EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany

Biography

  • PhD 2011, EMBL-EBI and Cambridge University.
    Postdoctoral research fellow, Stanford University.
    Group leader at EMBL since 2014.
    Joint appointment with the Genome Biology Unit and with EMBL-EBI.
    Group leader in the Molecular Medicine Partnership Unit.

Publications

Total: 18 publication(s)

2018

Ruiz-Velasco M, Zaugg J. (2018)

Structure meets function: How chromatin organisation conveys functionality.

Curr Opin Syst Biol 1:129-136. doi: 10.1016/j.coisb.2017.01.003
doi


2017

Ruiz-Velasco M, Kumar M, Lai MC, Bhat P, Solis-Pinson AB, Reyes A, Kleinsorg S, Noh KM, Gibson TJ, Zaugg JB. (2017)

CTCF-Mediated Chromatin Loops between Promoter and Gene Body Regulate Alternative Splicing across Individuals.

Cell Syst 5(6) doi: 10.1016/j.cels.2017.10.018
Europe PMC | doi

Saha A, Kim Y, Gewirtz ADH, Jo B, Gao C, McDowell IC, McDowell IC, Engelhardt BE, Battle A. (2017)

Co-expression networks reveal the tissue-specific regulation of transcription and splicing.

Genome Res 27(11):1843-1858. doi: 10.1101/gr.216721.116
Europe PMC | doi

Yang F, Wang JB, Pierce BL, Chen LS. (2017)

Identifying cis-mediators for trans-eQTLs across many human tissues using genomic mediation analysis

Genome Res. 27(11):1859-1871. doi: 10.1101/gr.216754.116
Europe PMC | doi

Lai MC, Bechy AL, Denk F, Collins E, Gavriliouk M, Zaugg JB, Ryan BJ, Wade-Martins R, Caffrey TM. (2017)

Haplotype-specific MAPT exon 3 expression regulated by common intronic polymorphisms associated with Parkinsonian disorders.

