Bart Deplancke

Bart Deplancke

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Bart Deplancke

Bart Deplancke

Publications by authors named "Bart Deplancke"

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cis-regulatory variation modulates susceptibility to enteric infection in the Drosophila genetic reference panel.

Genome Biol 2020 01 17;21(1). Epub 2020 Jan 17.

Laboratory of Systems Biology and Genetics, Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.

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http://dx.doi.org/10.1186/s13059-019-1912-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6966807PMC
January 2020

Enteric infection induces Lark-mediated intron retention at the 5' end of Drosophila genes.

Genome Biol 2020 01 17;21(1). Epub 2020 Jan 17.

Laboratory of Integrative Systems Physiology, Institue of Bioengineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.

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http://dx.doi.org/10.1186/s13059-019-1918-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6966827PMC
January 2020

Dynamic regulation of chromatin accessibility by pluripotency transcription factors across the cell cycle.

Elife 2019 12 3;8. Epub 2019 Dec 3.

Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.

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http://dx.doi.org/10.7554/eLife.50087DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6890464PMC
December 2019

Systems-Genetics-Based Inference of a Core Regulatory Network Underlying White Fat Browning.

Cell Rep 2019 Dec;29(12):4099-4113.e5

Chair for Molecular Nutritional Medicine, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Gregor-Mendel-Str. 2, 85354 Freising, Germany; EKFZ-Else Kröner-Fresenius Center for Nutritional Medicine, Technical University of Munich, Gregor-Mendel-Str. 2, 85354 Freising, Germany. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2019.11.053DOI Listing
December 2019

Sex-dependent and sex-independent regulatory systems of size variation in natural populations.

Mol Syst Biol 2019 11;15(11):e9012

Institute of Molecular Systems Biology, ETH Zurich, Zürich, Switzerland.

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http://dx.doi.org/10.15252/msb.20199012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6878047PMC
November 2019

Commensal Gut Bacteria Buffer the Impact of Host Genetic Variants on Drosophila Developmental Traits under Nutritional Stress.

iScience 2019 Sep 2;19:436-447. Epub 2019 Aug 2.

Institut de Génomique Fonctionnelle de Lyon (IGFL), Université de Lyon, Ecole Normale Supérieure de Lyon, Centre National de la Recherche Scientifique, Université Claude Bernard Lyon 1, Unité Mixte de Recherche 5242, 69364 Cedex 07, Lyon, France. Electronic address:

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http://dx.doi.org/10.1016/j.isci.2019.07.048DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6704380PMC
September 2019

Simplified Drop-seq workflow with minimized bead loss using a bead capture and processing microfluidic chip.

Lab Chip 2019 04;19(9):1610-1620

Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland. and Swiss Institute of Bioinformatics, Lausanne, Switzerland.

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http://dx.doi.org/10.1039/c9lc00014cDOI Listing
April 2019

A Comprehensive Drosophila melanogaster Transcription Factor Interactome.

Cell Rep 2019 04;27(3):955-970.e7

Department of Medicine, Division of Genetics, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Systems Biology Graduate Program, Harvard University, Cambridge, MA 02138, USA; Bioinformatics and Integrative Genomics Ph.D. Program, Harvard University, Cambridge, MA 02138, USA; Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2019.03.071DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6485956PMC
April 2019

BRB-seq: ultra-affordable high-throughput transcriptomics enabled by bulk RNA barcoding and sequencing.

Genome Biol 2019 04 19;20(1):71. Epub 2019 Apr 19.

Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland.

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http://dx.doi.org/10.1186/s13059-019-1671-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6474054PMC
April 2019

ZFP30 promotes adipogenesis through the KAP1-mediated activation of a retrotransposon-derived Pparg2 enhancer.

Nat Commun 2019 04 18;10(1):1809. Epub 2019 Apr 18.

Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland.

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http://www.nature.com/articles/s41467-019-09803-9
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http://dx.doi.org/10.1038/s41467-019-09803-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6472429PMC
April 2019

The NAD-Booster Nicotinamide Riboside Potently Stimulates Hematopoiesis through Increased Mitochondrial Clearance.

