Browse by Research Team

2024

Genome-wide screening identifies Trim33 as an essential regulator of dendritic cell differentiation.
Tiniakou, I. and Hsu, P.F. and Lopez-Zepeda, L.S. and Garipler, G. and Esteva, E. and Adams, N.M. and Jang, G. and Soni, C. and Lau, C.M. and Liu, F. and Khodadadi-Jamayran, A. and Rodrick, T.C. and Jones, D. and Tsirigos, A. and Ohler, U. and Bedford, M.T. and Nimer, S.D. and Kaartinen, V. and Mazzoni, E.O. and Reizis, B.
Science Immunology 9 (94): eadi1023. 12 April 2024

DCGG: drug combination prediction using GNN and GAE.
Ziaee, S.S. and Rahmani, H. and Tabatabaei, M. and Vlot, A.H.C. and Bender, A.
Progress in Artificial Intelligence 13 : 17-30. March 2024

The artificial intelligence-based model ANORAK improves histopathological grading of lung adenocarcinoma.
Pan, X. and AbdulJabbar, K. and Coelho-Lima, J. and Grapa, A.I. and Zhang, H. and Cheung, A.H.K. and Baena, J. and Karasaki, T. and Wilson, C.R. and Sereno, M. and Veeriah, S. and Aitken, S.J. and Hackshaw, A. and Nicholson, A.G. and Jamal-Hanjani, M. and Swanton, C. and Yuan, Y. and Le Quesne, J. and Moore, D.A.
Nature Cancer 5 (2): 347-363. February 2024

2023

Stress-induced nuclear speckle reorganization is linked to activation of immediate early gene splicing.
Sung, H.M. and Schott, J. and Boss, P. and Lehmann, J.A. and Hardt, M.R. and Lindner, D. and Messens, J. and Bogeski, I. and Ohler, U. and Stoecklin, G.
Journal of Cell Biology 222 (12): e202111151. 4 December 2023

Toward identification of functional sequences and variants in noncoding DNA.
Monti, R. and Ohler, U.
Annual Review of Biomedical Data Science 6 : 191-210. August 2023

Antibodies against endogenous retroviruses promote lung cancer immunotherapy.
Ng, K.W. and Boumelha, J. and Enfield, K.S.S. and Almagro, J. and Cha, H. and Pich, O. and Karasaki, T. and Moore, D.A. and Salgado, R. and Sivakumar, M. and Young, G. and Molina-Arcas, M. and de Carné Trécesson, S. and Anastasiou, P. and Fendler, A. and Au, L. and Shepherd, S.T.C. and Martínez-Ruiz, C. and Puttick, C. and Black, J.R.M. and Watkins, T.B.K. and Kim, H. and Shim, S. and Faulkner, N. and Attig, J. and Veeriah, S. and Magno, N. and Ward, S. and Frankell, A.M. and Al Bakir, M. and Lim, E.L. and Hill, M.S. and Wilson, G.A. and Cook, D.E. and Birkbak, N.J. and Behrens, A. and Yousaf, N. and Popat, S. and Hackshaw, A. and Hiley, C.T. and Litchfield, K. and McGranahan, N. and Jamal-Hanjani, M. and Larkin, J. and Lee, S.H. and Turajlic, S. and Swanton, C. and Downward, J. and Kassiotis, G.
Nature 616 (7957): 563-573. 20 April 2023

Genomic–transcriptomic evolution in lung cancer and metastasis.
Martínez-Ruiz, C. and Black, J.R.M. and Puttick, C. and Hill, M.S. and Demeulemeester, J. and Larose Cadieux, E. and Thol, K. and Jones, T.P. and Veeriah, S. and Naceur-Lombardelli, C. and Toncheva, A. and Prymas, P. and Rowan, A. and Ward, S. and Cubitt, L. and Athanasopoulou, F. and Pich, O. and Karasaki, T. and Moore, D.A. and Salgado, R. and Colliver, E. and Castignani, C. and Dietzen, M. and Huebner, A. and Al Bakir, M. and Tanić, M. and Watkins, T.B.K. and Lim, E.L. and Al-Rashed, A.M. and Lang, D. and Clements, J. and Cook, D.E. and Rosenthal, R. and Wilson, G. A. and Frankell, A.M. and de Carné Trécesson, S. and East, P. and Kanu, N. and Litchfield, K. and Birkbak, N.J. and Hackshaw, A. and Beck, S. and Van Loo, P. and Jamal-Hanjani, M. and McGranahan, N. and Swanton, C.
Nature 616 (7957): 543-552. 20 April 2023

Lung adenocarcinoma promotion by air pollutants.
Hill, W. and Lim, E.L. and Weeden, C.E. and Lee, C. and Augustine, M. and Chen, K. and Kuan, F.C. and Marongiu, F. and Evans, E.J. and Moore, D.A. and Rodrigues, F.S. and Pich, O. and Bakker, B. and Cha, H. and Myers, R. and van Maldegem, F. and Boumelha, J. and Veeriah, S. and Rowan, A. and Naceur-Lombardelli, C. and Karasaki, T. and Sivakumar, M. and De, S. and Caswell, D.R. and Nagano, A. and Black, J.R.M. and Martínez-Ruiz, C. and Ryu, M.H. and Huff, R.D. and Li, S. and Favé, M.J. and Magness, A. and Suárez-Bonnet, A. and Priestnall, S.L. and Lüchtenborg, M. and Lavelle, K. and Pethick, J. and Hardy, S. and McRonald, F.E. and Lin, M.H. and Troccoli, C.I. and Ghosh, M. and Miller, Y.E. and Merrick, D.T. and Keith, R.L. and Al Bakir, M. and Bailey, C. and Hill, M.S. and Saal, L.H. and Chen, Y. and George, A.M. and Abbosh, C. and Kanu, N. and Lee, S.H. and McGranahan, N. and Berg, C.D. and Sasieni, P. and Houlston, R. and Turnbull, C. and Lam, S. and Awadalla, P. and Grönroos, E. and Downward, J. and Jacks, T. and Carlsten, C. and Malanchi, I. and Hackshaw, A. and Litchfield, K. and DeGregori, J. and Jamal-Hanjani, M. and Swanton, C.
Nature 616 (7955): 159-167. 6 April 2023

Brassinosteroid gene regulatory networks at cellular resolution in the Arabidopsis root.
Nolan, T.M. and Vukašinović, N. and Hsu, C.W. and Zhang, J. and Vanhoutte, I. and Shahan, R. and Taylor, I.W. and Greenstreet, L. and Heitz, M. and Afanassiev, A. and Wang, P. and Szekely, P. and Brosnan, A. and Yin, Y. and Schiebinger, G. and Ohler, U. and Russinova, E. and Benfey, P.N.
Science 379 (6639): eadf4721. 31 March 2023

A computational map of the human-SARS-CoV-2 protein-RNA interactome predicted at single-nucleotide resolution.
Horlacher, M. and Oleshko, S. and Hu, Y. and Ghanbari, M. and Cantini, G. and Schinke, P. and Vergara, E.E. and Bittner, F. and Mueller, N.S and Ohler, U. and Moyon, L. and Marsico, A.
NAR Genomics and Bioinformatics 5 (1): lqad010. March 2023

SMITH: spatially constrained stochastic model for simulation of intra-tumour heterogeneity.
Streck, A. and Kaufmann, T.L. and Schwarz, R.F.
Bioinformatics 39 (3): btad102. March 2023

Altered and allele-specific open chromatin landscape reveals epigenetic and genetic regulators of innate immunity in COVID-19.
Zhang, B. and Zhang, Z. and Koeken, V.A.C.M. and Kumar, S. and Aillaud, M. and Tsay, H.C. and Liu, Z. and Kraft, A.R.M. and Soon, C.F. and Odak, I. and Bošnjak, B. and Vlot, A. and Swertz, M.A. and Ohler, U. and Geffers, R. and Illig, T. and Huehn, J. and Saliba, A.E. and Sander, L.E. and Förster, R. and Xu, C.J. and Cornberg, M. and Schulte, L.N. and Li, Y.
Cell Genomics 3 (2): 100232. 8 February 2023

2022

Liam tackles complex multimodal single-cell data integration challenges.
Rautenstrauch, P. and Ohler, U.
bioRxiv : 2022.12.21.521399. 22 December 2022

Protocol for fast scRNA-seq raw data processing using scKB and non-arbitrary quality control with COPILOT.
Hsu, C.W. and Shahan, R. and Nolan, T.M. and Benfey, P.N. and Ohler, U.
STAR Protocols 3 (4): 101729. 16 December 2022

A critical period of translational control during brain development at codon resolution.
Harnett, D. and Ambrozkiewicz, M.C. and Zinnall, U. and Rusanova, A. and Borisova, E. and Drescher, A.N. and Couce-Iglesias, M. and Villamil, G. and Dannenberg, R. and Imami, K. and Münster-Wandowski, A. and Fauler, B. and Mielke, T. and Selbach, M. and Landthaler, M. and Spahn, C.M.T. and Tarabykin, V. and Ohler, U. and Kraushar, M.L.
Nature Structural & Molecular Biology 29 (12): 1277-1290. December 2022

Cluster-independent marker feature identification from single-cell omics data using SEMITONES.
Vlot, A.H.C. and Maghsudi, S. and Ohler, U.
Nucleic Acids Research 50 (18): e107. 14 October 2022

