All publications

2021

Journal Articles

Disparate temperature-dependent virus-host dynamics for SARS-CoV-2 and SARS-CoV in the human respiratory epithelium

P. V’kovski; M. Gultom; J. N. Kelly; S. Steiner; J. Russeil et al. 

Plos Biology. 2021-03-01. Vol. 19, num. 3, p. e3001158. DOI : 10.1371/journal.pbio.3001158.

The Hippo pathway controls myofibril assembly and muscle fiber growth by regulating sarcomeric gene expression

A. Kaya-Copur; F. Marchiano; M. Y. Hein; D. Alpern; J. Russeil et al. 

Elife. 2021-01-06. Vol. 10, p. e63726. DOI : 10.7554/eLife.63726.

Extensive tissue-specific expression variation and novel regulators underlying circadian behavior

M. Litovchenko; A. C. A. Meireles-Filho; M. Frochaux; R. P. J. Bevers; A. Prunotto et al. 

Science Advances. 2021-01-01. Vol. 7, num. 5, p. eahc3781. DOI : 10.1126/sciadv.abc3781.

Theses

Developing new tools to study and program cell fate at the single-cell level

M. Biocanin / B. Deplancke (Dir.)  

Lausanne, EPFL, 2021. 

Towards scalable and deterministic single cell gene expression profiling

J. J. Bues / B. Deplancke (Dir.)  

Lausanne, EPFL, 2021. 

2020

Journal Articles

Inter-embryo gene expression variability recapitulates the hourglass pattern of evo-devo

J. Liu; M. Frochaux; V. Gardeux; B. Deplancke; M. Robinson-Rechavi 

Bmc Biology. 2020-09-19. Vol. 18, num. 1, p. 129. DOI : 10.1186/s12915-020-00842-z.

Genomic Analysis of European Drosophila melanogaster Populations Reveals Longitudinal Structure, Continent-Wide Selection, and Previously Unknown DNA Viruses

M. Kapun; M. G. Barron; F. Staubach; D. J. Obbard; R. A. W. Wiberg et al. 

Molecular Biology And Evolution. 2020-09-01. Vol. 37, num. 9, p. 2661-2678. DOI : 10.1093/molbev/msaa120.

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

P. Turelli; C. Playfoot; D. Grun; C. Raclot; J. Pontis et al. 

Science Advances. 2020-08-28. Vol. 6, num. 35, p. eaba3200. DOI : 10.1126/sciadv.aba3200.

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

F. P. A. David; M. Litovchenko; B. Deplancke; V. Gardeux 

Nucleic Acids Research. 2020-07-02. Vol. 48, num. W1, p. W403-W414. DOI : 10.1093/nar/gkaa412.

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

R. Dainese; V. Gardeux; G. Llimos; D. Alpern; J. Y. Jiang et al. 

Proceedings Of The National Academy Of Sciences Of The United States Of America. 2020-06-16. Vol. 117, num. 24, p. 13828-13838. DOI : 10.1073/pnas.1913261117.

Selective Retrieval of Individual Cells from Microfluidic Arrays Combining Dielectrophoretic Force and Directed Hydrodynamic Flow

P-E. M. Thiriet; J. Pezoldt; G. Gambardella; K. Keim; B. Deplancke et al. 

Micromachines. 2020-03-20. Vol. 11, num. 3, p. 322. DOI : 10.3390/mi11030322.

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

M. V. Frochaux; M. B. Sleiman; V. Gardeux; R. Dainese; B. Hollis et al. 

Genome Biology. 2020-01-17. Vol. 21, num. 1, p. 6. DOI : 10.1186/s13059-019-1912-z.

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

M. Bou Sleiman; M. V. Frochaux; T. Andreani; D. Osman; R. Guigo et al. 

Genome Biology. 2020-01-17. Vol. 21, num. 1, p. 4. DOI : 10.1186/s13059-019-1918-6.

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

M. Weger; D. Alpern; A. Cherix; S. Ghosal; J. Grosse et al. 

Sci Rep. 2020. Vol. 10, num. 1, p. 18308. DOI : 10.1038/s41598-020-75326-9.

Reviews

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

R. Ferrero; P. Rainer; B. Deplancke 

Trends In Cell Biology. 2020-12-01. Vol. 30, num. 12, p. 937-950. DOI : 10.1016/j.tcb.2020.09.007.