Mol Neurodegener 12(1) doi: 10.1186/s13024-017-0224-6
Europe PMC | doi

Aguet F, Brown AA, Castel SE, Davis JR, He Y, Jo B, Mohammadi P, Park Y, Parsana P, Segre AV, Strober BJ, Zappala Z, Cummings BB, Gelfand ET, Hadley K, Huang KH, Lek M, Li X, Nedzel JL, Nguyen DY, Noble MS, Sullivan TJ, Tukiainen T, MacArthur DG, Getz G, Management NP, Addington A, Guan P, Koester S, Little AR, Lockhart NC, Moore HM, Rao A, Struewing JP, Volpi S, Collection B, Brigham LE, Hasz R, Hunter M, Johns C, Johnson M, Kopen G, Leinweber WF, Lonsdale JT, McDonald A, Mestichelli B, Myer K, Roe B, Salvatore M, Shad S, Thomas JA, Walters G, Washington M, Wheeler J, Bridge J, Foster BA, Gillard BM, Karasik E, Kumar R, Miklos M, Moser MT, Jewell SD, Montroy RG, Rohrer DC, Valley D, Mash DC, Davis DA, Sobin L, Barcus ME, Branton PA, Grp EMW, Abell NS, Balliu B, Delaneau O, Fresard L, Gamazon ER, Garrido-Martin D, Gewirtz ADH, Gliner G, Gloudemans MJ, Han B, He AZ, Hormozdiari F, Li X, Liu B, Kang EY, McDowell IC, Ongen H, Palowitch JJ, Peterson CB, Quon G, Ripke S, Saha A, Shabalin AA, Shimko TC, Sul JH, Teran NA, Tsang EK, Zhang H, Zhou YH, Bustamante CD, Cox NJ, Guigo R, Kellis M, McCarthy MI, Conrad DF, Eskin E, Li G, Nobel AB, Sabatti C, Stranger BE, Wen X, Wright FA, Ardlie KG, Dermitzakis ET, Lappalainen T, Battle A, Brown CD, Engelhardt BE, Montgomery SB, Aguet F, Ardlie KG, Cummings BB, Gelfand ET, Getz G, Hadley K, Handsaker RE, Huang KH, Kashin S, Karczewski KJ, Lek M, Li X, MacArthur DG, Nedzel JL, Nguyen DT, Noble MS, Segre AV, Trowbridge CA, Tukiainen T, Abell NS, Balliu B, Barshir R, Basha O, Battle A, Bogu GK, Brown A, Brown CD, Castel SE, Chen LS, Chiang C, Conrad DF, Cox NJ, Damani FN, Davis JR, Delaneau O, Dermitzakis ET, Engelhardt BE, Eskin E, Ferreira PG, Fresard L, Gamazon ER, Garrido-Martin D, Gewirtz ADH, Gliner G, Gloudemans MJ, Guigo R, Hall IM, Han B, He Y, Hormozdiari F, Howald C, Im HK, Jo B, Kang EY, Kim Y, Kim-Hellmuth S, Lappalainen T, Li G, Li X, Liu B, Mangul S, McCarthy MI, McDowell IC, Mohammadi P, Monlong J, Montgomery SB, Munoz-Aguirre M, Ndungu AW, Nicolae DL, Nobel AB, Oliva M, Ongen H, Palowitch JJ, Panousis N, Papasaikas P, Park Y, Parsana P, Payne AJ, Peterson CB, Quan J, Reverter F, Sabatti C, Saha A, Sammeth M, Scott AJ, Shabalin AA, Sodaei R, Stephens M, Stranger BE, Strober BJ, Sul JH, Tsang EK, Urbut S, De Bunt MV, Wang G, Wen X, Wright FA, Xi HS, Yeger-Lotem E, Zappala Z, Zaugg JB, Zhou YH, Akey JM, Bates D, Chan J, Chen LS, Claussnitzer M, Demanelis K, Diegel M, Doherty JA, Feinberg AP, Fernando MS, Halow J, Hansen KD, Haugen E, Hickey PF, Hou L, Jasmine F, Jian R, Jiang L, Johnson A, Kaul R, Kellis M, Kibriya MG, Lee K, Li JB, Li Q, Li X, Lin J, Lin S, Linder S, Linke C, Liu Y, Maurano MT, Molinie B, Montgomery SB, Nelson J, Neri FJ, Oliva M, Park Y, Pierce BL, Rinaldi NJ, Rizzardi LF, Sandstrom R, Skol A, Smith KS, Snyder MP, Stamatoyannopoulos J, Stranger BE, Tang H, Tsang EK, Wang L, Wang M, Van Wittenberghe N, Wu F, Zhang R, Fund NC, Nierras CR, Nci N, Branton PA, Carithers LJ, Guan P, Moore HM, Rao A, Vaught JB, Nhgri N, Gould SE, Lockart NC, Martin C, Struewing JP, Volpi S, Nimh N, Addington AM, Koester SE, Nida N, Little AR, Brigham LE, Hasz R, Hunter M, Johns C, Johnson M, Kopen G, Leinweber WF, Lonsdale JT, McDonald A, Mestichelli B, Myer K, Roe B, Salvatore M, Shad S, Thomas JA, Walters G, Washington M, Wheeler J, Bridge J, Foster BA, Gillard BM, Karasik E, Kumar R, Miklos M, Moser MT, Jewell SD, Montroy RG, Rohrer DC, Valley DR, Davis DA, Mash DC, Undale AH, Smith AM, Tabor DE, Roche NV, McLean JA, Vatanian N, Robinson KL, Sobin L, Barcus ME, Valentino KM, Qi L, Hunter S, Hariharan P, Singh S, Um KS, Matose T, Tomaszewski MM, Study E, Barker LK, Mosavel M, Siminoff LA, Traino HM, Flicek P, Juettemann T, Ruffier M, Sheppard D, Taylor K, Trevanion SJ, Zerbino DR, Craft B, Goldman M, Haeussler M, Kent WJ, Lee CM, Paten B, Rosenbloom KR, Vivian J, Zhu J. (2017)

Genetic effects on gene expression across human tissues

NATURE 550(7675):204. doi: 10.1038/nature24277
Europe PMC | doi

Li X, Kim Y, Sang EKT, Davis JR, Damani FN, Hiang CC, Hess GT, Zappala Z, Strober BJ, Scott AJ, Li A, Ganna A, Assik MCB, Merker JD, Hall IM, Attle AB, Montgomery SB. (2017)

The impact of rare variation on gene expression across tissues.

