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1

The Human Cell Atlas

Regev, Aviv, Teichmann, Sarah A, Lander, Eric S, Amit, Ido, Benoist, Christophe, Birney, Ewan, Bodenmiller, Bernd, Campbell, Peter, Carninci, Piero, Clatworthy, Menna, Clevers, Hans, Deplancke, Bart,

Journal:

Year:

2017

Language:

english

File:

PDF, 16.27 MB

english, 2017

2

The Genetics of Transcription Factor DNA Binding Variation

Deplancke, Bart, Alpern, Daniel, Gardeux, Vincent

Journal:

Year:

2016

Language:

english

File:

PDF, 1.82 MB

english, 2016

3

Mitochondrial gene signature in the prefrontal cortex for differential susceptibility to chronic stress

Weger, Meltem, Alpern, Daniel, Cherix, Antoine, Ghosal, Sriparna, Grosse, Jocelyn, Russeil, Julie, Gruetter, Rolf, de Kloet, E. Ronald, Deplancke, Bart, Sandi, Carmen

Journal:

Scientific Reports

Year:

2020

File:

PDF, 2.83 MB

2020

4

[Methods in Molecular Biology] Gene Regulatory Networks Volume 786 || MITOMI: A Microfluidic Platform for In Vitro Characterization of Transcription Factor–DNA Interaction

Deplancke, Bart, Gheldof, Nele

Year:

2012

Language:

english

File:

PDF, 491 KB

english, 2012

5

Multilevel regulation of the glass locus during Drosophila eye development

Fritsch, Cornelia, Bernardo-Garcia, F. Javier, Humberg, Tim-Henning, Mishra, Abhishek Kumar, Miellet, Sara, Almeida, Silvia, Frochaux, Michael V., Deplancke, Bart, Huber, Armin, Sprecher, Simon G., Ku

Journal:

Year:

2019

Language:

english

File:

PDF, 3.35 MB

english, 2019

6

[Methods in Molecular Biology] Gene Regulatory Networks Volume 786 || Computational Analysis of Protein–DNA Interactions from ChIP-seq Data

Deplancke, Bart, Gheldof, Nele

Year:

2012

Language:

english

File:

PDF, 248 KB

english, 2012

7

Author Correction: Mitochondrial haplotypes affect metabolic phenotypes in the Drosophila Genetic Reference Panel

Bevers, Roel P. J., Litovchenko, Maria, Kapopoulou, Adamandia, Braman, Virginie S., Robinson, Matthew R., Auwerx, Johan, Hollis, Brian, Deplancke, Bart

Journal:

Nature Metabolism

Year:

2020

File:

PDF, 608 KB

2020

8

[Methods in Molecular Biology] Gene Regulatory Networks Volume 786 || Detecting Long-Range Chromatin Interactions Using the Chromosome Conformation Capture Sequencing (4C-seq) Method

Deplancke, Bart, Gheldof, Nele

Year:

2012

Language:

english

File:

PDF, 316 KB

english, 2012

9

[Methods in Molecular Biology] Gene Regulatory Networks Volume 786 ||

Deplancke, Bart, Gheldof, Nele

Year:

2012

Language:

english

File:

PDF, 9.52 MB

english, 2012

10

Toward a Consensus View of Mammalian Adipocyte Stem and Progenitor Cell Heterogeneity

Ferrero, Radiana, Rainer, Pernille, Deplancke, Bart

Journal:

Trends in Cell Biology

Year:

2020

File:

PDF, 79 KB

2020

11

Integrative Genomics Identifies the Corepressor SMRT as a Gatekeeper of Adipogenesis through the Transcription Factors C/EBPβ and KAISO

Sunil K. Raghav, Sebastian M. Waszak, Irina Krier, Carine Gubelmann, Alina Isakova, Tarjei S. Mikkelsen, Bart Deplancke

Journal:

Year:

2012

Language:

english

File:

PDF, 2.01 MB

english, 2012

12

Automated protein-DNA interaction screening of Drosophila regulatory elements

Hens, Korneel, Feuz, Jean-Daniel, Isakova, Alina, Iagovitina, Antonina, Massouras, Andreas, Bryois, Julien, Callaerts, Patrick, Celniker, Susan E, Deplancke, Bart

Journal:

Year:

2011

Language:

english

File:

PDF, 1.26 MB

english, 2011

13

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

Schertel, Claus, Albarca, Monica, Rockel-Bauer, Claudia, Kelley, Nicholas W., Bischof, Johannes, Hens, Korneel, van Nimwegen, Erik, Basler, Konrad, Deplancke, Bart

