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Items: 1 to 50 of 96

1.

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

Thiriet PE, Pezoldt J, Gambardella G, Keim K, Deplancke B, Guiducci C.

Micromachines (Basel). 2020 Mar 20;11(3). pii: E322. doi: 10.3390/mi11030322.

2.

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

Bou Sleiman M, Frochaux MV, Andreani T, Osman D, Guigo R, Deplancke B.

Genome Biol. 2020 Jan 17;21(1):4. doi: 10.1186/s13059-019-1918-6.

3.

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

Frochaux MV, Bou Sleiman M, Gardeux V, Dainese R, Hollis B, Litovchenko M, Braman VS, Andreani T, Osman D, Deplancke B.

Genome Biol. 2020 Jan 17;21(1):6. doi: 10.1186/s13059-019-1912-z.

4.

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

Li Y, Schwalie PC, Bast-Habersbrunner A, Mocek S, Russeil J, Fromme T, Deplancke B, Klingenspor M.

Cell Rep. 2019 Dec 17;29(12):4099-4113.e5. doi: 10.1016/j.celrep.2019.11.053.

5.

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

Friman ET, Deluz C, Meireles-Filho AC, Govindan S, Gardeux V, Deplancke B, Suter DM.

Elife. 2019 Dec 3;8. pii: e50087. doi: 10.7554/eLife.50087.

6.

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

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

Mol Syst Biol. 2019 Nov;15(11):e9012. doi: 10.15252/msb.20199012.

7.

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

Ma D, Bou-Sleiman M, Joncour P, Indelicato CE, Frochaux M, Braman V, Litovchenko M, Storelli G, Deplancke B, Leulier F.

iScience. 2019 Sep 27;19:436-447. doi: 10.1016/j.isci.2019.07.048. Epub 2019 Aug 2.

8.

Multilevel regulation of the glass locus during Drosophila eye development.

Fritsch C, Bernardo-Garcia FJ, Humberg TH, Mishra AK, Miellet S, Almeida S, Frochaux MV, Deplancke B, Huber A, Sprecher SG.

PLoS Genet. 2019 Jul 12;15(7):e1008269. doi: 10.1371/journal.pgen.1008269. eCollection 2019 Jul.

9.

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

Chen W, Schwalie PC, Pankevich EV, Gubelmann C, Raghav SK, Dainese R, Cassano M, Imbeault M, Jang SM, Russeil J, Delessa T, Duc J, Trono D, Wolfrum C, Deplancke B.

Nat Commun. 2019 Apr 18;10(1):1809. doi: 10.1038/s41467-019-09803-9.

10.

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

Alpern D, Gardeux V, Russeil J, Mangeat B, Meireles-Filho ACA, Breysse R, Hacker D, Deplancke B.

Genome Biol. 2019 Apr 19;20(1):71. doi: 10.1186/s13059-019-1671-x.

11.

A Comprehensive Drosophila melanogaster Transcription Factor Interactome.

Shokri L, Inukai S, Hafner A, Weinand K, Hens K, Vedenko A, Gisselbrecht SS, Dainese R, Bischof J, Furger E, Feuz JD, Basler K, Deplancke B, Bulyk ML.

Cell Rep. 2019 Apr 16;27(3):955-970.e7. doi: 10.1016/j.celrep.2019.03.071.

12.

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

Biočanin M, Bues J, Dainese R, Amstad E, Deplancke B.

Lab Chip. 2019 Apr 23;19(9):1610-1620. doi: 10.1039/c9lc00014c.

PMID:
30920557
13.

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

Vannini N, Campos V, Girotra M, Trachsel V, Rojas-Sutterlin S, Tratwal J, Ragusa S, Stefanidis E, Ryu D, Rainer PY, Nikitin G, Giger S, Li TY, Semilietof A, Oggier A, Yersin Y, Tauzin L, Pirinen E, Cheng WC, Ratajczak J, Canto C, Ehrbar M, Sizzano F, Petrova TV, Vanhecke D, Zhang L, Romero P, Nahimana A, Cherix S, Duchosal MA, Ho PC, Deplancke B, Coukos G, Auwerx J, Lutolf MP, Naveiras O.

Cell Stem Cell. 2019 Mar 7;24(3):405-418.e7. doi: 10.1016/j.stem.2019.02.012.