Cell Stem Cell 2019 03;24(3):405-418.e7

Laboratory of Regenerative Hematopoiesis, Swiss Institute for Experimental Cancer Research (ISREC) & Institute of Bioengineering (IBI), School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland; Service and Central Laboratory of Hematology, Departments of Oncology and of Laboratories, Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S19345909193006
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http://dx.doi.org/10.1016/j.stem.2019.02.012DOI Listing
March 2019

Cross-talk between emulsion drops: how are hydrophilic reagents transported across oil phases?

Lab Chip 2018 12;18(24):3903-3912

Soft Materials Laboratory, Institute of Materials, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland.

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http://xlink.rsc.org/?DOI=C8LC01000E
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http://dx.doi.org/10.1039/c8lc01000eDOI Listing
December 2018

Reversible De-differentiation of Mature White Adipocytes into Preadipocyte-like Precursors during Lactation.

Cell Metab 2018 08 14;28(2):282-288.e3. Epub 2018 Jun 14.

Touchstone Diabetes Center, Department of Internal Medicine, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-8549, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cmet.2018.05.022DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6535147PMC
August 2018

A stromal cell population that inhibits adipogenesis in mammalian fat depots.

Nature 2018 07 20;559(7712):103-108. Epub 2018 Jun 20.

Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL) and Swiss Institute of Bioinformatics, Lausanne, Switzerland.

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http://dx.doi.org/10.1038/s41586-018-0226-8DOI Listing
July 2018

Engineered Multivalent Sensors to Detect Coexisting Histone Modifications in Living Stem Cells.

Cell Chem Biol 2018 01 22;25(1):51-56.e6. Epub 2017 Nov 22.

Laboratory of Biophysical Chemistry of Macromolecules (LCBM), Institute of Chemical Sciences and Engineering (ISIC), Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland. Electronic address:

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http://dx.doi.org/10.1016/j.chembiol.2017.10.008DOI Listing
January 2018

Cross-Tissue Identification of Somatic Stem and Progenitor Cells Using a Single-Cell RNA-Sequencing Derived Gene Signature.

Stem Cells 2017 12 6;35(12):2390-2402. Epub 2017 Nov 6.

Laboratory of Systems Biology and Genetics, Institute of Bioengineering and Swiss Institute of Bioinformatics, CH-1015, Lausanne, Switzerland.

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http://dx.doi.org/10.1002/stem.2719DOI Listing
December 2017

Hippo, TGF-β, and Src-MAPK pathways regulate transcription of the upd3 cytokine in Drosophila enterocytes upon bacterial infection.

PLoS Genet 2017 Nov 6;13(11):e1007091. Epub 2017 Nov 6.

Cornell Institute of Host-Microbe Interactions and Disease. Department of Entomology. Cornell University, Ithaca, NY, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1007091DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5690694PMC
November 2017

ASAP: a web-based platform for the analysis and interactive visualization of single-cell RNA-seq data.

Bioinformatics 2017 Oct;33(19):3123-3125

Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne CH-1015, Switzerland.

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http://dx.doi.org/10.1093/bioinformatics/btx337DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5870842PMC
October 2017

Profiling of Single-Cell Transcriptomes.

Curr Protoc Mouse Biol 2017 Sep 8;7(3):145-175. Epub 2017 Sep 8.

Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland.

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http://dx.doi.org/10.1002/cpmo.30DOI Listing
September 2017

Gene regulatory mechanisms underlying the intestinal innate immune response.

Curr Opin Genet Dev 2017 Apr 20;43:46-52. Epub 2016 Dec 20.

Laboratory of Systems Biology and Genetics, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland. Electronic address:

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http://dx.doi.org/10.1016/j.gde.2016.11.004DOI Listing
April 2017

The Zic family homologue Odd-paired regulates Alk expression in Drosophila.

PLoS Genet 2017 04 3;13(4):e1006617. Epub 2017 Apr 3.

Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.

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http://dx.doi.org/10.1371/journal.pgen.1006617DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5393633PMC
April 2017

Tissue-specific enhancer repression through molecular integration of cell signaling inputs.

PLoS Genet 2017 04 10;13(4):e1006718. Epub 2017 Apr 10.

