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Article

Interpreting deep neural networks for the prediction of translation rates.
Korbel, F., Eroshok, E. and Ohler, U.
BMC Genomics 25 (1): 1061. 9 November 2024

Arabidopsis uses a molecular grounding mechanism and a biophysical circuit breaker to limit floral abscission signaling.
Taylor, I.W., Patharkar, O.R., Mijar, M., Hsu, C.W., Baer, J., Niederhuth, C.E., Ohler, U., Benfey, P.N. and Walker, J.C.
Proceedings of the National Academy of Sciences of the United States of America 121 (44): e2405806121. 29 October 2024

Copy-number dosage regulates telomere maintenance and disease-associated pathways in neuroblastoma.
Burkert, M., Blanc, E., Thiessen, N., Weber, C., Toedling, J., Monti, R., Dombrowe, V.M., de Biase, M.S., Kaufmann, T.L., Haase, K., Waszak, S.M., Eggert, A., Beule, D., Schulte, J.H., Ohler, U. and Schwarz, R.F.
iScience 27 (10): 110918. 18 October 2024

MHC Hammer reveals genetic and non-genetic HLA disruption in cancer evolution.
Puttick, C., Jones, T.P., Leung, M.M., Galvez-Cancino, F., Liu, J., Varas-Godoy, M., Rowan, A., Pich, O., Martinez-Ruiz, C., Bentham, R., Dijkstra, K.K., Black, J.R.M., Rosenthal, R., Kanu, N., Litchfield, K., Salgado, R., Moore, D.A., Van Loo, P., Jamal-Hanjani, M., Quezada, S.A., Swanton, C. and McGranahan, N.
Nature Genetics 56 (10): 2121-2131. October 2024

MatK impacts differential chloroplast translation by limiting spliced tRNA-K(UUU) abundance.
Muino, J.M., Ruwe, H., Qu, Y., Maschmann, S., Chen, W., Zoschke, R., Ohler, U., Kaufmann, K. and Schmitz-Linneweber, C.
Plant Journal 119 (6): 2737-2752. September 2024

Metadata-guided feature disentanglement for functional genomics.
Rakowski, A., Monti, R., Huryn, V., Lemanczyk, M., Ohler, U. and Lippert, C.
Bioinformatics 40 (Suppl 2): ii4-ii10. September 2024

Evaluation of polygenic scoring methods in five biobanks shows larger variation between biobanks than methods and finds benefits of ensemble learning.
Monti, R., Eick, L., Hudjashov, G., Läll, K., Kanoni, S., Wolford, B.N., Wingfield, B., Pain, O., Wharrie, S., Jermy, B., McMahon, A., Hartonen, T., Heyne, H., Mars, N., Lambert, S., Hveem, K., Inouye, M., van Heel, D.A., Mägi, R., Marttinen, P., Ripatti, S., Ganna, A. and Lippert, C.
American Journal of Human Genetics 111 (7): 1431-1447. 11 July 2024

Liam tackles complex multimodal single-cell data integration challenges.
Rautenstrauch, P. and Ohler, U.
Nucleic Acids Research 52 (12): e52. 8 July 2024

Genome-wide screening identifies Trim33 as an essential regulator of dendritic cell differentiation.
Tiniakou, I., Hsu, P.F., Lopez-Zepeda, L.S., Garipler, G., Esteva, E., Adams, N.M., Jang, G., Soni, C., Lau, C.M., Liu, F., Khodadadi-Jamayran, A., Rodrick, T.C., Jones, D., Tsirigos, A., Ohler, U., Bedford, M.T., Nimer, S.D., Kaartinen, V., 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., Rahmani, H., Tabatabaei, M., 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., AbdulJabbar, K., Coelho-Lima, J., Grapa, A.I., Zhang, H., Cheung, A.H.K., Baena, J., Karasaki, T., Wilson, C.R., Sereno, M., Veeriah, S., Aitken, S.J., Hackshaw, A., Nicholson, A.G., Jamal-Hanjani, M., Swanton, C., Yuan, Y., Le Quesne, J. and Moore, D.A.
Nature Cancer 5 (2): 347-363. February 2024

