Scholars@Duke

• Background
• 

  Education, Training, & Certifications

  • Postdoctoral Research Advisor, Department Of Biology, Massachusetts Institute of Technology 2002 - 2004
  • Ph.D., Friedrich-Alexander-Universität Erlangen-Nürnberg (Germany) 2002
• 

  Previous Appointments & Affiliations

  • Adjunct Associate Professor in the Department of Biostatistics & Bioinformatics, Biostatistics & Bioinformatics, Basic Science Departments 2014 - 2022
  • Associate Professor of Biostatistics and Bioinformatics, Biostatistics & Bioinformatics, Basic Science Departments 2011 - 2014
  • Associate Professor in the Department of Computer Science, Computer Science, Trinity College of Arts & Sciences 2011 - 2013
  • Assistant Professor of Biostatistics and Bioinformatics, Biostatistics & Bioinformatics, Basic Science Departments 2005 - 2011
• Recognition
• 

  Awards & Honors

  • Sloan Research Fellowship-Molecular Biology. Alfred P. Sloan Foundation. 2005
• Research
• 

  Selected Grants

  • Genome-Wide Mapping of Enhancer Elements for Neuronal Differentiation Genes awarded by National Institutes of Health 2013 - 2016
  • Arabidopsis 2010: Regulatory Networks Controlling Root Growth and Differentiation awarded by  National Science Foundation 2010 - 2015
  • Novel pathways modulating Raf-mediated cardiac hypertrophy awarded by National Institutes of Health 2013 - 2015
  • CAREER: Computational modeling and analysis of gene expression patterns from microscopy image data awarded by  National Science Foundation 2010 - 2013
  • Modeling the structure & evolution of regulatory regions in eukaryotic genomes awarded by National Institutes of Health 2007 - 2013
  • Functional regulatory circuits induced by transcription factors and small RNAs awarded by National Institutes of Health 2011 - 2012
  • Genome-wide exploring miRNA-mediated network motifs awarded by  National Science Foundation 2008 - 2012
  • Function of alpha herpesvirus microRNAs awarded by National Institutes of Health 2010 - 2011
  • Arabidopsis 2010: Identifying Transcriptional Networks at Cellular Resolution awarded by  National Science Foundation 2006 - 2010
  • High-performance Computing System for Bioinformatics awarded by National Institutes of Health 2009 - 2010
• Publications & Artistic Works
• 

