2015 Waszak SM, Delaneau O, Gschwind AR, Kilpinen H, Raghav SK, Witwicki RM, Orioli A, Wiederkehr M, Panousis NI, Yurovsky A, Romano-Palumbo L, Planchon A, Bielser D, Padioleau I, Udin G, ... ... Deplancke B, et al. Population Variation and Genetic Control of Modular Chromatin Architecture in Humans. Cell. 162: 1039-50. PMID 26300124 DOI: 10.1016/J.Cell.2015.08.001  0.96
2015 Nitta KR, Jolma A, Yin Y, Morgunova E, Kivioja T, Akhtar J, Hens K, Toivonen J, Deplancke B, Furlong EE, Taipale J. Conservation of transcription factor binding specificities across 600 million years of bilateria evolution. Elife. 4. PMID 25779349 DOI: 10.7554/Elife.04837  0.96
2015 Moullan N, Mouchiroud L, Wang X, Ryu D, Williams EG, Mottis A, Jovaisaite V, Frochaux MV, Quiros PM, Deplancke B, Houtkooper RH, Auwerx J. Tetracyclines Disturb Mitochondrial Function across Eukaryotic Models: A Call for Caution in Biomedical Research. Cell Reports. PMID 25772356 DOI: 10.1016/J.Celrep.2015.02.034  0.96
2015 Schertel C, Albarca M, Rockel-Bauer C, Kelley NW, Bischof J, Hens K, van Nimwegen E, Basler K, Deplancke B. A large-scale, in vivo transcription factor screen defines bivalent chromatin as a key property of regulatory factors mediating Drosophila wing development. Genome Research. 25: 514-23. PMID 25568052 DOI: 10.1101/Gr.181305.114  0.96
2015 Simicevic J, Moniatte M, Hamelin R, Ahrné E, Deplancke B. A mammalian transcription factor-specific peptide repository for targeted proteomics. Proteomics. 15: 752-6. PMID 25407602 DOI: 10.1002/Pmic.201400355  0.96
2015 Bou Sleiman MS, Osman D, Massouras A, Hoffmann AA, Lemaitre B, Deplancke B. Genetic, molecular and physiological basis of variation in Drosophila gut immunocompetence Nature Communications. 6. DOI: 10.1038/ncomms8829  0.96
2014 Williams EG, Mouchiroud L, Frochaux M, Pandey A, Andreux PA, Deplancke B, Auwerx J. An evolutionarily conserved role for the aryl hydrocarbon receptor in the regulation of movement. Plos Genetics. 10: e1004673. PMID 25255223 DOI: 10.1371/Journal.Pgen.1004673  0.96
2014 Gubelmann C, Schwalie PC, Raghav SK, Röder E, Delessa T, Kiehlmann E, Waszak SM, Corsinotti A, Udin G, Holcombe W, Rudofsky G, Trono D, Wolfrum C, Deplancke B. Identification of the transcription factor ZEB1 as a central component of the adipogenic gene regulatory network. Elife. 3: e03346. PMID 25163748 DOI: 10.7554/Elife.03346  0.96
2014 Huang W, Massouras A, Inoue Y, Peiffer J, Ràmia M, Tarone AM, Turlapati L, Zichner T, Zhu D, Lyman RF, Magwire MM, Blankenburg K, Carbone MA, Chang K, Ellis LL, ... ... Deplancke B, et al. Natural variation in genome architecture among 205 Drosophila melanogaster Genetic Reference Panel lines. Genome Research. 24: 1193-208. PMID 24714809 DOI: 10.1101/Gr.171546.113  0.96
2014 Bonhoure N, Bounova G, Bernasconi D, Praz V, Lammers F, Canella D, Willis IM, Herr W, Hernandez N, Delorenzi M, Deplancke B, Desvergne B, Guex N, Naef F, Rougemont J, et al. Quantifying ChIP-seq data: A spiking method providing an internal reference for sample-to-sample normalization Genome Research. 24: 1157-1168. PMID 24709819 DOI: 10.1101/Gr.168260.113  0.96
2014 Gilardi F, Migliavacca E, Naldi A, Baruchet M, Canella D, Le Martelot G, Guex N, Desvergne B, Delorenzi M, Deplancke B, Herr W, Naef F, Rougemont J, Schibler U, Andersin T, et al. Genome-Wide Analysis of SREBP1 Activity around the Clock Reveals Its Combined Dependency on Nutrient and Circadian Signals Plos Genetics. 10. PMID 24603613 DOI: 10.1371/journal.pgen.1004155  0.96