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

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

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

Lung adenocarcinoma promotion by air pollutants.
Hill, W., Lim, E.L., Weeden, C.E., Lee, C., Augustine, M., Chen, K., Kuan, F.C., Marongiu, F., Evans, E.J., Moore, D.A., Rodrigues, F.S., Pich, O., Bakker, B., Cha, H., Myers, R., van Maldegem, F., Boumelha, J., Veeriah, S., Rowan, A., Naceur-Lombardelli, C., Karasaki, T., Sivakumar, M., De, S., Caswell, D.R., Nagano, A., Black, J.R.M., Martínez-Ruiz, C., Ryu, M.H., Huff, R.D., Li, S., Favé, M.J., Magness, A., Suárez-Bonnet, A., Priestnall, S.L., Lüchtenborg, M., Lavelle, K., Pethick, J., Hardy, S., McRonald, F.E., Lin, M.H., Troccoli, C.I., Ghosh, M., Miller, Y.E., Merrick, D.T., Keith, R.L., Al Bakir, M., Bailey, C., Hill, M.S., Saal, L.H., Chen, Y., George, A.M., Abbosh, C., Kanu, N., Lee, S.H., McGranahan, N., Berg, C.D., Sasieni, P., Houlston, R., Turnbull, C., Lam, S., Awadalla, P., Grönroos, E., Downward, J., Jacks, T., Carlsten, C., Malanchi, I., Hackshaw, A., Litchfield, K., DeGregori, J., 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., Vukašinović, N., Hsu, C.W., Zhang, J., Vanhoutte, I., Shahan, R., Taylor, I.W., Greenstreet, L., Heitz, M., Afanassiev, A., Wang, P., Szekely, P., Brosnan, A., Yin, Y., Schiebinger, G., Ohler, U., 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., Oleshko, S., Hu, Y., Ghanbari, M., Cantini, G., Schinke, P., Vergara, E.E., Bittner, F., Mueller, N.S, Ohler, U., 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., 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., Zhang, Z., Koeken, V.A.C.M., Kumar, S., Aillaud, M., Tsay, H.C., Liu, Z., Kraft, A.R.M., Soon, C.F., Odak, I., Bošnjak, B., Vlot, A., Swertz, M.A., Ohler, U., Geffers, R., Illig, T., Huehn, J., Saliba, A.E., Sander, L.E., Förster, R., Xu, C.J., Cornberg, M., Schulte, L.N. and Li, Y.
Cell Genomics 3 (2): 100232. 8 February 2023

Protocol for fast scRNA-seq raw data processing using scKB and non-arbitrary quality control with COPILOT.
Hsu, C.W., Shahan, R., Nolan, T.M., 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., Ambrozkiewicz, M.C., Zinnall, U., Rusanova, A., Borisova, E., Drescher, A.N., Couce-Iglesias, M., Villamil, G., Dannenberg, R., Imami, K., Münster-Wandowski, A., Fauler, B., Mielke, T., Selbach, M., Landthaler, M., Spahn, C.M.T., Tarabykin, V., 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., 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., Lebedeva, S., Schott, J., Lindner, D., 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., Rautenstrauch, P., Ghanbari, M., James, A.R., Kirchler, M., Ohler, U., Konigorski, S. and Lippert, C.
Nature Communications 13 (1): 5332. 10 September 2022

Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements.
Baranasic, D., Hörtenhuber, M., Balwierz, P.J., Zehnder, T., Mukarram, A.K., Nepal, C., Várnai, C., Hadzhiev, Y., Jimenez-Gonzalez, A., Li, N., Wragg, J., D'Orazio, F.M., Relic, D., Pachkov, M., Díaz, N., Hernández-Rodríguez, B., Chen, Z., Stoiber, M., Dong, M., Stevens, I., Ross, S.E., Eagle, A., Martin, R., Obasaju, O., Rastegar, S., McGarvey, A.C., Kopp, W., Chambers, E., Wang, D., Kim, H.R., Acemel, R.D., Naranjo, S., Łapiński, M., Chong, V., Mathavan, S., Peers, B., Sauka-Spengler, T., Vingron, M., Carninci, P., Ohler, U., Lacadie, S.A., Burgess, S.M., Winata, C., van Eeden, F., Vaquerizas, J.M., Gómez-Skarmeta, J.L., Onichtchouk, D., Brown, B.J., Bogdanovic, O., van Nimwegen, E., Westerfield, M., Wardle, F.C, Daub, C.O., Lenhard, B. and Müller, F.
Nature Genetics 54 (7): 1037-1050. 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., Houwaart, T., Finzer, P., Ehlkes, L., Tyshaieva, A., Damagnez, M., Strelow, D., Duplessis, A., Nicolai, J., Wienemann, T., Tamayo, T., Kohns Vasconcelos, M., Hülse, L., Hoffmann, K., Lübke, N., Hauka, S., Andree, M., Däumer, M.P., Thielen, A., Kolbe-Busch, S., Göbels, K., Zotz, R., Pfeffer, K., 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., Lu, C., Morrissey, Al., Lopez-Zepeda, L.S., Pei, Y., Vidal, S.E., Zen Petisco Fiore, A.P., Aydin, B., Stadtfeld, M., Ohler, U., Mahony, S., 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., Hsu, C.W., Nolan, T.M., Cole, B.J., Taylor, I.W., Greenstreet, L., Zhang, S., Afanassiev, A., Vlot, A.H.C., Schiebinger, G., 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., Enders, D., Walker, J. and Ohler, U.
BMC Medical Informatics and Decision Making 22 (1): 32. 3 February 2022

SLM2 is a novel cardiac splicing factor involved in heart failure due to dilated cardiomyopathy.
Boeckel, J.N., Möbius-Winkler, M., Müller, M., Rebs, S., Eger, N., Schoppe, L., Tappu, R., Kokot, K.E., Kneuer, J.M., Gaul, S., Bordalo, D.M., Lai, A., Haas, J., Ghanbari, M., Drewe-Boss, P., Liss, M., Katus, H.A., Ohler, U., Gotthardt, M., Laufs, U., 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., Akalin, A. and Ohler, U.
Nature Machine Intelligence 4 (2): 162-168. February 2022

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

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

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

How to find genomic regions relevant for gene regulation.
Guo, X., 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., Mojica, J.P., Wang, B., Chen, C.Y., Lin, Y.P., Prasad, K.V.S.K, Chan, E., Hsu, C.W., Keith, R., Nuñez, C.L., Olson-Manning, C.F., Rushworth, C.A., Wagner, M.R., Wang, J., Yeh, P.M., Reichelt, M., Ghattas, K., Gershenzon, J., 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., Wellman, K., Baldwin, A., Rege, J., Walters, K., Hirsekorn, A., Riemondy, K., 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., Schöning, V., 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., Pfeuffer, J., Louloupi, A., Ørom, U.A.V. and Piro, R.M.
BMC Bioinformatics 22 (1): 368. 15 July 2021

Spatio-temporal mRNA tracking in the early zebrafish embryo.
Holler, K., Neuschulz, A., Drewe-Boß, P., Mintcheva, J., Spanjaard, B., Arsiè, R., Ohler, U., 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., Trautwein, C., Fendel, R., Krickeberg, N., Berezhnoy, G., Bissinger, R., Ossowski, S., Salker, M.S., Casadei, N. and Riess, O.
Heliyon 7 (6): e07147. June 2021