Theses

Computational study of transcription factor binding sites

R. F. P. Groux / B. Deplancke; P. Bucher (Dir.)  

Lausanne, EPFL, 2020. 

A single-cell-based identification and characterisation of Aregs, an inhibitory subpopulation of adipose stem and precursor cells

M. Zachara / B. Deplancke (Dir.)  

Lausanne, EPFL, 2020. 

Multi-omics reveals abundant mitochondrial genomic and circadian expression variation in the Drosophila Genetic Reference Panel

M. Litovchenko / B. Deplancke (Dir.)  

Lausanne, EPFL, 2020. 

2019

Journal Articles

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

Y. Li; P. C. Schwalie; A. Bast-Habersbrunner; S. Mocek; J. Russeil et al. 

Cell Reports. 2019-12-17. Vol. 29, num. 12, p. 4099-+. DOI : 10.1016/j.celrep.2019.11.053.

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

E. T. Friman; C. Deluz; A. C. A. Meireles-Filho; S. Govindan; V. Gardeux et al. 

Elife. 2019-12-03. Vol. 8, p. e50087. DOI : 10.7554/eLife.50087.

Mitochondrial haplotypes affect metabolic phenotypes in the Drosophila Genetic Reference Panel

R. P. J. Bevers; M. Litovchenko; A. Kapopoulou; V. S. Braman; M. R. Robinson et al. 

Nature Metabolism. 2019-12-01. Vol. 1, num. 12, p. 1226-+. DOI : 10.1038/s42255-019-0147-3.

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

H. Okada; R. Yagi; V. Gardeux; B. Deplancke; E. Hafen 

Molecular Systems Biology. 2019-11-01. Vol. 15, num. 11, p. e9012. DOI : 10.15252/msb.20199012.

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

D. Ma; M. Bou-Sleiman; P. Joncour; C-E. Indelicato; M. Frochaux et al. 

Iscience. 2019-09-27. Vol. 19, p. 436-+. DOI : 10.1016/j.isci.2019.07.048.

Multilevel regulation of the glass locus during Drosophila eye development

C. Fritsch; F. J. Bernardo-Garcia; T-H. Humberg; A. K. Mishra; S. Miellet et al. 

Plos Genetics. 2019-07-01. Vol. 15, num. 7, p. e1008269. DOI : 10.1371/journal.pgen.1008269.

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

M. Biocanin; J. Bues; R. Dainese; E. Amstad; B. Deplancke 

Lab On A Chip. 2019-05-07. Vol. 19, num. 9, p. 1610-1620. DOI : 10.1039/c9lc00014c.

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

D. Alpern; V. Gardeux; J. Russeil; B. Mangeat; A. C. A. Meireles-Filho et al. 

Genome Biology. 2019-04-19. Vol. 20, p. 71. DOI : 10.1186/s13059-019-1671-x.

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

W. Chen; P. C. Schwalie; E. V. Pankevich; C. Gubelmann; S. K. Raghav et al. 

Nature Communications. 2019-04-18. Vol. 10, num. 1. DOI : 10.1038/s41467-019-09803-9.

A Comprehensive Drosophila melanogaster Transcription Factor Interactome

L. Shokri; S. Inukai; A. Hafner; K. Weinand; K. Hens et al. 

Cell Reports. 2019-04-16. Vol. 27, num. 3, p. 955-+. DOI : 10.1016/j.celrep.2019.03.071.

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

N. Vannini; V. Campos; M. Girotra; V. Trachsel; S. Rojas-Sutterlin et al. 

Cell Stem Cell. 2019-03-07. Vol. 24, num. 3, p. 405-+. DOI : 10.1016/j.stem.2019.02.012.

Differential regulation of RNA polymerase III genes during liver regeneration

M. Yeganeh; V. Praz; C. Carmeli; D. Villeneuve; L. Rib et al. 

Nucleic Acids Research. 2019-02-28. Vol. 47, num. 4, p. 1786-1796. DOI : 10.1093/nar/gky1282.

Conference Papers

Epigenomic landscape defines immuno-modulatory properties across lymph node stromal cell subsets

J. Pezoldt; C. Wiechers; M. Zou; M. Litovchenko; K. Sitnik et al. 

2019-09-01. 2nd Joint Meeting of the German-Society-for-Immunology (DGfl) and the Italian-Society-of-Immunology-Clinical-Immunology-and-Allergology (SIICA), Munich, GERMANY, Sep 10-13, 2019. p. 38-39.

