Total: 120 publication(s)


Schraivogel D, Gschwind AR, Milbank JH, Leonce DR, Jakob P, Mathur L, Korbel JO, Merten CA, Velten L, Steinmetz LM. (2020)

Targeted Perturb-seq enables genome-scale genetic screens in single cells.

Nat. Methods 17(6):629-635. doi: 10.1038/s41592-020-0837-5
Europe PMC | doi

Eduati F, Jaaks P, Wappler J, Cramer T, Merten CA, Garnett MJ, Saez-Rodriguez J. (2020)

Patient-specific logic models of signaling pathways from screenings on cancer biopsies to prioritize personalized combination therapies.

Mol Syst Biol 16(2) doi: 10.15252/msb.20188664
Europe PMC | doi


Mathur L, Ballinger M, Utharala R, Merten CA. (2019)

Microfluidics as an enabling technology for personalized cancer therapy.

Small 16(9) doi: 10.1002/smll.201904321
Europe PMC | doi

Viets K, Sauria MEG, Chernoff C, Rodriguez Viales R, Echterling M, Anderson C, Tran S, Dove A, Goyal R, Voortman L, Gordus A, Furlong EEM, Taylor J, Johnston RJ. (2019)

Characterization of button loci that promote homologous chromosome pairing and cell-type-specific interchromosomal gene regulation.

Dev. Cell 51(3):341-356.e7. doi: 10.1016/j.devcel.2019.09.007
Europe PMC | doi

Mir M, Bickmore W, Furlong EEM, Narlikar G. (2019)

Chromatin topology, condensates and gene regulation: shifting paradigms or just a phase?

Development 146(19) doi: 10.1242/dev.182766
Europe PMC | doi

Zhou J, Schor IE, Yao V, Theesfeld CL, Marco-Ferreres R, Tadych A, Furlong EEM, Troyanskaya OG. (2019)

Accurate genome-wide predictions of spatio-temporal gene expression during embryonic development.

PLoS Genet. 15(9) doi: 10.1371/journal.pgen.1008382
Europe PMC | doi

Ghavi-Helm Y, Jankowski A, Meiers S, Viales RR, Korbel JO, Furlong EEM. (2019)

Highly rearranged chromosomes reveal uncoupling between genome topology and gene expression.

Nat. Genet. 51(8) doi: 10.1038/s41588-019-0462-3
Europe PMC | doi

Khoueiry P, Ward Gahlawat A, Petretich M, Michon AM, Simola D, Lam E, Furlong EE, Benes V, Dawson MA, Prinjha RK, Drewes G, Grandi P. (2019)

BRD4 bimodal binding at promoters and drug-induced displacement at Pol II pause sites associates with I-BET sensitivity.

Epigenetics Chromatin 12(1) doi: 10.1186/s13072-019-0286-5
Europe PMC | doi

Peng PC, Khoueiry P, Girardot C, Reddington JP, Garfield DA, Furlong EEM, Sinha S. (2019)

The role of chromatin accessibility in cis-regulatory evolution.

Genome Biol Evol 11(7) doi: 10.1093/gbe/evz103
Europe PMC | doi

Wu WH, Kuo TH, Kao CW, Girardot C, Hung SJ, Liu T, Furlong EEM, Liu YH. (2019)

Expanding the mesodermal transcriptional network by genome-wide identification of Zinc finger homeodomain 1 (Zfh1) targets.

FEBS Lett. 593(14):1698-1710. doi: 10.1002/1873-3468.13443
Europe PMC | doi

van Steensel B, Furlong EEM. (2019)

The role of transcription in shaping the spatial organization of the genome.

Nat. Rev. Mol. Cell Biol. 20(6):327-337. doi: 10.1038/s41580-019-0114-6
Europe PMC | doi

Sonnen KF, Merten CA. (2019)

Microfluidics as an emerging precision tool in developmental biology.