Control of immediate early gene expression by CPEB4-repressor complex-mediated mRNA degradation.
Poetz, F. and Lebedeva, S. and Schott, J. and Lindner, D. and Ohler, U. and Stoecklin, G.
Genome Biology 23 (1): 193. 12 September 2022

Identifying interpretable gene-biomarker associations with functionally informed kernel-based tests in 190,000 exomes.
Monti, R. and Rautenstrauch, P. and Ghanbari, M. and James, A.R. and Kirchler, M. and Ohler, U. and Konigorski, S. and Lippert, C.
Nature Communications 13 (1): 5332. 10 September 2022

SMITH: spatially constrained stochastic model for simulation of intra-tumour heterogeneity.
Streck, A. and Kaufmann, T. and Schwarz, R.F.
bioRxiv : 2022.07.22.501136. 24 July 2022

Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements.
Baranasic, D. and Hörtenhuber, M. and Balwierz, P.J. and Zehnder, T. and Mukarram, A.K. and Nepal, C. and Várnai, C. and Hadzhiev, Y. and Jimenez-Gonzalez, A. and Li, N. and Wragg, J. and D'Orazio, F.M. and Relic, D. and Pachkov, M. and Díaz, N. and Hernández-Rodríguez, B. and Chen, Z. and Stoiber, M. and Dong, M. and Stevens, I. and Ross, S.E. and Eagle, A. and Martin, R. and Obasaju, O. and Rastegar, S. and McGarvey, A.C. and Kopp, W. and Chambers, E. and Wang, D. and Kim, H.R. and Acemel, R.D. and Naranjo, S. and Łapiński, M. and Chong, V. and Mathavan, S. and Peers, B. and Sauka-Spengler, T. and Vingron, M. and Carninci, P. and Ohler, U. and Lacadie, S.A. and Burgess, S.M. and Winata, C. and van Eeden, F. and Vaquerizas, J.M. and Gómez-Skarmeta, J.L. and Onichtchouk, D. and Brown, B.J. and Bogdanovic, O. and van Nimwegen, E. and Westerfield, M. and Wardle, F.C and Daub, C.O. and Lenhard, B. and Müller, F.
Nature Genetics 54 (7): 1037-1050. July 2022

Standardized annotation of translated open reading frames.
Mudge, J.M. and Ruiz-Orera, J. and Prensner, J.R. and Brunet, M.A. and Calvet, F. and Jungreis, I. and Gonzalez, Jo.M. and Magrane, M. and Martinez, T.F. and Schulz, J.F. and Yang, Y.T. and Albà, M.M. and Aspden, J.L. and Baranov, P.V. and Bazzini, A.A. and Bruford, E. and Martin, M.J. and Calviello, L. and Carvunis, A.R. and Chen, J. and Couso, J.P. and Deutsch, E.W. and Flicek, P. and Frankish, A. and Gerstein, M. and Hubner, N. and Ingolia, N.T. and Kellis, M. and Menschaert, G. and Moritz, R.L. and Ohler, U. and Roucou, X. and Saghatelian, A. and Weissman, J.S. and van Heesch, S.
Nature Biotechnology 40 (7): 994–999. July 2022

Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection clusters based on integrated genomic surveillance, outbreak analysis and contact tracing in an urban setting.
Walker, A. and Houwaart, T. and Finzer, P. and Ehlkes, L. and Tyshaieva, A. and Damagnez, M. and Strelow, D. and Duplessis, A. and Nicolai, J. and Wienemann, T. and Tamayo, T. and Kohns Vasconcelos, M. and Hülse, L. and Hoffmann, K. and Lübke, N. and Hauka, S. and Andree, M. and Däumer, M.P. and Thielen, A. and Kolbe-Busch, S. and Göbels, K. and Zotz, R. and Pfeffer, K. and Timm, J. and Dilthey, A.T.
Clinical Infectious Diseases 74 (6): 1039-1046. 15 March 2022

The BTB transcription factors ZBTB11 and ZFP131 maintain pluripotency by repressing pro-differentiation genes.
Garipler, G. and Lu, C. and Morrissey, Al. and Lopez-Zepeda, L.S. and Pei, Y. and Vidal, S.E. and Zen Petisco Fiore, A.P. and Aydin, B. and Stadtfeld, M. and Ohler, U. and Mahony, S. and Sanjana, N.E. and Mazzoni, E.O.
Cell Reports 38 (11): 110524. 15 March 2022

A single-cell Arabidopsis root atlas reveals developmental trajectories in wild-type and cell identity mutants.
Shahan, R. and Hsu, C.W. and Nolan, T.M. and Cole, B.J. and Taylor, I.W. and Greenstreet, L. and Zhang, S. and Afanassiev, A. and Vlot, A.H.C. and Schiebinger, G. and Benfey, P.N. and Ohler, U.
Developmental Cell 57 (4): 543-560. 28 February 2022

Deep learning for prediction of population health costs.
Drewe-Boss, P. and Enders, D. and Walker, J. and Ohler, U.
BMC Medical Informatics and Decision Making 22 (1): 32. 3 February 2022

Intricacies of single-cell multi-omics data integration.
Rautenstrauch, P. and Vlot, A.H.C. and Saran, S. and Ohler, U.
Trends in Genetics 38 (2): 128-139. February 2022

SLM2 is a novel cardiac splicing factor involved in heart failure due to dilated cardiomyopathy.
Boeckel, J.N. and Möbius-Winkler, M. and Müller, M. and Rebs, S. and Eger, N. and Schoppe, L. and Tappu, R. and Kokot, K.E. and Kneuer, J.M. and Gaul, S. and Bordalo, D.M. and Lai, A. and Haas, J. and Ghanbari, M. and Drewe-Boss, P. and Liss, M. and Katus, H.A. and Ohler, U. and Gotthardt, M. and Laufs, U. and Streckfuss-Bömeke, K. and Meder, B.
Genomics Proteomics & Bioinformatics 20 (1): 129-146. February 2022

Simultaneous dimensionality reduction and integration for single-cell ATAC-seq data using deep learning.
Kopp, W. and Akalin, A. and Ohler, U.
Nature Machine Intelligence 4 (2): 162-168. February 2022

Identifying interpretable gene-biomarker associations with functionally informed kernel-based tests in 190,000 exomes.
Monti, R. and Rautenstrauch, P. and Ghanbari, M. and James, A.R. and Ohler, U. and Konigorski, S. and Lippert, C.
bioRxiv : 2021.05.27.444972. 20 January 2022

Single-cell-resolved dynamics of chromatin architecture delineate cell and regulatory states in zebrafish embryos.
McGarvey, A.C. and Kopp, W. and Vučićević, D. and Mattonet, K. and Kempfer, R. and Hirsekorn, A. and Bilić, I. and Gil, M. and Trinks, A. and Merks, A.M. and Panáková, D. and Pombo, A. and Akalin, A. and Junker, J.P. and Stainier, D.Y.R. and Garfield, D. and Ohler, U. and Lacadie, S.A.
Cell Genomics 2 (1): 100083. 13 January 2022

2021

RNF219 attenuates global mRNA decay through inhibition of CCR4-NOT complex-mediated deadenylation.
Poetz, F. and Corbo, J. and Levdansky, Y. and Spiegelhalter, A. and Lindner, D. and Magg, V. and Lebedeva, S. and Schweiggert, J. and Schott, J. and Valkov, E. and Stoecklin, G.
Nature Communications 12 (1): 7175. 9 December 2021

Modeling Structure-Activity Relationship of AMPK Activation.
Drewe, J. and Küsters, E. and Hammann, F. and Kreuter, M. and Boss, P. and Schöning, V.
Molecules 26 (21): 6508. 1 November 2021

How to find genomic regions relevant for gene regulation.
Guo, X. and Ohler, U. and Yildirim, F.
Medizinische Genetik 33 (2): 157-165. 14 August 2021

Ecological factors influence balancing selection on leaf chemical profiles of a wildflower.
Carley, L.N. and Mojica, J.P. and Wang, B. and Chen, C.Y. and Lin, Y.P. and Prasad, K.V.S.K and Chan, E. and Hsu, C.W. and Keith, R. and Nuñez, C.L. and Olson-Manning, C.F. and Rushworth, C.A. and Wagner, M.R. and Wang, J. and Yeh, P.M. and Reichelt, M. and Ghattas, K. and Gershenzon, J. and Lee, C.R. and Mitchell-Olds, T.
Nature Ecology & Evolution 5 : 1135–1144. August 2021

RNA-binding proteins regulate aldosterone homeostasis in human steroidogenic cells.
Fu, R. and Wellman, K. and Baldwin, A. and Rege, J. and Walters, K. and Hirsekorn, A. and Riemondy, K. and Rainey, W.E and Mukherjee, N.
RNA 27 (8): 933-945. August 2021

A comparison of nine machine learning mutagenicity models and their application for predicting pyrrolizidine alkaloids.
Helma, C. and Schöning, V. and Drewe, J. and Boss, P.
Frontiers in Pharmacology 12 : 708050. 22 July 2021

SPLICE-q: a Python tool for genome-wide quantification of splicing efficiency.
de Melo Costa, V.R. and Pfeuffer, J. and Louloupi, A. and Ørom, U.A.V. and Piro, R.M.
BMC Bioinformatics 22 (1): 368. 15 July 2021

