Uwe Ohler - Publications

Affiliations: 
Computational Biology and Bioinformatics Duke University, Durham, NC 
Area:
Bioinformatics, Computer Science, Statistics

110 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Nolan TM, Vukašinović N, Hsu CW, Zhang J, Vanhoutte I, Shahan R, Taylor IW, Greenstreet L, Heitz M, Afanassiev A, Wang P, Szekely P, Brosnan A, Yin Y, Schiebinger G, ... Ohler U, et al. Brassinosteroid gene regulatory networks at cellular resolution in the root. Science (New York, N.Y.). 379: eadf4721. PMID 36996230 DOI: 10.1126/science.adf4721  0.305
2022 McGarvey AC, Kopp W, Vučićević D, Mattonet K, Kempfer R, Hirsekorn A, Bilić I, Gil M, Trinks A, Merks AM, Panáková D, Pombo A, Akalin A, Junker JP, Stainier DYR, ... ... Ohler U, et al. Single-cell-resolved dynamics of chromatin architecture delineate cell and regulatory states in zebrafish embryos. Cell Genomics. 2: 100083. PMID 36777038 DOI: 10.1016/j.xgen.2021.100083  0.343
2022 Harnett D, Ambrozkiewicz MC, Zinnall U, Rusanova A, Borisova E, Drescher AN, Couce-Iglesias M, Villamil G, Dannenberg R, Imami K, Münster-Wandowski A, Fauler B, Mielke T, Selbach M, Landthaler M, ... ... Ohler U, et al. A critical period of translational control during brain development at codon resolution. Nature Structural & Molecular Biology. PMID 36482253 DOI: 10.1038/s41594-022-00882-9  0.304
2022 Garipler G, Lu C, Morrissey A, Lopez-Zepeda LS, Pei Y, Vidal SE, Zen Petisco Fiore AP, Aydin B, Stadtfeld M, Ohler U, Mahony S, Sanjana NE, Mazzoni EO. The BTB transcription factors ZBTB11 and ZFP131 maintain pluripotency by repressing pro-differentiation genes. Cell Reports. 38: 110524. PMID 35294876 DOI: 10.1016/j.celrep.2022.110524  0.32
2021 Harnett D, Meerdink E, Calviello L, Sydow D, Ohler U. Genome-Wide Analysis of Actively Translated Open Reading Frames Using RiboTaper/ORFquant. Methods in Molecular Biology (Clifton, N.J.). 2252: 331-346. PMID 33765284 DOI: 10.1007/978-1-0716-1150-0_16  0.312
2020 Lenzen B, Rühle T, Lehniger MK, Okuzaki A, Labs M, Muino JM, Ohler U, Leister D, Schmitz-Linneweber C. 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. International Journal of Molecular Sciences. 21. PMID 32781615 DOI: 10.3390/Ijms21165633  0.423
2020 Kopp W, Monti R, Tamburrini A, Ohler U, Akalin A. Deep learning for genomics using Janggu. Nature Communications. 11: 3488. PMID 32661261 DOI: 10.1038/S41467-020-17155-Y  0.354
2020 Calviello L, Hirsekorn A, Ohler U. Quantification of translation uncovers the functions of the alternative transcriptome. Nature Structural & Molecular Biology. PMID 32601440 DOI: 10.1038/S41594-020-0450-4  0.509
2020 Ghanbari M, Ohler U. Deep neural networks for interpreting RNA-binding protein target preferences. Genome Research. PMID 31992613 DOI: 10.1101/Gr.247494.118  0.429
2019 Galupa R, Nora EP, Worsley-Hunt R, Picard C, Gard C, van Bemmel JG, Servant N, Zhan Y, El Marjou F, Johanneau C, Diabangouaya P, Le Saux A, Lameiras S, Pipoli da Fonseca J, Loos F, ... ... Ohler U, et al. A Conserved Noncoding Locus Regulates Random Monoallelic Xist Expression across a Topological Boundary. Molecular Cell. PMID 31759823 DOI: 10.1016/J.Molcel.2019.10.030  0.411
2019 van Heesch S, Witte F, Schneider-Lunitz V, Schulz JF, Adami E, Faber AB, Kirchner M, Maatz H, Blachut S, Sandmann CL, Kanda M, Worth CL, Schafer S, Calviello L, Merriott R, ... ... Ohler U, et al. The Translational Landscape of the Human Heart. Cell. PMID 31155234 DOI: 10.1016/J.Cell.2019.05.010  0.408