Dev. Cell 48(3):293-311. doi: 10.1016/j.devcel.2019.01.015
Europe PMC | doi

Hildebrand F, Moitinho-Silva L, Blasche S, Jahn MTT, Gossmann TI, Huerta Cepas J, Hercog R, Luetge M, Bahram M, Pryszlak A, Alves RJ, Waszak SM, Zhu A, Ye L, Costea PI, Belzer C, Aalvink S, Sunagawa S, Forslund SK, Merten C, Hentschel U, Benes V, Patil KR, Bork P. (2019)

Antibiotics-induced monodominance of a novel gut bacterial order.

Gut 68(10):1781-1790. doi: 10.1136/gutjnl-2018-317715
Europe PMC | doi


Schor IE, Bussotti G, Maleš M, Forneris M, Viales RR, Enright AJ, Furlong EEM. (2018)

Non-coding RNA expression, function, and variation during Drosophila embryogenesis.

Curr. Biol. 28(22):3547-3561. doi: 10.1016/j.cub.2018.09.026
Europe PMC | doi

Gambetta MC, Furlong EEM. (2018)

The Insulator Protein CTCF Is Required for Correct Hox Gene Expression, but Not for Embryonic Development in Drosophila.

Genetics 210(1) doi: 10.1534/genetics.118.301350
Europe PMC | doi

Furlong EEM, Levine M. (2018)

Developmental enhancers and chromosome topology.

Science 361(6409):1341-1345. doi: 10.1126/science.aau0320
Europe PMC | doi

Eduati F, Utharala R, Madhavan D, Neumann UP, Longerich T, Cramer T, Saez-Rodriguez J, Merten CA. (2018)

A microfluidics platform for combinatorial drug screening on cancer biopsies.

Nat Commun 9(1) doi: 10.1038/s41467-018-04919-w
Europe PMC | doi

Utharala R, Tseng Q, Furlong EEM, Merten CA. (2018)

A versatile, low-cost, multiway microfluidic sorter for droplets, cells, and embryos.

Anal Chem 90(10):5982-5988. doi: 10.1021/acs.analchem.7b04689
Europe PMC | doi

Cusanovich DA, Reddington JP, Garfield DA, Daza RM, Aghamirzaie D, Marco-Ferreres R, Pliner HA, Christiansen L, Qiu X, Steemers FJ, Trapnell C, Shendure J, Furlong EEM. (2018)

The cis-regulatory dynamics of embryonic development at single-cell resolution.

Nature 555(7697):538-542. doi: 10.1038/nature25981
Europe PMC | doi

Sonnen KF, Lauschke VM, Uraji J, Falk HJ, Petersen Y, Funk MC, Beaupeux M, François P, Merten CA, Aulehla A. (2018)

Modulation of phase shift between wnt and notch signaling oscillations controls mesoderm segmentation.

Cell 172(5):1079-1090.e12. doi: 10.1016/j.cell.2018.01.026
Europe PMC | doi

Shembekar N, Hu H, Eustace D, Merten CA. (2018)

Single-cell droplet microfluidic screening for antibodies specifically binding to target cells.

Cell Rep 22(8):2206-2215. doi: 10.1016/j.celrep.2018.01.071
Europe PMC | doi

Seah YFS, Hu H, Merten CA. (2018)

Microfluidic single-cell technology in immunology and antibody screening.

Mol. Aspects Med. 59 doi: 10.1016/j.mam.2017.09.004
Europe PMC | doi

Lehmann LH, Jebessa ZH, Kreusser MM, Horsch A, He T, Kronlage M, Dewenter M, Sramek V, Oehl U, Krebs-Haupenthal J, von der Lieth AH, Schmidt A, Sun Q, Ritterhoff J, Finke D, Völkers M, Jungmann A, Sauer SW, Thiel C, Nickel A, Kohlhaas M, Schäfer M, Sticht C, Maack C, Gretz N, Wagner M, El-Armouche A, Maier LS, Londoño JEC, Meder B, Freichel M, Gröne HJ, Most P, Müller OJ, Herzig S, Furlong EEM, Katus HA, Backs J. (2018)

A proteolytic fragment of histone deacetylase 4 protects the heart from failure by regulating the hexosamine biosynthetic pathway.