Timed global reorganization of protein synthesis during neocortex neurogenesis at codon resolution.
Harnett, D. and Ambrozkiewicz, M.C. and Zinnall, U. and Borisova, E. and Rusanova, A. and Dannenberg, R. and Imami, K. and Münster-Wandowski, A. and Fauler, B. and Mielke, T. and Selbach, M. and Landthaler, M. and Spahn, C.M.T. and Tarabykin, V. and Ohler, U. and Kraushar, M.L.
bioRxiv : 2021.06.23.449626. 24 June 2021

A community-driven roadmap to advance research on translated open reading frames detected by Ribo-seq.
Mudge, J.M. and Ruiz-Orera, J. and Prensner, J.R. and Brunet, M.A. and Gonzalez, J.M. and Magrane, M. and Martinez, T. and Schulz, J.F. and Yang, Y.T. and Albà, M.M. and Baranov, P.V. and Bazzini, A. and Bruford, E. and Martin, M.J. and Carvunis, A.R. and Chen, J. and Couso, J.P. and Flicek, P. and Frankish, A. and Gerstein, M. and Hubner, N. and Ingolia, N.T. and Menschaert, G. and Ohler, U. and Roucou, X. and Saghatelian, A. and Weissman, J. and van Heesch, S.
bioRxiv : 2021.06.10.447896. 10 June 2021

Spatio-temporal mRNA tracking in the early zebrafish embryo.
Holler, K. and Neuschulz, A. and Drewe-Boß, P. and Mintcheva, J. and Spanjaard, B. and Arsiè, R. and Ohler, U. and Landthaler, M. and Junker, J.P.
Nature Communications 12 : 3358. 7 June 2021

SARS-CoV-2 infection paralyzes cytotoxic and metabolic functions of the immune cells.
Singh, Y. and Trautwein, C. and Fendel, R. and Krickeberg, N. and Berezhnoy, G. and Bissinger, R. and Ossowski, S. and Salker, M.S. and Casadei, N. and Riess, O.
Heliyon 7 (6): e07147. June 2021

Simultaneous dimensionality reduction and integration for single-cell ATAC-seq data using deep learning.
Kopp, W. and Akalin, A. and Ohler, U.
bioRxiv : 2021.05.11.443540. 12 May 2021

Ythdf is a N6-methyladenosine reader that modulates Fmr1 target mRNA selection and restricts axonal growth in Drosophila.
Worpenberg, L. and Paolantoni, C. and Longhi, S. and Mulorz, M.M. and Lence, T. and Wessels, H.H. and Dassi, E. and Aiello, G. and Sutandy, F.X.R. and Scheibe, M. and Edupuganti, R.R. and Busch, A. and Möckel, M.M. and Vermeulen, M. and Butter, F. and König, J. and Notarangelo, M. and Ohler, U. and Dieterich, C. and Quattrone, A. and Soldano, A. and Roignant, J.Y.
EMBO Journal 40 (4): e104975. 15 February 2021

Inferring time series chromatin states for promoter-enhancer pairs based on Hi-C data.
Miko, H. and Qiu, Y. and Gaertner, B. and Sander, M. and Ohler, U.
BMC Genomics 22 (1): 84. 28 January 2021

Protein synthesis in the developing neocortex at near-atomic resolution reveals Ebp1-mediated neuronal proteostasis at the 60S tunnel exit.
Kraushar, M.L. and Krupp, F. and Harnett, D. and Turko, P. and Ambrozkiewicz, M.C. and Sprink, T. and Imami, K. and Günnigmann, M. and Zinnall, U. and Vieira-Vieira, C.H. and Schaub, T. and Münster-Wandowski, A. and Bürger, J. and Borisova, E. and Yamamoto, H. and Rasin, M.R. and Ohler, U. and Beule, D. and Mielke, T. and Tarabykin, V. and Landthaler, M. and Kramer, G. and Vida, I. and Selbach, M. and Spahn, C.M.T.
Molecular Cell 81 (2): 304-322. 21 January 2021

Disease severity-specific neutrophil signatures in blood transcriptomes stratify COVID-19 patients.
Aschenbrenner, A.C. and Mouktaroudi, M. and Krämer, B. and Oestreich, M. and Antonakos, N. and Nuesch-Germano, M. and Gkizeli, K. and Bonaguro, L. and Reusch, N. and Baßler, K. and Saridaki, M. and Knoll, R. and Pecht, T. and Kapellos, T.S. and Doulou, S. and Kröger, C. and Herbert, M. and Holsten, L. and Horne, A. and Gemünd, I.D. and Rovina, N. and Agrawal, S. and Dahm, K. and van Uelft, M. and Drews, A. and Lenkeit, L. and Bruse, N. and Gerretsen, J. and Gierlich, J. and Becker, M. and Händler, K. and Kraut, M. and Theis, H. and Mengiste, S. and Domenico, E. and Schulte-Schrepping, J. and Seep, L. and Raabe, J. and Hoffmeister, C. and ToVinh, M. and Keitel, V. and Rieke, G. and Talevi, V. and Skowasch, D. and Aziz, N.A. and Pickkers, P. and van de Veerdonk, F.L. and Netea, M.G. and Schultze, J.L. and Kox, M. and Breteler, M.M.B. and Nattermann, J. and Koutsoukou, A. and Giamarellos-Bourboulis, E.J. and Ulas, T.
Genome Medicine 13 (1): 7. 13 January 2021

Genome-wide analysis of actively translated open reading frames using riboTaper/ORFquant.
Harnett, D. and Meerdink, E. and Calviello, L. and Sydow, D. and Ohler, U.
Methods in Molecular Biology 2252 : 331-346. 2021

2020

Longitudinal multi-omics analyses identify responses of megakaryocytes, erythroid cells, and plasmablasts as hallmarks of severe COVID-19.
Bernardes, J.P. and Mishra, N. and Tran, F. and Bahmer, T. and Best, L. and Blase, J.I. and Bordoni, D. and Franzenburg, J. and Geisen, U. and Josephs-Spaulding, J. and Köhler, P. and Künstner, A. and Rosati, E. and Aschenbrenner, A.C. and Bacher, P. and Baran, N. and Boysen, T. and Brandt, B. and Bruse, N. and Dörr, J. and Dräger, A. and Elke, G. and Ellinghaus, D. and Fischer, J. and Forster, M. and Franke, A. and Franzenburg, S. and Frey, N. and Friedrichs, A. and Fuß, J. and Glück, A. and Hamm, J. and Hinrichsen, F. and Hoeppner, M.P. and Imm, S. and Junker, R. and Kaiser, S. and Kan, Y.H. and Knoll, R. and Lange, C. and Laue, G. and Lier, C. and Lindner, M. and Marinos, G. and Markewitz, R. and Nattermann, J. and Noth, R. and Pickkers, P. and Rabe, K.F. and Renz, A. and Röcken, C. and Rupp, J. and Schaffarzyk, A. and Scheffold, A. and Schulte-Schrepping, J. and Schunk, D. and Skowasch, D. and Ulas, T. and Wandinger, K.P. and Wittig, M. and Zimmermann, J. and Busch, H. and Hoyer, B.F. and Kaleta, C. and Heyckendorf, J. and Kox, M. and Rybniker, J. and Schreiber, S. and Schultze, J.L. and Rosenstiel, P.
Immunity 53 (6): 1296-1314. 15 December 2020

Lineage-resolved enhancer and promoter usage during a time course of embryogenesis.
Reddington, J.P. and Garfield, D.A. and Sigalova, O.M. and Karabacak Calviello, A. and Marco-Ferreres, R. and Girardot, C. and Viales, R.R. and Degner, J.F. and Ohler, U. and Furlong, E.E.M.
Developmental Cell 55 (5): 648-664. 7 December 2020

Using gradient boosting with stability selection on health insurance claims data to identify disease trajectories in chronic obstructive pulmonary disease.
Ploner, T. and Heß, S. and Grum, M. and Drewe-Boss, P. and Walker, J.
Statistical Methods in Medical Research 29 (12): 3684-3694. 1 December 2020

The BTB transcription factors ZBTB11 and ZFP131 maintain pluripotency by pausing POL II at pro-differentiation genes.
Garipler, G. and Lu, C. and Morrissey, A. and Lopez-Zepeda, L.S. and Vidal, S.E. and Aydin, B. and Stadtfeld, M. and Ohler, U. and Mahony, S. and Sanjana, N.E. and Mazzoni, E.O.
bioRxiv : 2020.11.23.391771. 23 November 2020

Spatio-temporal mRNA dynamics in the early zebrafish embryo.
Holler, K. and Neuschulz, A. and Drewe-Boß, P. and Mintcheva, J. and Spanjaard, B. and Arsiè, R. and Ohler, U. and Landthaler, M. and Junker, J.P.
bioRxiv : 020.11.19.389809. 20 November 2020

SEMITONES: Single-cEll Marker IdentificaTiON by Enrichment Scoring.
Vlot, A.H.C. and Maghsudi, S. and Ohler, U.
bioRxiv : 2020.11.17.386664. 18 November 2020

SPLICE-q: a Python tool for genome-wide quantification of splicing efficiency.
Costa, V.R.M. and Pfeuffer, J. and Louloupi, A. and Ørom, U.A.V. and Piro, R.M.
bioRxiv : 2020.10.12.318808. 12 October 2020