14.

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

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

Lab Chip. 2018 Dec 4;18(24):3903-3912. doi: 10.1039/c8lc01000e.

PMID:
30465575
15.

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

Schwalie PC, Dong H, Zachara M, Russeil J, Alpern D, Akchiche N, Caprara C, Sun W, Schlaudraff KU, Soldati G, Wolfrum C, Deplancke B.

Nature. 2018 Jul;559(7712):103-108. doi: 10.1038/s41586-018-0226-8. Epub 2018 Jun 20.

PMID:
29925944
16.

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

Wang QA, Song A, Chen W, Schwalie PC, Zhang F, Vishvanath L, Jiang L, Ye R, Shao M, Tao C, Gupta RK, Deplancke B, Scherer PE.

Cell Metab. 2018 Aug 7;28(2):282-288.e3. doi: 10.1016/j.cmet.2018.05.022. Epub 2018 Jun 14.

17.

The Human Cell Atlas.

Regev A, Teichmann SA, Lander ES, Amit I, Benoist C, Birney E, Bodenmiller B, Campbell P, Carninci P, Clatworthy M, Clevers H, Deplancke B, Dunham I, Eberwine J, Eils R, Enard W, Farmer A, Fugger L, Göttgens B, Hacohen N, Haniffa M, Hemberg M, Kim S, Klenerman P, Kriegstein A, Lein E, Linnarsson S, Lundberg E, Lundeberg J, Majumder P, Marioni JC, Merad M, Mhlanga M, Nawijn M, Netea M, Nolan G, Pe'er D, Phillipakis A, Ponting CP, Quake S, Reik W, Rozenblatt-Rosen O, Sanes J, Satija R, Schumacher TN, Shalek A, Shapiro E, Sharma P, Shin JW, Stegle O, Stratton M, Stubbington MJT, Theis FJ, Uhlen M, van Oudenaarden A, Wagner A, Watt F, Weissman J, Wold B, Xavier R, Yosef N; Human Cell Atlas Meeting Participants.

Elife. 2017 Dec 5;6. pii: e27041. doi: 10.7554/eLife.27041.

18.

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

Delachat AM, Guidotti N, Bachmann AL, Meireles-Filho ACA, Pick H, Lechner CC, Deluz C, Deplancke B, Suter DM, Fierz B.

Cell Chem Biol. 2018 Jan 18;25(1):51-56.e6. doi: 10.1016/j.chembiol.2017.10.008. Epub 2017 Nov 22.

19.

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

Houtz P, Bonfini A, Liu X, Revah J, Guillou A, Poidevin M, Hens K, Huang HY, Deplancke B, Tsai YC, Buchon N.

PLoS Genet. 2017 Nov 6;13(11):e1007091. doi: 10.1371/journal.pgen.1007091. eCollection 2017 Nov.

20.

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

Schwalie PC, Ordóñez-Morán P, Huelsken J, Deplancke B.

Stem Cells. 2017 Dec;35(12):2390-2402. doi: 10.1002/stem.2719. Epub 2017 Nov 6.

21.

Profiling of Single-Cell Transcriptomes.

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

Curr Protoc Mouse Biol. 2017 Sep 8;7(3):145-175. doi: 10.1002/cpmo.30.

PMID:
28884792
22.

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

McDaid AF, Joshi PK, Porcu E, Komljenovic A, Li H, Sorrentino V, Litovchenko M, Bevers RPJ, Rüeger S, Reymond A, Bochud M, Deplancke B, Williams RW, Robinson-Rechavi M, Paccaud F, Rousson V, Auwerx J, Wilson JF, Kutalik Z.

Nat Commun. 2017 Jul 27;8:15842. doi: 10.1038/ncomms15842.

23.

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

Gardeux V, David FPA, Shajkofci A, Schwalie PC, Deplancke B.

Bioinformatics. 2017 Oct 1;33(19):3123-3125. doi: 10.1093/bioinformatics/btx337.

24.

Editorial overview: Genome architecture and expression.

Deplancke B, Sagerström C.

Curr Opin Genet Dev. 2017 Apr;43:iv-v. doi: 10.1016/j.gde.2017.04.002. Epub 2017 May 1. No abstract available.