Nat. Med. 24(1):62-72. doi: 10.1038/nm.4452
Europe PMC | doi

Mikhaylichenko O, Bondarenko V, Harnett D, Schor IE, Males M, Viales RR, Furlong EEM. (2018)

The degree of enhancer or promoter activity is reflected by the levels and directionality of eRNA transcription.

Genes Dev 32(1):42-57. doi: 10.1101/gad.308619.117
Europe PMC | doi


Zolotarev N, Maksimenko O, Kyrchanova O, Sokolinskaya E, Osadchiy I, Girardot C, Bonchuk A, Ciglar L, Furlong EEM, Georgiev P. (2017)

Opbp is a new architectural/insulator protein required for ribosomal gene expression.

Nucleic Acids Res. 45(21):12285-12300. doi: 10.1093/nar/gkx840
Europe PMC | doi

Khoueiry P, Girardot C, Ciglar L, Peng PC, Gustafson EH, Sinha S, Furlong EE. (2017)

Uncoupling evolutionary changes in DNA sequence, transcription factor occupancy and enhancer activity.

Elife 6 doi: 10.7554/eLife.28440
Europe PMC | doi

Schauer T, Ghavi-Helm Y, Sexton T, Albig C, Regnard C, Cavalli G, Furlong EE, Becker PB. (2017)

Chromosome topology guides the Drosophila Dosage Compensation Complex for target gene activation.

EMBO Rep. 18(10) doi: 10.15252/embr.201744292
Europe PMC | doi

Monfort M, Furlong EE, Girardot C. (2017)

Dynamix: Dynamic visualization by automatic selection of informative tracks from hundreds of genomic data sets.

Bioinformatics 33(14) doi: 10.1093/bioinformatics/btx141
Europe PMC | doi

Chaipan C, Pryszlak A, Dean H, Poignard P, Benes V, Griffiths AD, Merten CA. (2017)

Single-virus droplet microfluidics for high-throughput screening of neutralizing epitopes on HIV particles.

Cell Chem Biol 24(6):751-757. doi: 10.1016/j.chembiol.2017.05.009
Europe PMC | doi

Pollex T, Furlong EEM. (2017)

Correlation Does Not Imply Causation: Histone Methyltransferases, but Not Histone Methylation, SET the Stage for Enhancer Activation

Mol Cell 66(4):439-441. doi: 10.1016/j.molcel.2017.05.005
Europe PMC | doi

Schor IE, Degner JF, Harnett D, Cannavò E, Casale FP, Shim H, Garfield DA, Birney E, Stephens M, Stegle O, Furlong EE. (2017)

Promoter shape varies across populations and affects promoter evolution and expression noise.

Nat. Genet. 49(4):550-558. doi: 10.1038/ng.3791
Europe PMC | doi

Erceg J, Pakozdi T, Marco-Ferreres R, Ghavi-Helm Y, Girardot C, Bracken AP, Furlong EE. (2017)

Dual functionality of cis-regulatory elements as developmental enhancers and Polycomb response elements.

Genes Dev. 31(6):590-602. doi: 10.1101/gad.292870.116
Europe PMC | doi

Frenzel D, Merten CA. (2017)

Microfluidic train station: highly robust and multiplexable sorting of droplets on electric rails.

Lab Chip 17(6):1024-1030. doi: 10.1039/c6lc01544a
Europe PMC | doi

Cannavò E, Koelling N, Harnett D, Garfield D, Casale FP, Ciglar L, Gustafson HE, Viales RR, Marco-Ferreres R, Degner JF, Zhao B, Stegle O, Birney E, Furlong EE. (2017)

Genetic variants regulating expression levels and isoform diversity during embryogenesis.