The chloroplast RNA binding protein CP31A has a preference for mRNAs encoding the subunits of the chloroplast NAD(P)H dehydrogenase complex and is required for their accumulation.
Lenzen, B. and Rühle, T. and Lehniger, M.K. and Okuzaki, A. and Labs, M. and Muino, J.M. and Ohler, U. and Leister, D. and Schmitz-Linneweber, C.
International Journal of Molecular Sciences 21 (16): 5633. 6 August 2020

Quantification of translation uncovers the functions of the alternative transcriptome.
Calviello, L. and Hirsekorn, A. and Ohler, U.
Nature Structural & Molecular Biology 27 (8): 717-725. August 2020

Deep learning for genomics using Janggu.
Kopp, W. and Monti, R. and Tamburrini, A. and Ohler, U. and Akalin, A.
Nature Communications 11 (1): 3488. 13 July 2020

A single cell Arabidopsis root atlas reveals developmental trajectories in wild type and cell identity mutants.
Shahan, R. and Hsu, C.W. and Nolan, T.M. and Cole, B.J. and Taylor, I.W. and Vlot, A.H.C. and Benfey, P.N. and Ohler, U.
bioRxiv : 2020.06.29.178863. 30 June 2020

Single-cell-resolved dynamics of chromatin architecture delineate cell and regulatory states in wildtype and cloche/npas4l mutant zebrafish embryos.
McGarvey, A.C. and Kopp, W. and Vučićević, D. and Kempfer, R. and Mattonet, K. and Hirsekorn, A. and Bilić, I. and Trinks, A. and Merks, A.M. and Panáková, D. and Pombo, A. and Akalin, A. and Junker, J.P. and Stainier, D.Y.R. and Garfield, D. and Ohler, U. and Lacadie, S.A.
bioRxiv : 2020.06.26.173377. 26 June 2020

Towards a deeper annotation of human lncRNAs.
Szcześniak, M.W. and Wanowska, E. and Mukherjee, N. and Ohler, U. and Makałowska, I.
Biochimica et Biophysica Acta - Gene Regulatory Mechanisms 1863 (4): 194385. April 2020

Deep learning for prediction of population health costs.
Drewe-Boss, P. and Enders, D. and Walker, J. and Ohler, U.
arXiv : 2003.03466. 10 March 2020

Integrated proteogenomic deep sequencing and analytics accurately identify non-canonical peptides in tumor immunopeptidomes.
Chong, C. and Müller, M. and Pak, H.S. and Harnett, D. and Huber, F. and Grun, D. and Leleu, M. and Auger, A. and Arnaud, M. and Stevenson, B.J. and Michaux, J. and Bilic, I. and Hirsekorn, A. and Calviello, L. and Simó-Riudalbas, L. and Planet, E. and Lubiński, J. and Bryśkiewicz, M. and Wiznerowicz, M. and Xenarios, I. and Zhang, L. and Trono, D. and Harari, A. and Ohler, U. and Coukos, G. and Bassani-Sternberg, M.
Nature Communications 11 (1): 1293. 10 March 2020

The architecture of protein synthesis in the developing neocortex at near-atomic resolution reveals Ebp1-mediated neuronal proteostasis at the 60S tunnel exit.
Kraushar, M.L. and Krupp, F. and Turko, P. and Ambrozkiewicz, M.C. and Sprink, T. and Imami, K. and Vieira-Vieira, C.H. and Schaub, T. and Harnett, D. and Münster-Wandowski, A. and Bürger, J. and Zinnall, U. and Borisova, E. and Yamamoto, H. and Rasin, M.R. and Beule, D. and Landthaler, M. and Mielke, T. and Tarabykin, V. and Vida, I. and Selbach, M. and Spahn, C.M.T.
bioRxiv : 2020.02.08.939488. 10 February 2020

Deep neural networks for interpreting RNA-binding protein target preferences.
Ghanbari, M. and Ohler, U.
Genome Research 30 (2): 214-226. February 2020

A conserved noncoding locus regulates random monoallelic Xist expression across a topological boundary.
Galupa, R. and Nora, E.P. and Worsley-Hunt, R. and Picard, C. and Gard, C. and van Bemmel, J.G. and Servant, N. and Zhan, Y. and El Marjou, F. and Johanneau, C. and Diabangouaya, P. and Le Saux, A. and Lameiras, S. and Pipoli da Fonseca, J. and Loos, F. and Gribnau, J. and Baulande, S. and Ohler, U. and Giorgetti, L. and Heard, E.
Molecular Cell 77 (2): 352-367. 16 January 2020

Extrachromosomal circular DNA drives oncogenic genome remodeling in neuroblastoma.
Koche, R.P. and Rodriguez-Fos, E. and Helmsauer, K. and Burkert, M. and MacArthur, I.C. and Maag, J. and Chamorro, R. and Munoz-Perez, N. and Puiggròs, M. and Dorado Garcia, H. and Bei, Y. and Röefzaad, C. and Bardinet, V. and Szymansky, A. and Winkler, A. and Thole, T. and Timme, N. and Kasack, K. and Fuchs, S. and Klironomos, F. and Thiessen, N. and Blanc, E. and Schmelz, K. and Künkele, A. and Hundsdörfer, P. and Rosswog, C. and Theissen, J. and Beule, D. and Deubzer, H. and Sauer, S. and Toedling, J. and Fischer, M. and Hertwig, F. and Schwarz, R.F. and Eggert, A. and Torrents, D. and Schulte, J.H. and Henssen, A.G.
Nature Genetics 52 (1): 29-34. January 2020

2019

Chloroplast cold-resistance is mediated by the acidic domain of the RNA binding protein CP31A.
Okuzaki, A. and Lehniger, M.K. and Muino, J.M. and Lenzen, B. and Rühe, Thilo and Leister, D. and Ohler, U. and Schmitz-Linneweber, C.
bioRxiv : 832337. 5 December 2019

Applying synergy metrics to oncology combination screening data: agreements, disagreements and pitfalls.
Vlot, A.H.C. and Aniceto, N. and Menden, M.P. and Ulrich-Merzenich, G. and Bender, A.
Drug Discovery Today 24 (12): 2286-2298. December 2019

Integrated proteogenomic deep sequencing and analytics accurately identify non-canonical peptides in tumor immunopeptidomes.
Chong, C. and Müller, M. and Pak, H.S. and Harnett, D. and Huber, F. and Grun, D. and Leleu, M. and Auger, A. and Arnaud, M. and Stevenson, B.J. and Michaux, J. and Bilic, I. and Hirsekorn, A. and Calviello, L. and Simó-Riudalbas, L. and Planet, E. and Lubiński, J. and Bryśkiewicz, M. and Wiznerowicz, M. and Xenarios, I. and Zhang, L. and Trono, D. and Harari, A. and Ohler, U. and Coukos, G. and Bassani-Sternberg, M.
bioRxiv : 758680. 6 September 2019

Janggu: deep learning for genomics.
Kopp, W. and Monti, R. and Tamburrini, A. and Ohler, U. and Akalin, A.
bioRxiv : 700450. 16 July 2019

The translational landscape of the human heart.
van Heesch, S. and Witte, F. and Schneider-Lunitz, V. and Schulz, J.F. and Adami, E. and Faber, A. and Kirchner, M. and Maatz, H. and Blachut, S. and Sandmann, C.L. and Kanda, M. and Worth, C.L. and Schafer, S. and Calviello, L. and Merriott, R. and Patone, G. and Hummel, O. and Wyler, E. and Obermayer, B. and Mücke, M. and Lindberg, E.L. and Trnka, F. and Memczak, S. and Schilling, M. and Felkin, L.E. and Barton, P.J.R. and Quaife, N.M. and Vanezis, K. and Diecke, S. and Mukai, M. and Mah, N. and Oh, S.J. and Kurtz, A. and Schramm, C. and Schwinge, D. and Sebode, M. and Harakalova, M. and Asselbergs, F.W. and Vink, A. and de Weger, R.A. and Viswanathan, S. and Widjaja, A.A. and Gärtner-Rommel, A. and Milting, H. and Dos Remedios, C. and Knosalla, C. and Mertins, P. and Landthaler, M. and Vingron, M. and Linke, W.A. and Seidman, J.G. and Seidman, C.E. and Rajewsky, N. and Ohler, U. and Cook, S.A. and Hubner, N.
Cell 178 (1): 242-260. 27 June 2019

SaTAnn quantifies translation on the functionally heterogeneous transcriptome.
Calviello, L. and Hirsekorn, A. and Ohler, U.
bioRxiv : 608794. 14 April 2019

Global identification of functional microRNA-mRNA interactions in Drosophila.
Wessels, H.H. and Lebedeva, S. and Hirsekorn, A. and Wurmus, R. and Akalin, A. and Mukherjee, N. and Ohler, U.
Nature Communications 10 (1): 1626. 9 April 2019

Ribo-seQC: comprehensive analysis of cytoplasmic and organellar ribosome profiling data.
Calviello, L. and Sydow, D. and Harnett, D. and Ohler, U.
bioRxiv : 601468. 8 April 2019

Purification of cross-linked RNA-protein complexes by phenol-toluol extraction.
Urdaneta, E.C. and Vieira-Vieira, C.H. and Hick, T. and Wessels, H.H. and Figini, D. and Moschall, R. and Medenbach, J. and Ohler, U. and Granneman, S. and Selbach, M. and Beckmann, B.M.
Nature Communications 10 (1): 990. 1 March 2019

