Computational Regulatory Genomics

Publications

Reproducible inference of transcription factor footprints in ATAC-seq and DNase-seq datasets using protocol-specific bias modeling

Aslihan Karabacak Antje Hirsekorn,  Wurmus, Ricardo,  Yusuf, Dilmurat,  Uwe Ohler 
Genome Biology 2019;   DOI   PubMed  

Purification of cross-linked RNA-protein complexes by phenol-toluol extraction

Vieira-Vieira, Erika C. Urdanetaand Carlos H.,  Hick, Timon,  Hans-Hermann Wessels,  Figini, Davide,  Moschall, Rebecca,  Medenbach, Jan,  Uwe Ohler,  Granneman, Sander,  Selbach, Matthias,  Beckmann, Benedikt M. 
Nature Communications 2019;   DOI  

Global identification of functional microRNA-mRNA interactions in Drosophila

Hans-Hermann Wessels Svetlana Lebedeva Antje Hirsekorn,  Wurmus, Ricardo,  Altuna Akalin Neelanjan Mukherjee Uwe Ohler 
Nature Communications 2019;   DOI  

Deciphering human ribonucleoprotein regulatory networks

Neelanjan Mukherjee Hans-Hermann Wessels Svetlana Lebedeva,  Sajek, Marcin,  Mahsa Ghanbari,  Garzia, Aitor,  Alina-Cristina Munteanu,  Yusuf, Dilmurat,  Farazi, Thalia,  Hoell, Jessica I.,  Akat, Kemal M.,  Altuna Akalin,  Tuschl, Thomas,  Uwe Ohler 
Nucleic Acids Research 2019;   DOI  

Expanding the map of protein-RNA interaction sites via cell fusion followed by PAR-CLIP

Hinze, Florian,  Drewe-Boss, Philipp,  Milek, Miha,  Uwe Ohler,  Landthaler, Markus,  Gotthardt, Michael 
RNA Biology 2018;  

omniCLIP: probabilistic identification of protein-RNA interactions from CLIP-seq data

Drewe-Boss, Philipp,  Hans-Hermann Wessels Uwe Ohler 
Genome Biology 2018;   DOI  

JACUSA: site-specific identification of RNA editing events from replicate sequencing data

Piechotta, M.,  Wyler, E.,  Uwe Ohler,  Landthaler, M.,  Dieterich, C. 
BMC Bioinformatics 2017;   DOI   PubMed  

Genome-wide identification of regulatory elements in Sertoli cells

Maatouk, D. M.,  Natarajan, A.,  Shibata, Y.,  Song, L.,  Crawford, G. E.,  Uwe Ohler,  Capel, B. 
Development 2017;   DOI   PubMed  

A Multi-step Transcriptional and Chromatin State Cascade Underlies Motor Neuron Programming from Embryonic Stem Cells

Velasco, Silvia,  Mahmoud Ibrahim,  Kakumanu, Akshay,  Garipler, Gorkem,  Aydin, Begum,  Al-Sayegh, Mohamed Ahmed,  Antje Hirsekorn,  Abdul-Rahman, Farah,  Satija, Rahul,  Uwe Ohler,  Mahony, Shaun,  Mazzoni, Esteban O 
Cell Stem Cell 2017;   DOI   PubMed  

The RNA workbench: best practices for RNA and high-throughput sequencing bioinformatics in Galaxy

Gruning, 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.,  Altuna Akalin Uwe Ohler,  Stadler, P. F.,  Backofen, R. 
Nucleic Acids Res. 2017;   DOI   PubMed  

RCAS: an RNA centric annotation system for transcriptome-wide regions of interest

Uyar, B.,  Yusuf, D.,  Wurmus, R.,  Rajewsky, N.,  Uwe Ohler Altuna Akalin 
Nucleic Acids Res. 2017;   DOI   PubMed  

RNA-bioinformatics: Tools, services and databases for the analysis of RNA-based regulation

Backofen, R.,  Engelhardt, J.,  Erxleben, A.,  Fallmann, J.,  Gruning, B.,  Uwe Ohler,  Rajewsky, N.,  Stadler, P. F. 
J. Biotechnol. 2017;   DOI   PubMed  