PMID:
28473185
25.

Transcriptional regulatory logic of the diurnal cycle in the mouse liver.

Sobel JA, Krier I, Andersin T, Raghav S, Canella D, Gilardi F, Kalantzi AS, Rey G, Weger B, Gachon F, Dal Peraro M, Hernandez N, Schibler U, Deplancke B, Naef F; CycliX consortium.

PLoS Biol. 2017 Apr 17;15(4):e2001069. doi: 10.1371/journal.pbio.2001069. eCollection 2017 Apr.

26.

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

Mojica-Vázquez LH, Benetah MH, Baanannou A, Bernat-Fabre S, Deplancke B, Cribbs DL, Bourbon HM, Boube M.

PLoS Genet. 2017 Apr 10;13(4):e1006718. doi: 10.1371/journal.pgen.1006718. eCollection 2017 Apr.

27.

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

Mendoza-García P, Hugosson F, Fallah M, Higgins ML, Iwasaki Y, Pfeifer K, Wolfstetter G, Varshney G, Popichenko D, Gergen JP, Hens K, Deplancke B, Palmer RH.

PLoS Genet. 2017 Apr 3;13(4):e1006617. doi: 10.1371/journal.pgen.1006617. eCollection 2017 Apr.

28.

Dissecting the brown adipogenic regulatory network using integrative genomics.

Pradhan RN, Bues JJ, Gardeux V, Schwalie PC, Alpern D, Chen W, Russeil J, Raghav SK, Deplancke B.

Sci Rep. 2017 Feb 9;7:42130. doi: 10.1038/srep42130.

29.

A systems perspective on brown adipogenesis and metabolic activation.

Pradhan RN, Zachara M, Deplancke B.

Obes Rev. 2017 Feb;18 Suppl 1:65-81. doi: 10.1111/obr.12512. Review.

PMID:
28164456
30.

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

Grossman SR, Zhang X, Wang L, Engreitz J, Melnikov A, Rogov P, Tewhey R, Isakova A, Deplancke B, Bernstein BE, Mikkelsen TS, Lander ES.

Proc Natl Acad Sci U S A. 2017 Feb 14;114(7):E1291-E1300. doi: 10.1073/pnas.1621150114. Epub 2017 Jan 30.

31.

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

Isakova A, Groux R, Imbeault M, Rainer P, Alpern D, Dainese R, Ambrosini G, Trono D, Bucher P, Deplancke B.

Nat Methods. 2017 Mar;14(3):316-322. doi: 10.1038/nmeth.4143. Epub 2017 Jan 16.

PMID:
28092692
32.

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

David FP, Rougemont J, Deplancke B.

Nucleic Acids Res. 2017 Jan 4;45(D1):D56-D60. doi: 10.1093/nar/gkw913. Epub 2016 Oct 7.

33.

Gene regulatory mechanisms underlying the intestinal innate immune response.

Meireles-Filho AC, Deplancke B.

Curr Opin Genet Dev. 2017 Apr;43:46-52. doi: 10.1016/j.gde.2016.11.004. Epub 2016 Dec 20. Review.

PMID:
28011293
34.

Transcription factor proteomics-Tools, applications, and challenges.

Simicevic J, Deplancke B.

Proteomics. 2017 Feb;17(3-4). doi: 10.1002/pmic.201600317. Epub 2017 Jan 24. Review.

PMID:
27860250
35.

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

Mezan S, Feuz JD, Deplancke B, Kadener S.

Cell Rep. 2016 Oct 11;17(3):708-719. doi: 10.1016/j.celrep.2016.09.048.

36.

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

Mouchiroud L, Sorrentino V, Williams EG, Cornaglia M, Frochaux MV, Lin T, Nicolet-Dit-Félix AA, Krishnamani G, Ouhmad T, Gijs MA, Deplancke B, Auwerx J.

Curr Protoc Neurosci. 2016 Oct 3;77:8.37.1-8.37.21. doi: 10.1002/cpns.17.

PMID:
27696358
37.

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

Kalay G, Lusk R, Dome M, Hens K, Deplancke B, Wittkopp PJ.

G3 (Bethesda). 2016 Oct 13;6(10):3419-3430. doi: 10.1534/g3.116.032607.

38.