Nature 550(7675):239-243. doi: 10.1038/nature24267
Europe PMC | doi

Tan MH, Li Q, Shanmugam R, Piskol R, Kohler J, Young AN, Liu KI, Zhang R, Amaswami GR, Ariyoshi K, Gupte A, Keegan LP, George CX, Amu AR, Huang N, Pollina EA, Leeman DS, Ustighi AR, Goh YPS, Hawla AC, Del Sal G, Peltz G, Runet AB, Onrad DFC, Samuel CE, O'Connell MA, Walkley CR, Nishikura K, Li JB. (2017)

Dynamic landscape and regulation of RNA editing in mammals

Nature 550(7675):249-254. doi: 10.1038/nature24041
Europe PMC | doi

Tukiainen T, Villani AC, Yen A, Rivas MA, Marshall JL, Satija R, Aguirre M, Gauthier L, Fleharty M, Kirby A, Ummings BBC, Astel SEC, Karczewski KJ, Aguet F, Byrnes A, Lappalainen T, Regev A, Ardlie KG, Hacohen N, MacArthur DG. (2017)

Landscape of X chromosome inactivation across human tissues.

Nature 550(7675):244-248. doi: 10.1038/nature24265
Europe PMC | doi


2016

Cakiroglu SA, Zaugg JB, Luscombe NM. (2016)

Backmasking in the yeast genome: encoding overlapping information for protein-coding and RNA degradation.

Nucleic Acids Res. 44(17):8065-8072. doi: 10.1093/nar/gkw683
Europe PMC | doi

Arnold C, Bhat P, Zaugg JB. (2016)

SNPhood: investigate, quantify and visualise the epigenomic neighbourhood of SNPs using NGS data.

Bioinformatics 32(15):2359-2360. doi: 10.1093/bioinformatics/btw127
Europe PMC | doi

Ignatiadis N, Klaus B, Zaugg JB, Huber W. (2016)

Data-driven hypothesis weighting increases detection power in genome-scale multiple testing.

Nat. Methods 13(7):577-580. doi: 10.1038/nmeth.3885
Europe PMC | doi

Zaugg LK, Lenherr P, Zaugg JB, Weiger R, Krastl G. (2016)

Influence of the bleaching interval on the luminosity of long-term discolored enamel-dentin discs.

Clin Oral Investig 20(3):451-458. doi: 10.1007/s00784-015-1545-x
Europe PMC | doi


2015

Grubert F, Zaugg JB, Kasowski M, Ursu O, Spacek DV, Martin AR, Greenside P, Srivas R, Phanstiel DH, Pekowska A, Heidari N, Euskirchen G, Huber W, Pritchard JK, Bustamante CD, Steinmetz LM, Kundaje A, Snyder M. (2015)

Genetic Control of Chromatin States in Humans Involves Local and Distal Chromosomal Interactions.

Cell 162(5):1051-1065. doi: 10.1016/j.cell.2015.07.048
Europe PMC | doi


2014

Castelnuovo M, Zaugg JB, Guffanti E, Maffioletti A, Camblong J, Xu Z, Clauder-Münster S, Steinmetz LM, Luscombe NM, Stutz F. (2014)

Role of histone modifications and early termination in pervasive transcription and antisense-mediated gene silencing in yeast.

Nucleic Acids Res. 42(7):4348-4362. doi: 10.1093/nar/gku100
Europe PMC | doi


2013

Kasowski M, Kyriazopoulou-Panagiotopoulou S, Grubert F, Zaugg JB, Kundaje A, Liu Y, Boyle AP, Zhang QC, Zakharia F, Spacek DV, Li J, Xie D, Olarerin-George A, Steinmetz LM, Hogenesch JB, Kellis M, Batzoglou S, Snyder M. (2013)

Extensive variation in chromatin states across humans

Science 342(6159):750-752. doi: 10.1126/science.1242510
Europe PMC | doi


2012

Tan-Wong SM, Zaugg JB, Camblong J, Xu Z, Zhang DW, Mischo HE, Ansari AZ, Luscombe NM, Steinmetz LM, Proudfoot NJ. (2012)

Gene loops enhance transcriptional directionality

Science 338(6107):671-675. doi: 10.1126/science.1224350
Europe PMC | doi

Zaugg JB, Luscombe NM. (2012)

A genomic model of condition-specific nucleosome behavior explains transcriptional activity in yeast

Genome Res. 22(1):84-94. doi: 10.1101/gr.124099.111
Europe PMC | doi