2014 Waszak SM, Kilpinen H, Gschwind AR, Orioli A, Raghav SK, Witwicki RM, Migliavacca E, Yurovsky A, Lappalainen T, Hernandez N, Reymond A, Dermitzakis ET, Deplancke B. Identification and removal of low-complexity sites in allele-specific analysis of ChIP-seq data. Bioinformatics (Oxford, England). 30: 165-71. PMID 24255646 DOI: 10.1093/Bioinformatics/Btt667  0.96
2013 Waszak SM, Deplancke B. Rounding up natural gene expression variation during development. Developmental Cell. 27: 601-3. PMID 24369832 DOI: 10.1016/J.Devcel.2013.12.007  0.96
2013 Kilpinen H, Waszak SM, Gschwind AR, Raghav SK, Witwicki RM, Orioli A, Migliavacca E, Wiederkehr M, Gutierrez-Arcelus M, Panousis NI, Yurovsky A, Lappalainen T, Romano-Palumbo L, Planchon A, Bielser D, ... ... Deplancke B, et al. Coordinated effects of sequence variation on DNA binding, chromatin structure, and transcription. Science (New York, N.Y.). 342: 744-7. PMID 24136355 DOI: 10.1126/Science.1242463  0.96
2013 Gubelmann C, Waszak SM, Isakova A, Holcombe W, Hens K, Iagovitina A, Feuz JD, Raghav SK, Simicevic J, Deplancke B. A yeast one-hybrid and microfluidics-based pipeline to map mammalian gene regulatory networks. Molecular Systems Biology. 9: 682. PMID 23917988 DOI: 10.1038/Msb.2013.38  0.96
2013 Kim Y, Iagovitina A, Ishihara K, Fitzgerald KM, Deplancke B, Papatsenko D, Shvartsman SY. Context-dependent transcriptional interpretation of mitogen activated protein kinase signaling in the Drosophila embryo. Chaos (Woodbury, N.Y.). 23: 025105. PMID 23822503 DOI: 10.1063/1.4808157  0.96
2013 Buchon N, Osman D, David FP, Fang HY, Boquete JP, Deplancke B, Lemaitre B. Morphological and molecular characterization of adult midgut compartmentalization in Drosophila. Cell Reports. 3: 1725-38. PMID 23643535 DOI: 10.1016/J.Celrep.2013.04.001  0.96
2013 Simicevic J, Schmid AW, Gilardoni PA, Zoller B, Raghav SK, Krier I, Gubelmann C, Lisacek F, Naef F, Moniatte M, Deplancke B. Absolute quantification of transcription factors during cellular differentiation using multiplexed targeted proteomics. Nature Methods. 10: 570-6. PMID 23584187 DOI: 10.1038/Nmeth.2441  0.96
2013 Ritter AD, Shen Y, Fuxman Bass J, Jeyaraj S, Deplancke B, Mukhopadhyay A, Xu J, Driscoll M, Tissenbaum HA, Walhout AJ. Complex expression dynamics and robustness in C. elegans insulin networks. Genome Research. 23: 954-65. PMID 23539137 DOI: 10.1101/Gr.150466.112  0.96
2013 Corsinotti A, Kapopoulou A, Gubelmann C, Imbeault M, Santoni de Sio FR, Rowe HM, Mouscaz Y, Deplancke B, Trono D. Global and stage specific patterns of Krüppel-associated-box zinc finger protein gene expression in murine early embryonic cells. Plos One. 8: e56721. PMID 23451074 DOI: 10.1371/Journal.Pone.0056721  0.96
2013 Rockel S, Geertz M, Hens K, Deplancke B, Maerkl SJ. iSLIM: a comprehensive approach to mapping and characterizing gene regulatory networks. Nucleic Acids Research. 41: e52. PMID 23258699 DOI: 10.1093/Nar/Gks1323  0.96
2012 Le Martelot G, Canella D, Symul L, Migliavacca E, Gilardi F, Liechti R, Martin O, Harshman K, Delorenzi M, Desvergne B, Herr W, Deplancke B, Schibler U, Rougemont J, Guex N, et al. Genome-wide RNA polymerase II profiles and RNA accumulation reveal kinetics of transcription and associated epigenetic changes during diurnal cycles. Plos Biology. 10: e1001442. PMID 23209382 DOI: 10.1371/Journal.Pbio.1001442  0.96