Nature 541(7637):402-406. doi: 10.1038/nature20802
Europe PMC | doi


Seyres D, Ghavi-Helm Y, Junion G, Taghli-Lamallem O, Guichard C, Röder L, Girardot C, Furlong EE, Perrin L. (2016)

Identification and in silico modeling of enhancers reveals new features of the cardiac differentiation network.

Development 143(23):4533-4542. doi: 10.1242/dev.140822
Europe PMC | doi

Ghavi-Helm Y, Zhao B, Furlong EE. (2016)

Chromatin Immunoprecipitation for Analyzing Transcription Factor Binding and Histone Modifications in Drosophila.

Methods Mol. Biol. 1478:263-277. doi: 10.1007/978-1-4939-6371-3_16
Europe PMC | doi

Girardot C, Scholtalbers J, Sauer S, Su SY, Furlong EE. (2016)

Je, a versatile suite to handle multiplexed NGS libraries with unique molecular identifiers.

BMC Bioinformatics 17(1) doi: 10.1186/s12859-016-1284-2
Europe PMC | doi

Ghavi-Helm Y, Klein FA, Pakozdi T, Ciglar L, Noordermeer D, Huber W, Furlong EEM. (2016)

Corrigendum: Enhancer loops appear stable during development and are associated with paused polymerase

NATURE 537(7619) doi: 10.1038/nature18962
Europe PMC | doi

Mbodj A, Gustafson EH, Ciglar L, Junion G, Gonzalez A, Girardot C, Perrin L, Furlong EE, Thieffry D. (2016)

Qualitative Dynamical Modelling Can Formally Explain Mesoderm Specification and Predict Novel Developmental Phenotypes.

PLoS Comput. Biol. 12(9) doi: 10.1371/journal.pcbi.1005073
Europe PMC | doi

Tica J, Lee E, Untergasser A, Meiers S, Garfield DA, Gokcumen O, Furlong EE, Park PJ, Stütz AM, Korbel JO. (2016)

Next-generation sequencing-based detection of germline L1-mediated transductions.

BMC Genomics 17(1) doi: 10.1186/s12864-016-2670-x
Europe PMC | doi

Shembekar N, Chaipan C, Utharala R, Merten CA. (2016)

Droplet-based microfluidics in drug discovery, transcriptomics and high-throughput molecular genetics.

Lab Chip 16(8):1314-1331. doi: 10.1039/c6lc00249h
Europe PMC | doi

Cannavò E, Khoueiry P, Garfield DA, Geeleher P, Zichner T, Gustafson EH, Ciglar L, Korbel JO, Furlong EE. (2016)

Shadow Enhancers Are Pervasive Features of Developmental Regulatory Networks.

Curr. Biol. 26(1):38-51. doi: 10.1016/j.cub.2015.11.034
Europe PMC | doi


Ramanathan N, Simakov O, Merten CA, Arendt D. (2015)

Quantifying preferences and responsiveness of marine zooplankton to changing environmental conditions using microfluidics.

PLoS ONE 10(10) doi: 10.1371/journal.pone.0140553
Europe PMC | doi

Hu H, Eustace D, Merten CA. (2015)

Efficient cell pairing in droplets using dual-color sorting.

Lab Chip 15(20):3989-3993. doi: 10.1039/c5lc00686d
Europe PMC | doi

Klein FA, Pakozdi T, Anders S, Ghavi-Helm Y, Furlong EE, Huber W. (2015)

FourCSeq: Analysis of 4C sequencing data.

Bioinformatics 31(19):3085-3091. doi: 10.1093/bioinformatics/btv335
Europe PMC | doi

Hara Y, Merten CA. (2015)

Dynein-based accumulation of membranes regulates nuclear expansion in xenopus laevis egg extracts.

