Publications
Cluster-Independent Marker Feature Identification from Single-Cell Omics Data using SEMITONES
Vlot, Anna H. C., Maghsudi, Setareh, Uwe OhlerNucleic Acids Research 2022;
Quantification of translation uncovers the functions of the alternative transcriptome
Lorenzo Calviello, Antje Hirsekorn, Uwe OhlerNat Struct Mol Biol 2020;
DOI
PubMed
Lineage-Resolved Enhancer and Promoter Usage during a Time Course of Embryogenesis
Reddington, J. P., Garfield, D. A., Sigalova, O. M., Aslihan Karabacak, Marco-Ferreres, R., Girardot, C., Viales, R. R., Degner, J. F., Uwe Ohler, Furlong, E. E. M.Dev Cell 2020;
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 OhlerGenome 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, Akalin, Altuna, Neelanjan Mukherjee, Uwe OhlerNature Communications 2019;
DOI
Towards a deeper annotation of human lncRNAs.
Michal Szczesniak, Wanowska, E., Neelanjan Mukherjee, Uwe Ohler, Makalowska, IzabelaBiochimica et biophysica acta. Gene regulatory mechanisms 2019;
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PubMed
Deep neural networks for interpreting RNA binding protein target preferences
Mahsa Ghanbari, Uwe OhlerbioRxiv 2019;
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A Conserved Noncoding Locus Regulates Random Monoallelic Xist Expression Across a Topological Boundary
Galupa, Rafael, Nora, Elphege Pierre, Hunt, Rebecca Worsley, Picard, Christel, Gard, Chris, van Bemmel, Joke Gerarda, Servant, Nicolas, Zhan, Yinxiu, Marjou, Fatima El, Johanneau, Colin, Diabangouaya, Patricia, Saux, Agnes Le, Lameiras, Sonia, da Fonseca, Juliana Pipoli, Loos, Friedemann, Gribnau, Joost, Baulande, Sylvain, Uwe Ohler, Giorgetti, Luca, Heard, EdithMolecular Cell 2019;
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PubMed
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, MichaelRNA Biology 2018;
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., Akalin, Altuna, Tuschl, Thomas, Uwe OhlerNucleic Acids Research 2018;
DOI
omniCLIP: probabilistic identification of protein-RNA interactions from CLIP-seq data
Drewe-Boss, Philipp, Hans-Hermann Wessels, Uwe OhlerGenome Biology 2018;
DOI
Redundant regulation.
Scott Allen Lacadie, Uwe OhlerNature ecology and evolution 2018;
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PubMed
Finding RNA structure in the unstructured RBPome.
Orenstein, Yaron, Uwe Ohler, Berger, BonnieDOI
PubMed
SSMART: sequence-structure motif identification for RNA-binding proteins.
Alina-Cristina Munteanu, Neelanjan Mukherjee, Uwe OhlerDOI
PubMed
Determinants of promoter and enhancer transcription directionality in metazoans.
Mahmoud Ibrahim, Aslihan Karabacak, Glahs, Alexander, Kolundzic, Ena, Antje Hirsekorn, Carda, Alexa, Tursun, Baris, Zinzen, Robert P, Scott Allen Lacadie, Uwe OhlerNature communications 2018;
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PubMed
Ectopic Transplastomic Expression of a Synthetic MatK Gene Leads to Cotyledon-Specific Leaf Variegation.