2012 Massouras A, Waszak SM, Albarca-Aguilera M, Hens K, Holcombe W, Ayroles JF, Dermitzakis ET, Stone EA, Jensen JD, Mackay TF, Deplancke B. Genomic variation and its impact on gene expression in Drosophila melanogaster. Plos Genetics. 8: e1003055. PMID 23189034 DOI: 10.1371/Journal.Pgen.1003055  0.96
2012 Schröter C, Ares S, Morelli LG, Isakova A, Hens K, Soroldoni D, Gajewski M, Jülicher F, Maerkl SJ, Deplancke B, Oates AC. Topology and dynamics of the zebrafish segmentation clock core circuit. Plos Biology. 10: e1001364. PMID 22911291 DOI: 10.1371/Journal.Pbio.1001364  0.96
2012 Raghav SK, Waszak SM, Krier I, Gubelmann C, Isakova A, Mikkelsen TS, Deplancke B. Integrative genomics identifies the corepressor SMRT as a gatekeeper of adipogenesis through the transcription factors C/EBPβ and KAISO. Molecular Cell. 46: 335-50. PMID 22521691 DOI: 10.1016/J.Molcel.2012.03.017  0.96
2012 Canella D, Bernasconi D, Gilardi F, LeMartelot G, Migliavacca E, Praz V, Cousin P, Delorenzi M, Hernandez N. A multiplicity of factors contributes to selective RNA polymerase III occupancy of a subset of RNA polymerase III genes in mouse liver. Genome Research. 22: 666-80. PMID 22287103 DOI: 10.1101/Gr.130286.111  0.96
2012 Deplancke B, Verstrepen KJ. Genetics. Variable outcome of mutations. Science (New York, N.Y.). 335: 44-5. PMID 22223795 DOI: 10.1126/Science.1216823  0.96
2012 Hens K, Feuz JD, Deplancke B. A high-throughput gateway-compatible yeast one-hybrid screen to detect protein-DNA interactions. Methods in Molecular Biology (Clifton, N.J.). 786: 335-55. PMID 21938636 DOI: 10.1007/978-1-61779-292-2_20  0.96
2012 Raghav SK, Deplancke B. Genome-wide profiling of DNA-binding proteins using barcode-based multiplex Solexa sequencing. Methods in Molecular Biology (Clifton, N.J.). 786: 247-62. PMID 21938631 DOI: 10.1007/978-1-61779-292-2_15  0.96
2012 Deplancke B, Gheldof N. Preface Methods in Molecular Biology. 786.  0.96
2011 Hens K, Feuz JD, Isakova A, Iagovitina A, Massouras A, Bryois J, Callaerts P, Celniker SE, Deplancke B. Automated protein-DNA interaction screening of Drosophila regulatory elements. Nature Methods. 8: 1065-70. PMID 22037703 DOI: 10.1038/Nmeth.1763  0.96
2011 Gubelmann C, Gattiker A, Massouras A, Hens K, David F, Decouttere F, Rougemont J, Deplancke B. GETPrime: a gene- or transcript-specific primer database for quantitative real-time PCR. Database : the Journal of Biological Databases and Curation. 2011: bar040. PMID 21917859 DOI: 10.1093/Database/Bar040  0.96
2011 Tabuchi TM, Deplancke B, Osato N, Zhu LJ, Barrasa MI, Harrison MM, Horvitz HR, Walhout AJ, Hagstrom KA. Chromosome-biased binding and gene regulation by the Caenorhabditis elegans DRM complex. Plos Genetics. 7: e1002074. PMID 21589891 DOI: 10.1371/Journal.Pgen.1002074  0.36
2011 Baitsch L, Baumgaertner P, Devêvre E, Raghav SK, Legat A, Barba L, Wieckowski S, Bouzourene H, Deplancke B, Romero P, Rufer N, Speiser DE. Exhaustion of tumor-specific CD8⁺ T cells in metastases from melanoma patients. The Journal of Clinical Investigation. 121: 2350-60. PMID 21555851 DOI: 10.1172/Jci46102  0.96