2019 Szcześniak MW, Wanowska E, Mukherjee N, Ohler U, Makałowska I. Towards a deeper annotation of human lncRNAs. Biochimica Et Biophysica Acta. Gene Regulatory Mechanisms. PMID 31128317 DOI: 10.1016/J.Bbagrm.2019.05.003  0.621
2019 Wessels HH, Lebedeva S, Hirsekorn A, Wurmus R, Akalin A, Mukherjee N, Ohler U. Global identification of functional microRNA-mRNA interactions in Drosophila. Nature Communications. 10: 1626. PMID 30967537 DOI: 10.1038/S41467-019-09586-Z  0.608
2019 Urdaneta EC, Vieira-Vieira CH, Hick T, Wessels HH, Figini D, Moschall R, Medenbach J, Ohler U, Granneman S, Selbach M, Beckmann BM. Purification of cross-linked RNA-protein complexes by phenol-toluol extraction. Nature Communications. 10: 990. PMID 30824702 DOI: 10.1038/S41467-019-08942-3  0.386
2019 Karabacak Calviello A, Hirsekorn A, Wurmus R, Yusuf D, Ohler U. Reproducible inference of transcription factor footprints in ATAC-seq and DNase-seq datasets using protocol-specific bias modeling. Genome Biology. 20: 42. PMID 30791920 DOI: 10.1186/S13059-019-1654-Y  0.494
2018 Mukherjee N, Wessels HH, Lebedeva S, Sajek M, Ghanbari M, Garzia A, Munteanu A, Yusuf D, Farazi T, Hoell JI, Akat KM, Akalin A, Tuschl T, Ohler U. Deciphering human ribonucleoprotein regulatory networks. Nucleic Acids Research. PMID 30517751 DOI: 10.1093/Nar/Gky1185  0.643
2018 Drewe-Boss P, Wessels HH, Ohler U. omniCLIP: probabilistic identification of protein-RNA interactions from CLIP-seq data. Genome Biology. 19: 183. PMID 30384847 DOI: 10.1186/S13059-018-1521-2  0.402
2018 Ibrahim MM, Karabacak A, Glahs A, Kolundzic E, Hirsekorn A, Carda A, Tursun B, Zinzen RP, Lacadie SA, Ohler U. Determinants of promoter and enhancer transcription directionality in metazoans. Nature Communications. 9: 4472. PMID 30367057 DOI: 10.1038/S41467-018-06962-Z  0.44
2018 Qu Y, Legen J, Arndt J, Henkel S, Hoppe G, Thieme C, Ranzini G, Muino JM, Weihe A, Ohler U, Weber G, Ostersetzer O, Schmitz-Linneweber C. Ectopic Transplastomic Expression of a Synthetic MatK Gene Leads to Cotyledon-Specific Leaf Variegation. Frontiers in Plant Science. 9: 1453. PMID 30337934 DOI: 10.3389/Fpls.2018.01453  0.462
2018 Munteanu A, Mukherjee N, Ohler U. SSMART: Sequence-structure motif identification for RNA-binding proteins. Bioinformatics (Oxford, England). PMID 29893814 DOI: 10.1093/bioinformatics/bty404  0.616
2018 Orenstein Y, Ohler U, Berger B. Finding RNA structure in the unstructured RBPome. Bmc Genomics. 19: 154. PMID 29463232 DOI: 10.1186/S12864-018-4540-1  0.386
2017 Hafez D, Karabacak A, Krueger S, Hwang YC, Wang LS, Zinzen RP, Ohler U. McEnhancer: predicting gene expression via semi-supervised assignment of enhancers to target genes. Genome Biology. 18: 199. PMID 29070071 DOI: 10.1186/S13059-017-1316-X  0.464
2017 Hinze F, Drewe-Boß P, Milek M, Ohler U, Landthaler M, Gotthardt M. Expanding the map of protein-RNA interaction sites via cell fusion followed by PAR-CLIP. Rna Biology. 0. PMID 29028411 DOI: 10.1080/15476286.2017.1384120  0.429
2017 Heller D, Krestel R, Ohler U, Vingron M, Marsico A. ssHMM: extracting intuitive sequence-structure motifs from high-throughput RNA-binding protein data. Nucleic Acids Research. PMID 28977546 DOI: 10.1093/Nar/Gkx756  0.42
2017 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, et al. RNA localization is a key determinant of neurite-enriched proteome. Nature Communications. 8: 583. PMID 28928394 DOI: 10.1038/S41467-017-00690-6  0.338