Reproducible inference of transcription factor footprints in ATAC-seq and DNase-seq datasets using protocol-specific bias modeling.
Karabacak Calviello, A. and Hirsekorn, A. and Wurmus, R. and Yusuf, D. and Ohler, U.
Genome Biology 20 (1): 42. 21 February 2019

Deciphering human ribonucleoprotein regulatory networks.
Mukherjee, N. and Wessels, H.H. and Lebedeva, S. and Sajek, M. and Ghanbari, M. and Garzia, A. and Munteanu, A. and Yusuf, D. and Farazi, T. and Hoell, J.I. and Akat, K.M. and Akalin, A. and Tuschl, T. and Ohler, U.
Nucleic Acids Research 47 (2): 570-581. 25 January 2019

Deep neural networks for interpreting RNA binding protein target preferences.
Ghanbari, M. and Ohler, U.
bioRxiv : 518191. 11 January 2019

2018

SSMART: Sequence-structure motif identification for RNA-binding proteins.
Munteanu, A. and Mukherjee, N. and Ohler, U.
Bioinformatics 34 (23): 3990-3998. 1 December 2018

omniCLIP: probabilistic identification of protein-RNA interactions from CLIP-seq data.
Drewe-Boss, P. and Wessels, H.H. and Ohler, U.
Genome Biology 19 : 183. 1 November 2018

Determinants of promoter and enhancer transcription directionality in metazoans.
Ibrahim, M.M. and Karabacak, A. and Glahs, A. and Kolundzic, E. and Hirsekorn, A. and Carda, A. and Tursun, B. and Zinzen, R.P. and Lacadie, S.A. and Ohler, U.
Nature Communications 9 (1): 4472. 26 October 2018

Ectopic transplastomic expression of a synthetic MatK gene leads to cotyledon-specific leaf variegation.
Qu, Y. and Legen, J. and Arndt, J. and Henkel, S. and Hoppe, G. and Thieme, C. and Ranzini, G. and Muino, J.M. and Weihe, A. and Ohler, U. and Weber, G. and Ostersetzer, O. and Schmitz-Linneweber, C.
Frontiers in Plant Science 9 : 1453. October 2018

FACT sets a barrier for cell fate reprogramming in Caenorhabditis elegans and human cells.
Kolundzic, E. and Ofenbauer, A. and Bulut, S.I. and Uyar, B. and Baytek, G. and Sommermeier, A. and Seelk, S. and He, M. and Hirsekorn, A. and Vucicevic, D. and Akalin, A. and Diecke, S. and Lacadie, S.A. and Tursun, B.
Developmental Cell 46 (5): 611-626. 10 September 2018

Global identification of functional microRNA::mRNA interactions in Drosophila.
Wessels, H.H. and Lebedeva, S. and Hirsekorn, A. and Mukherjee, N. and Ohler, U.
bioRxiv : 395335. 22 August 2018

Purification of cross-linked RNA-protein complexes by phenol-toluol extraction.
Urdaneta, E.C. and Vieira-Vieira, C.H. and Hick, T. and Wessels, H.H. and Figini, D. and Moschall, R. and Medenbach, J. and Ohler, U. and Granneman, S. and Selbach, M. and Beckmann, B.M.
bioRxiv : 333385. 30 May 2018

Deciphering human ribonucleoprotein regulatory networks.
Mukherjee, N. and Wessels, H.H. and Lebedeva, S. and Sajek, M. and Ghanbari, M. and Garzia, A. and Munteanu, A. and Farazi, T. and Hoell, J.I. and Akat, K. and Tuschl, T. and Ohler, U.
bioRxiv : 295097. 10 April 2018

SSMART: Sequence-structure motif identification for RNA-binding proteins.
Munteanu, A. and Mukherjee, N. and Ohler, U.
bioRxiv : 287953. 23 March 2018

Reproducible inference of transcription factor footprints in ATAC-seq and DNase-seq datasets via protocol-specific bias modeling.
Karabacak Calviello, A. and Hirsekorn, A. and Wurmus, R. and Yusuf, D. and Ohler, U.
bioRxiv : 284364. 19 March 2018

Expanding the map of protein-RNA interaction sites via cell fusion followed by PAR-CLIP.
Hinze, F. and Drewe-Boss, P. and Milek, M. and Ohler, U. and Landthaler, M. and Gotthardt, M.
RNA Biology 15 (3): 359-368. 4 March 2018

Redundant regulation.
Lacadie, S.A. and Ohler, U.
Nature Ecology & Evolution 2 (3): 418-419. March 2018

Finding RNA structure in the unstructured RBPome.
Orenstein, Y. and Ohler, U. and Berger, B.
BMC Genomics 19 (1): 154. 20 February 2018

2017

Determinants of transcription initiation directionality in metazoans.
Ibrahim, M.M. and Karabacak, A. and Glahs, A. and Kolundzic, E. and Hirsekorn, A. and Carda, A. and Tursun, B. and Zinzen, R.P. and Lacadie, S.A. and Ohler, U.
bioRxiv : 224642. 24 November 2017

RNA-bioinformatics: tools, services and databases for the analysis of RNA-based regulation.
Backofen, R. and Engelhardt, J. and Erxleben, A. and Fallmann, J. and Grüning, B. and Ohler, U. and Rajewsky, N. and Stadler, P.F.
Journal of Biotechnology 261 : 76-84. 10 November 2017

ssHMM: extracting intuitive sequence-structure motifs from high-throughput RNA-binding protein data.
Heller, D. and Krestel, R. and Ohler, U. and Vingron, M. and Marsico, A.
Nucleic Acids Research 45 (19): 11004-11018. 2 November 2017

McEnhancer: predicting gene expression via semi-supervised assignment of enhancers to target genes.
Hafez, D. and Karabacak, A. and Krueger, S. and Hwang, Y.C. and Wang, L.S. and Zinzen, R.P. and Ohler, U.
Genome Biology 18 (1): 199. 26 October 2017

Beyond read-counts: Ribo-seq data analysis to understand the functions of the transcriptome.
Calviello, L. and Ohler, U.
Trends in Genetics 33 (10): 728-744. October 2017

RNA localization is a key determinant of neurite-enriched proteome.
Zappulo, A. and van den Bruck, D. and Ciolli Mattioli, C. and Franke, V. and Imami, K. and McShane, E. and Moreno-Estelles, M. and Calviello, L. and Filipchyk, A. and Peguero-Sanchez, E. and Müller, T. and Woehler, A. and Birchmeier, C. and Merino, E. and Rajewsky, N. and Ohler, U. and Mazzoni, E.O. and Selbach, M. and Akalin, A. and Chekulaeva, M.
Nature Communications 8 (1): 583. 19 September 2017

FACT sets a barrier for cell fate reprogramming in C. elegans and human.
Kolundzic, E. and Ofenbauer, A. and Uyar, B. and Sommermeier, A. and Seelk, S. and He, M. and Baytek, G. and Akalin, A. and Diecke, S. and Lacadie, S.A. and Tursun, B.
bioRxiv : 185116. 6 September 2017

DDX54 regulates transcriptome dynamics during DNA damage response.
Milek, M. and Imami, K. and Mukherjee, N. and De Bortoli, F. and Zinnall, U. and Hazapis, O. and Trahan, C. and Oeffinger, M. and Heyd, F. and Ohler, U. and Selbach, M. and Landthaler, M.
Genome Research 27 (8): 1344-1359. August 2017

omniCLIP: Bayesian identification of protein-RNA interactions from CLIP-Seq data.
Drewe-Boss, P. and Wessels, H.H. and Ohler, U.
bioRxiv : 161877. 11 July 2017

The RNA workbench: best practices for RNA and high-throughput sequencing bioinformatics in Galaxy.
Grüning, B.A. and Fallmann, J. and Yusuf, D. and Will, S. and Erxleben, A. and Eggenhofer, F. and Houwaart, T. and Batut, B. and Videm, P. and Bagnacani, A. and Wolfien, M. and Lott, S.C. and Hoogstrate, Y. and Hess, W.R. and Wolkenhauer, O. and Hoffmann, S. and Akalin, A. and Ohler, U. and Stadler, P.F. and Backofen, R.
Nucleic Acids Research 45 (W1): W560-W566. 3 July 2017

RCAS: an RNA centric annotation system for transcriptome-wide regions of interest.
Uyar, B. and Yusuf, D. and Wurmus, R. and Rajewsky, N. and Ohler, U. and Akalin, A.
Nucleic Acids Research 45 (10): e91. 2 June 2017

Genome-wide identification of regulatory elements in Sertoli cells.
Maatouk, D.M. and Natarajan, A. and Shibata, Y. and Song, L. and Crawford, G.E. and Ohler, U. and Capel, B.
Development 144 (4): 720-730. 15 February 2017

A multi-step transcriptional and chromatin state cascade underlies motor neuron programming from embryonic stem cells.
Velasco, S. and Ibrahim, M.M. and Kakumanu, A. and Garipler, G. and Aydin, B. and Al-Sayegh, M.A. and Hirsekorn, A. and Abdul-Rahman, F. and Satija, R. and Ohler, U. and Mahony, S. and Mazzoni, E.O.
Cell Stem Cell 20 (2): 205-217. 2 February 2017