Ythdf is a N6-methyladenosine reader that modulates Fmr1 target mRNA selection and restricts axonal growth in Drosophila.
Worpenberg, L., Paolantoni, C., Longhi, S., Mulorz, M.M., Lence, T., Wessels, H.H., Dassi, E., Aiello, G., Sutandy, F.X.R., Scheibe, M., Edupuganti, R.R., Busch, A., Möckel, M.M., Vermeulen, M., Butter, F., König, J., Notarangelo, M., Ohler, U., Dieterich, C., Quattrone, A., 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., Qiu, Y., Gaertner, B., 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., Krupp, F., Harnett, D., Turko, P., Ambrozkiewicz, M.C., Sprink, T., Imami, K., Günnigmann, M., Zinnall, U., Vieira-Vieira, C.H., Schaub, T., Münster-Wandowski, A., Bürger, J., Borisova, E., Yamamoto, H., Rasin, M.R., Ohler, U., Beule, D., Mielke, T., Tarabykin, V., Landthaler, M., Kramer, G., Vida, I., 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., Mouktaroudi, M., Krämer, B., Oestreich, M., Antonakos, N., Nuesch-Germano, M., Gkizeli, K., Bonaguro, L., Reusch, N., Baßler, K., Saridaki, M., Knoll, R., Pecht, T., Kapellos, T.S., Doulou, S., Kröger, C., Herbert, M., Holsten, L., Horne, A., Gemünd, I.D., Rovina, N., Agrawal, S., Dahm, K., van Uelft, M., Drews, A., Lenkeit, L., Bruse, N., Gerretsen, J., Gierlich, J., Becker, M., Händler, K., Kraut, M., Theis, H., Mengiste, S., Domenico, E., Schulte-Schrepping, J., Seep, L., Raabe, J., Hoffmeister, C., ToVinh, M., Keitel, V., Rieke, G., Talevi, V., Skowasch, D., Aziz, N.A., Pickkers, P., van de Veerdonk, F.L., Netea, M.G., Schultze, J.L., Kox, M., Breteler, M.M.B., Nattermann, J., Koutsoukou, A., 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., Meerdink, E., Calviello, L., Sydow, D. and Ohler, U.
Methods in Molecular Biology 2252 : 331-346. 2021

Longitudinal multi-omics analyses identify responses of megakaryocytes, erythroid cells, and plasmablasts as hallmarks of severe COVID-19.
Bernardes, J.P., Mishra, N., Tran, F., Bahmer, T., Best, L., Blase, J.I., Bordoni, D., Franzenburg, J., Geisen, U., Josephs-Spaulding, J., Köhler, P., Künstner, A., Rosati, E., Aschenbrenner, A.C., Bacher, P., Baran, N., Boysen, T., Brandt, B., Bruse, N., Dörr, J., Dräger, A., Elke, G., Ellinghaus, D., Fischer, J., Forster, M., Franke, A., Franzenburg, S., Frey, N., Friedrichs, A., Fuß, J., Glück, A., Hamm, J., Hinrichsen, F., Hoeppner, M.P., Imm, S., Junker, R., Kaiser, S., Kan, Y.H., Knoll, R., Lange, C., Laue, G., Lier, C., Lindner, M., Marinos, G., Markewitz, R., Nattermann, J., Noth, R., Pickkers, P., Rabe, K.F., Renz, A., Röcken, C., Rupp, J., Schaffarzyk, A., Scheffold, A., Schulte-Schrepping, J., Schunk, D., Skowasch, D., Ulas, T., Wandinger, K.P., Wittig, M., Zimmermann, J., Busch, H., Hoyer, B.F., Kaleta, C., Heyckendorf, J., Kox, M., Rybniker, J., Schreiber, S., 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., Garfield, D.A., Sigalova, O.M., Karabacak Calviello, A., Marco-Ferreres, R., Girardot, C., Viales, R.R., Degner, J.F., 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., Heß, S., Grum, M., Drewe-Boss, P. and Walker, J.
Statistical Methods in Medical Research 29 (12): 3684-3694. 1 December 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., Rühle, T., Lehniger, M.K., Okuzaki, A., Labs, M., Muino, J.M., Ohler, U., 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., Hirsekorn, A. and Ohler, U.
Nature Structural & Molecular Biology 27 (8): 717-725. August 2020

