Beyond the exome

DFG funded Research Group

People of Beyond the exome

Prof. Dr.-Ing. Uwe Ohler

Testbeschreibung Institutes of Biology and Computer Science
Humboldt-Universität zu Berlin
Unter den Linden 6
D-10099 Berlin, Germany

Phone: +49 (0)30 9406 1810
FAX: +49 (0)30 9406 1752

Uwe Ohler, Dr.-Ing, has been a senior group leader at the Max Delbrueck Center in Berlin since 2012 and is appointed as full professor in the Department of Biology (primary) and the Department of Computer Science (secondary) at Humboldt University Berlin. He studied computer science with a minor in biology at the University of Erlangen-Nuremberg in Germany, graduating in 1996. While being a student, he became fascinated with computational biology during a research internship involving computational DNA sequence analyis. In 1998, he started his PhD research at the Chair for Pattern Recognition (Professor Heinrich Niemann) at the same university. He was a Boehringer Ingelheim pre-doctoral fellow from 1998-2001 and a visiting researcher with the Berkeley Drosophila Genome Project (Professor Gerald Rubin). He obtained his PhD with distinction in 2002 for the McPromoter system for computational identification of promoters in eukaryotic genomes. Before returning to Germany, Uwe lived in the US for more than a decade and followed his interests in gene regulation and applied machine learning. From 2002-2004, he worked as a postdoctoral researcher in the Department of Biology (Professor Chris Burge) at the Massa-chusetts Institute of Technology, where he was also a member of the cross-departmental Computational and Systems Biology Initiative. In 2005, he joined the faculty of the Institute of Genome Sciences & Policy at Duke University, Durham NC, USA, where he received tenure in 2011. He taught in the cross-departmental graduate program in Computational Biology & Bioinformatics, and was core faculty of the Duke Center for Systems Biology. During this time, he received fellowships from the Alfred P Sloan Foundation, as well as HFSP, NSF CAREER, and NIH Transformative Research awards. In Berlin, his group now combines experimental high-throughput genomics lab work with computational approaches. Members of the group utilize the resulting large datasets to gain insights on transcriptional and post-transcriptional regulatory mechanisms. Current research projects are funded by multiple BMBF and DFG awards. Uwe is a member of the Berlin Center for Machine Learning ( and co-director of two cross-institutional graduate training programs, the Helmholtz Einstein International Berlin Research School in Data Science ( and the DFG-funded International Research Training Group with Duke University on “Dissecting and Re-Engineering the Regulatory Genome” (

Publications (selection)

Mukherjee N, Calviello L, Hirsekorn A, de Pretis S, Pelizzola M, Ohler U. Integrative classification of human coding and noncoding genes through RNA metabolism profiles. Nat Struct Mol Biol 2017;24:86-96.

Calviello L, Mukherjee N, Wyler E, Zauber H, Hirsekorn A, Selbach M, Landthaler M, Obermayer B, Ohler U. Detecting actively translated open reading frames in ribosome profiling data. Nat Methods 2016;13:165-70.

Duttke S, Lacadie SA, Ibrahim MM, Glass CK, Corcoran DL, Benner C, Heinz S, Kadonaga JT*, Ohler U*. Human promoters are intrinsically directional. Mol Cell 2015;57:674-684

Natarajan A, Yardimci GG, Sheffield NC, Crawford GE*, Ohler U*. Predicting cell-type specific gene expres-sion from regions of open chromatin. Genome Res 2012;22:1711-1722

Ascano M Jr, Mukherjee N, Bandaru P, Miller JB, Nusbaum JD, Corcoran DL, Langlois C, Munschauer M, Dewell S, Hafner M, Williams Z, Ohler U*, Tuschl T*. FMR1 targets distinct mRNA sequence elements to regulate pro-tein expression. Nature 2012;492:382-386