Journal:

Genome Research

Year:

2015

Language:

english

File:

PDF, 4.48 MB

english, 2015

14

[Methods in Molecular Biology] Gene Regulatory Networks Volume 786 || Analyzing Transcription Factor Occupancy During Embryo Development Using ChIP-seq

Deplancke, Bart, Gheldof, Nele

Year:

2012

Language:

english

File:

PDF, 162 KB

english, 2012

15

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

Yamei Wang, Seung Wook Oh, Bart Deplancke, Jianyuan Luo, Albertha J.M. Walhout, Heidi A. Tissenbaum

Journal:

Mechanisms of Ageing and Development

Year:

2006

Language:

english

File:

PDF, 751 KB

english, 2006

16

A Gene-Centered C. elegans Protein-DNA Interaction Network

Bart Deplancke, Arnab Mukhopadhyay, Wanyuan Ao, Ahmed M. Elewa, Christian A. Grove, Natalia J. Martinez, Reynaldo Sequerra, Lynn Doucette-Stamm, John S. Reece-Hoyes, Ian A. Hope, Heidi A. Tissenbaum,

Journal:

Year:

2006

Language:

english

File:

PDF, 901 KB

english, 2006

17

Systematic dissection of genomic features determining transcription factor binding and enhancer function

Grossman, Sharon R., Zhang, Xiaolan, Wang, Li, Engreitz, Jesse, Melnikov, Alexandre, Rogov, Peter, Tewhey, Ryan, Isakova, Alina, Deplancke, Bart, Bernstein, Bradley E., Mikkelsen, Tarjei S., Lander, E

Journal:

Proceedings of the National Academy of Sciences

Year:

2017

Language:

english

File:

PDF, 1.10 MB

english, 2017

18

C. elegans tubby regulates life span and fat storage by two independent mechanisms

Arnab Mukhopadhyay, Bart Deplancke, Albertha J.M. Walhout, Heidi A. Tissenbaum

Journal:

Cell Metabolism

Year:

2005

Language:

english

File:

PDF, 391 KB

english, 2005

19

[Methods in Molecular Biology] Gene Regulatory Networks Volume 786 || Sample Preparation for Small RNA Massive Parallel Sequencing

Deplancke, Bart, Gheldof, Nele

Year:

2012

Language:

english

File:

PDF, 162 KB

english, 2012

20

A mammalian transcription factor-specific peptide repository for targeted proteomics

Simicevic, Jovan, Moniatte, Marc, Hamelin, Romain, Ahrné, Erik, Deplancke, Bart

Journal:

Year:

2015

Language:

english

File:

PDF, 345 KB

english, 2015

21

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

Vermeirssen, Vanessa, Deplancke, Bart, Barrasa, M Inmaculada, Reece-Hoyes, John S, Arda, H Efsun, Grove, Christian A, Martinez, Natalia J, Sequerra, Reynaldo, Doucette-Stamm, Lynn, Brent, Michael R

Journal:

Year:

2007

Language:

english

File:

PDF, 272 KB

english, 2007

22

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

Delachat, Aurore M.-F., Guidotti, Nora, Bachmann, Andreas L., Meireles-Filho, Antonio C.A., Pick, Horst, Lechner, Carolin C., Deluz, Cédric, Deplancke, Bart, Suter, David M., Fierz, Beat

Journal:

Cell Chemical Biology

Year:

2017

Language:

english

File:

PDF, 2.11 MB

english, 2017

23

Global and Stage Specific Patterns of Krüppel-Associated-Box Zinc Finger Protein Gene Expression in Murine Early Embryonic Cells

Corsinotti, Andrea, Kapopoulou, Adamandia, Gubelmann, Carine, Imbeault, Michael, Santoni de Sio, Francesca R., Rowe, Helen M., Mouscaz, Yoann, Deplancke, Bart, Trono, Didier, Wilusz, Carol J.

Journal:

Year:

2013

Language:

english

File:

PDF, 3.43 MB

english, 2013

24

[Methods in Molecular Biology] Gene Regulatory Networks Volume 786 || Using cisTargetX to Predict Transcriptional Targets and Networks in Drosophila

Deplancke, Bart, Gheldof, Nele

Year:

2012

Language:

english

File:

PDF, 1.04 MB

english, 2012

25

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

Gubelmann, Carine, Waszak, Sebastian M, Isakova, Alina, Holcombe, Wiebke, Hens, Korneel, Iagovitina, Antonina, Feuz, Jean-Daniel, Raghav, Sunil K, Simicevic, Jovan, Deplancke, Bart

Journal:

Molecular Systems Biology

Year:

2013

Language:

english

File:

PDF, 3.68 MB

english, 2013

26

An Evolutionarily Conserved Role for the Aryl Hydrocarbon Receptor in the Regulation of Movement

Williams, Evan G., Mouchiroud, Laurent, Frochaux, Michael, Pandey, Ashutosh, Andreux, Pénélope A., Deplancke, Bart, Auwerx, Johan, Barsh, Gregory S.