2017 Calviello L, Ohler U. Beyond Read-Counts: Ribo-seq Data Analysis to Understand the Functions of the Transcriptome. Trends in Genetics : Tig. PMID 28887026 DOI: 10.1016/J.Tig.2017.08.003  0.444
2017 Milek M, Imami K, Mukherjee N, De Bortoli F, Zinnall U, Hazapis O, Trahan C, Oeffinger M, Heyd F, Ohler U, Selbach M, Landthaler M. DDX54 regulates transcriptome dynamics during DNA damage response. Genome Research. PMID 28596291 DOI: 10.1101/Gr.218438.116  0.608
2017 Grüning BA, Fallmann J, Yusuf D, Will S, Erxleben A, Eggenhofer F, Houwaart T, Batut B, Videm P, Bagnacani A, Wolfien M, Lott SC, Hoogstrate Y, Hess WR, Wolkenhauer O, ... ... Ohler U, et al. The RNA workbench: best practices for RNA and high-throughput sequencing bioinformatics in Galaxy. Nucleic Acids Research. PMID 28582575 DOI: 10.1093/Nar/Gkx409  0.361
2017 Backofen R, Engelhardt J, Erxleben A, Fallmann J, Grüning B, Ohler U, Rajewsky N, Stadler PF. RNA-bioinformatics: Tools, Services and Databases for the Analysis of RNA-based Regulation. Journal of Biotechnology. PMID 28554830 DOI: 10.1016/J.Jbiotec.2017.05.019  0.418
2017 Uyar B, Yusuf D, Wurmus R, Rajewsky N, Ohler U, Akalin A. RCAS: an RNA centric annotation system for transcriptome-wide regions of interest. Nucleic Acids Research. PMID 28334930 DOI: 10.1093/Nar/Gkx120  0.399
2017 Maatouk DM, Natarajan A, Shibata Y, Song L, Crawford GE, Ohler U, Capel B. Genome-wide identification of regulatory elements in Sertoli cells. Development (Cambridge, England). PMID 28087634 DOI: 10.1242/Dev.142554  0.484
2017 Piechotta M, Wyler E, Ohler U, Landthaler M, Dieterich C. JACUSA: site-specific identification of RNA editing events from replicate sequencing data. Bmc Bioinformatics. 18: 7. PMID 28049429 DOI: 10.1186/S12859-016-1432-8  0.427
2016 Velasco S, Ibrahim MM, Kakumanu A, Garipler G, Aydin B, Al-Sayegh MA, Hirsekorn A, Abdul-Rahman F, Satija R, Ohler U, Mahony S, Mazzoni EO. A Multi-step Transcriptional and Chromatin State Cascade Underlies Motor Neuron Programming from Embryonic Stem Cells. Cell Stem Cell. PMID 27939218 DOI: 10.1016/J.Stem.2016.11.006  0.371
2016 Mukherjee N, Calviello L, Hirsekorn A, de Pretis S, Pelizzola M, Ohler U. Integrative classification of human coding and noncoding genes through RNA metabolism profiles. Nature Structural & Molecular Biology. PMID 27870833 DOI: 10.1038/Nsmb.3325  0.622
2016 Li S, Yamada M, Han X, Ohler U, Benfey PN. High-Resolution Expression Map of the Arabidopsis Root Reveals Alternative Splicing and lincRNA Regulation. Developmental Cell. 39: 508-522. PMID 27840108 DOI: 10.1016/J.Devcel.2016.10.012  0.437
2016 Hsu PY, Calviello L, Wu HL, Li FW, Rothfels CJ, Ohler U, Benfey PN. Super-resolution ribosome profiling reveals unannotated translation events in Arabidopsis. Proceedings of the National Academy of Sciences of the United States of America. PMID 27791167 DOI: 10.1073/Pnas.1614788113  0.456
2016 Wessels HH, Imami K, Baltz AG, Kolinksi M, Beldovskaya A, Selbach M, Small S, Ohler U, Landthaler M. The mRNA-bound proteome of the early fly embryo. Genome Research. PMID 27197210 DOI: 10.1101/Gr.200386.115  0.469
2016 Lacadie SA, Ibrahim MM, Gokhale SA, Ohler U. Divergent Transcription and Epigenetic Directionality of Human Promoters. The Febs Journal. PMID 27115538 DOI: 10.1111/Febs.13747  0.445
2016 Wessels HH, Hirsekorn A, Ohler U, Mukherjee N. Identifying RBP Targets with RIP-seq. Methods in Molecular Biology (Clifton, N.J.). 1358: 141-52. PMID 26463382 DOI: 10.1007/978-1-4939-3067-8_9  0.625