Dev. Cell 33(5) doi: 10.1016/j.devcel.2015.04.016
Europe PMC | doi

Eicher D, Ramanathan N, Merten CA. (2015)

Soft compartmentalization: Combining droplet-based microfluidics with freely accessible cells

Eng. Life Sci. 15(3):297-305. doi: 10.1002/elsc.201400184

Nitta KR, Jolma A, Yin Y, Morgunova E, Kivioja T, Akhtar J, Hens K, Toivonen J, Deplancke B, Furlong EE, Taipale J. (2015)

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

Elife 4 doi: 10.7554/elife.04837
Europe PMC | doi


El Debs B, Utharala R, Merten CA. (2014)

Screening cellular metabolic activity.

Nat. Biotechnol. 32(11) doi: 10.1038/nbt.3058
Europe PMC | doi

Hughes CS, Foehr S, Garfield DA, Furlong EE, Steinmetz LM, Krijgsveld J. (2014)

Ultrasensitive proteome analysis using paramagnetic bead technology.

Mol. Syst. Biol. 10(10) doi: 10.15252/msb.20145625
Europe PMC | doi

Ghavi-Helm Y, Klein FA, Pakozdi T, Ciglar L, Noordermeer D, Huber W, Furlong EE. (2014)

Enhancer loops appear stable during development and are associated with paused polymerase

Nature 512(7512):96-100. doi: 10.1038/nature13417
Europe PMC | doi

Ciglar L, Girardot C, Wilczyński B, Braun M, Furlong EE. (2014)

Coordinated repression and activation of two transcriptional programs stabilizes cell fate during myogenesis

Development 141(13):2633-2643. doi: 10.1242/dev.101956
Europe PMC | doi

Rembold M, Ciglar L, Yáñez-Cuna JO, Zinzen RP, Girardot C, Jain A, Welte MA, Stark A, Leptin M, Furlong EE. (2014)

A conserved role for Snail as a potentiator of active transcription

Genes Dev. 28(2):167-181. doi: 10.1101/gad.230953.113
Europe PMC | doi

Erceg J, Saunders TE, Girardot C, Devos DP, Hufnagel L, Furlong EE. (2014)

Subtle changes in motif positioning cause tissue-specific effects on robustness of an enhancer's activity

PLoS Genet. 10(1):e1004060. doi: 10.1371/journal.pgen.1004060
Europe PMC | doi


Mbodj A, Junion G, Brun C, Furlong EE, Thieffry D. (2013)

Logical modelling of Drosophila signalling pathways

Mol Biosyst 9(9):2248-2258. doi: 10.1039/c3mb70187e
Europe PMC | doi

Zichner T, Garfield DA, Rausch T, Stütz AM, Cannavó E, Braun M, Furlong EE, Korbel JO. (2013)

Impact of genomic structural variation in Drosophila melanogaster based on population-scale sequencing

Genome Res. 23(3):568-579. doi: 10.1101/gr.142646.112
Europe PMC | doi


Tseng Q, Lomonosov AM, Furlong EE, Merten CA. (2012)

Fragmentation of DNA in a sub-microliter microfluidic sonication device

Lab Chip 12(22):4677-4682. doi: 10.1039/c2lc40595d
Europe PMC | doi

Delhomme N, Padioleau I, Furlong EE, Steinmetz LM. (2012)

easyRNASeq: a bioconductor package for processing RNA-Seq data

Bioinformatics 28(19):2532-2533. doi: 10.1093/bioinformatics/bts477
Europe PMC | doi

Spitz F, Furlong EE. (2012)

Transcription factors: from enhancer binding to developmental control

Nat. Rev. Genet. 13(9):613-626. doi: 10.1038/nrg3207
Europe PMC | doi

El Debs B, Utharala R, Balyasnikova IV, Griffiths AD, Merten CA. (2012)

Functional single-cell hybridoma screening using droplet-based microfluidics

Proc. Natl. Acad. Sci. U.S.A. 109(29):11570-11575. doi: 10.1073/pnas.1204514109
Europe PMC | doi