Theses

Elucidating regulatory mechanisms shaping the transcriptome and proteome of the gut immune response in Drosophila melanogaster

M. V. Frochaux / B. Deplancke (Dir.)  

Lausanne, EPFL, 2019. 

The role of the transcriptional regulator BCL6 in adipose tissue development and remodeling

T. Didonna / B. Deplancke (Dir.)  

Lausanne, EPFL, 2019. 

Mechanistic insights into AMP-activated protein kinase-dependent gene expression

C. Collodet / P. Descombes; B. Deplancke (Dir.)  

Lausanne, EPFL, 2019. 

Integrated microfluidic tools for the characterization of protein/DNA interactions in vitro and in vivo

R. Dainese / B. Deplancke (Dir.)  

Lausanne, EPFL, 2019. 

Patents

System for capture or immunoprecipitation of a protein-dna complex

B. Deplancke; R. Dainese 

WO2019116306.

2019.

2018

Journal Articles

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

G. Etienne; A. Vian; M. Biočanin; B. Deplancke; E. Amstad 

Lab on a Chip. 2018-11-13. Vol. 18, num. 24, p. 3903-3912. DOI : 10.1039/C8LC01000E.

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

A. M-F. Delachat; N. Guidotti; A. L. Bachmann; A. C. Meireles-Filho; H. Pick et al. 

Cell Chemical Biology. 2018-01-18. Vol. 25, num. 1, p. 51-56. DOI : 10.1016/j.chembiol.2017.10.008.

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

Q. Wang; A. Song; W. Chen; P. Schwalie; F. Zhang et al. 

CELL METABOLISM. 2018. Vol. 28, num. 2, p. 282-+. DOI : 10.1016/j.cmet.2018.05.022.

A stromal cell population that inhibits adipogenesis in mammalian fat depots

P. Schwalie; H. Dong; M. Zachara; J. Russeil; D. Alpern et al. 

NATURE. 2018. Vol. 559, num. 7712, p. 103-+. DOI : 10.1038/s41586-018-0226-8.

Conference Papers

The NAD plus Salvage Pathway Potently Stimulates Hematopoiesis through Increased Mitochondrial Clearance and Asymmetric Division

N. Vannini; V. Campos; M. Girotra; S. Rojas-Sutterlin; J. Tratwal et al. 

2018-11-29. 60th Annual Meeting of the American-Society-of-Hematology (ASH), San Diego, CA, Dec 01-04, 2018. DOI : 10.1182/blood-2018-99-117388.

Theses

Genetic determinants of healthy human immune variance: from humoral response to microbiome diversity

P. Scepanovic / J. Fellay; B. Deplancke (Dir.)  

Lausanne, EPFL, 2018. 

The phenotypic impact of naturally occurring genetic and molecular mitochondrial variation in a Drosophila Genetic Reference Population

R. P. J. Bevers / B. Deplancke (Dir.)  

Lausanne, EPFL, 2018. 

Computational and Statistical analyses of Molecular Evolution and Demography using Large-scale Sequencing Data

A. Kapopoulou / B. Deplancke; J. D. Jensen (Dir.)  

Lausanne, EPFL, 2018. 

Patents

Device for high throughput single-cell studies

B. Deplancke; J. Bues; R. Dainese; M. Biocanin 

US2019240664; WO2018051242.

2018.

2017

Journal Articles

Profiling of Single-Cell Transcriptomes

W. Chen; V. Gardeux; A. Meireles-Filho; B. Deplancke 

Current Protocols in Mouse Biology. 2017. Vol. 7, num. 3, p. 145-175. DOI : 10.1002/cpmo.30.

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

P. C. Schwalie; P. Ordonez-Moran; J. Huelsken; B. Deplancke 

Stem Cells. 2017. Vol. 35, num. 12, p. 2390-2402. DOI : 10.1002/stem.2719.

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

P. Houtz; A. Bonfini; X. Liu; J. Revah; A. Guillou et al. 

Plos Genetics. 2017. Vol. 13, num. 11, p. e1007091. DOI : 10.1371/journal.pgen.1007091.

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

V. Gardeux; F. P. A. David; A. Shajkofci; P. C. Schwalie; B. Deplancke 

Bioinformatics. 2017. Vol. 33, num. 19, p. 3123-3125. DOI : 10.1093/bioinformatics/btx337.