2015 Calviello L, Mukherjee N, Wyler E, Zauber H, Hirsekorn A, Selbach M, Landthaler M, Obermayer B, Ohler U. Detecting actively translated open reading frames in ribosome profiling data. Nature Methods. PMID 26657557 DOI: 10.1038/Nmeth.3688  0.652
2015 Moreno-Risueno MA, Sozzani R, Yardımcı GG, Petricka JJ, Vernoux T, Blilou I, Alonso J, Winter CM, Ohler U, Scheres B, Benfey PN. Transcriptional control of tissue formation throughout root development. Science (New York, N.Y.). 350: 426-30. PMID 26494755 DOI: 10.1126/Science.Aad1171  0.718
2015 Mino T, Murakawa Y, Fukao A, Vandenbon A, Wessels HH, Ori D, Uehata T, Tartey S, Akira S, Suzuki Y, Vinuesa CG, Ohler U, Standley DM, Landthaler M, Fujiwara T, et al. Regnase-1 and Roquin Regulate a Common Element in Inflammatory mRNAs by Spatiotemporally Distinct Mechanisms. Cell. 161: 1058-73. PMID 26000482 DOI: 10.1016/J.Cell.2015.04.029  0.354
2015 Duttke SH, Lacadie SA, Ibrahim MM, Glass CK, Corcoran DL, Benner C, Heinz S, Kadonaga JT, Ohler U. Human promoters are intrinsically directional. Molecular Cell. 57: 674-84. PMID 25639469 DOI: 10.1016/J.Molcel.2014.12.029  0.481
2015 Ibrahim MM, Lacadie SA, Ohler U. JAMM: a peak finder for joint analysis of NGS replicates. Bioinformatics (Oxford, England). 31: 48-55. PMID 25223640 DOI: 10.1093/Bioinformatics/Btu568  0.349
2014 Yard?mc? GGü, Frank CL, Crawford GE, Ohler U. Explicit DNase sequence bias modeling enables high-resolution transcription factor footprint detection Nucleic Acids Research. 42: 11865-11878. PMID 25294828 DOI: 10.1093/Nar/Gku810  0.437
2014 Morton T, Petricka J, Corcoran DL, Li S, Winter CM, Carda A, Benfey PN, Ohler U, Megraw M. Paired-end analysis of transcription start sites in Arabidopsis reveals plant-specific promoter signatures. The Plant Cell. 26: 2746-60. PMID 25035402 DOI: 10.1105/Tpc.114.125617  0.466
2014 Munteanu A, Ohler U, Gordân R. COUGER--co-factors associated with uniquely-bound genomic regions. Nucleic Acids Research. 42: W461-7. PMID 24861628 DOI: 10.1093/Nar/Gku435  0.41
2014 Farazi TA, Leonhardt CS, Mukherjee N, Mihailovic A, Li S, Max KE, Meyer C, Yamaji M, Cekan P, Jacobs NC, Gerstberger S, Bognanni C, Larsson E, Ohler U, Tuschl T. Identification of the RNA recognition element of the RBPMS family of RNA-binding proteins and their transcriptome-wide mRNA targets. Rna (New York, N.Y.). 20: 1090-102. PMID 24860013 DOI: 10.1261/Rna.045005.114  0.61
2014 Majoros WH, Lebeck N, Ohler U, Li S. Improved transcript isoform discovery using ORF graphs. Bioinformatics (Oxford, England). 30: 1958-64. PMID 24659106 DOI: 10.1093/Bioinformatics/Btu160  0.411
2014 Mukherjee N, Jacobs NC, Hafner M, Kennington EA, Nusbaum JD, Tuschl T, Blackshear PJ, Ohler U. Global target mRNA specification and regulation by the RNA-binding protein ZFP36. Genome Biology. 15: R12. PMID 24401661 DOI: 10.1186/Gb-2014-15-1-R12  0.666
2013 Ohler U. Using machine learning to identify disease-relevant regulatory RNAs. Proceedings of the National Academy of Sciences of the United States of America. 110: 15516-7. PMID 24046375 DOI: 10.1073/Pnas.1315199110  0.48
2013 Ni T, Yang Y, Hafez D, Yang W, Kiesewetter K, Wakabayashi Y, Ohler U, Peng W, Zhu J. Distinct polyadenylation landscapes of diverse human tissues revealed by a modified PA-seq strategy. Bmc Genomics. 14: 615. PMID 24025092 DOI: 10.1186/1471-2164-14-615  0.38
2013 Megraw M, Mukherjee S, Ohler U. Sustained-input switches for transcription factors and microRNAs are central building blocks of eukaryotic gene circuits. Genome Biology. 14: R85. PMID 23972209 DOI: 10.1186/Gb-2013-14-8-R85  0.356