Bonn S, Zinzen RP, Perez-Gonzalez A, Riddell A, Gavin AC, Furlong EE. (2012)

Cell type-specific chromatin immunoprecipitation from multicellular complex samples using BiTS-ChIP

Nat Protoc 7(5):978-994. doi: 10.1038/nprot.2012.049
Europe PMC | doi

Bonn S, Zinzen RP, Girardot C, Gustafson EH, Perez-Gonzalez A, Delhomme N, Ghavi-Helm Y, Wilczyński B, Riddell A, Furlong EE. (2012)

Tissue-specific analysis of chromatin state identifies temporal signatures of enhancer activity during embryonic development

Nat. Genet. 44(2):148-156. doi: 10.1038/ng.1064
Europe PMC | doi

Junion G, Spivakov M, Girardot C, Braun M, Gustafson EH, Birney E, Furlong EE. (2012)

A transcription factor collective defines cardiac cell fate and reflects lineage history

Cell 148(3):473-486. doi: 10.1016/j.cell.2012.01.030
Europe PMC | doi

Clausell-Tormos J, Merten CA. (2012)

Micro segmented-flow in biochemical and cell-based assays

Front Biosci (Elite Ed) 4:1768-1779. doi: 10.2741/497
Europe PMC | doi

Ghavi-Helm Y, Furlong EE. (2012)

Analyzing transcription factor occupancy during embryo development using ChIP-seq

Methods Mol. Biol. 786:229-245. doi: 10.1007/978-1-61779-292-2_14
Europe PMC | doi

Spivakov M, Akhtar J, Kheradpour P, Beal K, Girardot C, Koscielny G, Herrero J, Kellis M, Furlong EE, Birney E. (2012)

Analysis of variation at transcription factor binding sites in Drosophila and humans

Genome Biol. 13(9):R49. doi: 10.1186/gb-2012-13-9-r49
Europe PMC | doi

Wilczynski B, Liu YH, Yeo ZX, Furlong EE. (2012)

Predicting spatial and temporal gene expression using an integrative model of transcription factor occupancy and chromatin state

PLoS Comput. Biol. 8(12):e1002798. doi: 10.1371/journal.pcbi.1002798
Europe PMC | doi


El Debs BW, Tschulena U, Griffiths AD, Merten CA. (2011)

A competitive co-cultivation assay for cancer drug specificity evaluation

J Biomol Screen 16(8):818-824. doi: 10.1177/1087057111414898
Europe PMC | doi

Eicher D, Merten CA. (2011)

Microfluidic devices for diagnostic applications

Expert Rev. Mol. Diagn. 11(5):505-519. doi: 10.1586/erm.11.25
Europe PMC | doi

Furlong EE. (2011)

Molecular biology: A fly in the face of genomics

Nature 471(7339):458-459. doi: 10.1038/471458a
Europe PMC | doi

Urban JH, Merten CA. (2011)

Retroviral display in gene therapy, protein engineering, and vaccine development

ACS Chem. Biol. 6(1):61-74. doi: 10.1021/cb100285n
Europe PMC | doi


Furlong EE. (2010)

The importance of being specified: cell fate decisions and their role in cell biology

Mol. Biol. Cell 21(22):3797-3798. doi: 10.1091/mbc.e10-05-0436
Europe PMC | doi

Vyawahare S, Griffiths AD, Merten CA. (2010)

Miniaturization and parallelization of biological and chemical assays in microfluidic devices

Chem. Biol. 17(10):1052-1065. doi: 10.1016/j.chembiol.2010.09.007
Europe PMC | doi

Cunha PM, Sandmann T, Gustafson EH, Ciglar L, Eichenlaub MP, Furlong EE. (2010)

Combinatorial binding leads to diverse regulatory responses: Lmd is a tissue-specific modulator of Mef2 activity

PLoS Genet. 6(7):e1001014. doi: 10.1371/journal.pgen.1001014
Europe PMC | doi

Merten CA. (2010)