  Selected Publications

  • Academic Articles

    • Maatouk, Danielle M., Anirudh Natarajan, Yoichiro Shibata, Lingyun Song, Gregory E. Crawford, Uwe Ohler, and Blanche Capel. “Genome-wide identification of regulatory elements in Sertoli cells.” Development 144, no. 4 (February 15, 2017): 720–30. https://doi.org/10.1242/dev.142554.
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    • Li, Song, Masashi Yamada, Xinwei Han, Uwe Ohler, and Philip N. Benfey. “High-Resolution Expression Map of the Arabidopsis Root Reveals Alternative Splicing and lincRNA Regulation.” Dev Cell 39, no. 4 (November 21, 2016): 508–22. https://doi.org/10.1016/j.devcel.2016.10.012.
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    • Hsu, Polly Yingshan, Lorenzo Calviello, Hsin-Yen Larry Wu, Fay-Wei Li, Carl J. Rothfels, Uwe Ohler, and Philip N. Benfey. “Super-resolution ribosome profiling reveals unannotated translation events in Arabidopsis.” Proc Natl Acad Sci U S A 113, no. 45 (November 8, 2016): E7126–35. https://doi.org/10.1073/pnas.1614788113.
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    • Duttke, Sascha H. C., Scott A. Lacadie, Mahmoud M. Ibrahim, Christopher K. Glass, David L. Corcoran, Christopher Benner, Sven Heinz, James T. Kadonaga, and Uwe Ohler. “Perspectives on Unidirectional versus Divergent Transcription.” Mol Cell 60, no. 3 (November 5, 2015): 348–49. https://doi.org/10.1016/j.molcel.2015.10.014.
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    • Moreno-Risueno, Miguel A., Rosangela Sozzani, Galip Gürkan Yardımcı, Jalean J. Petricka, Teva Vernoux, Ikram Blilou, Jose Alonso, et al. “Transcriptional control of tissue formation throughout root development.” Science 350, no. 6259 (October 23, 2015): 426–30. https://doi.org/10.1126/science.aad1171.
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    • Duttke, Sascha H. C., Scott A. Lacadie, Mahmoud M. Ibrahim, Christopher K. Glass, David L. Corcoran, Christopher Benner, Sven Heinz, James T. Kadonaga, and Uwe Ohler. “Human promoters are intrinsically directional.” Mol Cell 57, no. 4 (February 19, 2015): 674–84. https://doi.org/10.1016/j.molcel.2014.12.029.
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    • Yardımcı, Galip Gürkan, Christopher L. Frank, Gregory E. Crawford, and Uwe Ohler. “Explicit DNase sequence bias modeling enables high-resolution transcription factor footprint detection.” Nucleic Acids Res 42, no. 19 (October 29, 2014): 11865–78. https://doi.org/10.1093/nar/gku810.
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    • Majoros, William H., Niel Lebeck, Uwe Ohler, and Song Li. “Improved transcript isoform discovery using ORF graphs.” Bioinformatics 30, no. 14 (July 15, 2014): 1958–64. https://doi.org/10.1093/bioinformatics/btu160.
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    • Munteanu, Alina, Uwe Ohler, and Raluca Gordân. “COUGER--co-factors associated with uniquely-bound genomic regions.” Nucleic Acids Res 42, no. Web Server issue (July 2014): W461–67. https://doi.org/10.1093/nar/gku435.
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    • Farazi, Thalia A., Carl S. Leonhardt, Neelanjan Mukherjee, Aleksandra Mihailovic, Song Li, Klaas E. A. Max, Cindy Meyer, et al. “Identification of the RNA recognition element of the RBPMS family of RNA-binding proteins and their transcriptome-wide mRNA targets.” Rna 20, no. 7 (July 2014): 1090–1102. https://doi.org/10.1261/rna.045005.114.
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    • Morton, Taj, Jalean Petricka, David L. Corcoran, Song Li, Cara M. Winter, Alexa Carda, Philip N. Benfey, Uwe Ohler, and Molly Megraw. “Paired-end analysis of transcription start sites in Arabidopsis reveals plant-specific promoter signatures.” Plant Cell 26, no. 7 (July 2014): 2746–60. https://doi.org/10.1105/tpc.114.125617.
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    • Li, Song, Louisa M. Liberman, Neelanjan Mukherjee, Philip N. Benfey, and Uwe Ohler. “Integrated detection of natural antisense transcripts using strand-specific RNA sequencing data.” Genome Res 23, no. 10 (October 2013): 1730–39. https://doi.org/10.1101/gr.149310.112.
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    • Ni, Ting, Yanqin Yang, Dina Hafez, Wenjing Yang, Kurtis Kiesewetter, Yoshi Wakabayashi, Uwe Ohler, Weiqun Peng, and Jun Zhu. “Distinct polyadenylation landscapes of diverse human tissues revealed by a modified PA-seq strategy.” Bmc Genomics 14 (September 11, 2013): 615. https://doi.org/10.1186/1471-2164-14-615.