2013 Munger SC, Natarajan A, Looger LL, Ohler U, Capel B. Fine time course expression analysis identifies cascades of activation and repression and maps a putative regulator of mammalian sex determination. Plos Genetics. 9: e1003630. PMID 23874228 DOI: 10.1371/Journal.Pgen.1003630  0.405
2013 Li S, Liberman LM, Mukherjee N, Benfey PN, Ohler U. Integrated detection of natural antisense transcripts using strand-specific RNA sequencing data. Genome Research. 23: 1730-9. PMID 23816784 DOI: 10.1101/Gr.149310.112  0.61
2013 Pruteanu-Malinici I, Majoros WH, Ohler U. Automated annotation of gene expression image sequences via non-parametric factor analysis and conditional random fields. Bioinformatics (Oxford, England). 29: i27-35. PMID 23812993 DOI: 10.1093/Bioinformatics/Btt206  0.418
2013 Hafez D, Ni T, Mukherjee S, Zhu J, Ohler U. Genome-wide identification and predictive modeling of tissue-specific alternative polyadenylation. Bioinformatics (Oxford, England). 29: i108-16. PMID 23812974 DOI: 10.1093/Bioinformatics/Btt233  0.479
2013 Majoros WH, Lekprasert P, Mukherjee N, Skalsky RL, Corcoran DL, Cullen BR, Ohler U. MicroRNA target site identification by integrating sequence and binding information. Nature Methods. 10: 630-3. PMID 23708386 DOI: 10.1038/Nmeth.2489  0.755
2012 Ascano M, Mukherjee N, Bandaru P, Miller JB, Nusbaum JD, Corcoran DL, Langlois C, Munschauer M, Dewell S, Hafner M, Williams Z, Ohler U, Tuschl T. FMRP targets distinct mRNA sequence elements to regulate protein expression. Nature. 492: 382-6. PMID 23235829 DOI: 10.1038/Nature11737  0.617
2012 Tewari AK, Yardimci GG, Shibata Y, Sheffield NC, Song L, Taylor BS, Georgiev SG, Coetzee GA, Ohler U, Furey TS, Crawford GE, Febbo PG. Chromatin accessibility reveals insights into androgen receptor activation and transcriptional specificity. Genome Biology. 13: R88. PMID 23034120 DOI: 10.1186/Gb-2012-13-10-R88  0.763
2012 Busch W, Moore BT, Martsberger B, Mace DL, Twigg RW, Jung J, Pruteanu-Malinici I, Kennedy SJ, Fricke GK, Clark RL, Ohler U, Benfey PN. A microfluidic device and computational platform for high-throughput live imaging of gene expression. Nature Methods. 9: 1101-6. PMID 23023597 DOI: 10.1038/Nmeth.2185  0.744
2012 Katzenberger RJ, Rach EA, Anderson AK, Ohler U, Wassarman DA. The Drosophila Translational Control Element (TCE) is required for high-level transcription of many genes that are specifically expressed in testes. Plos One. 7: e45009. PMID 22984601 DOI: 10.1371/Journal.Pone.0045009  0.81
2012 Natarajan A, Yardimci GG, Sheffield NC, Crawford GE, Ohler U. Predicting cell-type-specific gene expression from regions of open chromatin. Genome Research. 22: 1711-22. PMID 22955983 DOI: 10.1101/Gr.135129.111  0.789
2012 Ding J, Li D, Ohler U, Guan J, Zhou S. Genome-wide search for miRNA-target interactions in Arabidopsis thaliana with an integrated approach. Bmc Genomics. 13: S3. PMID 22759612 DOI: 10.1186/1471-2164-13-S3-S3  0.379
2012 Petricka JJ, Schauer MA, Megraw M, Breakfield NW, Thompson JW, Georgiev S, Soderblom EJ, Ohler U, Moseley MA, Grossniklaus U, Benfey PN. The protein expression landscape of the Arabidopsis root. Proceedings of the National Academy of Sciences of the United States of America. 109: 6811-8. PMID 22447775 DOI: 10.1073/Pnas.1202546109  0.329