The Genetics of Transcription Factor DNA Binding Variation.

Deplancke B, Alpern D, Gardeux V.

Cell. 2016 Jul 28;166(3):538-554. doi: 10.1016/j.cell.2016.07.012. Review.

39.

Chromosomal contacts connect loci associated with autism, BMI and head circumference phenotypes.

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; 2p15 Consortium; 16p11.2 Consortium, Van Dijck A, Kooy RF, Sanlaville D, Rosenfeld JA, Shaffer LG, Andrieux J, Marshall C, Scherer SW, Shen Y, Gusella JF, Thorsteinsdottir U, Thorleifsson G, Dermitzakis ET, Deplancke B, Beckmann JS, Rougemont J, Jacquemont S, Reymond A.

Mol Psychiatry. 2017 Jun;22(6):836-849. doi: 10.1038/mp.2016.84. Epub 2016 May 31.

40.

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

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

J Biol Chem. 2016 May 6;291(19):10293-306. doi: 10.1074/jbc.M115.691154. Epub 2016 Feb 24.

41.

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

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, Thurnheer S, Hacker D, Hernandez N, Reymond A, Deplancke B, Dermitzakis ET.

Cell. 2015 Aug 27;162(5):1039-50. doi: 10.1016/j.cell.2015.08.001. Epub 2015 Aug 20.

42.

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

Bou Sleiman MS, Osman D, Massouras A, Hoffmann AA, Lemaitre B, Deplancke B.

Nat Commun. 2015 Jul 27;6:7829. doi: 10.1038/ncomms8829.

43.

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

Nitta KR, Jolma A, Yin Y, Morgunova E, Kivioja T, Akhtar J, Hens K, Toivonen J, Deplancke B, Furlong EE, Taipale J.

Elife. 2015 Mar 17;4. doi: 10.7554/eLife.04837.

44.

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

Moullan N, Mouchiroud L, Wang X, Ryu D, Williams EG, Mottis A, Jovaisaite V, Frochaux MV, Quiros PM, Deplancke B, Houtkooper RH, Auwerx J.

Cell Rep. 2015 Mar 17;10(10):1681-1691. doi: 10.1016/j.celrep.2015.02.034. Epub 2015 Mar 12.

45.

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

Schertel C, Albarca M, Rockel-Bauer C, Kelley NW, Bischof J, Hens K, van Nimwegen E, Basler K, Deplancke B.

Genome Res. 2015 Apr;25(4):514-23. doi: 10.1101/gr.181305.114. Epub 2015 Jan 7.

46.

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

Simicevic J, Moniatte M, Hamelin R, Ahrné E, Deplancke B.

Proteomics. 2015 Feb;15(4):752-6. doi: 10.1002/pmic.201400355. Epub 2015 Jan 14.

PMID:
25407602
47.

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

Williams EG, Mouchiroud L, Frochaux M, Pandey A, Andreux PA, Deplancke B, Auwerx J.

PLoS Genet. 2014 Sep 25;10(9):e1004673. doi: 10.1371/journal.pgen.1004673. eCollection 2014 Sep.

48.

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

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.

Elife. 2014 Aug 27;3:e03346. doi: 10.7554/eLife.03346.

49.

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

Masin M, Vazquez J, Rossi S, Groeneveld S, Samson N, Schwalie PC, Deplancke B, Frawley LE, Gouttenoire J, Moradpour D, Oliver TG, Meylan E.

Cancer Metab. 2014 Jul 29;2:11. doi: 10.1186/2049-3002-2-11. eCollection 2014.

50.

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

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, Fernandez S, Han Y, Highnam G, Hjelmen CE, Jack JR, Javaid M, Jayaseelan J, Kalra D, Lee S, Lewis L, Munidasa M, Ongeri F, Patel S, Perales L, Perez A, Pu L, Rollmann SM, Ruth R, Saada N, Warner C, Williams A, Wu YQ, Yamamoto A, Zhang Y, Zhu Y, Anholt RR, Korbel JO, Mittelman D, Muzny DM, Gibbs RA, Barbadilla A, Johnston JS, Stone EA, Richards S, Deplancke B, Mackay TF.

Genome Res. 2014 Jul;24(7):1193-208. doi: 10.1101/gr.171546.113. Epub 2014 Apr 8.

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