Centre de Biologie du Développement (CBD), Centre de Biologie Intégrative (CBI), Université Fédérale de Toulouse, UMR5547 CNRS/Université Paul Sabatier (UPS), Toulouse, France.

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http://dx.doi.org/10.1371/journal.pgen.1006718DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5402979PMC
April 2017

Editorial overview: Genome architecture and expression.

Curr Opin Genet Dev 2017 04 1;43:iv-v. Epub 2017 May 1.

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http://dx.doi.org/10.1016/j.gde.2017.04.002DOI Listing
April 2017

SMiLE-seq identifies binding motifs of single and dimeric transcription factors.

Nat Methods 2017 03 16;14(3):316-322. Epub 2017 Jan 16.

Institute of Bioengineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.

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http://dx.doi.org/10.1038/nmeth.4143DOI Listing
March 2017

Transcription factor proteomics-Tools, applications, and challenges.

Proteomics 2017 02 24;17(3-4). Epub 2017 Jan 24.

Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), and Swiss Institute of Bioinformatics, Lausanne, Switzerland.

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http://dx.doi.org/10.1002/pmic.201600317DOI Listing
February 2017

Dissecting the brown adipogenic regulatory network using integrative genomics.

Sci Rep 2017 02 9;7:42130. Epub 2017 Feb 9.

Institute of Bioengineering, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland.

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http://dx.doi.org/10.1038/srep42130DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5299609PMC
February 2017

GETPrime 2.0: gene- and transcript-specific qPCR primers for 13 species including polymorphisms.

Nucleic Acids Res 2017 01 7;45(D1):D56-D60. Epub 2016 Oct 7.

Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland

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http://dx.doi.org/10.1093/nar/gkw913DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5210624PMC
January 2017

Potential Direct Regulators of the Drosophila yellow Gene Identified by Yeast One-Hybrid and RNAi Screens.

G3 (Bethesda) 2016 10 13;6(10):3419-3430. Epub 2016 Oct 13.

Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109 Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48109

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http://dx.doi.org/10.1534/g3.116.032607DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5068961PMC
October 2016

The Movement Tracker: A Flexible System for Automated Movement Analysis in Invertebrate Model Organisms.

Curr Protoc Neurosci 2016 10 3;77:8.37.1-8.37.21. Epub 2016 Oct 3.

Laboratory of Integrative and Systems Physiology, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.

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http://dx.doi.org/10.1002/cpns.17DOI Listing
October 2016

PDF Signaling Is an Integral Part of the Drosophila Circadian Molecular Oscillator.

Cell Rep 2016 10;17(3):708-719

Biological Chemistry Department, Silberman Institute of Life Sciences, the Hebrew University, Jerusalem 91904, Israel. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2016.09.048DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5081397PMC
October 2016

The Genetics of Transcription Factor DNA Binding Variation.

Cell 2016 Jul;166(3):538-554

Laboratory of Systems Biology and Genetics, Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.

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http://dx.doi.org/10.1016/j.cell.2016.07.012DOI Listing
July 2016

Quantification of Cooperativity in Heterodimer-DNA Binding Improves the Accuracy of Binding Specificity Models.

J Biol Chem 2016 May 24;291(19):10293-306. Epub 2016 Feb 24.

From the Institute of Bioengineering, Swiss Institute of Bioinformatics (SIB), CH-1015 Lausanne, Switzerland

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http://dx.doi.org/10.1074/jbc.M115.691154DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4858977PMC
May 2016

Population Variation and Genetic Control of Modular Chromatin Architecture in Humans.

Cell 2015 Aug 20;162(5):1039-50. Epub 2015 Aug 20.

Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland; Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva 1211, Switzerland; Institute of Genetics and Genomics in Geneva, University of Geneva, Geneva 1211, Switzerland. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2015.08.001DOI Listing
August 2015

Genetic, molecular and physiological basis of variation in Drosophila gut immunocompetence.

Nat Commun 2015 Jul 27;6:7829. Epub 2015 Jul 27.

1] Institute of Bioengineering, School of Life Sciences, Station 19, EPFL, 1015 Lausanne, Switzerland [2] Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.