Bayesian association scan reveals loci associated with human lifespan and linked biomarkers

A. F. Mcdaid; P. K. Joshi; E. Porcu; A. Komljenovic; H. Li et al. 

Nature Communications. 2017. Vol. 8, p. 15842. DOI : 10.1038/ncomms15842.

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

L. H. Mojica-Vazquez; M. H. Benetah; A. Baanannou; S. Bernat-Fabre; B. Deplancke et al. 

Plos Genetics. 2017. Vol. 13, num. 4, p. e1006718. DOI : 10.1371/journal.pgen.1006718.

Transcriptional regulatory logic of the diurnal cycle in the mouse liver

J. A. Sobel; I. Krier; T. Andersin; S. Raghav; D. Canella et al. 

PLoS Biology. 2017. Vol. 15, num. 4, p. e2001069. DOI : 10.1371/journal.pbio.2001069.

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

F. P. A. David; J. Rougemont; B. Deplancke 

Nucleic Acids Research. 2017. Vol. 45, num. D1, p. D56-D60. DOI : 10.1093/nar/gkw913.

Dissecting the brown adipogenic regulatory network using integrative genomics

R. N. Pradhan; J. J. Bues; V. Gardeux; P. C. Schwalie; D. Alpern et al. 

Scientific Reports. 2017. Vol. 7, p. 42130. DOI : 10.1038/srep42130.

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

A. Isakova; R. Groux; M. Imbeault; P. Rainer; D. Alpern et al. 

Nature methods. 2017. Vol. 14, p. 316-322. DOI : 10.1038/nmeth.4143.

Conference Papers

Disease-Informed Bayesian Association Scan Reveals Novel Loci Associated with Human Lifespan and Linked Biomarkers

A. F. Mcdaid; P. K. Joshi; N. Mounier; E. Porcu; A. Komljenovic et al. 

2017. Annual Meeting of the International-Genetic-Epidemiology-Society (IGES), Queens Coll, Cambridge, ENGLAND, SEP 09-11, 2017. p. 648-649.

Reviews

Gene regulatory mechanisms underlying the intestinal innate immune response

A. C. A. Meireles-Filho; B. Deplancke 

Current Opinion In Genetics & Development. 2017. Vol. 43, p. 46-52. DOI : 10.1016/j.gde.2016.11.004.

A systems perspective on brown adipogenesis and metabolic activation

R. N. Pradhan; M. Zachara; B. Deplancke 

Obesity Reviews. 2017. Vol. 18, p. 65-81. DOI : 10.1111/obr.12512.

Transcription factor proteomics – Tools, applications, and challenges

J. Simicevic; B. Deplancke 

Proteomics. 2017. Vol. 17, num. 3-4, p. 1600317. DOI : 10.1002/pmic.201600317.

Theses

Gene regulatory dynamics underlying brown fat cell differentiation

R. N. Pradhan / B. Deplancke (Dir.)  

Lausanne, EPFL, 2017. 

2016

Journal Articles

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

G. Kalay; R. Lusk; M. Dome; K. Hens; B. Deplancke et al. 

G3-Genes Genomes Genetics. 2016-08-15. Vol. 6, num. 10, p. 3419-3430. DOI : 10.1534/g3.116.032607.

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

S. Mezan; J. D. Feuz; B. Deplancke; S. Kadener 

Cell Reports. 2016. Vol. 17, num. 3, p. 708-719. DOI : 10.1016/j.celrep.2016.09.048.

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

A. Isakova; Y. Berset; V. Hatzimanikatis; B. Deplancke 

Journal Of Biological Chemistry. 2016. Vol. 291, num. 19, p. 10293-+. DOI : 10.1074/jbc.M115.691154.

Reviews

The Genetics of Transcription Factor DNA Binding Variation

B. Deplancke; D. Alpern; V. Gardeux 

Cell. 2016. Vol. 166, num. 3, p. 538-554. DOI : 10.1016/j.cell.2016.07.012.

Theses

The Drosophila gut response to infection

M. Bou Sleiman / B. Lemaitre; B. Deplancke (Dir.)  

Lausanne, EPFL, 2016. 

Patents

Microfluidic device and method for isolation of nucleic acids

A. Isakova; B. Deplancke 

US2019091689; WO2016059619; WO2016059619.

2016.