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

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

Integrated proteogenomic deep sequencing and analytics accurately identify non-canonical peptides in tumor immunopeptidomes.
Chong, C., Müller, M., Pak, H.S., Harnett, D., Huber, F., Grun, D., Leleu, M., Auger, A., Arnaud, M., Stevenson, B.J., Michaux, J., Bilic, I., Hirsekorn, A., Calviello, L., Simó-Riudalbas, L., Planet, E., Lubiński, J., Bryśkiewicz, M., Wiznerowicz, M., Xenarios, I., Zhang, L., Trono, D., Harari, A., Ohler, U., Coukos, G. and Bassani-Sternberg, M.
Nature Communications 11 (1): 1293. 10 March 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., Nora, E.P., Worsley-Hunt, R., Picard, C., Gard, C., van Bemmel, J.G., Servant, N., Zhan, Y., El Marjou, F., Johanneau, C., Diabangouaya, P., Le Saux, A., Lameiras, S., Pipoli da Fonseca, J., Loos, F., Gribnau, J., Baulande, S., Ohler, U., 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., Rodriguez-Fos, E., Helmsauer, K., Burkert, M., MacArthur, I.C., Maag, J., Chamorro, R., Munoz-Perez, N., Puiggròs, M., Dorado Garcia, H., Bei, Y., Röefzaad, C., Bardinet, V., Szymansky, A., Winkler, A., Thole, T., Timme, N., Kasack, K., Fuchs, S., Klironomos, F., Thiessen, N., Blanc, E., Schmelz, K., Künkele, A., Hundsdörfer, P., Rosswog, C., Theissen, J., Beule, D., Deubzer, H., Sauer, S., Toedling, J., Fischer, M., Hertwig, F., Schwarz, R.F., Eggert, A., Torrents, D., Schulte, J.H. and Henssen, A.G.
Nature Genetics 52 (1): 29-34. January 2020

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

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

Purification of cross-linked RNA-protein complexes by phenol-toluol extraction.
Urdaneta, E.C., Vieira-Vieira, C.H., Hick, T., Wessels, H.H., Figini, D., Moschall, R., Medenbach, J., Ohler, U., Granneman, S., 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., Hirsekorn, A., Wurmus, R., Yusuf, D. and Ohler, U.
Genome Biology 20 (1): 42. 21 February 2019

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

SSMART: Sequence-structure motif identification for RNA-binding proteins.
Munteanu, A., 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., 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., Karabacak, A., Glahs, A., Kolundzic, E., Hirsekorn, A., Carda, A., Tursun, B., Zinzen, R.P., 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., Legen, J., Arndt, J., Henkel, S., Hoppe, G., Thieme, C., Ranzini, G., Muino, J.M., Weihe, A., Ohler, U., Weber, G., 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., Ofenbauer, A., Bulut, S.I., Uyar, B., Baytek, G., Sommermeier, A., Seelk, S., He, M., Hirsekorn, A., Vucicevic, D., Akalin, A., Diecke, S., Lacadie, S.A. and Tursun, B.
Developmental Cell 46 (5): 611-626. 10 September 2018

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

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

RNA-bioinformatics: tools, services and databases for the analysis of RNA-based regulation.
Backofen, R., Engelhardt, J., Erxleben, A., Fallmann, J., Grüning, B., Ohler, U., 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., Krestel, R., Ohler, U., 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., Karabacak, A., Krueger, S., Hwang, Y.C., Wang, L.S., Zinzen, R.P. and Ohler, U.
Genome Biology 18 (1): 199. 26 October 2017

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

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

The RNA workbench: best practices for RNA and high-throughput sequencing bioinformatics in Galaxy.
Grüning, B.A., Fallmann, J., Yusuf, D., Will, S., Erxleben, A., Eggenhofer, F., Houwaart, T., Batut, B., Videm, P., Bagnacani, A., Wolfien, M., Lott, S.C., Hoogstrate, Y., Hess, W.R., Wolkenhauer, O., Hoffmann, S., Akalin, A., Ohler, U., 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., Yusuf, D., Wurmus, R., Rajewsky, N., 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., Natarajan, A., Shibata, Y., Song, L., Crawford, G.E., 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., Ibrahim, M.M., Kakumanu, A., Garipler, G., Aydin, B., Al-Sayegh, M.A., Hirsekorn, A., Abdul-Rahman, F., Satija, R., Ohler, U., 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., Wyler, E., Ohler, U., 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., Karaletsos, T., Drewe, P., Sreedharan, V.T., Kuo, D., Singh, K., 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., Calviello, L., Hirsekorn, A., de Pretis, S., Pelizzola, M. and Ohler, U.
Nature Structural & Molecular Biology 24 (1): 86-96. January 2017