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http://dx.doi.org/10.1038/ncomms8829DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4525169PMC
July 2015

A large-scale, in vivo transcription factor screen defines bivalent chromatin as a key property of regulatory factors mediating Drosophila wing development.

Genome Res 2015 Apr 7;25(4):514-23. Epub 2015 Jan 7.

Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland;

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http://genome.cshlp.org/lookup/doi/10.1101/gr.181305.114
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http://dx.doi.org/10.1101/gr.181305.114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4381523PMC
April 2015

Tetracyclines Disturb Mitochondrial Function across Eukaryotic Models: A Call for Caution in Biomedical Research.

Cell Rep 2015 Mar 12;10(10):1681-1691. Epub 2015 Mar 12.

Laboratory for Integrative and Systems Physiology, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2015.02.034DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4565776PMC
March 2015

A mammalian transcription factor-specific peptide repository for targeted proteomics.

Proteomics 2015 Feb 14;15(4):752-6. Epub 2015 Jan 14.

Biozentrum, University of Basel, Basel, Switzerland; Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.

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http://dx.doi.org/10.1002/pmic.201400355DOI Listing
February 2015

An evolutionarily conserved role for the aryl hydrocarbon receptor in the regulation of movement.

PLoS Genet 2014 Sep 25;10(9):e1004673. Epub 2014 Sep 25.

Laboratory of Integrative and Systems Physiology, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.

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http://dx.doi.org/10.1371/journal.pgen.1004673DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4177751PMC
September 2014

GLUT3 is induced during epithelial-mesenchymal transition and promotes tumor cell proliferation in non-small cell lung cancer.

Cancer Metab 2014 29;2:11. Epub 2014 Jul 29.

Swiss Institute for Experimental Cancer Research, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne 1015, Switzerland.

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http://dx.doi.org/10.1186/2049-3002-2-11DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4122054PMC
August 2014

Identification of the transcription factor ZEB1 as a central component of the adipogenic gene regulatory network.

Elife 2014 Aug 27;3:e03346. Epub 2014 Aug 27.

Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Lausanne, Switzerland.

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http://dx.doi.org/10.7554/eLife.03346DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4359378PMC
August 2014

Identification and removal of low-complexity sites in allele-specific analysis of ChIP-seq data.

Bioinformatics 2014 Jan 18;30(2):165-71. Epub 2013 Nov 18.

Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland, Department of Genetic Medicine and Development, University of Geneva Medical School, Institute of Genetics and Genomics in Geneva, University of Geneva, 1211, Geneva, Switzerland and Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, 1011, Lausanne, Switzerland.

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http://dx.doi.org/10.1093/bioinformatics/btt667DOI Listing
January 2014

Rounding up natural gene expression variation during development.

Dev Cell 2013 Dec;27(6):601-3

Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, Swiss Federal Institute of Technology Lausanne (EPFL), 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland. Electronic address:

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http://dx.doi.org/10.1016/j.devcel.2013.12.007DOI Listing
December 2013

A yeast one-hybrid and microfluidics-based pipeline to map mammalian gene regulatory networks.

Mol Syst Biol 2013 Aug 6;9:682. Epub 2013 Aug 6.

Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.

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http://dx.doi.org/10.1038/msb.2013.38DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3779800PMC
August 2013

Complex expression dynamics and robustness in C. elegans insulin networks.

Genome Res 2013 Jun 28;23(6):954-65. Epub 2013 Mar 28.

Program in Systems Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA.

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http://dx.doi.org/10.1101/gr.150466.112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3668363PMC
June 2013

Absolute quantification of transcription factors during cellular differentiation using multiplexed targeted proteomics.

Nat Methods 2013 Jun 14;10(6):570-6. Epub 2013 Apr 14.

Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.

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http://dx.doi.org/10.1038/nmeth.2441DOI Listing
June 2013

Context-dependent transcriptional interpretation of mitogen activated protein kinase signaling in the Drosophila embryo.

Chaos 2013 Jun;23(2):025105

Department of Chemical and Biological Engineering and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA.

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http://dx.doi.org/10.1063/1.4808157DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3689791PMC
June 2013

Genomic variation and its impact on gene expression in Drosophila melanogaster.