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    • Megraw, Molly, Sayan Mukherjee, and Uwe Ohler. “Sustained-input switches for transcription factors and microRNAs are central building blocks of eukaryotic gene circuits.” Genome Biol 14, no. 8 (August 23, 2013): R85. https://doi.org/10.1186/gb-2013-14-8-r85.
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    • Hafez, Dina, Ting Ni, Sayan Mukherjee, Jun Zhu, and Uwe Ohler. “Genome-wide identification and predictive modeling of tissue-specific alternative polyadenylation.” Bioinformatics 29, no. 13 (July 1, 2013): i108–16. https://doi.org/10.1093/bioinformatics/btt233.
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    • Majoros, William H., Parawee Lekprasert, Neelanjan Mukherjee, Rebecca L. Skalsky, David L. Corcoran, Bryan R. Cullen, and Uwe Ohler. “MicroRNA target site identification by integrating sequence and binding information.” Nat Methods 10, no. 7 (July 2013): 630–33. https://doi.org/10.1038/nmeth.2489.
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    • Pruteanu-Malinici, Iulian, William H. Majoros, and Uwe Ohler. “Automated annotation of gene expression image sequences via non-parametric factor analysis and conditional random fields.” Bioinformatics 29, no. 13 (July 1, 2013): i27–35. https://doi.org/10.1093/bioinformatics/btt206.
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    • Majoros, W. H., P. Lekprasert, N. Mukherjee, R. L. Skalsky, D. L. Corcoran, B. R. Cullen, and U. Ohler. “MicroRNA target site identification by integrating sequence and binding information (Accepted).” Nature Methods, May 26, 2013. https://doi.org/10.138/nmeth.2489.
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    • Majoros, W. H., P. Lekprasert, N. Mukherjee, R. L. Skalsky, D. L. Corcoran, B. R. Cullen, and U. Ohler. “MicroRNA target site identification by integrating sequence and binding information.” Nature Methods 10, no. 7 (2013): 630–33. https://doi.org/10.1038/nmeth.2489.
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    • Munger, Steven C., Anirudh Natarajan, Loren L. Looger, Uwe Ohler, and Blanche Capel. “Fine time course expression analysis identifies cascades of activation and repression and maps a putative regulator of mammalian sex determination.” Plos Genet 9, no. 7 (2013): e1003630. https://doi.org/10.1371/journal.pgen.1003630.
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    • Ascano, Manuel, Neelanjan Mukherjee, Pradeep Bandaru, Jason B. Miller, Jeffrey D. Nusbaum, David L. Corcoran, Christine Langlois, et al. “FMRP targets distinct mRNA sequence elements to regulate protein expression.” Nature 492, no. 7429 (December 20, 2012): 382–86. https://doi.org/10.1038/nature11737.
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    • Busch, Wolfgang, Brad T. Moore, Bradley Martsberger, Daniel L. Mace, Richard W. Twigg, Jee Jung, Iulian Pruteanu-Malinici, et al. “A microfluidic device and computational platform for high-throughput live imaging of gene expression.” Nat Methods 9, no. 11 (November 2012): 1101–6. https://doi.org/10.1038/nmeth.2185.
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    • Tewari, Alok K., Galip Gürkan Yardimci, Yoichiro Shibata, Nathan C. Sheffield, Lingyun Song, Barry S. Taylor, Stoyan G. Georgiev, et al. “Chromatin accessibility reveals insights into androgen receptor activation and transcriptional specificity.” Genome Biol 13, no. 10 (October 3, 2012): R88. https://doi.org/10.1186/gb-2012-13-10-r88.
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    • Natarajan, Anirudh, Galip Gürkan Yardimci, Nathan C. Sheffield, Gregory E. Crawford, and Uwe Ohler. “Predicting cell-type-specific gene expression from regions of open chromatin.” Genome Res 22, no. 9 (September 2012): 1711–22. https://doi.org/10.1101/gr.135129.111.
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    • LaMonte, Gregory, Nisha Philip, Joseph Reardon, Joshua R. Lacsina, William Majoros, Lesley Chapman, Courtney D. Thornburg, et al. “Translocation of sickle cell erythrocyte microRNAs into Plasmodium falciparum inhibits parasite translation and contributes to malaria resistance.” Cell Host Microbe 12, no. 2 (August 16, 2012): 187–99. https://doi.org/10.1016/j.chom.2012.06.007.