DDX54 regulates transcriptome dynamics during DNA damage response

Milek, M.,  Imami, K.,  Neelanjan Mukherjee,  Bortoli, F.,  Zinnall, U.,  Hazapis, O.,  Trahan, C.,  Oeffinger, M.,  Heyd, F.,  Uwe Ohler,  Selbach, M.,  Landthaler, M. 
Genome Res. 2017;   DOI   PubMed  

ssHMM: extracting intuitive sequence-structure motifs from high-throughput RNA-binding protein data

Heller, D.,  Krestel, R.,  Uwe Ohler,  Vingron, M.,  Marsico, A. 
Nucleic Acids Res. 2017;   DOI   PubMed  

Beyond Read-Counts: Ribo-seq Data Analysis to Understand the Functions of the Transcriptome

Lorenzo Calviello Uwe Ohler 
Trends Genet. 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.,  Lorenzo Calviello,  Filipchyk, A.,  Peguero-Sanchez, E.,  Muller, T.,  Woehler, A.,  Birchmeier, C.,  Merino, E.,  Rajewsky, N.,  Uwe Ohler,  Mazzoni, E. O.,  Selbach, M.,  Altuna Akalin,  Chekulaeva, M. 
Nat Commun 2017;  

McEnhancer: predicting gene expression via semi-supervised assignment of enhancers to target genes

Dina Hafez Aslihan Karabacak,  Krueger, S.,  Hwang, Y. C.,  Wang, L. S.,  Zinzen, R. P.,  Uwe Ohler 
Genome Biol. 2017;  

Divergent Transcription and Epigenetic Directionality of Human Promoters

Scott Allen Lacadie Mahmoud Ibrahim Sucheta Arun Gokhale Uwe Ohler 
FEBS J. 2016;   DOI   PubMed  

CSEQ-SIMULATOR: A DATA SIMULATOR FOR CLIP-SEQ EXPERIMENTS

Wanja Kassuhn Uwe Ohler,  Drewe, P. 
Pac Symp Biocomput 2016;   PubMed  

Identifying RBP Targets with RIP-seq

Hans-Hermann Wessels Antje Hirsekorn Uwe Ohler Neelanjan Mukherjee 
Methods Mol. Biol. 2016;   DOI   PubMed  

The mRNA-bound proteome of the early fly embryo

Hans-Hermann Wessels,  Imami, K.,  Baltz, A. G.,  Kolinksi, M.,  Beldovskaya, M.,  Selbach, M.,  Small, S.,  Uwe Ohler,  Landthaler, M. 
Genome Res. 2016;   DOI  

Integrative classification of human coding and noncoding genes through RNA metabolism profiles

Neelanjan Mukherjee Lorenzo Calviello Antje Hirsekorn,  de Pretis, S.,  Pelizzola, M.,  Uwe Ohler 
Nat. Struct. Mol. Biol. 2016;   DOI   PubMed  

Super-resolution ribosome profiling reveals unannotated translation events in Arabidopsis

Hsu, Polly Yingshan,  Lorenzo Calviello,  Wu, Hsin-Yen Larry,  Li, Fay-Wei,  Rothfels, Carl J.,  Uwe Ohler,  Benfey, Philip N. 
Proceedings of the National Academy of Sciences 2016;  

Human Promoters Are Intrinsically Directional

Duttke, S. H.,  Scott Allen Lacadie Mahmoud Ibrahim,  Glass, C. K.,  Corcoran, D. L.,  Benner, C.,  Heinz, S.,  Kadonaga, J. T.,  Uwe Ohler 
Molecular Cell 2015;   DOI   PubMed  

Regnase-1 and Roquin Regulate a Common Element in Inflammatory mRNAs by Spatiotemporally Distinct Mechanisms

Mino, T.,  Murakawa, Y.,  Fukao, A.,  Vandenbon, A.,  Hans-Hermann Wessels,  Ori, D.,  Uehata, T.,  Tartey, S.,  Akira, S.,  Suzuki, Y.,  Vinuesa, C. G.,  Uwe Ohler,  Standley, D. M.,  Landthaler, M.,  Fujiwara, T.,  Takeuchi, O. 
Cell 2015;   DOI   PubMed  