PLoS Genet 2012 15;8(11):e1003055. Epub 2012 Nov 15.

Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.

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http://dx.doi.org/10.1371/journal.pgen.1003055DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3499359PMC
May 2013

Morphological and molecular characterization of adult midgut compartmentalization in Drosophila.

Cell Rep 2013 May 2;3(5):1725-38. Epub 2013 May 2.

Global Health Institute, School of Life Sciences, Station 19, EPFL, 1015 Lausanne, Switzerland.

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http://dx.doi.org/10.1016/j.celrep.2013.04.001DOI Listing
May 2013

iSLIM: a comprehensive approach to mapping and characterizing gene regulatory networks.

Nucleic Acids Res 2013 Feb 20;41(4):e52. Epub 2012 Dec 20.

Laboratory of Biological Network Characterization, Institute of Bioengineering, School of Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.

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http://dx.doi.org/10.1093/nar/gks1323DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3575842PMC
February 2013

Integrative genomics identifies the corepressor SMRT as a gatekeeper of adipogenesis through the transcription factors C/EBPβ and KAISO.

Mol Cell 2012 May 19;46(3):335-50. Epub 2012 Apr 19.

Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.

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http://dx.doi.org/10.1016/j.molcel.2012.03.017DOI Listing
May 2012

Genome-wide profiling of DNA-binding proteins using barcode-based multiplex Solexa sequencing.

Methods Mol Biol 2012 ;786:247-62

Laboratory of Systems Biology and Genetics, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.

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http://dx.doi.org/10.1007/978-1-61779-292-2_15DOI Listing
February 2012

A high-throughput gateway-compatible yeast one-hybrid screen to detect protein-DNA interactions.

Methods Mol Biol 2012 ;786:335-55

Laboratory of Systems Biology and Genetics, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.

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http://dx.doi.org/10.1007/978-1-61779-292-2_20DOI Listing
February 2012

Genetics. Variable outcome of mutations.

Science 2012 Jan;335(6064):44-5

Laboratory of Systems Biology and Genetics, Institute of Bio-Engineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland. bart.deplancke@epfl .ch

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http://dx.doi.org/10.1126/science.1216823DOI Listing
January 2012

GETPrime: a gene- or transcript-specific primer database for quantitative real-time PCR.

Database (Oxford) 2011 14;2011:bar040. Epub 2011 Sep 14.

Institute of Bio-engineering, School of Life Sciences, Laboratory of Systems Biology and Genetics, Lausanne, Switzerland.

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http://dx.doi.org/10.1093/database/bar040DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3173022PMC
December 2011

Automated protein-DNA interaction screening of Drosophila regulatory elements.

Nat Methods 2011 Oct 30;8(12):1065-70. Epub 2011 Oct 30.

Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.

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http://dx.doi.org/10.1038/nmeth.1763DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3929264PMC
October 2011

Chromosome-biased binding and gene regulation by the Caenorhabditis elegans DRM complex.

PLoS Genet 2011 May 12;7(5):e1002074. Epub 2011 May 12.

Program in Molecular Medicine and Program in Cell Dynamics, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3093354PMC
May 2011

WebPrInSeS: automated full-length clone sequence identification and verification using high-throughput sequencing data.

Nucleic Acids Res 2010 Jul 25;38(Web Server issue):W378-84. Epub 2010 May 25.

Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland.

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http://dx.doi.org/10.1093/nar/gkq431DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2896179PMC
July 2010

DNA-centered approaches to characterize regulatory protein-DNA interaction complexes.

Mol Biosyst 2010 Mar 2;6(3):462-8. Epub 2009 Dec 2.

Ecole Polytechnique Fédérale de Lausanne, School of Life Sciences, Institute of Bioengineering, Station 15, 1015 Lausanne, Switzerland.

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http://dx.doi.org/10.1039/b916137fDOI Listing
March 2010

The C. elegans Snail homolog CES-1 can activate gene expression in vivo and share targets with bHLH transcription factors.

Nucleic Acids Res 2009 Jun 16;37(11):3689-98. Epub 2009 Apr 16.

Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA.

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http://dx.doi.org/10.1093/nar/gkp232DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2699517PMC
June 2009

Experimental advances in the characterization of metazoan gene regulatory networks.