2012 Skalsky RL, Corcoran DL, Gottwein E, Frank CL, Kang D, Hafner M, Nusbaum JD, Feederle R, Delecluse HJ, Luftig MA, Tuschl T, Ohler U, Cullen BR. The viral and cellular microRNA targetome in lymphoblastoid cell lines. Plos Pathogens. 8: e1002484. PMID 22291592 DOI: 10.1371/Journal.Ppat.1002484  0.354
2012 Breakfield NW, Corcoran DL, Petricka JJ, Shen J, Sae-Seaw J, Rubio-Somoza I, Weigel D, Ohler U, Benfey PN. High-resolution experimental and computational profiling of tissue-specific known and novel miRNAs in Arabidopsis. Genome Research. 22: 163-76. PMID 21940835 DOI: 10.1101/Gr.123547.111  0.405
2012 Skalsky RL, Corcoran DL, Gottwein E, Frank CL, Hafner M, Nusbaum JD, Feederle R, Delecluse H, Luftig M, Tuschl T, Ohler U, Cullen BR. Analysis of the miRNA targetome in EBV-infected B cells Infectious Agents and Cancer. 7. DOI: 10.1186/1750-9378-7-S1-O2  0.374
2011 Gottwein E, Corcoran DL, Mukherjee N, Skalsky RL, Hafner M, Nusbaum JD, Shamulailatpam P, Love CL, Dave SS, Tuschl T, Ohler U, Cullen BR. Viral microRNA targetome of KSHV-infected primary effusion lymphoma cell lines. Cell Host & Microbe. 10: 515-26. PMID 22100165 DOI: 10.1016/J.Chom.2011.09.012  0.57
2011 Corcoran DL, Georgiev S, Mukherjee N, Gottwein E, Skalsky RL, Keene JD, Ohler U. PARalyzer: definition of RNA binding sites from PAR-CLIP short-read sequence data. Genome Biology. 12: R79. PMID 21851591 DOI: 10.1186/Gb-2011-12-8-R79  0.735
2011 Pruteanu-Malinici I, Mace DL, Ohler U. Automatic annotation of spatial expression patterns via sparse Bayesian factor models. Plos Computational Biology. 7: e1002098. PMID 21814502 DOI: 10.1371/Journal.Pcbi.1002098  0.775
2011 Mukherjee N, Corcoran DL, Nusbaum JD, Reid DW, Georgiev S, Hafner M, Ascano M, Tuschl T, Ohler U, Keene JD. Integrative regulatory mapping indicates that the RNA-binding protein HuR couples pre-mRNA processing and mRNA stability. Molecular Cell. 43: 327-39. PMID 21723170 DOI: 10.1016/J.Molcel.2011.06.007  0.739
2011 Lekprasert P, Mayhew M, Ohler U. Assessing the utility of thermodynamic features for microRNA target prediction under relaxed seed and no conservation requirements. Plos One. 6: e20622. PMID 21674004 DOI: 10.1371/Journal.Pone.0020622  0.747
2011 Rach EA, Winter DR, Benjamin AM, Corcoran DL, Ni T, Zhu J, Ohler U. Transcription initiation patterns indicate divergent strategies for gene regulation at the chromatin level. Plos Genetics. 7: e1001274. PMID 21249180 DOI: 10.1371/Journal.Pgen.1001274  0.816
2011 Brady SM, Zhang L, Megraw M, Martinez NJ, Jiang E, Yi CS, Liu W, Zeng A, Taylor-Teeples M, Kim D, Ahnert S, Ohler U, Ware D, Walhout AJ, Benfey PN. A stele-enriched gene regulatory network in the Arabidopsis root. Molecular Systems Biology. 7: 459. PMID 21245844 DOI: 10.1038/Msb.2010.114  0.488
2010 Majoros WH, Ohler U. Modeling the evolution of regulatory elements by simultaneous detection and alignment with phylogenetic pair HMMs. Plos Computational Biology. 6: e1001037. PMID 21187896 DOI: 10.1371/Journal.Pcbi.1001037  0.444
2010 Kalinka AT, Varga KM, Gerrard DT, Preibisch S, Corcoran DL, Jarrells J, Ohler U, Bergman CM, Tomancak P. Gene expression divergence recapitulates the developmental hourglass model. Nature. 468: 811-4. PMID 21150996 DOI: 10.1038/Nature09634  0.65
2010 Parry TJ, Theisen JW, Hsu JY, Wang YL, Corcoran DL, Eustice M, Ohler U, Kadonaga JT. The TCT motif, a key component of an RNA polymerase II transcription system for the translational machinery. Genes & Development. 24: 2013-8. PMID 20801935 DOI: 10.1101/Gad.1951110  0.481
