| 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 |
0.344 |
|
| 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 |
0.321 |
|
| 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 |
0.422 |
|
| 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 |
0.353 |
|
| 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 |
0.622 |
|
| 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 |
0.617 |
|
| 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 |
0.609 |
|
| 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 |
0.623 |
|
| 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 |
0.446 |
|
| 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 |
0.723 |
|
| 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 |
0.48 |
|
| 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 |
0.618 |
|
| 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 |
0.767 |
|
| 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 |
0.811 |
|
| 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 |
0.793 |
|
| 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 |
0.651 |
|
| 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 |
0.694 |
|
| 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 |
0.619 |
|
| 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 |
0.564 |
|
| 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 |
|
| Show low-probability matches. |