Detecting actively translated open reading frames in ribosome profiling data

Lorenzo Calviello Neelanjan Mukherjee,  Wyler, Emanuel,  Zauber, Henrik,  Antje Hirsekorn,  Selbach, Matthias,  Landthaler, Markus,  Obermayer, Benedikt,  Uwe Ohler 
Nature Methods 2015;   DOI   PubMed  

Perspectives on Unidirectional versus Divergent Transcription

Duttke, S. H.,  Scott Allen Lacadie Mahmoud Ibrahim,  Glass, C. K.,  Corcoran, D. L.,  Benner, C.,  Heinz, S.,  Kadonaga, J. T.,  Uwe Ohler 
Mol. Cell 2015;   DOI   PubMed  

COUGER-co-factors associated with uniquely-bound genomic regions

Alina-Cristina Munteanu Uwe Ohler,  Gordan, R. 
Nucleic Acids Res. 2014;   DOI   PubMed  

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.,  Neelanjan Mukherjee,  Mihailovic, A.,  Li, S.,  Max, K. E.,  Meyer, C.,  Yamaji, M.,  Cekan, P.,  Nicholas Charles Jacobs,  Gerstberger, S.,  Bognanni, C.,  Larsson, E.,  Uwe Ohler,  Tuschl, T. 
RNA 2014;   DOI   PubMed  

Improved transcript isoform discovery using ORF graphs

Majoros, W. H.,  Lebeck, N.,  Uwe Ohler,  Li, S. 
Bioinformatics 2014;   DOI   PubMed  

Global target mRNA specification and regulation by the RNA-binding protein ZFP36

Neelanjan Mukherjee Nicholas Charles Jacobs,  Hafner, M.,  Kennington, E. A.,  Nusbaum, J. D.,  Tuschl, T.,  Blackshear, P. J.,  Uwe Ohler 
Genome Biol. 2014;   DOI   PubMed  

JAMM: a peak finder for joint analysis of NGS replicates

Mahmoud Ibrahim Scott Allen Lacadie Uwe Ohler 
Bioinformatics 2014;   DOI   PubMed  

Paired-end analysis of transcription start sites in Arabidopsis reveals plant-specific promoter signatures

Morton, Taj,  Petricka, Jalean,  Corcoran, David L,  Li, Song,  Winter, Cara M,  Carda, Alexa,  Benfey, Philip N,  Uwe Ohler,  Megraw, Molly 
The Plant Cell 2014;   DOI   PubMed  

Explicit DNase sequence bias modeling enables high-resolution transcription factor footprint detection

Gurkan Yardimci,  Frank, Christopher L,  Crawford, Gregory E,  Uwe Ohler 
Nucleic acids research 2014;   DOI   PubMed  

Distinct polyadenylation landscapes of diverse human tissues revealed by a modified PA-seq strategy

Ni, T.,  Yang, Y.,  Dina Hafez,  Yang, W.,  Kiesewetter, K.,  Wakabayashi, Y.,  Uwe Ohler,  Peng, W.,  Zhu, J. 
BMC Genomics 2013;   PubMed Central   DOI   PubMed  

Sustained-input switches for transcription factors and microRNAs are central building blocks of eukaryotic gene circuits

Megraw, M.,  Mukherjee, S.,  Uwe Ohler 
Genome Biol. 2013;   DOI   PubMed  

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.,  Uwe Ohler,  Capel, B. 
PLoS Genet. 2013;   PubMed Central   DOI   PubMed  

Integrated detection of natural antisense transcripts using strand-specific RNA sequencing data

Li, S.,  Liberman, L. M.,  Neelanjan Mukherjee,  Benfey, P. N.,  Uwe Ohler 
Genome Res. 2013;   PubMed Central   DOI   PubMed  

Automated annotation of gene expression image sequences via non-parametric factor analysis and conditional random fields

Pruteanu-Malinici, I.,  Majoros, W. H.,  Uwe Ohler 
Bioinformatics 2013;   PubMed Central   DOI   PubMed  

Genome-wide identification and predictive modeling of tissue-specific alternative polyadenylation

Dina Hafez,  Ni, T.,  Mukherjee, S.,  Zhu, J.,  Uwe Ohler 
Bioinformatics 2013;   PubMed Central   DOI   PubMed  

MicroRNA target site identification by integrating sequence and binding information