2010 Massouras A, Hens K, Gubelmann C, Uplekar S, Decouttere F, Rougemont J, Cole ST, Deplancke B. Primer-initiated sequence synthesis to detect and assemble structural variants. Nature Methods. 7: 485-6. PMID 20543844 DOI: 10.1038/Nmeth.F.308  0.96
2010 Massouras A, Decouttere F, Hens K, Deplancke B. WebPrInSeS: automated full-length clone sequence identification and verification using high-throughput sequencing data. Nucleic Acids Research. 38: W378-84. PMID 20501601 DOI: 10.1093/nar/gkq431  0.96
2010 Simicevic J, Deplancke B. DNA-centered approaches to characterize regulatory protein-DNA interaction complexes. Molecular Biosystems. 6: 462-8. PMID 20174675 DOI: 10.1039/B916137F  0.96
2009 Reece-Hoyes JS, Deplancke B, Barrasa MI, Hatzold J, Smit RB, Arda HE, Pope PA, Gaudet J, Conradt B, Walhout AJ. The C. elegans Snail homolog CES-1 can activate gene expression in vivo and share targets with bHLH transcription factors. Nucleic Acids Research. 37: 3689-98. PMID 19372275 DOI: 10.1093/Nar/Gkp232  0.96
2009 Deplancke B. Experimental advances in the characterization of metazoan gene regulatory networks. Briefings in Functional Genomics & Proteomics. 8: 12-27. PMID 19324929 DOI: 10.1093/Bfgp/Elp001  0.96
2008 Mukhopadhyay A, Deplancke B, Walhout AJ, Tissenbaum HA. Chromatin immunoprecipitation (ChIP) coupled to detection by quantitative real-time PCR to study transcription factor binding to DNA in Caenorhabditis elegans. Nature Protocols. 3: 698-709. PMID 18388953 DOI: 10.1038/Nprot.2008.38  0.96
2007 Vermeirssen V, Deplancke B, Barrasa MI, Reece-Hoyes JS, Arda HE, Grove CA, Martinez NJ, Sequerra R, Doucette-Stamm L, Brent MR, Walhout AJ. Matrix and Steiner-triple-system smart pooling assays for high-performance transcription regulatory network mapping. Nature Methods. 4: 659-64. PMID 17589517 DOI: 10.1038/Nmeth1063  0.96
2006 Deplancke B, Vermeirssen V, Arda HE, Martinez NJ, Walhout AJ. Gateway-compatible yeast one-hybrid screens. Csh Protocols. 2006. PMID 22485967 DOI: 10.1101/Pdb.Prot4590  0.36
2006 Wang Y, Oh SW, Deplancke B, Luo J, Walhout AJ, Tissenbaum HA. C. elegans 14-3-3 proteins regulate life span and interact with SIR-2.1 and DAF-16/FOXO. Mechanisms of Ageing and Development. 127: 741-7. PMID 16860373 DOI: 10.1016/J.Mad.2006.05.005  0.96
2006 Deplancke B, Mukhopadhyay A, Ao W, Elewa AM, Grove CA, Martinez NJ, Sequerra R, Doucette-Stamm L, Reece-Hoyes JS, Hope IA, Tissenbaum HA, Mango SE, Walhout AJ. A gene-centered C. elegans protein-DNA interaction network. Cell. 125: 1193-205. PMID 16777607 DOI: 10.1016/J.Cell.2006.04.038  0.96
2005 Reece-Hoyes JS, Deplancke B, Shingles J, Grove CA, Hope IA, Walhout AJ. A compendium of Caenorhabditis elegans regulatory transcription factors: a resource for mapping transcription regulatory networks. Genome Biology. 6: R110. PMID 16420670 DOI: 10.1186/Gb-2005-6-13-R110  0.96
2005 Mukhopadhyay A, Deplancke B, Walhout AJ, Tissenbaum HA. C. elegans tubby regulates life span and fat storage by two independent mechanisms. Cell Metabolism. 2: 35-42. PMID 16054097 DOI: 10.1016/J.Cmet.2005.06.004  0.96
2004 Dupuy D, Li QR, Deplancke B, Boxem M, Hao T, Lamesch P, Sequerra R, Bosak S, Doucette-Stamm L, Hope IA, Hill DE, Walhout AJ, Vidal M. A first version of the Caenorhabditis elegans Promoterome. Genome Research. 14: 2169-75. PMID 15489340 DOI: 10.1101/Gr.2497604  0.96
2004 Deplancke B, Dupuy D, Vidal M, Walhout AJ. A gateway-compatible yeast one-hybrid system. Genome Research. 14: 2093-101. PMID 15489331 DOI: 10.1101/Gr.2445504  0.96