JACUSA: site-specific identification of RNA editing events from replicate sequencing data.
Piechotta, M. and Wyler, E. and Ohler, U. and Landthaler, M. and Dieterich, C.
BMC Bioinformatics 18 (1): 7. 3 January 2017

RiboDiff: detecting changes of mRNA translation efficiency from ribosome footprints.
Zhong, Y. and Karaletsos, T. and Drewe, P. and Sreedharan, V.T. and Kuo, D. and Singh, K. and Wendel, H.G. and Raetsch, G.
Bioinformatics 33 (1): 139-141. 1 January 2017

Integrative classification of human coding and noncoding genes through RNA metabolism profiles.
Mukherjee, N. and Calviello, L. and Hirsekorn, A. and de Pretis, S. and Pelizzola, M. and Ohler, U.
Nature Structural & Molecular Biology 24 (1): 86-96. January 2017

How are different transcripts in our genome translated into proteins?
Ohler, U.
[Video] 2017

2016

Divergent transcription and epigenetic directionality of human promoters.
Lacadie, S.A. and Ibrahim, M.M. and Gokhale, S.A. and Ohler, U.
FEBS Journal 283 (23): 4214-4222. December 2016

High-resolution expression map of the arabidopsis root reveals alternative splicing and lincRNA regulation.
Li, S. and Yamada, M. and Han, X. and Ohler, U. and Benfey, P.N.
Developmental Cell 39 (4): 508-522. 21 November 2016

Super-resolution ribosome profiling reveals unannotated translation events in Arabidopsis.
Hsu, P.Y. and Calviello, L. and Wu, H.Y.L. and Li, F.W. and Rothfels, C.J. and Ohler, U. and Benfey, P.N.
Proceedings of the National Academy of Sciences of the United States of America 113 (45): E7126-E7135. 8 November 2016

Alternative splicing substantially diversifies the transcriptome during early photomorphogenesis and correlates with the energy availability in arabidopsis.
Hartmann, L. and Drewe-Boss, P. and Wiessner, T. and Wagner, G. and Geue, S. and Lee, H.C. and Obermueller, D.M. and Kahles, A. and Behr, J. and Sinz, F.H. and Raetsch, G. and Wachter, A.
Plant Cell 28 (11): 2715-2734. November 2016

ssHMM: Extracting intuitive sequence-structure motifs from high-throughput RNA-binding protein data.
Heller, D. and Krestel, R. and Ohler, U. and Vingron, M. and Marsico, A.
bioRxiv : 076034. 11 October 2016

Integrative classification of human coding and non-coding genes based on RNA metabolism profiles.
Mukherjee, N. and Calviello, L. and Hirsekorn, A. and de Pretis, S. and Pelizzola, M. and Ohler, U.
bioRxiv : 073643. 6 September 2016

The mRNA-bound proteome of the early fly embryo.
Wessels, H.H. and Imami, K. and Baltz, A.G. and Kolinski, M. and Beldovskaya, A. and Selbach, M. and Small, S. and Ohler, U. and Landthaler, M.
Genome Research 26 (7): 1000-1009. July 2016

The long non-coding RNA PARROT is an upstream regulator of c-Myc and affects proliferation and translation.
Vučićević, D. and Gehre, M. and Dhamija, S. and Friis-Hansen, L. and Meierhofer, D. and Sauer, S. and Ørom, U.A.
Oncotarget 7 (23): 33934-33947. 7 June 2016

Delivery of therapeutics targeting the mRNA-binding protein HuR using 3DNA nanocarriers suppresses ovarian tumor growth.
Huang, Y.H. and Peng, W. and Furuuchi, N. and Gerhart, J. and Rhodes, K. and Mukherjee, N. and Jimbo, M. and Gonye, G.E. and Brody, J.R. and Getts, R.C. and Sawicki, J.A.
Cancer Research 76 (6): 1549-1559. 15 March 2016

Detecting actively translated open reading frames in ribosome profiling data.
Calviello, L. and Mukherjee, N. and Wyler, E. and Zauber, H. and Hirsekorn, A. and Selbach, M. and Landthaler, M. and Obermayer, B. and Ohler, U.
Nature Methods 13 (2): 165-170. February 2016

RiboDiff: detecting changes of translation efficiency from ribosome footprints.
Zhong, Y. and Karaletsos, T. and Drewe, P. and Sreedharan, V. and Kuo, D. and Singh, K. and Wendel, H.G. and Raetsch, G.
bioRxiv : 017111. 11 January 2016

Cseq-simulator: a data simulator for CLIP-Seq experiments.
Kassuhn, W. and Ohler, U. and Drewe, P.
In: Pacific Symposium on Biocomputing (PSB) 2016, 4-8 Jan 2016, The Big Island of Hawaii, USA. January 2016

Identifying RBP targets with RIP-seq.
Wessels, H.H. and Hirsekorn, A. and Ohler, U. and Mukherjee, N.
Methods in Molecular Biology 1358 : 141-152. 2016

On fine stochastic simulations of liposome-encapsulated PUREsystem(TM).
Calviello, L. and Lazzerini-Ospri, L. and Marangoni, R.
In: 10th Italian Workshop on Artificial Life and Evolutionary Computation, WIVACE 2015, 22-25 Sept 2015, Bari, Italy. 2016

2015

A spectral analysis approach to detect actively translated open reading frames in high-resolution ribosome profiling data.
Calviello, L. and Mukherjee, N. and Wyler, E. and Zauber, H. and Hirsekorn, A. and Selbach, M. and Landthaler, M. and Obermayer, B. and Ohler, U.
bioRxiv : 031625. 13 November 2015

Perspectives on unidirectional versus divergent transcription.
Duttke, S.H.C. and Lacadie, S.A. and Ibrahim, M.M. and Glass, C.K. and Corcoran, D.L. and Benner, C. and Heinz, S. and Kadonaga, J.T. and Ohler, U.
Molecular Cell 60 (3): 348-349. 5 November 2015

Transcriptional control of tissue formation throughout root development.
Moreno-Risueno, M.A. and Sozzani, R. and Yardımcı, G.G. and Petricka, J.J. and Vernoux, T. and Blilou, I. and Alonso, J. and Winter, C.M. and Ohler, U. and Scheres, B. and Benfey, P.N.
Science 350 (6259): 426-430. 23 October 2015

Ancient gene duplications have shaped developmental stage-specific expression in Pristionchus pacificus.
Baskaran, P. and Roedelsperger, C. and Prabh, N. and Serobyan, V. and Markov, G.V. and Hirsekorn, A. and Dieterich, C.
BMC Evolutionary Biology 15 (1): 185. 15 September 2015

Extensive identification and analysis of conserved small ORFs in animals.
Mackowiak, S.D. and Zauber, H. and Bielow, C. and Thiel, D. and Kutz, K. and Calviello, L. and Mastrobuoni, G. and Rajewsky, N. and Kempa, S. and Selbach, M. and Obermayer, B.
Genome Biology 16 : 179. 14 September 2015

miR-184 regulates pancreatic β-cell function according to glucose metabolism.
Tattikota, S.G. and Rathjen, T. and Hausser, J. and Khedkar, A. and Kabra, U.D. and Pandey, V.K. and Sury, M.D. and Wessels, H.H. and Mollet, I.G. and Eliasson, L. and Selbach, M. and Zinzen, R.P. and Zavolan, M. and Kadener, S. and Tschöp, M. and Jastroch, M. and Friedländer, M.R. and Poy, M.N.
Journal of Biological Chemistry 290 (33): 20284-20294. 14 August 2015

Regnase-1 and roquin regulate a common element in inflammatory mRNAs by spatiotemporally distinct mechanisms.
Mino, T. and Murakawa, Y. and Fukao, A. and Vandenbon, A. and Wessels, H.H. and Ori, D. and Uehata, T. and Tartey, S. and Akira, S. and Suzuki, Y. and Vinuesa, C.G. and Ohler, U. and Standley, D.M. and Landthaler, M. and Fujiwara, T. and Takeuchi, O.
Cell 161 (5): 1058-1073. 21 May 2015

Human promoters are intrinsically directional.
Duttke, S.H.C. and Lacadie, S.A. and Ibrahim, M.M. and Glass, C.K. and Corcoran, D.L. and Benner, C. and Heinz, S. and Kadonaga, J.T. and Ohler, U.
Molecular Cell 57 (4): 674-684. 19 February 2015

JAMM: a peak finder for joint analysis of NGS replicates.
Ibrahim, M.M. and Lacadie, S.A. and Ohler, U.
Bioinformatics 31 (1): 48-55. 1 January 2015

2014

Explicit DNase sequence bias modeling enables high-resolution transcription factor footprint detection.
Yardımcı, G.G. and Frank, C.L. and Crawford, G.E. and Ohler, U.
Nucleic Acids Research 42 (19): 11865-11878. 29 October 2014

Effective diagnosis of genetic disease by computational phenotype analysis of the disease-associated genome.
Zemojtel, T. and Koehler, S. and Mackenroth, L. and Jaeger, M. and Hecht, J. and Krawitz, P. and Graul-Neumann, L. and Doelken, S. and Ehmke, N. and Spielmann, M. and Oien, N.C. and Schweiger, M.R. and Krueger, U. and Frommer, G. and Fischer, B. and Kornak, U. and Floettmann, R. and Ardeshirdavani, A. and Moreau, Y. and Lewis, S.E. and Haendel, M. and Smedley, D. and Horn, D. and Mundlos, S. and Robinson, P.N.
Science Translational Medicine 6 (252): 252ra123. 3 September 2014