High-resolution expression map of the arabidopsis root reveals alternative splicing and lincRNA regulation.
Li, S., Yamada, M., Han, X., 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., Calviello, L., Wu, H.Y.L., Li, F.W., Rothfels, C.J., 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., Drewe-Boss, P., Wiessner, T., Wagner, G., Geue, S., Lee, H.C., Obermueller, D.M., Kahles, A., Behr, J., Sinz, F.H., Raetsch, G. and Wachter, A.
Plant Cell 28 (11): 2715-2734. November 2016

The mRNA-bound proteome of the early fly embryo.
Wessels, H.H., Imami, K., Baltz, A.G., Kolinski, M., Beldovskaya, A., Selbach, M., Small, S., 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., Gehre, M., Dhamija, S., Friis-Hansen, L., Meierhofer, D., 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., Peng, W., Furuuchi, N., Gerhart, J., Rhodes, K., Mukherjee, N., Jimbo, M., Gonye, G.E., Brody, J.R., 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., Mukherjee, N., Wyler, E., Zauber, H., Hirsekorn, A., Selbach, M., Landthaler, M., Obermayer, B. and Ohler, U.
Nature Methods 13 (2): 165-170. February 2016

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

Transcriptional control of tissue formation throughout root development.
Moreno-Risueno, M.A., Sozzani, R., Yardımcı, G.G., Petricka, J.J., Vernoux, T., Blilou, I., Alonso, J., Winter, C.M., Ohler, U., 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., Roedelsperger, C., Prabh, N., Serobyan, V., Markov, G.V., 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., Zauber, H., Bielow, C., Thiel, D., Kutz, K., Calviello, L., Mastrobuoni, G., Rajewsky, N., Kempa, S., 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., Rathjen, T., Hausser, J., Khedkar, A., Kabra, U.D., Pandey, V.K., Sury, M.D., Wessels, H.H., Mollet, I.G., Eliasson, L., Selbach, M., Zinzen, R.P., Zavolan, M., Kadener, S., Tschöp, M., Jastroch, M., 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., Murakawa, Y., Fukao, A., Vandenbon, A., Wessels, H.H., Ori, D., Uehata, T., Tartey, S., Akira, S., Suzuki, Y., Vinuesa, C.G., Ohler, U., Standley, D.M., Landthaler, M., Fujiwara, T. and Takeuchi, O.
Cell 161 (5): 1058-1073. 21 May 2015

Human promoters are intrinsically directional.
Duttke, S.H.C., Lacadie, S.A., Ibrahim, M.M., Glass, C.K., Corcoran, D.L., Benner, C., Heinz, S., 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., Lacadie, S.A. and Ohler, U.
Bioinformatics 31 (1): 48-55. 1 January 2015

Explicit DNase sequence bias modeling enables high-resolution transcription factor footprint detection.
Yardımcı, G.G., Frank, C.L., 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., Koehler, S., Mackenroth, L., Jaeger, M., Hecht, J., Krawitz, P., Graul-Neumann, L., Doelken, S., Ehmke, N., Spielmann, M., Oien, N.C., Schweiger, M.R., Krueger, U., Frommer, G., Fischer, B., Kornak, U., Floettmann, R., Ardeshirdavani, A., Moreau, Y., Lewis, S.E., Haendel, M., Smedley, D., Horn, D., 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., Lebeck, N., Ohler, U. and Li, S.
Bioinformatics 30 (14): 1958-1964. 15 July 2014

COUGER-co-factors associated with uniquely-bound genomic regions.
Munteanu, A., 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., Leonhardt, C.S., Mukherjee, N., Mihailovic, A., Li, S., Max, K.E.A., Meyer, C., Yamaji, M., Cekan, P., Jacobs, N.C., Gerstberger, S., Bognanni, C., Larsson, E., 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., Petricka, J., Corcoran, D.L., Li, S., Winter, C.M., Carda, A., Benfey, P.N., 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., Jacobs, N.C., Hafner, M., Kennington, E.A., Nusbaum, J.D., Tuschl, T., Blackshear, P.J. and Ohler, U.
Genome Biology 15 (1): R12. 8 January 2014

