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2018

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

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

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

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

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

SSMART: Sequence-structure motif identification for RNA-binding proteins.
Munteanu, A. and Mukherjee, N. and Ohler, U.
Bioinformatics 11 June 2018 (In Press)

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

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

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

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

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

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

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

2017

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

2016

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

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

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

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

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

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

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

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

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

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

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

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

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

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

2015

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

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

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

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

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

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

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

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

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

2014

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

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

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

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

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

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

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

2013

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

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

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

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

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

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

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

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

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

2012

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

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

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

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

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

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

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

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

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

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

2011

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

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

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

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

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

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

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

2010

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

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

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

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

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

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

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

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

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

2009

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

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

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

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

2008

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

2007

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

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

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

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

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

2006

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

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

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

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

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

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

2005

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

2004

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

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

2002

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

2001

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

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

2000

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

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

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

1999

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

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

This list was generated on Wed Nov 14 02:19:11 2018 CET.
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