Screening Europe 2010: an update about the latest technologies and applications in high-throughput screening

Expert Rev. Mol. Diagn. 10(5):559-563. doi: 10.1586/erm.10.42
Europe PMC | doi

Wilczyński B, Furlong EE. (2010)

Dynamic CRM occupancy reflects a temporal map of developmental progression

Mol. Syst. Biol. 6:383. doi: 10.1038/msb.2010.35
Europe PMC | doi

Clausell-Tormos J, Griffiths AD, Merten CA. (2010)

An automated two-phase microfluidic system for kinetic analyses and the screening of compound libraries

Lab Chip 10(10):1302-1307. doi: 10.1039/b921754a
Europe PMC | doi

Clausell-Tormos J, Griffiths AD, Merten CA. (2010)

Coupling the inhibition of viral transduction with a positive fluorescence signal

Comb. Chem. High Throughput Screen. 13(4):352-357. doi: 10.2174/138620710791054312
Europe PMC | doi

Honkela A, Girardot C, Gustafson EH, Liu YH, Furlong EE, Lawrence ND, Rattray M. (2010)

Model-based method for transcription factor target identification with limited data

Proc. Natl. Acad. Sci. U.S.A. 107(17):7793-7798. doi: 10.1073/pnas.0914285107
Europe PMC | doi

Upert G, Merten CA, Wennemers H. (2010)

Nanoliter plates--versatile tools for the screening of split-and-mix libraries on-bead and off-bead

Chem. Commun. (Camb.) 46(13):2209-2211. doi: 10.1039/b927017e
Europe PMC | doi

Wilczynski B, Furlong EE. (2010)

Challenges for modeling global gene regulatory networks during development: insights from Drosophila

Dev. Biol. 340(2):161-169. doi: 10.1016/j.ydbio.2009.10.032
Europe PMC | doi

Granieri L, Baret JC, Griffiths AD, Merten CA. (2010)

High-throughput screening of enzymes by retroviral display using droplet-based microfluidics

Chem. Biol. 17(3):229-235. doi: 10.1016/j.chembiol.2010.02.011
Europe PMC | doi


Ciglar L, Furlong EE. (2009)

Conservation and divergence in developmental networks: a view from Drosophila myogenesis

Curr. Opin. Cell Biol. 21(6):754-760. doi: 10.1016/
Europe PMC | doi

Zinzen RP, Girardot C, Gagneur J, Braun M, Furlong EE. (2009)

Combinatorial binding predicts spatio-temporal cis-regulatory activity

Nature 462(7269):65-70. doi: 10.1038/nature08531
Europe PMC | doi

Granieri L, Miller OJ, Griffiths AD, Merten CA. (2009)

A competition-based assay for the screening of species-specific antibiotics

J. Antimicrob. Chemother. 64(1):62-68. doi: 10.1093/jac/dkp137
Europe PMC | doi

Pianowski Z, Gorska K, Oswald L, Merten CA, Winssinger N. (2009)

Imaging of mRNA in live cells using nucleic acid-templated reduction of azidorhodamine probes

J. Am. Chem. Soc. 131(18):6492-6497. doi: 10.1021/ja809656k
Europe PMC | doi

Liu YH, Jakobsen JS, Valentin G, Amarantos I, Gilmour DT, Furlong EE. (2009)

A systematic analysis of Tinman function reveals Eya and JAK-STAT signaling as essential regulators of muscle development

Dev. Cell 16(2):280-291. doi: 10.1016/j.devcel.2009.01.006
Europe PMC | doi

Baret JC, Taly V, Ryckelynck M, Merten CA, Griffiths AD. (2009)

[Droplets and emulsions: very high-throughput screening in biology]

Med Sci (Paris) 25(6-7):627-632. doi: 10.1051/medsci/2009256-7627
Europe PMC | doi