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    • Petricka, Jalean J., Monica A. Schauer, Molly Megraw, Natalie W. Breakfield, J Will Thompson, Stoyan Georgiev, Erik J. Soderblom, et al. “The protein expression landscape of the Arabidopsis root.” Proc Natl Acad Sci U S A 109, no. 18 (May 1, 2012): 6811–18. https://doi.org/10.1073/pnas.1202546109.
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    • Katzenberger, Rebeccah J., Elizabeth A. Rach, Ashley K. Anderson, Uwe Ohler, and David A. Wassarman. “The Drosophila Translational Control Element (TCE) is required for high-level transcription of many genes that are specifically expressed in testes.” Plos One 7, no. 9 (2012): e45009. https://doi.org/10.1371/journal.pone.0045009.
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    • Skalsky, Rebecca L., David L. Corcoran, Eva Gottwein, Christopher L. Frank, Dong Kang, Markus Hafner, Jeffrey D. Nusbaum, et al. “The viral and cellular microRNA targetome in lymphoblastoid cell lines.” Plos Pathog 8, no. 1 (January 2012): e1002484. https://doi.org/10.1371/journal.ppat.1002484.
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    • Breakfield, Natalie W., David L. Corcoran, Jalean J. Petricka, Jeffrey Shen, Juthamas Sae-Seaw, Ignacio Rubio-Somoza, Detlef Weigel, Uwe Ohler, and Philip N. Benfey. “High-resolution experimental and computational profiling of tissue-specific known and novel miRNAs in Arabidopsis.” Genome Res 22, no. 1 (January 2012): 163–76. https://doi.org/10.1101/gr.123547.111.
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    • Ding, J., S. Yu, U. Ohler, J. Guan, and S. Zhou. “imiRTP: An integrated method to identifying miRNA-target interactions in Arabidopsis thaliana.” Proceedings  2011 Ieee International Conference on Bioinformatics and Biomedicine, Bibm 2011, December 1, 2011, 100–104. https://doi.org/10.1109/BIBM.2011.13.
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    • Gottwein, Eva, David L. Corcoran, Neelanjan Mukherjee, Rebecca L. Skalsky, Markus Hafner, Jeffrey D. Nusbaum, Priscilla Shamulailatpam, et al. “Viral microRNA targetome of KSHV-infected primary effusion lymphoma cell lines.” Cell Host Microbe 10, no. 5 (November 17, 2011): 515–26. https://doi.org/10.1016/j.chom.2011.09.012.
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    • Corcoran, David L., Stoyan Georgiev, Neelanjan Mukherjee, Eva Gottwein, Rebecca L. Skalsky, Jack D. Keene, and Uwe Ohler. “PARalyzer: definition of RNA binding sites from PAR-CLIP short-read sequence data.” Genome Biol 12, no. 8 (August 18, 2011): R79. https://doi.org/10.1186/gb-2011-12-8-r79.
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    • Mukherjee, Neelanjan, David L. Corcoran, Jeffrey D. Nusbaum, David W. Reid, Stoyan Georgiev, Markus Hafner, Manuel Ascano, Thomas Tuschl, Uwe Ohler, and Jack D. Keene. “Integrative regulatory mapping indicates that the RNA-binding protein HuR couples pre-mRNA processing and mRNA stability.” Mol Cell 43, no. 3 (August 5, 2011): 327–39. https://doi.org/10.1016/j.molcel.2011.06.007.
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    • Pruteanu-Malinici, Iulian, Daniel L. Mace, and Uwe Ohler. “Automatic annotation of spatial expression patterns via sparse Bayesian factor models.” Plos Comput Biol 7, no. 7 (July 2011): e1002098. https://doi.org/10.1371/journal.pcbi.1002098.
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    • Brady, Siobhan M., Lifang Zhang, Molly Megraw, Natalia J. Martinez, Eric Jiang, Charles S. Yi, Weilin Liu, et al. “A stele-enriched gene regulatory network in the Arabidopsis root.” Mol Syst Biol 7 (January 18, 2011): 459. https://doi.org/10.1038/msb.2010.114.
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    • Rach, Elizabeth A., Deborah R. Winter, Ashlee M. Benjamin, David L. Corcoran, Ting Ni, Jun Zhu, and Uwe Ohler. “Transcription initiation patterns indicate divergent strategies for gene regulation at the chromatin level.” Plos Genet 7, no. 1 (January 13, 2011): e1001274. https://doi.org/10.1371/journal.pgen.1001274.
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    • Lekprasert, Parawee, Michael Mayhew, and Uwe Ohler. “Assessing the utility of thermodynamic features for microRNA target prediction under relaxed seed and no conservation requirements.” Plos One 6, no. 6 (2011): e20622. https://doi.org/10.1371/journal.pone.0020622.
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    • Majoros, William H., and Uwe Ohler. “Modeling the evolution of regulatory elements by simultaneous detection and alignment with phylogenetic pair HMMs.” Plos Comput Biol 6, no. 12 (December 16, 2010): e1001037. https://doi.org/10.1371/journal.pcbi.1001037.