Qu, Yujiao, Legen, Julia, Arndt, Juergen, Henkel, Stephanie, Hoppe, Galina, Thieme, Christopher, Ranzini, Giovanna, Muino, Jose M, Weihe, Andreas, Uwe Ohler, Weber, Gert, Ostersetzer, Oren, Schmitz-Linneweber, ChristianFrontiers in plant science 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;
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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;
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PubMed
Integrative classification of human coding and noncoding genes through RNA metabolism profiles
Neelanjan Mukherjee, Lorenzo Calviello, Antje Hirsekorn, de Pretis, S., Pelizzola, M., Uwe OhlerNat. Struct. Mol. Biol. 2017;
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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 OCell Stem Cell 2017;
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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., Akalin, A., Uwe Ohler, Stadler, P. F., Backofen, R.Nucleic Acids Res. 2017;
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PubMed
RCAS: an RNA centric annotation system for transcriptome-wide regions of interest
Uyar, B., Yusuf, D., Wurmus, R., Rajewsky, N., Uwe Ohler, Akalin, A.Nucleic Acids Res. 2017;
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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;
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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;
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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 OhlerTrends Genet. 2017;
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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., Akalin, A., Chekulaeva, M.Nat Commun 2017;
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McEnhancer: predicting gene expression via semi-supervised assignment of enhancers to target genes
Dina Hafez, Aslihan Karabacak, Krueger, Sabrina, Hwang, Yih-Chii, Wang, Li-San, Zinzen, Robert P., Uwe OhlerGenome Biology 2017;
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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 OhlerNature Methods 2016;
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PubMed
Divergent Transcription and Epigenetic Directionality of Human Promoters
Scott Allen Lacadie, Mahmoud Ibrahim, Sucheta Arun Gokhale, Uwe OhlerFEBS J. 2016;
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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 MukherjeeMethods Mol. Biol. 2016;
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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
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.DOI
PNAS
High-Resolution Expression Map of the Arabidopsis Root Reveals Alternative Splicing and lincRNA Regulation.
Li, Song, Yamada, Masashi, Han, Xinwei, Uwe Ohler, Benfey, Philip NDOI
PubMed
JAMM: a peak finder for joint analysis of NGS replicates
Mahmoud Ibrahim, Scott Allen Lacadie, Uwe OhlerBioinformatics 2015;
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PubMed
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 OhlerMolecular Cell 2015;
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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;
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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 OhlerMol. Cell 2015;
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PubMed
Transcriptional control of tissue formation throughout root development
Moreno-Risueno, M. A., Sozzani, R., Gurkan Yardimci, Petricka, J. J., Vernoux, T., Blilou, I., Alonso, J., Winter, C. M., Uwe Ohler, Scheres, B., Benfey, P. N.Science 2015;
DOI
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;
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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 OhlerGenome Biol. 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, MollyThe Plant Cell 2014;
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PubMed
Explicit DNase sequence bias modeling enables high-resolution transcription factor footprint detection
Gurkan Yardimci, Frank, Christopher L, Crawford, Gregory E, Uwe OhlerNucleic 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 OhlerGenome Biol. 2013;
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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 OhlerPubMed 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 OhlerBioinformatics 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 OhlerBioinformatics 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 OhlerNat. Methods 2013;
PubMed Central
DOI
PubMed
Using machine learning to identify disease-relevant regulatory RNAs
Uwe OhlerProc. 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 OhlerGenome 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 OhlerGenome Biol. 2011;
PubMed Central
DOI
PubMed
Automatic annotation of spatial expression patterns via sparse Bayesian factor models
Pruteanu-Malinici, I., Mace, D. L., Uwe OhlerPLoS 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 OhlerPLoS 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 OhlerPLoS 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 OhlerPLoS 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;
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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 OhlerBioinformatics 2010;
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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 OhlerGenome Biol. 2010;
PubMed Central
DOI
PubMed
Evidence-ranked motif identification
Georgiev, S., Boyle, A. P., Jayasurya, K., Ding, X., Mukherjee, S., Uwe OhlerGenome 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 OhlerBioinformatics 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 OhlerGenome 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 OhlerBioinformatics 2009;
PubMed Central
DOI
PubMed
Strategies for identifying RNA splicing regulatory motifs and predicting alternative splicing events
Holste, D., Uwe OhlerPLoS 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;
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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 OhlerGenome Biol. 2007;
PubMed Central
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PubMed
Spatial preferences of microRNA targets in 3' untranslated regions
Majoros, W. H., Uwe OhlerBMC 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;
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PubMed
Identification of core promoter modules in Drosophila and their application in accurate transcription start site prediction
Uwe OhlerNucleic 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
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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;
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PubMed
Quantification of transcription factor expression from Arabidopsis images
Mace, D. L., Lee, J. Y., Twigg, R. W., Colinas, J., Benfey, P. N., Uwe OhlerBioinformatics 2006;
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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
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PubMed
Recognition of unknown conserved alternatively spliced exons
Uwe Ohler, Shomron, N., Burge, C. B.PLoS Comput. Biol. 2005;
PubMed Central
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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 OhlerGenome 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