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

Distinct polyadenylation landscapes of diverse human tissues revealed by a modified PA-seq strategy.
Ni, T., Yang, Y., Hafez, D., Yang, W., Kiesewetter, K., Wakabayashi, Y., Ohler, U., 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., 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., Natarajan, A., Looger, L.L., 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., 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., Ni, T., Mukherjee, S., 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., Lekprasert, P., Mukherjee, N., Skalsky, R.L., Corcoran, D.L., Cullen, B.R. and Ohler, U.
Nature Methods 10 (7): 630-633. July 2013

FMRP targets distinct mRNA sequence elements to regulate protein expression.
Ascano, M., Mukherjee, N., Bandaru, P., Miller, J.B., Nusbaum, J.D., Corcoran, D.L., Langlois, C., Munschauer, M., Dewell, S., Hafner, M., Williams, Z., 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., Moore, B.T., Martsberger, B., Mace, D.L., Twigg, R.W., Jung, J., Pruteanu-Malinici, I., Kennedy, S.J., Fricke, G.K., Clark, R.L., 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., Yardimci, G.G., Shibata, Y., Sheffield, N.C., Song, L., Taylor, B.S., Georgiev, S.G., Coetzee, GA., Ohler, U., Furey, T.S., 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., Rach, E.A., Anderson, A.K., 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., Yardimci, G.G., Sheffield, N.C., 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., Philip, N., Reardon, J., Lacsina, J.R., Majoros, W., Chapman, L., Thornburg, C.D., Telen, M.J., Ohler, U., Nicchitta, C.V., 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., Li, D., Ohler, U., 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., Schauer, M.A., Megraw, M., Breakfield, N.W., Thompson, J.W., Georgiev, S., Soderblom, E.J., Ohler, U., Moseley, M.A., 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., Corcoran, D.L., Gottwein, E., Frank, C.L., Kang, D., Hafner, M., Nusbaum, J.D., Feederle, R., Delecluse, H.J., Luftig, M.A., Tuschl, T., 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., Corcoran, D.L., Petricka, J.J., Shen, J., Sae-Seaw, J., Rubio-Somoza, I., Weigel, D., Ohler, U. and Benfey, P.N.
Genome Research 22 (1): 163-176. January 2012

Viral microRNA targetome of KSHV-infected primary effusion lymphoma cell lines.
Gottwein, E., Corcoran, D.L., Mukherjee, N., Skalsky, R.L., Hafner, M., Nusbaum, J.D., Shamulailatpam, P., Love, C.L., Dave, S.S., Tuschl, T., 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., Georgiev, S., Mukherjee, N., Gottwein, E., Skalsky, R.L., 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., Corcoran, D.L., Nusbaum, J.D., Reid, D.W., Georgiev, S., Hafner, M., Ascano, M., Tuschl, T., 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., 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., 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., Zhang, L., Megraw, M., Martinez, N.J., Jiang, E., Yi, C.S., Liu, W., Zeng, A., Taylor-Teeples, M., Kim, D., Ahnert, S., Ohler, U., Ware, D., 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., Winter, D.R., Benjamin, A.M., Corcoran, D.L., Ni, T., Zhu, J. and Ohler, U.
PLoS Genetics 7 (1): e1001274. 13 January 2011

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., Varga, K.M., Gerrard, D.T., Preibisch, S., Corcoran, D.L., Jarrells, J., Ohler, U., 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., Theisen, J.W.M., Hsu, J.Y., Wang, Y.L., Corcoran, D.L., Eustice, M., 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., Jayasurya, K., 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., Corcoran, D.L., Rach, E.A., Song, S., Spana, E.P., Gao, Y., Ohler, U. and Zhu, J.
Nature Methods 7 (7): 521-527. July 2010

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

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

Motif composition, conservation and condition-specificity of single and alternative transcription start sites in the Drosophila genome.
Rach, E.A., Yuan, H.Y., Majoros, W.H., 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., 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., Pereira, F., Jensen, S.T., 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