Majoros, W. H.,  Lekprasert, P.,  Neelanjan Mukherjee,  Skalsky, R. L.,  Corcoran, D. L.,  Cullen, B. R.,  Uwe Ohler 
Nat. Methods 2013;   PubMed Central   DOI   PubMed  

Using machine learning to identify disease-relevant regulatory RNAs

Uwe Ohler 
Proc. Natl. Acad. Sci. U.S.A. 2013;   PubMed Central   DOI   PubMed  

FMRP targets distinct mRNA sequence elements to regulate protein expression

Ascano, M.,  Neelanjan Mukherjee,  Bandaru, P.,  Miller, J. B.,  Nusbaum, J. D.,  Corcoran, D. L.,  Langlois, C.,  Munschauer, M.,  Dewell, S.,  Hafner, M.,  Williams, Z.,  Uwe Ohler,  Tuschl, T. 
Nature 2012;   PubMed Central   DOI   PubMed  

Chromatin accessibility reveals insights into androgen receptor activation and transcriptional specificity

Tewari, A. K.,  Gurkan Yardimci,  Shibata, Y.,  Sheffield, N. C.,  Song, L.,  Taylor, B. S.,  Georgiev, S. G.,  Coetzee, G. A.,  Uwe Ohler,  Furey, T. S.,  Crawford, G. E.,  Febbo, P. G. 
Genome Biol. 2012;   PubMed Central   DOI   PubMed  

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.,  Uwe Ohler,  Benfey, P. N. 
Nat. Methods 2012;   PubMed Central   DOI   PubMed  

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.,  Uwe Ohler,  Wassarman, D. A. 
PLoS ONE 2012;   PubMed Central   DOI   PubMed  

Predicting cell-type-specific gene expression from regions of open chromatin

Natarajan, A.,  Gurkan Yardimci,  Sheffield, N. C.,  Crawford, G. E.,  Uwe Ohler 
Genome Res. 2012;   PubMed Central   DOI   PubMed  

Translocation of sickle cell erythrocyte microRNAs into Plasmodium falciparum inhibits parasite translation and contributes to malaria resistance

LaMonte, G.,  Philip, N.,  Reardon, J.,  Lacsina, J. R.,  Majoros, W.,  Chapman, L.,  Thornburg, C. D.,  Telen, M. J.,  Uwe Ohler,  Nicchitta, C. V.,  Haystead, T.,  Chi, J. T. 
Cell Host Microbe 2012;   PubMed Central   DOI   PubMed  

Genome-wide search for miRNA-target interactions in Arabidopsis thaliana with an integrated approach

Ding, J.,  Li, D.,  Uwe Ohler,  Guan, J.,  Zhou, S. 
BMC Genomics 2012;   PubMed Central   DOI   PubMed  

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.,  Uwe Ohler,  Moseley, M. A.,  Grossniklaus, U.,  Benfey, P. N. 
Proc. Natl. Acad. Sci. U.S.A. 2012;   PubMed Central   DOI   PubMed  

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.,  Uwe Ohler,  Cullen, B. R. 
PLoS Pathog. 2012;   PubMed Central   DOI   PubMed  

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.,  Uwe Ohler,  Benfey, P. N. 
Genome Res. 2012;   PubMed Central   DOI   PubMed  

Viral microRNA targetome of KSHV-infected primary effusion lymphoma cell lines

Gottwein, E.,  Corcoran, D. L.,  Neelanjan Mukherjee,  Skalsky, R. L.,  Hafner, M.,  Nusbaum, J. D.,  Shamulailatpam, P.,  Love, C. L.,  Dave, S. S.,  Tuschl, T.,  Uwe Ohler,  Cullen, B. R. 
Cell Host Microbe 2011;   PubMed Central   DOI   PubMed  

PARalyzer: definition of RNA binding sites from PAR-CLIP short-read sequence data

Corcoran, D. L.,  Georgiev, S.,  Neelanjan Mukherjee,  Gottwein, E.,  Skalsky, R. L.,  Keene, J. D.,  Uwe Ohler 
Genome Biol. 2011;   PubMed Central   DOI   PubMed  

Automatic annotation of spatial expression patterns via sparse Bayesian factor models

Pruteanu-Malinici, I.,  Mace, D. L.,  Uwe Ohler 
PLoS Comput. Biol. 2011;   PubMed Central   DOI   PubMed  