2015

Journal Articles

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

M. S. B. Sleiman; D. Osman; A. Massouras; A. A. Hoffmann; B. Lemaitre et al. 

Nature Communications. 2015. Vol. 6, p. 7829. DOI : 10.1038/ncomms8829.

Population Variation and Genetic Control of Modular Chromatin Architecture in Humans

S. M. Waszak; O. Delaneau; A. R. Gschwind; H. Kilpinen; S. K. Raghav et al. 

Cell. 2015. Vol. 162, num. 5, p. 1039-1050. DOI : 10.1016/j.cell.2015.08.001.

Conservation of transcription factor binding specificities across 600 million years of bilateria evolution

K. R. Nitta; A. Jolma; Y. Yin; E. Morgunova; T. Kivioja et al. 

Elife. 2015. Vol. 4, p. e04837. DOI : 10.7554/eLife.04837.

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

C. Schertel; M. Albarca; C. Rockel-Bauer; N. W. Kelley; J. Bischof et al. 

Genome Research. 2015. Vol. 25, num. 4, p. 514-523. DOI : 10.1101/gr.181305.114.

A mammalian transcription factor-specific peptide repository for targeted proteomics

J. Simicevic; M. Moniatte; R. Hamelin; E. Ahrne; B. Deplancke 

Proteomics. 2015. Vol. 15, num. 4, p. 752-756. DOI : 10.1002/pmic.201400355.

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

N. Moullan; L. Mouchiroud; X. Wang; D. Ryu; E. G. Williams et al. 

Cell Reports. 2015. Vol. 10, num. 10, p. 1681-1691. DOI : 10.1016/j.celrep.2015.02.034.

2014

Journal Articles

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

E. G. Williams; L. Mouchiroud; M. Frochaux; P. Ashutosh; P. A. Andreux et al. 

PLoS genetics. 2014. Vol. 10, num. 9, p. e1004673. DOI : 10.1371/journal.pgen.1004673.

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

C. Gubelmann; P. C. Schwalie; S. K. Raghav; E. Roeder; T. Delessa et al. 

Elife. 2014. Vol. 3, p. e03346. DOI : 10.7554/eLife.03346.

Natural variation in genome architecture among 205 Drosophila melanogaster Genetic Reference Panel lines

W. Huang; A. Massouras; Y. Inoue; J. Peiffer; M. Ramia et al. 

Genome Research. 2014. Vol. 24, num. 7, p. 1193-1208. DOI : 10.1101/gr.171546.113.

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

M. Masin; J. Vazquez; S. Rossi; S. Groeneveld; N. Samson et al. 

Cancer & metabolism. 2014. Vol. 2, p. 11. DOI : 10.1186/2049-3002-2-11.

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

S. M. Waszak; H. Kilpinen; A. R. Gschwind; A. Orioli; S. K. Raghav et al. 

Bioinformatics. 2014. Vol. 30, num. 2, p. 165-171. DOI : 10.1093/bioinformatics/btt667.

Theses

An integrative genomics approach toward deciphering the regulatory logic of phase-specific circadian transcription in the mouse liver

I. Krier / B. Deplancke; J. Rougemont (Dir.)  

Lausanne, EPFL, 2014. 

Context-specific regulation of BMAL1 target genes during the circadian rhythm in mouse

J. C. Cajan / F. Naef; B. Deplancke (Dir.)  

Lausanne, EPFL, 2014. 

Dissecting the DNA binding principles of transcription factor monomers and heterodimers

A. Isakova / B. Deplancke (Dir.)  

Lausanne, EPFL, 2014. 

A systems approach to elucidate the genetic architecture of molecular phenotypes

S. M. Waszak / B. Deplancke (Dir.)  

Lausanne, EPFL, 2014. 

2013

Journal Articles

Rounding Up Natural Gene Expression Variation during Development

S. M. Waszak; B. Deplancke 

Developmental Cell. 2013. Vol. 27, num. 6, p. 601-603. DOI : 10.1016/j.devcel.2013.12.007.

Coordinated Effects of Sequence Variation on DNA Binding, Chromatin Structure, and Transcription

H. Kilpinen; S. M. Waszak; A. R. Gschwind; S. K. Raghav; R. M. Witwicki et al. 

Science. 2013. Vol. 342, num. 6159, p. 744-747. DOI : 10.1126/science.1242463.