2010 Arunachalam M, Jayasurya K, Tomancak P, Ohler U. An alignment-free method to identify candidate orthologous enhancers in multiple Drosophila genomes. Bioinformatics (Oxford, England). 26: 2109-15. PMID 20624780 DOI: 10.1093/Bioinformatics/Btq358  0.693
2010 Ni T, Corcoran DL, Rach EA, Song S, Spana EP, Gao Y, Ohler U, Zhu J. A paired-end sequencing strategy to map the complex landscape of transcription initiation. Nature Methods. 7: 521-7. PMID 20495556 DOI: 10.1038/Nmeth.1464  0.821
2010 Tomancak P, Ohler U. Mapping the complexity of transcription control in higher eukaryotes. Genome Biology. 11: 115. PMID 20441601 DOI: 10.1186/Gb-2010-11-4-115  0.677
2010 Georgiev S, Boyle AP, Jayasurya K, Ding X, Mukherjee S, Ohler U. Evidence-ranked motif identification. Genome Biology. 11: R19. PMID 20156354 DOI: 10.1186/Gb-2010-11-2-R19  0.421
2010 Ohler U, Wassarman DA. Promoting developmental transcription. Development (Cambridge, England). 137: 15-26. PMID 20023156 DOI: 10.1242/Dev.035493  0.724
2010 Mace DL, Varnado N, Zhang W, Frise E, Ohler U. Extraction and comparison of gene expression patterns from 2D RNA in situ hybridization images. Bioinformatics (Oxford, England). 26: 761-9. PMID 19942587 DOI: 10.1093/Bioinformatics/Btp658  0.768
2010 Ni T, Corcoran D, Carda A, Rach E, Song S, Xie B, Gao Y, Ohler U, Zhu J. Paired-end analysis of transcriptional start sites Nature Protocols. DOI: 10.1038/Nprot.2010.55  0.793
2009 Rach EA, Yuan HY, Majoros WH, Tomancak P, Ohler U. Motif composition, conservation and condition-specificity of single and alternative transcription start sites in the Drosophila genome. Genome Biology. 10: R73. PMID 19589141 DOI: 10.1186/Gb-2009-10-7-R73  0.817
2009 Yokoyama KD, Ohler U, Wray GA. Measuring spatial preferences at fine-scale resolution identifies known and novel cis-regulatory element candidates and functional motif-pair relationships. Nucleic Acids Research. 37: e92. PMID 19483094 DOI: 10.1093/Nar/Gkp423  0.442
2009 Megraw M, Pereira F, Jensen ST, Ohler U, Hatzigeorgiou AG. A transcription factor affinity-based code for mammalian transcription initiation. Genome Research. 19: 644-56. PMID 19141595 DOI: 10.1101/Gr.085449.108  0.539
2008 Holste D, Ohler U. Strategies for identifying RNA splicing regulatory motifs and predicting alternative splicing events. Plos Computational Biology. 4: e21. PMID 18225947 DOI: 10.1371/Journal.Pcbi.0040021  0.386
2007 Gottwein E, Mukherjee N, Sachse C, Frenzel C, Majoros WH, Chi JT, Braich R, Manoharan M, Soutschek J, Ohler U, Cullen BR. A viral microRNA functions as an orthologue of cellular miR-155. Nature. 450: 1096-9. PMID 18075594 DOI: 10.1038/Nature05992  0.56
2007 Brady SM, Orlando DA, Lee JY, Wang JY, Koch J, Dinneny JR, Mace D, Ohler U, Benfey PN. A high-resolution root spatiotemporal map reveals dominant expression patterns. Science (New York, N.Y.). 318: 801-6. PMID 17975066 DOI: 10.1126/Science.1146265  0.777
2007 Huang W, Nevins JR, Ohler U. Phylogenetic simulation of promoter evolution: estimation and modeling of binding site turnover events and assessment of their impact on alignment tools. Genome Biology. 8: R225. PMID 17956628 DOI: 10.1186/Gb-2007-8-10-R225  0.422
2007 Majoros WH, Ohler U. Spatial preferences of microRNA targets in 3' untranslated regions. Bmc Genomics. 8: 152. PMID 17555584 DOI: 10.1186/1471-2164-8-152  0.468
2007 Ruvinsky I, Ohler U, Burge CB, Ruvkun G. Detection of broadly expressed neuronal genes in C. elegans. Developmental Biology. 302: 617-26. PMID 17046742 DOI: 10.1016/J.Ydbio.2006.09.014  0.618