Improved transcript isoform discovery using ORF graphs.
Majoros, W.H. and Lebeck, N. and Ohler, U. and Li, S.
Bioinformatics 30 (14): 1958-1964. 15 July 2014

COUGER-co-factors associated with uniquely-bound genomic regions.
Munteanu, A. and Ohler, U. and Gordân, R.
Nucleic Acids Research 42 (Web Server issue): W461-W467. July 2014

Identification of the RNA recognition element of the RBPMS family of RNA-binding proteins and their transcriptome-wide mRNA targets.
Farazi, T.A. and Leonhardt, C.S. and Mukherjee, N. and Mihailovic, A. and Li, S. and Max, K.E.A. and Meyer, C. and Yamaji, M. and Cekan, P. and Jacobs, N.C. and Gerstberger, S. and Bognanni, C. and Larsson, E. and Ohler, U. and Tuschl, T.
RNA 20 (7): 1090-1102. July 2014

Paired-end analysis of transcription start sites in Arabidopsis reveals plant-specific promoter signatures.
Morton, T. and Petricka, J. and Corcoran, D.L. and Li, S. and Winter, C.M. and Carda, A. and Benfey, P.N. and Ohler, U. and Megraw, M.
Plant Cell 26 (7): 2746-2760. July 2014

Global target mRNA specification and regulation by the RNA-binding protein ZFP36.
Mukherjee, N. and Jacobs, N.C. and Hafner, M. and Kennington, E.A. and Nusbaum, J.D. and Tuschl, T. and Blackshear, P.J. and Ohler, U.
Genome Biology 15 (1): R12. 8 January 2014

2013

Integrated detection of natural antisense transcripts using strand-specific RNA sequencing data.
Li, S. and Liberman, L. and Mukherjee, N. and Benfey, P. and Ohler, U.
Genome Research 23 (10): 1730-1739. October 2013

Using machine learning to identify disease-relevant regulatory RNAs.
Ohler, U.
Proceedings of the National Academy of Sciences of the United States of America 110 (39): 15516-15517. 24 September 2013

Distinct polyadenylation landscapes of diverse human tissues revealed by a modified PA-seq strategy.
Ni, T. and Yang, Y. and Hafez, D. and Yang, W. and Kiesewetter, K. and Wakabayashi, Y. and Ohler, U. and Peng, W. and Zhu, J.
BMC Genomics 14 (1): 615. 11 September 2013

Sustained-input switches for transcription factors and microRNAs are central building blocks of eukaryotic gene circuits.
Megraw, M. and Mukherjee, S. and Ohler, U.
Genome Biology 14 (8): R85. 23 August 2013

Fine time course expression analysis identifies cascades of activation and repression and maps a putative regulator of Mammalian sex determination.
Munger, S.C. and Natarajan, A. and Looger, L.L. and Ohler, U. and Capel, B.
PLoS Genetics 9 (7): e1003630. 11 July 2013

Automated annotation of gene expression image sequences via non-parametric factor analysis and conditional random fields.
Pruteanu-Malinici, I. and Majoros, W.H. and Ohler, U.
Bioinformatics 29 (13): i27-i35. 1 July 2013

Genome-wide identification and predictive modeling of tissue-specific alternative polyadenylation.
Hafez, D. and Ni, T. and Mukherjee, S. and Zhu, J. and Ohler, U.
Bioinformatics 29 (13): i108-i116. 1 July 2013

MicroRNA target site identification by integrating sequence and binding information.
Majoros, W.H. and Lekprasert, P. and Mukherjee, N. and Skalsky, R.L. and Corcoran, D.L. and Cullen, B.R. and Ohler, U.
Nature Methods 10 (7): 630-633. July 2013

NextGen speaks.
Lacadie, S.A.
Science 340 (6128): 29. April 2013

2012

FMRP targets distinct mRNA sequence elements to regulate protein expression.
Ascano, M. and Mukherjee, N. and Bandaru, P. and Miller, J.B. and Nusbaum, J.D. and Corcoran, D.L. and Langlois, C. and Munschauer, M. and Dewell, S. and Hafner, M. and Williams, Z. and Ohler, U. and Tuschl, T.
Nature 492 (7429): 382-386. 20 December 2012

A microfluidic device and computational platform for high-throughput live imaging of gene expression.
Busch, W. and Moore, B.T. and Martsberger, B. and Mace, D.L. and Twigg, R.W. and Jung, J. and Pruteanu-Malinici, I. and Kennedy, S.J. and Fricke, G.K. and Clark, R.L. and Ohler, U. and Benfey, P.N.
Nature Methods 9 (11): 1101-1106. November 2012

Chromatin accessibility reveals insights into androgen receptor activation and transcriptional specificity.
Tewari, A.K. and Yardimci, G.G. and Shibata, Y. and Sheffield, N.C. and Song, L. and Taylor, B.S. and Georgiev, S.G. and Coetzee, GA. and Ohler, U. and Furey, T.S. and Crawford, G.E. and Febbo, P.G.
Genome Biology 13 (10): R88. 3 October 2012

The Drosophila translational control element (TCE) is required for high-level transcription of many genes that are specifically expressed in testes.
Katzenberger, R.J. and Rach, E.A. and Anderson, A.K. and Ohler, U. and Wassarman, D.A.
PLoS ONE 7 (9): e45009. 11 September 2012

Predicting cell-type-specific gene expression from regions of open chromatin.
Natarajan, A. and Yardimci, G.G. and Sheffield, N.C. and Crawford, G.E. and Ohler, U.
Genome Research 22 (9): 1711-1722. September 2012

Translocation of sickle cell erythrocyte microRNAs into plasmodium falciparum inhibits parasite rranslation and contributes to malaria resistance.
Lamonte, G. and Philip, N. and Reardon, J. and Lacsina, J.R. and Majoros, W. and Chapman, L. and Thornburg, C.D. and Telen, M.J. and Ohler, U. and Nicchitta, C.V. and Haystead, T. and Chi, J.T.
Cell Host & Microbe 12 (2): 187-199. 16 August 2012

Genome-wide search for miRNA-target interactions in Arabidopsis thaliana with an integrated approach.
Ding, J. and Li, D. and Ohler, U. and Guan, J. and Zhou, S.
BMC Genomics 13 (Suppl 3): S3. 11 June 2012

The protein expression landscape of the Arabidopsis root.
Petricka, J.J. and Schauer, M.A. and Megraw, M. and Breakfield, N.W. and Thompson, J.W. and Georgiev, S. and Soderblom, E.J. and Ohler, U. and Moseley, M.A. and Grossniklaus, U. and Benfey, P.N.
Proceedings of the National Academy of Sciences of the United States of America 109 (18): 6811-6818. 1 May 2012

The viral and cellular microRNA targetome in lymphoblastoid cell lines.
Skalsky, R.L. and Corcoran, D.L. and Gottwein, E. and Frank, C.L. and Kang, D. and Hafner, M. and Nusbaum, J.D. and Feederle, R. and Delecluse, H.J. and Luftig, M.A. and Tuschl, T. and Ohler, U. and Cullen, B.R.
PLoS Pathogens 8 (1): e1002484. 26 January 2012

High-resolution experimental and computational profiling of tissue-specific known and novel miRNAs in Arabidopsis.
Breakfield, N.W. and Corcoran, D.L. and Petricka, J.J. and Shen, J. and Sae-Seaw, J. and Rubio-Somoza, I. and Weigel, D. and Ohler, U. and Benfey, P.N.
Genome Research 22 (1): 163-176. January 2012

2011

Viral microRNA targetome of KSHV-infected primary effusion lymphoma cell lines.
Gottwein, E. and Corcoran, D.L. and Mukherjee, N. and Skalsky, R.L. and Hafner, M. and Nusbaum, J.D. and Shamulailatpam, P. and Love, C.L. and Dave, S.S. and Tuschl, T. and Ohler, U. and Cullen, B.R.
Cell Host & Microbe 10 (5): 515-526. 17 November 2011

PARalyzer: definition of RNA binding sites from PAR-CLIP short-read sequence data.
Corcoran, D.L. and Georgiev, S. and Mukherjee, N. and Gottwein, E. and Skalsky, R.L. and Keene, J.D. and Ohler, U.
Genome Biology 12 (8): R79. 18 August 2011

Integrative regulatory mapping indicates that the RNA-binding protein HuR couples pre-mRNA processing and mRNA stability.
Mukherjee, N. and Corcoran, D.L. and Nusbaum, J.D. and Reid, D.W. and Georgiev, S. and Hafner, M. and Ascano, M. and Tuschl, T. and Ohler, U. and Keene, J.D.
Molecular Cell 43 (3): 327-339. 5 August 2011

Automatic annotation of spatial expression patterns via sparse Bayesian factor models.
Pruteanu-Malinici, I. and Mace, D.L. and Ohler, U.
PLoS Computational Biology 7 (7): e1002098. July 2011

Assessing the utility of thermodynamic features for microRNA target prediction under relaxed seed and no conservation requirements.
Lekprasert, P. and Mayhew, M. and Ohler, U.
PLoS ONE 6 (6): e20622. 6 June 2011