Morphological and Molecular Characterization of Adult Midgut Compartmentalization in Drosophila

N. Buchon; D. Osman; F. P. A. David; H. Y. Fang; J-P. Boquete et al. 

Cell Reports. 2013. Vol. 3, num. 5, p. 1725-1738. DOI : 10.1016/j.celrep.2013.04.001.

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

Y. Kim; A. Iagovitina; K. Ishihara; K. M. Fitzgerald; B. Deplancke et al. 

Chaos. 2013. Vol. 23, num. 2. DOI : 10.1063/1.4808157.

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

J. Simicevic; A. W. Schmid; P. A. Gilardoni; B. Zoller; S. K. Raghav et al. 

Nature methods. 2013. Vol. 10, num. 6, p. 570-6. DOI : 10.1038/nmeth.2441.

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

C. Gubelmann; S. M. Waszak; A. Isakova; W. Holcombe; K. Hens et al. 

Molecular Systems Biology. 2013. Vol. 9, num. 682. DOI : 10.1038/msb.2013.38.

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

S. Rockel; M. Geertz; K. Hens; B. Deplancke; S. J. Maerkl 

Nucleic Acids Research. 2013. Vol. 41, num. 4, p. e52. DOI : 10.1093/nar/gks1323.

Global and stage specific patterns of krüppel-associated-box zinc finger protein gene expression in murine early embryonic cells

A. Corsinotti; A. Kapopoulou; C. Gubelmann; M. Imbeault; S. de Sio et al. 

PloS One. 2013. Vol. 8, num. 2, p. e56721. DOI : 10.1371/journal.pone.0056721.

Theses

Development and application of experimental tools to elucidate the gene regulatory network underlying adipogenesis

C. Delattre-Gubelmann / B. Deplancke (Dir.)  

Lausanne, EPFL, 2013. 

Discovery and functional characterisation of structural genomic variation in a natural population

A. Massouras / B. Deplancke (Dir.)  

Lausanne, EPFL, 2013. 

2012

Journal Articles

Topology and dynamics of the zebrafish segmentation clock core circuit

C. Schröter; S. Ares; L. G. Morelli; A. Isakova; K. Hens et al. 

PLoS Biology. 2012. Vol. 10, num. 7, p. e1001364. DOI : 10.1371/journal.pbio.1001364.

Genome-Wide RNA Polymerase II Profiles and RNA Accumulation Reveal Kinetics of Transcription and Associated Epigenetic Changes During Diurnal Cycles

G. Le Martelot; D. Canella; L. Symul; E. Migliavacca; F. Gilardi et al. 

Plos Biology. 2012. Vol. 10, num. 11. DOI : 10.1371/journal.pbio.1001442.

Genomic Variation and Its Impact on Gene Expression in Drosophila melanogaster

A. Massouras; S. M. Waszak; M. Albarca-Aguilera; K. Hens; W. Holcombe et al. 

Plos Genetics. 2012. Vol. 8, num. 11, p. e1003055. DOI : 10.1371/journal.pgen.1003055.

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

S. K. Raghav; S. M. Waszak; I. Krier; C. Gubelmann; A. Isakova et al. 

Molecular cell. 2012. Vol. 46, num. 3, p. 335-50. DOI : 10.1016/j.molcel.2012.03.017.

Variable Outcome of Mutations

B. Deplancke; K. J. Verstrepen 

Science. 2012. Vol. 335, p. 44-45. DOI : 10.1126/science.1216823.

Theses

Dissecting Gene Regulatory Networks Using Targeted Quantitative Proteomics

J. Simicevic / B. Deplancke (Dir.)  

Lausanne, EPFL, 2012. 

2011

Journal Articles

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

C. Gubelmann; A. Gattiker; A. Massouras; K. Hens; F. David et al. 

Database-The Journal Of Biological Databases And Curation. 2011.  p. bar040. DOI : 10.1093/database/bar040.

Automated protein-DNA interaction screening of Drosophila regulatory elements

K. Hens; J-D. Feuz; A. Isakova; A. Iagovitina; A. Massouras et al. 

Nature Methods. 2011. Vol. 8, num. 12, p. 1065-1070. DOI : 10.1038/nmeth.1763.

Exhaustion of tumor-specific CD8(+) T cells in metastases from melanoma patients

L. Baitsch; P. Baumgaertner; E. Devevre; S. K. Raghav; A. Legat et al. 

Journal Of Clinical Investigation. 2011. Vol. 121, num. 6, p. 2350-2360. DOI : 10.1172/JCI46102.