Integrative regulatory mapping indicates that the RNA-binding protein HuR couples pre-mRNA processing and mRNA stability

Neelanjan Mukherjee,  Corcoran, D. L.,  Nusbaum, J. D.,  Reid, D. W.,  Georgiev, S.,  Hafner, M.,  Ascano, M.,  Tuschl, T.,  Uwe Ohler,  Keene, J. D. 
Mol. Cell 2011;   PubMed Central   DOI   PubMed  

Assessing the utility of thermodynamic features for microRNA target prediction under relaxed seed and no conservation requirements

Lekprasert, P.,  Mayhew, M.,  Uwe Ohler 
PLoS ONE 2011;   PubMed Central   DOI   PubMed  

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.,  Uwe Ohler 
PLoS Genet. 2011;   PubMed Central   DOI   PubMed  

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.,  Uwe Ohler,  Ware, D.,  Walhout, A. J.,  Benfey, P. N. 
Mol. Syst. Biol. 2011;   PubMed Central   DOI   PubMed  

Modeling the evolution of regulatory elements by simultaneous detection and alignment with phylogenetic pair HMMs

Majoros, W. H.,  Uwe Ohler 
PLoS Comput. Biol. 2010;   PubMed Central   DOI   PubMed  

Gene expression divergence recapitulates the developmental hourglass model

Kalinka, A. T.,  Varga, K. M.,  Gerrard, D. T.,  Preibisch, S.,  Corcoran, D. L.,  Jarrells, J.,  Uwe Ohler,  Bergman, C. M.,  Tomancak, P. 
Nature 2010;   DOI   PubMed  

The TCT motif, a key component of an RNA polymerase II transcription system for the translational machinery

Parry, T. J.,  Theisen, J. W.,  Hsu, J. Y.,  Wang, Y. L.,  Corcoran, D. L.,  Eustice, M.,  Uwe Ohler,  Kadonaga, J. T. 
Genes Dev. 2010;   PubMed Central   DOI   PubMed  

An alignment-free method to identify candidate orthologous enhancers in multiple Drosophila genomes

Arunachalam, M.,  Jayasurya, K.,  Tomancak, P.,  Uwe Ohler 
Bioinformatics 2010;   PubMed Central   DOI   PubMed  

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.,  Uwe Ohler,  Zhu, J. 
Nat. Methods 2010;   PubMed Central   DOI   PubMed  

Mapping the complexity of transcription control in higher eukaryotes

Tomancak, P.,  Uwe Ohler 
Genome Biol. 2010;   PubMed Central   DOI   PubMed  

Evidence-ranked motif identification

Georgiev, S.,  Boyle, A. P.,  Jayasurya, K.,  Ding, X.,  Mukherjee, S.,  Uwe Ohler 
Genome Biol. 2010;   PubMed Central   DOI   PubMed  

Promoting developmental transcription

Uwe Ohler,  Wassarman, D. A. 
Development 2010;   PubMed Central   DOI   PubMed  

Extraction and comparison of gene expression patterns from 2D RNA in situ hybridization images

Mace, D. L.,  Varnado, N.,  Zhang, W.,  Frise, E.,  Uwe Ohler 
Bioinformatics 2010;   PubMed Central   DOI   PubMed  

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.,  Uwe Ohler 
Genome Biol. 2009;   PubMed Central   DOI   PubMed  

Measuring spatial preferences at fine-scale resolution identifies known and novel cis-regulatory element candidates and functional motif-pair relationships

Yokoyama, K. D.,  Uwe Ohler,  Wray, G. A. 
Nucleic Acids Res. 2009;   PubMed Central   DOI   PubMed  

A transcription factor affinity-based code for mammalian transcription initiation

Megraw, M.,  Pereira, F.,  Jensen, S. T.,  Uwe Ohler,  Hatzigeorgiou, A. G. 
Genome Res. 2009;   PubMed Central   DOI   PubMed  

Complexity reduction in context-dependent DNA substitution models

Majoros, W. H.,  Uwe Ohler 
Bioinformatics 2009;   PubMed Central   DOI   PubMed  

Strategies for identifying RNA splicing regulatory motifs and predicting alternative splicing events