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

A viral microRNA functions as an orthologue of cellular miR-155.
Gottwein, E., Mukherjee, N., Sachse, C., Frenzel, C., Majoros, W.H., Chi, J.T.A., Braich, R., Manoharan, M., Soutschek, J., 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., Orlando, D.A., Lee, J.Y., Wang, J.Y., Koch, J., Dinneny, J.R., Mace, D., 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., 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., Ohler, U., Burge, C.B. and Ruvkun, G.
Developmental Biology 302 (2): 617-626. 15 February 2007

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., Gordan, R., 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., Lee, J.Y., Twigg, R.W., Colinas, J., Benfey, P.N. and Ohler, U.
Bioinformatics 22 (14): e323-231. 15 July 2006

Optimized mixed Markov models for motif identification.
Huang, W., Umbach, D.M., 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., Colinas, J., Wang, J.Y., Mace, D., 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

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

Patterns of flanking sequence conservation and a characteristic upstream motif for microRNA gene identification.
Ohler, U., Yekta, S., Lim, L.P., 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., Santoso, B., Boulay, T., Dong, E., Ohler, U. and Kadonaga, J.T.
Genes & Development 18 (13): 1606-1617. 1 July 2004

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

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., Niemann, H, Liao, G.C. and Rubin, G.M.
Bioinformatics 17 Suppl 1 : S199-206. 2001

Genome annotation assessment in Drosophila melanogaster.
Reese, M.G., Hartzell, G., Harris, N.L., Ohler, U., 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., Stemmer, G., Harbeck, S. and Niemann, H.
Pacific Symposium on Biocomputing : 380-391. 2000

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

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

Conference or Workshop Item

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

On fine stochastic simulations of liposome-encapsulated PUREsystem(TM).
Calviello, L., 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

Review

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

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

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

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

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

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

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

Letter

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

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

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

Editorial

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

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

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

Preprint

Sensitive dissection of a genomic regulatory landscape using bulk and targeted single-cell activation.
Vučićević, D., Hsu, C.W., Lopez Zepeda, L.S., Burkert, M., Hirsekorn, A., Bilić, I., Kastelić, N., Landthaler, M., Lacadie, S.A. and Ohler, U.
bioRxiv : 2024.09.12.612198. 12 September 2024

High-quality peptide evidence for annotating non-canonical open reading frames as human proteins.
Deutsch, Eric W, Kok, Leron W, Mudge, Jonathan M, Ruiz-Orera, J., Fierro-Monti, Ivo, Sun, Zhi, Abelin, Jennifer G, Alba, M Mar, Aspden, Julie L, Bazzini, Ariel A, Bruford, Elspeth, Brunet, Marie A, Calviello, L., Carr, Steven A, Carvunis, Anne-Ruxandra, Chothani, Sonia, Clauwaert, Jim, Dean, Kellie, Faridi, Pouya, Frankish, Adam, Hubner, N., Ingolia, Nicholas, Magrane, Michele, Martin, Maria Jesus, Martinez, Thomas F, Menschaert, Gerben, Ohler, U., Orchard, Sandra, Rackham, Owen, Roucou, Xavier, Slavoff, Sarah A, Valen, Eivind, Wacholder, Aaron C, Weissman, Jonathan S., Wu, Wei, Xie, Zhi, Choudhary, Jyoti, Bassani-Sternberg, Michal, Vizcaino, Juan Antonio, Ternette, Nicola, Moritz, Robert L., Prensner, John and van Heesch, S.
bioRxiv : 2024.09.09.612016. 9 September 2024

Insights, opportunities and challenges provided by large cell atlases.
Hemberg, M., Marini, F., Ghazanfar, S., Al Ajami, A., Abassi, N., Anchang, B., Benayoun, B.A., Cao, Y., Chen, K., Cuesta-Astroz, Y., DeBruine, Z., Dendrou, K.A., De Vlaminck, I., Imkeller, K., Korsunsky, I., Lederer, A.R., Meysman, P., Miller, C., Mullan, K., Ohler, U., Patikas, N., Schuck, N., Siu, J.H.Y., Triche, T.J., Tsankov, A., van der Laan, S.W., Yajima, M., Yang, J., Zanini, F. and Jelic, I.
arXiv : 2408.06563. 13 August 2024

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

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

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

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

Video

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