Journal:

Year:

2014

Language:

english

File:

PDF, 2.77 MB

english, 2014

27

Cross-Tissue Identification Of Somatic Stem And Progenitor Cells Using A Single-Cell RNA-Seq Derived Gene Signature

Schwalie, Petra C., Ordonez Moran, Paloma, Huelsken, Joerg, Deplancke, Bart

Journal:

Year:

2017

Language:

english

File:

PDF, 1.43 MB

english, 2017

28

Microbial modulation of innate defense: goblet cells and the intestinal mucus layer

Deplancke, Bart, Gaskins, H Rex

Journal:

American Journal of Clinical Nutrition

Year:

2001

Language:

english

File:

PDF, 566 KB

english, 2001

29

Exhaustion of tumour-specific CD8+ T cells in metastases from melanoma patients

Baitsch, Lukas, Baumgaertner, Petra, Devevre, Estelle, Raghav, Sunil K, Legat, Amandine, Barba, Leticia, Wieckowski, Sebastien, Bouzourene, Hanifa, Deplancke, Bart, Romero, Pedro, Rufer, Nathalie, Spe

Journal:

Journal of Clinical Investigation

Year:

2011

Language:

english

File:

PDF, 1.80 MB

english, 2011

30

ASAP 2020 update: an open, scalable and interactive web-based portal for (single-cell) omics analyses

David, Fabrice P A, Litovchenko, Maria, Deplancke, Bart, Gardeux, Vincent

Journal:

Nucleic Acids Research

Year:

2020

File:

PDF, 4.06 MB

2020

31

[Methods in Molecular Biology] Gene Regulatory Networks Volume 786 || How Do You Find Transcription Factors? Computational Approaches to Compile and Annotate Repertoires of Regulators for Any Genome

Deplancke, Bart, Gheldof, Nele

Year:

2012

Language:

english

File:

PDF, 307 KB

english, 2012

32

Morphological and Molecular Characterization of Adult Midgut Compartmentalization in Drosophila

Buchon, Nicolas, Osman, Dani, David, Fabrice P.A., Yu Fang, Hsiao, Boquete, Jean-Philippe, Deplancke, Bart, Lemaitre, Bruno

Journal:

Year:

2013

Language:

english

File:

PDF, 4.92 MB

english, 2013

33

Diurnal regulation of RNA polymerase III transcription is under the control of both the feeding–fasting response and the circadian clock

Mange, François, Praz, Viviane, Migliavacca, Eugenia, Willis, Ian M., Schütz, Frédéric, Hernandez, Nouria, Hernandez, Nouria, Delorenzi, Mauro, Deplancke, Bart, Desvergne, Béatrice, Guex, Nicolas, Her

Journal:

Genome Research

Year:

2017

Language:

english

File:

PDF, 7.06 MB

english, 2017

34

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

Okada, Hirokazu, Yagi, Ryohei, Gardeux, Vincent, Deplancke, Bart, Hafen, Ernst

Journal:

Molecular Systems Biology

Year:

2019

File:

PDF, 2.96 MB

2019

35

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

Kim, Yoosik, Iagovitina, Antonina, Ishihara, Keisuke, Fitzgerald, Kate M., Deplancke, Bart, Papatsenko, Dmitri, Shvartsman, Stanislav Y.

Journal:

Chaos An Interdisciplinary Journal of Nonlinear Science

Year:

2013

Language:

english

File:

PDF, 4.17 MB

english, 2013

36

A parallelized, automated platform enabling individual or sequential ChIP of histone marks and transcription factors

Dainese, Riccardo, Gardeux, Vincent, Llimos, Gerard, Alpern, Daniel, Jiang, Jia Yuan, Meireles-Filho, Antonio Carlos Alves, Deplancke, Bart

Journal:

Proceedings of the National Academy of Sciences

Year:

2020

File:

PDF, 6.88 MB

2020

37

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

Mukhopadhyay, Arnab, Deplancke, Bart, Walhout, Albertha J M, Tissenbaum, Heidi A

Journal:

