Axel Visel

 Education

• Ph.D. (Dr. rer. nat.) in Biology, Max Planck Institute, Germany
• Postdoctoral training, Lawrence Berkeley National Laboratory, Berkeley, CA

Summary

Dr. Visel joined the DOE Joint Genome Institute in 2010.  As the Deputy for Science Programs, he focuses on the development and implementation of strategic initiatives at the JGI. Dr. Visel received his Ph.D. in 2004 from the Max Planck Institute in Hanover, Germany, where he developed novel tools for large-scale in situ gene expression analysis in multicellular organisms.  During his postdoctoral training at Lawrence Berkeley National Laboratory, he developed and applied novel computational and experimental sequence-based methods for elucidating the gene regulatory landscape of vertebrate genomes, which led to the discovery of thousands of genetic switches implicated in developmental and disease processes in the human genome.  In addition to his appointment at the DOE Joint Genome Institute, Dr. Visel also holds appointments as a Senior Staff Scientist at Lawrence Berkeley National Laboratory and as an Adjunct Professor at the School of Natural Sciences at the University of California, Merced. Dr. Visel also served as JGI Interim Director from March 2016 – March 2017.

Awards and Honors

2014 LBNL Director’s Award for Exceptional Achievement, 2009 LBNL Outstanding Performance Award, 2006 AHA Lievre Fellowship Award, 2000 Boehringer Ingelheim Fellow.

Reviewer for major funding agencies and journals including National Institutes of Health, American Heart Association, Medical Research Council (UK), Nature, Cell, Nature Genetics, Nature Methods, Genome Research (Editorial Board), Cell Reports, Nature Structural and Molecular Biology, PLoS Computational Biology, Nucleic Acids Research.

Over 80 publications in peer-reviewed journals including Nature, Science, Cell, and Nature Genetics.

Selected Publications

• Ngan CY, Wong CH, Choi C, Yoshinaga Y, Louie K, Jia J, Chen C, Bowen B, Cheng H, Leonelli L, Kuo R, Baran R, García-Cerdán JG, Pratap A, Wang M, Lim J, Tice H, Daum C, Xu J, Northen T, Visel A, Bristow J, Niyogi KK, Wei CL (2015). Lineage-specific chromatin signatures reveal a regulator of lipid metabolism in microalgae. Nature Plants1: 15107
• Lupiáñez DG, Kraft K, Heinrich V, Krawitz P, Brancati F, Klopocki E, Horn D, Kayserili H, Opitz JM, Laxova R, Santos-Simarro F, Gilbert-Dussardier B, Wittler L, Borschiwer M, Haas SA, Osterwalder M, Franke M, Timmermann B, Hecht J, Spielmann M, Visel A, Mundlos S. (2015). Disruptions of topological chromatin domains cause pathogenic rewiring of gene-enhancer interactions. Cell 161, 1012-25
• Ivanova NN, Schwientek P, Tripp HJ, Rinke C, Pati A, Huntemann M, Visel A, Woyke T, Kyrpides NC, Rubin EM (2014).  Stop codon reassignments in the wild.  Science344:909-13
• Nord AS, Blow MJ, Attanasio C, Akiyama JA, Holt A, Hosseini R, Phouanenavong S, Plajzer-Frick I, Shoukry M, Afzal V, Rubenstein JL, Rubin EM, Pennacchio LA*, Visel A* (2013). Rapid and Pervasive Changes in Genome-wide Enhancer Usage during Mammalian Development. Cell 155, 1521-31.
• Attanasio C, Nord AS, Zhu Y, Blow MJ, Li Z, Liberton DK, Morrison H, Plajzer-Frick I, Holt A, Hosseini R, Phouanenavong S, Akiyama JA, Shoukry M, Afzal V, Rubin EM, FitzPatrick DR, Ren B, Hallgrímsson B, Pennacchio LA, Visel A (2013). Fine tuning of craniofacial morphology by distant-acting enhancers. Science 342, 1241006.
• Visel A*, Taher L, Girgis H, May D, Golonzhka O, Hoch RV, McKinsey GL, Pattabiraman K, Silberberg SN, Blow MJ, Hansen DV, Nord AS, Akiyama JA, Holt A, Hosseini R, Phouanenavong S, Plajzer-Frick I, Shoukry M, Afzal V, Kaplan T, Kriegstein AR, Rubin EM, Ovcharenko I, Pennacchio LA, Rubenstein JL (2013, * corresponding author). A high-resolution enhancer atlas of the developing telencephalon. Cell 152, 895-908.
• Gross SM, Martin JA, Simpson J, Abraham-Juarez MJ, Wang Z, Visel A (2013). De novo transcriptome assembly of drought tolerant CAM plants, Agave deserti and Agave tequilana. BMC Genomics 14, 563.
• May D, Blow MJ, Kaplan T, McCulley DJ, Jensen BC, Akiyama JA, Holt A, Plajzer-Frick I, Shoukry M, Wright C, Afzal V, Simpson PC, Rubin EM, Black BL, Bristow J, Pennacchio LA*, Visel A* (2012). Large-scale discovery of enhancers from human heart tissue. Nature Genetics 44, 89-93.
• Hess M, Sczyrba A, Egan R, Kim TW, Chokhawala H, Schroth G, Luo S, Clark DS, Chen F, Zhang T, Mackie RI, Pennacchio LA, Tringe SG, Visel A, Woyke T, Wang Z, Rubin EM (2011). Metagenomic discovery of biomass-degrading genes and genomes from cow rumen. Science 331, 463-7.
• Visel A, Zhu Y, May D, Afzal V, Gong E, Attanasio C, Blow MJ, Cohen JC, Rubin EM, Pennacchio LA (2010). Targeted deletion of the 9p21 non-coding coronary artery disease risk interval in mice. Nature 464, 409-12.
• Visel A, Blow MJ, Li Z, Zhang T, Akiyama JA, Holt A, Plajzer-Frick I, Shoukry M, Wright C, Chen F, Afzal V, Ren B, Rubin EM, Pennacchio LA (2009). ChIP-seq accurately predicts tissue-specific activity of enhancers. Nature 457, 854-8.