Authors:
Bart Deplancke

Brief Funct Genomic Proteomic 2009 Jan;8(1):12-27

Ecole Polytechnique Fédérale de Lausanne, School of Life Sciences, Institute of Bioengineering, Lausanne, Switzerland.

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January 2009

Chromatin immunoprecipitation (ChIP) coupled to detection by quantitative real-time PCR to study transcription factor binding to DNA in Caenorhabditis elegans.

Nat Protoc 2008 ;3(4):698-709

Program in Gene Function and Expression, Program in Molecular Medicine, Aaron Lazare Research Building, University of Massachusetts Medical School, 364 Plantation Street, Worcester, Massachusetts 01605, USA.

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http://dx.doi.org/10.1038/nprot.2008.38DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2681100PMC
October 2008

Matrix and Steiner-triple-system smart pooling assays for high-performance transcription regulatory network mapping.

Nat Methods 2007 Aug 24;4(8):659-64. Epub 2007 Jun 24.

Program in Gene Function and Expression and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA.

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August 2007

Gateway-compatible yeast one-hybrid screens.

CSH Protoc 2006 Oct 1;2006(5). Epub 2006 Oct 1.

Program in Gene Function and Expression and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA.

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October 2006

C. elegans 14-3-3 proteins regulate life span and interact with SIR-2.1 and DAF-16/FOXO.

Mech Ageing Dev 2006 Sep 24;127(9):741-7. Epub 2006 Jul 24.

Program in Gene Function and Expression, Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, 01605, USA.

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September 2006

A compendium of Caenorhabditis elegans regulatory transcription factors: a resource for mapping transcription regulatory networks.

Genome Biol 2005 30;6(13):R110. Epub 2005 Dec 30.

Institute of Integrative and Comparative Biology, Faculty of Biological Sciences, School of Biology, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, UK.

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http://dx.doi.org/10.1186/gb-2005-6-13-r110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1414109PMC
July 2006

A gene-centered C. elegans protein-DNA interaction network.

Cell 2006 Jun;125(6):1193-205

Program in Gene Function and Expression and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, 01605, USA.

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http://dx.doi.org/10.1016/j.cell.2006.04.038DOI Listing
June 2006

A gateway-compatible yeast one-hybrid system.

Genome Res 2004 Oct;14(10B):2093-101

Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC528925PMC
October 2004

A first version of the Caenorhabditis elegans Promoterome.

Genome Res 2004 Oct;14(10B):2169-75

Center for Cancer Systems Biology and Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, USA.

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October 2004

Hydrogen sulfide induces serum-independent cell cycle entry in nontransformed rat intestinal epithelial cells.

FASEB J 2003 Jul 8;17(10):1310-2. Epub 2003 May 8.

Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.

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July 2003

Gastrointestinal and microbial responses to sulfate-supplemented drinking water in mice.

Exp Biol Med (Maywood) 2003 Apr;228(4):424-33

Division of Nutritional Sciences, and Department of Animal Sciences, University of Illinois, Urbana, Illinois 61801, USA.

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April 2003

Selective growth of mucolytic bacteria including Clostridium perfringens in a neonatal piglet model of total parenteral nutrition.

Am J Clin Nutr 2002 Nov;76(5):1117-25

Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, 61801, USA.

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November 2002

Roles of Vibrio fischeri and nonsymbiotic bacteria in the dynamics of mucus secretion during symbiont colonization of the Euprymna scolopes light organ.

Appl Environ Microbiol 2002 Oct;68(10):5113-22

Pacific Biomedical Research Center, Kewalo Marine Laboratory, University of Hawaii, Honolulu, Hawaii 96813, USA.

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http://dx.doi.org/10.1128/aem.68.10.5113-5122.2002DOI Listing
October 2002

Redox control of the transsulfuration and glutathione biosynthesis pathways.

Curr Opin Clin Nutr Metab Care 2002 Jan;5(1):85-92

Division of Nutritional Sciences, Department of Animal Sciences, University of Illinois at Urbana-Champaign, 1207 W. Gregory Drive, Urbana, IL 61801, USA.

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January 2002