2003 Collier CT, Smiricky-Tjardes MR, Albin DM, Wubben JE, Gabert VM, Deplancke B, Bane D, Anderson DB, Gaskins HR. Molecular ecological analysis of porcine ileal microbiota responses to antimicrobial growth promoters. Journal of Animal Science. 81: 3035-45. PMID 14677859 DOI: 10.2527/2003.81123035X  0.96
2003 Collier CT, van der Klis JD, Deplancke B, Anderson DB, Gaskins HR. Effects of tylosin on bacterial mucolysis, Clostridium perfringens colonization, and intestinal barrier function in a chick model of necrotic enteritis. Antimicrobial Agents and Chemotherapy. 47: 3311-7. PMID 14506046 DOI: 10.1128/Aac.47.10.3311-3317.2003  0.96
2003 Deplancke B, Gaskins HR. Hydrogen sulfide induces serum-independent cell cycle entry in nontransformed rat intestinal epithelial cells. Faseb Journal : Official Publication of the Federation of American Societies For Experimental Biology. 17: 1310-2. PMID 12738807 DOI: 10.1096/Fj.02-0883Fje  0.96
2003 Deplancke B, Finster K, Graham WV, Collier CT, Thurmond JE, Gaskins HR. Gastrointestinal and microbial responses to sulfate-supplemented drinking water in mice. Experimental Biology and Medicine (Maywood, N.J.). 228: 424-33. PMID 12671187 DOI: 10.1177/153537020322800413  0.96
2002 Deplancke B, Vidal O, Ganessunker D, Donovan SM, Mackie RI, Gaskins HR. Selective growth of mucolytic bacteria including Clostridium perfringens in a neonatal piglet model of total parenteral nutrition. The American Journal of Clinical Nutrition. 76: 1117-25. PMID 12399288 DOI: 10.1093/Ajcn/76.5.1117  0.96
2002 Nyholm SV, Deplancke B, Gaskins HR, Apicella MA, McFall-Ngai MJ. Roles of Vibrio fischeri and nonsymbiotic bacteria in the dynamics of mucus secretion during symbiont colonization of the Euprymna scolopes light organ. Applied and Environmental Microbiology. 68: 5113-22. PMID 12324362 DOI: 10.1128/Aem.68.10.5113-5122.2002  0.96
2002 Vermeirssen V, Deplancke B, Tappenden KA, Van Camp J, Gaskins HR, Verstraete W. Intestinal transport of the lactokinin Ala-Leu-Pro-Met-His-Ile-Arg through a Caco-2 Bbe monolayer. Journal of Peptide Science : An Official Publication of the European Peptide Society. 8: 95-100. PMID 11931586 DOI: 10.1002/Psc.371  0.96
2002 Deplancke B, Gaskins HR. Redox control of the transsulfuration and glutathione biosynthesis pathways. Current Opinion in Clinical Nutrition and Metabolic Care. 5: 85-92. PMID 11790955 DOI: 10.1097/00075197-200201000-00015  0.96
2001 Deplancke B, Gaskins HR. Microbial modulation of innate defense: goblet cells and the intestinal mucus layer. The American Journal of Clinical Nutrition. 73: 1131S-1141S. PMID 11393191 DOI: 10.1093/Ajcn/73.6.1131S  0.96
2000 De Boever P, Deplancke B, Verstraete W. Fermentation by gut microbiota cultured in a simulator of the human intestinal microbial ecosystem is improved by supplementing a soygerm powder Journal of Nutrition. 130: 2599-2606. PMID 11015496 DOI: 10.1093/Jn/130.10.2599  0.96
2000 Deplancke B, Hristova KR, Oakley HA, McCracken VJ, Aminov R, Mackie RI, Gaskins HR. Molecular ecological analysis of the succession and diversity of sulfate-reducing bacteria in the mouse gastrointestinal tract. Applied and Environmental Microbiology. 66: 2166-74. PMID 10788396 DOI: 10.1128/Aem.66.5.2166-2174.2000  0.96
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