Holste, D.,  Uwe Ohler 
PLoS Comput. Biol. 2008;   PubMed Central   DOI   PubMed  

A viral microRNA functions as an orthologue of cellular miR-155

Gottwein, E.,  Neelanjan Mukherjee,  Sachse, C.,  Frenzel, C.,  Majoros, W. H.,  Chi, J. T.,  Braich, R.,  Manoharan, M.,  Soutschek, J.,  Uwe Ohler,  Cullen, B. R. 
Nature 2007;   PubMed Central   DOI   PubMed  

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.,  Uwe Ohler,  Benfey, P. N. 
Science 2007;   DOI   PubMed  

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.,  Uwe Ohler 
Genome Biol. 2007;   PubMed Central   DOI   PubMed  

Spatial preferences of microRNA targets in 3' untranslated regions

Majoros, W. H.,  Uwe Ohler 
BMC Genomics 2007;   PubMed Central   DOI   PubMed  

Detection of broadly expressed neuronal genes in C. elegans

Ruvinsky, I.,  Uwe Ohler,  Burge, C. B.,  Ruvkun, G. 
Dev. Biol. 2007;   DOI   PubMed  

Identification of core promoter modules in Drosophila and their application in accurate transcription start site prediction

Uwe Ohler 
Nucleic Acids Res. 2006;   PubMed Central   DOI   PubMed  

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.,  Uwe Ohler,  Solovyev, V. V.,  Tan, S. L. 
Genome Biol. 2006;   PubMed Central   DOI   PubMed  

Informative priors based on transcription factor structural class improve de novo motif discovery

Narlikar, L.,  Gordan, R.,  Uwe Ohler,  Hartemink, A. J. 
Bioinformatics 2006;   DOI   PubMed  

Quantification of transcription factor expression from Arabidopsis images

Mace, D. L.,  Lee, J. Y.,  Twigg, R. W.,  Colinas, J.,  Benfey, P. N.,  Uwe Ohler 
Bioinformatics 2006;   DOI   PubMed  

Optimized mixed Markov models for motif identification

Huang, W.,  Umbach, D. M.,  Uwe Ohler,  Li, L. 
BMC Bioinformatics 2006;   PubMed Central   DOI   PubMed  

Transcriptional and posttranscriptional regulation of transcription factor expression in Arabidopsis roots

Lee, J. Y.,  Colinas, J.,  Wang, J. Y.,  Mace, D.,  Uwe Ohler,  Benfey, P. N. 
Proc. Natl. Acad. Sci. U.S.A. 2006;   PubMed Central   DOI   PubMed  

Recognition of unknown conserved alternatively spliced exons

Uwe Ohler,  Shomron, N.,  Burge, C. B. 
PLoS Comput. Biol. 2005;   PubMed Central   DOI   PubMed  

Patterns of flanking sequence conservation and a characteristic upstream motif for microRNA gene identification

Uwe Ohler,  Yekta, S.,  Lim, L. P.,  Bartel, D. P.,  Burge, C. B. 
RNA 2004;   PubMed Central   DOI   PubMed  

The MTE, a new core promoter element for transcription by RNA polymerase II

Lim, C. Y.,  Santoso, B.,  Boulay, T.,  Dong, E.,  Uwe Ohler,  Kadonaga, J. T. 
Genes Dev. 2004;   PubMed Central   DOI   PubMed  

Computational analysis of core promoters in the Drosophila genome

Uwe Ohler,  Liao, G. C.,  Niemann, H.,  Rubin, G. M. 
Genome Biol. 2002;   PubMed Central   PubMed  

Promoter prediction on a genomic scale--the Adh experience

Uwe Ohler 
Genome Res. 2000;   PubMed Central   PubMed  

Genome annotation assessment in Drosophila melanogaster

Reese, M. G.,  Hartzell, G.,  Harris, N. L.,  Uwe Ohler,  Abril, J. F.,  Lewis, S. E. 
Genome Res. 2000;   PubMed Central   PubMed  

Stochastic segment models of eukaryotic promoter regions

Uwe Ohler,  Stemmer, G.,  Harbeck, S.,  Niemann, H. 
Pac Symp Biocomput 2000;   PubMed  

Interpolated markov chains for eukaryotic promoter recognition

Uwe Ohler,  Harbeck, S.,  Niemann, H.,  Noth, E.,  Reese, M. G. 
Bioinformatics 1999;   PubMed  
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