A stele-enriched gene regulatory network in the Arabidopsis root.
Brady, S.M. and Zhang, L. and Megraw, M. and Martinez, N.J. and Jiang, E. and Yi, C.S. and Liu, W. and Zeng, A. and Taylor-Teeples, M. and Kim, D. and Ahnert, S. and Ohler, U. and Ware, D. and Walhout, A.J.M. and Benfey, P.N.
Molecular Systems Biology 7 : 459. 18 January 2011

Transcription initiation patterns indicate divergent strategies for gene regulation at the chromatin level.
Rach, E.A. and Winter, D.R. and Benjamin, A.M. and Corcoran, D.L. and Ni, T. and Zhu, J. and Ohler, U.
PLoS Genetics 7 (1): e1001274. 13 January 2011

2010

Modeling the evolution of regulatory elements by simultaneous detection and alignment with phylogenetic pair HMMs.
Majoros, W.H. and Ohler, U.
PLoS Computational Biology 6 (12): e1001037. 16 December 2010

Gene expression divergence recapitulates the developmental hourglass model.
Kalinka, A.T. and Varga, K.M. and Gerrard, D.T. and Preibisch, S. and Corcoran, D.L. and Jarrells, J. and Ohler, U. and Bergman, C.M. and Tomancak, P.
Nature 468 (7325): 811-814. 9 December 2010

The TCT motif, a key component of an RNA polymerase II transcription system for the translational machinery.
Parry, T.J. and Theisen, J.W.M. and Hsu, J.Y. and Wang, Y.L. and Corcoran, D.L. and Eustice, M. and Ohler, U. and Kadonaga, J.T.
Genes & Development 24 (18): 2013-2018. 15 September 2010

An alignment-free method to identify candidate orthologous enhancers in multiple Drosophila genomes.
Arunachalam, M. and Jayasurya, K. and Tomancak, P. and Ohler, U.
Bioinformatics 26 (17): 2109-2115. 1 September 2010

A paired-end sequencing strategy to map the complex landscape of transcription initiation.
Ni, T. and Corcoran, D.L. and Rach, E.A. and Song, S. and Spana, E.P. and Gao, Y. and Ohler, U. and Zhu, J.
Nature Methods 7 (7): 521-527. July 2010

Mapping the complexity of transcription control in higher eukaryotes.
Tomancak, P. and Ohler, U.
Genome Biology 11 (4): 115. 30 April 2010

Extraction and comparison of gene expression patterns from 2D RNA in situ hybridization images.
Mace, D.L. and Varnado, N. and Zhang, W. and Frise, E. and Ohler, U.
Bioinformatics 26 (6): 761-769. 15 March 2010

Evidence-ranked motif identification.
Georgiev, S. and Boyle, A.P. and Jayasurya, K. and Ding, X. and Mukherjee, S. and Ohler, U.
Genome Biology 11 (2): R19. 15 February 2010

Promoting developmental transcription.
Ohler, U. and Wassarman, D.A.
Development 137 (1): 15-26. January 2010

2009

Motif composition, conservation and condition-specificity of single and alternative transcription start sites in the Drosophila genome.
Rach, E.A. and Yuan, H.Y. and Majoros, W.H. and Tomancak, P. and Ohler, U.
Genome Biology 10 (7): R73. 9 July 2009

Measuring spatial preferences at fine-scale resolution identifies known and novel cis-regulatory element candidates and functional motif-pair relationships.
Yokoyama, K.D. and Ohler, U. and Wray, G.A.
Nucleic Acids Research 37 (13): e92. July 2009

A transcription factor affinity-based code for mammalian transcription initiation.
Megraw, M. and Pereira, F. and Jensen, S.T. and Ohler, U. and Hatzigeorgiou, A.G.
Genome Research 19 (4): 644-656. April 2009

Complexity reduction in context-dependent DNA substitution models.
Majoros, W.H. and Ohler, U.
Bioinformatics 25 (2): 175-182. 15 January 2009

2008

Strategies for identifying RNA splicing regulatory motifs and predicting alternative splicing events.
Holste, D. and Ohler, U.
PLoS Computational Biology 4 (1): e21. 25 January 2008

2007

A viral microRNA functions as an orthologue of cellular miR-155.
Gottwein, E. and Mukherjee, N. and Sachse, C. and Frenzel, C. and Majoros, W.H. and Chi, J.T.A. and Braich, R. and Manoharan, M. and Soutschek, J. and Ohler, U. and Cullen, B.R.
Nature 450 (7172): 1096-1099. 13 December 2007

A high-resolution root spatiotemporal map reveals dominant expression patterns.
Brady, S.M. and Orlando, D.A. and Lee, J.Y. and Wang, J.Y. and Koch, J. and Dinneny, J.R. and Mace, D. and Ohler, U. and Benfey, P.N.
Science 318 (5851): 801-806. 2 November 2007

Phylogenetic simulation of promoter evolution: estimation and modeling of binding site turnover events and assessment of their impact on alignment tools.
Huang, W. and Nevins, J.R. and Ohler, U.
Genome Biology 8 (10): R225. 24 October 2007

Spatial preferences of microRNA targets in 3' untranslated regions.
Majoros, W.H. and Ohler, U.
BMC Genomics 8 : 152. 7 June 2007

Detection of broadly expressed neuronal genes in C. elegans.
Ruvinsky, I. and Ohler, U. and Burge, C.B. and Ruvkun, G.
Developmental Biology 302 (2): 617-626. 15 February 2007

2006

Identification of core promoter modules in Drosophila and their application in accurate transcription start site prediction.
Ohler, U.
Nucleic Acids Research 34 (20): 5943-5950. November 2006

Informative priors based on transcription factor structural class improve de novo motif discovery.
Narlikar, L. and Gordan, R. and Ohler, U. and Hartemink, A.J.
Bioinformatics 22 (14): e384-392. 15 July 2006

Quantification of transcription factor expression from Arabidopsis images.
Mace, D.L. and Lee, J.Y. and Twigg, R.W. and Colinas, J. and Benfey, P.N. and Ohler, U.
Bioinformatics 22 (14): e323-231. 15 July 2006

Optimized mixed Markov models for motif identification.
Huang, W. and Umbach, D.M. and Ohler, U. and Li, L.
BMC Bioinformatics 7 : 279. 2 June 2006

Transcriptional and posttranscriptional regulation of transcription factor expression in Arabidopsis roots.
Lee, J.Y. and Colinas, J. and Wang, J.Y. and Mace, D. and Ohler, U. and Benfey, P.N.
Proceedings of the National Academy of Sciences of the United States of America 103 (15): 6055-6060. 11 April 2006

Performance assessment of promoter predictions on ENCODE regions in the EGASP experiment.
Bajic, V.B. and Brent, M.R. and Brown, R.H. and Frankish, A. and Harrow, J. and Ohler, U. and Solovyev, V.V. and Tan, S.L.
Genome Biology 7 Suppl 1 : S3.1-13. 2006

2005

Recognition of unknown conserved alternatively spliced exons.
Ohler, U. and Shomron, N. and Burge, C.B.
PLoS Computational Biology 1 (2): 113-122. July 2005

2004

Patterns of flanking sequence conservation and a characteristic upstream motif for microRNA gene identification.
Ohler, U. and Yekta, S. and Lim, L.P. and Bartel, D.P. and Burge, C.B.
RNA 10 (9): 1309-1322. September 2004

The MTE, a new core promoter element for transcription by RNA polymerase II.
Lim, C.Y. and Santoso, B. and Boulay, T. and Dong, E. and Ohler, U. and Kadonaga, J.T.
Genes & Development 18 (13): 1606-1617. 1 July 2004

2002

Computational analysis of core promoters in the Drosophila genome.
Ohler, U. and Liao, G.C. and Niemann, H. and Rubin, G.M.
Genome Biology 3 (12): RESEARCH0087. 2002

2001

Identification and analysis of eukaryotic promoters: recent computational approaches.
Ohler, U. and Niemann, H.
Trends in Genetics 17 (2): 56-60. February 2001

Joint modeling of DNA sequence and physical properties to improve eukaryotic promoter recognition.
Ohler, U. and Niemann, H and Liao, G.C. and Rubin, G.M.
Bioinformatics 17 Suppl 1 : S199-206. 2001

2000

Genome annotation assessment in Drosophila melanogaster.
Reese, M.G. and Hartzell, G. and Harris, N.L. and Ohler, U. and Abril, J.F. and Lewis, S.E.
Genome Research 10 (4): 483-501. April 2000

Promoter prediction on a genomic scale-the Adh experience.
Ohler, U.
Genome Research 10 (4): 539-542. April 2000

Stochastic segment models of eukaryotic promoter regions.
Ohler, U. and Stemmer, G. and Harbeck, S. and Niemann, H.
Pacific Symposium on Biocomputing : 380-391. 2000

1999

Interpolated markov chains for eukaryotic promoter recognition.
Ohler, U. and Harbeck, S. and Niemann, H. and Noeth, E. and Reese, M.G.
Bioinformatics 15 (5): 362-369. May 1999

Information theoretic based segments for language identification.
Harbeck, S. and Ohler, U. and Noth, E. and Niemann, H.
Lecture Notes in Computer Science 1692 : 187-192. 1999