Nature Protocols

Year:

2008

Language:

english

File:

PDF, 316 KB

english, 2008

38

A compendium ofCaenorhabditis elegansregulatory transcription factors: a resource for mapping transcription regulatory networks

John S Reece-Hoyes, Bart Deplancke, Jane Shingles, Christian A Grove…

Journal:

Year:

2005

Language:

english

File:

PDF, 703 KB

english, 2005

39

Fermentation by Gut Microbiota Cultured in a Simulator of the Human Intestinal Microbial Ecosystem Is Improved by Supplementing a Soygerm Powder

Patrick De Boever,, Deplancke, Bart, Verstraete, Willy

Journal:

Journal of Nutrition

Year:

2000

Language:

english

File:

PDF, 492 KB

english, 2000

40

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

Frochaux, Michael V., Bou Sleiman, Maroun, Gardeux, Vincent, Dainese, Riccardo, Hollis, Brian, Litovchenko, Maria, Braman, Virginie S., Andreani, Tommaso, Osman, Dani, Deplancke, Bart

Journal:

Year:

2020

Language:

english

File:

PDF, 2.27 MB

english, 2020

41

Primate-restricted KRAB zinc finger proteins and target retrotransposons control gene expression in human neurons

Turelli, Priscilla, Playfoot, Christopher, Grun, Dephine, Raclot, CharlÃ¨ne, Pontis, Julien, Coudray, Alexandre, Thorball, Christian, Duc, Julien, Pankevich, Eugenia V., Deplancke, Bart, Busskamp, Vol

Journal:

Science Advances

Year:

2020

File:

PDF, 1.65 MB

2020

42

Morphological and Molecular Characterization of Adult Midgut Compartmentalization in Drosophila

Buchon, Nicolas, Osman, Dani, David, Fabrice P.A., Fang, Hsiao Yu, Boquete, Jean-Philippe, Deplancke, Bart, Lemaitre, Bruno

Journal:

Year:

2013

Language:

english

File:

PDF, 46 KB

english, 2013

43

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

Li, Yongguo, Schwalie, Petra C., Bast-Habersbrunner, Andrea, Mocek, Sabine, Russeil, Julie, Fromme, Tobias, Deplancke, Bart, Klingenspor, Martin

Journal:

Year:

2019

File:

PDF, 5.43 MB

2019

44

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

Bou Sleiman, Maroun, Frochaux, Michael Vincent, Andreani, Tommaso, Osman, Dani, Guigo, Roderic, Deplancke, Bart

Journal:

Year:

2020

Language:

english

File:

PDF, 3.84 MB

english, 2020

45

[Methods in Molecular Biology] Gene Regulatory Networks Volume 786 || BioTapestry: A Tool to Visualize the Dynamic Properties of Gene Regulatory Networks

Deplancke, Bart, Gheldof, Nele

Year:

2012

Language:

english

File:

PDF, 764 KB

english, 2012

46

Transcription factor proteomics - tools, applications, and challenges

Simicevic, Jovan, Deplancke, Bart

Journal:

Year:

2016

Language:

english

File:

PDF, 639 KB

english, 2016

47

Topology and Dynamics of the Zebrafish Segmentation Clock Core Circuit

Schröter, Christian, Ares, Saúl, Morelli, Luis G., Isakova, Alina, Hens, Korneel, Soroldoni, Daniele, Gajewski, Martin, Jülicher, Frank, Maerkl, Sebastian J., Deplancke, Bart, Oates, Andrew C., Storey

Journal:

Year:

2012

Language:

english

File:

PDF, 3.46 MB

english, 2012

48

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

Isakova, Alina, Groux, Romain, Imbeault, Michael, Rainer, Pernille, Alpern, Daniel, Dainese, Riccardo, Ambrosini, Giovanna, Trono, Didier, Bucher, Philipp, Deplancke, Bart

Journal:

Year:

2017

Language:

english

File:

PDF, 2.50 MB

english, 2017

49

[Methods in Molecular Biology] Gene Regulatory Networks Volume 786 || Proteomic Methodologies to Study Transcription Factor Function

Deplancke, Bart, Gheldof, Nele

Year:

2012

Language:

english

File:

PDF, 331 KB

english, 2012

50

Gene regulatory mechanisms underlying the intestinal innate immune response

Meireles-Filho, Antonio CA, Deplancke, Bart

Journal:

Current Opinion in Genetics & Development

Year:

2017

Language:

english

File:

PDF, 1.75 MB

english, 2017

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