Bonn S, Furlong EE. (2008)

cis-Regulatory networks during development: a view of Drosophila

Curr. Opin. Genet. Dev. 18(6):513-520. doi: 10.1016/j.gde.2008.09.005
Europe PMC | doi

Oktaba K, Gutiérrez L, Gagneur J, Girardot C, Sengupta AK, Furlong EE, Müller J. (2008)

Dynamic regulation by polycomb group protein complexes controls pattern formation and the cell cycle in Drosophila

Dev. Cell 15(6):877-889. doi: 10.1016/j.devcel.2008.10.005
Europe PMC | doi

Köster S, Angilè FE, Duan H, Agresti JJ, Wintner A, Schmitz C, Rowat AC, Merten CA, Pisignano D, Griffiths AD, Weitz DA. (2008)

Drop-based microfluidic devices for encapsulation of single cells

Lab Chip 8(7):1110-1115. doi: 10.1039/b802941e
Europe PMC | doi

Clausell-Tormos J, Lieber D, Baret JC, El-Harrak A, Miller OJ, Frenz L, Blouwolff J, Humphry KJ, Köster S, Duan H, Holtze C, Weitz DA, Griffiths AD, Merten CA. (2008)

Droplet-based microfluidic platforms for the encapsulation and screening of Mammalian cells and multicellular organisms

Chem. Biol. 15(5):427-437. doi: 10.1016/j.chembiol.2008.04.004
Europe PMC | doi

Furlong EE. (2008)

A topographical map of spatiotemporal patterns of gene expression

Dev. Cell 14(5):639-640. doi: 10.1016/j.devcel.2008.04.007
Europe PMC | doi

Haudry Y, Berube H, Letunic I, Weeber PD, Gagneur J, Girardot C, Kapushesky M, Arendt D, Bork P, Brazma A, Furlong EE, Wittbrodt J, Henrich T. (2008)

4DXpress: a database for cross-species expression pattern comparisons

Nucleic Acids Res. 36(Database issue):D847-53. doi: 10.1093/nar/gkm797
Europe PMC | doi

Shah PK, Tripathi LP, Jensen LJ, Gahnim M, Mason C, Furlong EE, Rodrigues V, White KP, Bork P, Sowdhamini R. (2008)

Enhanced function annotations for Drosophila serine proteases: a case study for systematic annotation of multi-member gene families

Gene 407(1-2):199-215. doi: 10.1016/j.gene.2007.10.012
Europe PMC | doi

Zinzen RP, Furlong EE. (2008)

Divergence in cis-regulatory networks: taking the 'species' out of cross-species analysis

Genome Biol. 9(11):240. doi: 10.1186/gb-2008-9-11-240
Europe PMC | doi


Jakobsen JS, Braun M, Astorga J, Gustafson EH, Sandmann T, Karzynski M, Carlsson P, Furlong EE. (2007)

Temporal ChIP-on-chip reveals Biniou as a universal regulator of the visceral muscle transcriptional network

Genes Dev. 21(19):2448-2460. doi: 10.1101/gad.437607
Europe PMC | doi

Girardot C, Sklyar O, Grosz S, Huber W, Furlong EE. (2007)

CoCo: a web application to display, store and curate ChIP-on-chip data integrated with diverse types of gene expression data

Bioinformatics 23(6):771-773. doi: 10.1093/bioinformatics/btl641
Europe PMC | doi

Sandmann T, Girardot C, Brehme M, Tongprasit W, Stolc V, Furlong EE. (2007)

A core transcriptional network for early mesoderm development in Drosophila melanogaster

Genes Dev. 21(4):436-449. doi: 10.1101/gad.1509007
Europe PMC | doi

Hooper SD, Boué S, Krause R, Jensen LJ, Mason CE, Ghanim M, White KP, Furlong EE, Bork P. (2007)

Identification of tightly regulated groups of genes during Drosophila melanogaster embryogenesis

Mol. Syst. Biol. 3:72. doi: 10.1038/msb4100112
Europe PMC | doi