2006 Ohler U. Identification of core promoter modules in Drosophila and their application in accurate transcription start site prediction. Nucleic Acids Research. 34: 5943-50. PMID 17068082 DOI: 10.1093/Nar/Gkl608  0.51
2006 Bajic VB, Brent MR, Brown RH, Frankish A, Harrow J, Ohler U, Solovyev VV, Tan SL. Performance assessment of promoter predictions on ENCODE regions in the EGASP experiment. Genome Biology. 7: S3.1-13. PMID 16925837 DOI: 10.1186/Gb-2006-7-S1-S3  0.381
2006 Narlikar L, Gordân R, Ohler U, Hartemink AJ. Informative priors based on transcription factor structural class improve de novo motif discovery. Bioinformatics (Oxford, England). 22: e384-92. PMID 16873497 DOI: 10.1093/Bioinformatics/Btl251  0.427
2006 Mace DL, Lee JY, Twigg RW, Colinas J, Benfey PN, Ohler U. Quantification of transcription factor expression from Arabidopsis images. Bioinformatics (Oxford, England). 22: e323-31. PMID 16873489 DOI: 10.1093/Bioinformatics/Btl228  0.759
2006 Huang W, Umbach DM, Ohler U, Li L. Optimized mixed Markov models for motif identification. Bmc Bioinformatics. 7: 279. PMID 16749929 DOI: 10.1186/1471-2105-7-279  0.406
2006 Lee JY, Colinas J, Wang JY, Mace D, Ohler U, Benfey PN. Transcriptional and posttranscriptional regulation of transcription factor expression in Arabidopsis roots. Proceedings of the National Academy of Sciences of the United States of America. 103: 6055-60. PMID 16581911 DOI: 10.1073/Pnas.0510607103  0.808
2005 Ohler U, Shomron N, Burge CB. Recognition of unknown conserved alternatively spliced exons. Plos Computational Biology. 1: 113-22. PMID 16110330 DOI: 10.1371/Journal.Pcbi.0010015  0.669
2005 Ohler U, Shomron N, Burge CB. Recognition of unknown conserved alternatively spliced exons Plos Computational Biology. 1: 0113-0122. DOI: 10.1371/journal.pcbi.0010015  0.563
2004 Ohler U, Yekta S, Lim LP, Bartel DP, Burge CB. Patterns of flanking sequence conservation and a characteristic upstream motif for microRNA gene identification. Rna (New York, N.Y.). 10: 1309-22. PMID 15317971 DOI: 10.1261/Rna.5206304  0.674
2004 Lim CY, Santoso B, Boulay T, Dong E, Ohler U, Kadonaga JT. The MTE, a new core promoter element for transcription by RNA polymerase II. Genes & Development. 18: 1606-17. PMID 15231738 DOI: 10.1101/Gad.1193404  0.45
2002 Ohler U, Liao GC, Niemann H, Rubin GM. Computational analysis of core promoters in the Drosophila genome. Genome Biology. 3: RESEARCH0087. PMID 12537576 DOI: 10.1186/Gb-2002-3-12-Research0087  0.73
2001 Ohler U, Niemann H, Liao Gc, Rubin GM. Joint modeling of DNA sequence and physical properties to improve eukaryotic promoter recognition. Bioinformatics (Oxford, England). 17: S199-206. PMID 11473010 DOI: 10.1093/Bioinformatics/17.Suppl_1.S199  0.529
2001 Ohler U, Niemann H. Identification and analysis of eukaryotic promoters: Recent computational approaches Trends in Genetics. 17: 56-60. PMID 11173099 DOI: 10.1016/S0168-9525(00)02174-0  0.45
2000 Ohler U. Promoter prediction on a genomic scale - The Adh experience Genome Research. 10: 539-542. PMID 10779494 DOI: 10.1101/Gr.10.4.539  0.39
2000 Reese MG, Hartzell G, Harris NL, Ohler U, Abril JF, Lewis SE. Genome annotation assessment in Drosophila melanogaster Genome Research. 10: 483-501. PMID 10779488 DOI: 10.1101/Gr.10.4.483  0.798
1999 Ohler U, Harbeck S, Niemann H, Nöth E, Reese MG. Interpolated Markov chains for eukaryotic promoter recognition Bioinformatics. 15: 362-369. PMID 10366656 DOI: 10.1093/Bioinformatics/15.5.362  0.407
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