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    • Kalinka, Alex T., Karolina M. Varga, Dave T. Gerrard, Stephan Preibisch, David L. Corcoran, Julia Jarrells, Uwe Ohler, Casey M. Bergman, and Pavel Tomancak. “Gene expression divergence recapitulates the developmental hourglass model.” Nature 468, no. 7325 (December 9, 2010): 811–14. https://doi.org/10.1038/nature09634.
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    • Parry, Trevor J., Joshua W. M. Theisen, Jer-Yuan Hsu, Yuan-Liang Wang, David L. Corcoran, Moriah Eustice, Uwe Ohler, and James T. Kadonaga. “The TCT motif, a key component of an RNA polymerase II transcription system for the translational machinery.” Genes Dev 24, no. 18 (September 15, 2010): 2013–18. https://doi.org/10.1101/gad.1951110.
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    • Arunachalam, Manonmani, Karthik Jayasurya, Pavel Tomancak, and Uwe Ohler. “An alignment-free method to identify candidate orthologous enhancers in multiple Drosophila genomes.” Bioinformatics 26, no. 17 (September 1, 2010): 2109–15. https://doi.org/10.1093/bioinformatics/btq358.
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    • Ni, Ting, David L. Corcoran, Elizabeth A. Rach, Shen Song, Eric P. Spana, Yuan Gao, Uwe Ohler, and Jun Zhu. “A paired-end sequencing strategy to map the complex landscape of transcription initiation.” Nat Methods 7, no. 7 (July 2010): 521–27. https://doi.org/10.1038/nmeth.1464.
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    • Mace, Daniel L., Nicole Varnado, Weiping Zhang, Erwin Frise, and Uwe Ohler. “Extraction and comparison of gene expression patterns from 2D RNA in situ hybridization images.” Bioinformatics 26, no. 6 (March 15, 2010): 761–69. https://doi.org/10.1093/bioinformatics/btp658.
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    • Georgiev, Stoyan, Alan P. Boyle, Karthik Jayasurya, Xuan Ding, Sayan Mukherjee, and Uwe Ohler. “Evidence-ranked motif identification.” Genome Biol 11, no. 2 (2010): R19. https://doi.org/10.1186/gb-2010-11-2-r19.
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    • Ohler, Uwe, and David A. Wassarman. “Promoting developmental transcription.” Development 137, no. 1 (January 2010): 15–26. https://doi.org/10.1242/dev.035493.
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    • Tomancak, Pavel, and Uwe Ohler. “Mapping the complexity of transcription control in higher eukaryotes.” Genome Biol 11, no. 4 (2010): 115. https://doi.org/10.1186/gb-2010-11-4-115.
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    • Yokoyama, Ken Daigoro, Uwe Ohler, and Gregory A. Wray. “Measuring spatial preferences at fine-scale resolution identifies known and novel cis-regulatory element candidates and functional motif-pair relationships.” Nucleic Acids Res 37, no. 13 (July 2009): e92. https://doi.org/10.1093/nar/gkp423.
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    • Megraw, Molly, Fernando Pereira, Shane T. Jensen, Uwe Ohler, and Artemis G. Hatzigeorgiou. “A transcription factor affinity-based code for mammalian transcription initiation.” Genome Res 19, no. 4 (April 2009): 644–56. https://doi.org/10.1101/gr.085449.108.
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    • Majoros, William H., and Uwe Ohler. “Complexity reduction in context-dependent DNA substitution models.” Bioinformatics 25, no. 2 (January 15, 2009): 175–82. https://doi.org/10.1093/bioinformatics/btn598.
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    • Rach, Elizabeth A., Hsiang-Yu Yuan, William H. Majoros, Pavel Tomancak, and Uwe Ohler. “Motif composition, conservation and condition-specificity of single and alternative transcription start sites in the Drosophila genome.” Genome Biol 10, no. 7 (2009): R73. https://doi.org/10.1186/gb-2009-10-7-r73.
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    • Holste, D., and U. Ohler. “Strategies for identifying RNA splicing regulatory motifs and predicting alternative splicing events.” Plos Computational Biology 4, no. 1 (2008): e21. https://doi.org/10.1371/journal.pcbi.0040021.
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    • Holste, Dirk, and Uwe Ohler. “Strategies for identifying RNA splicing regulatory motifs and predicting alternative splicing events.” Plos Comput Biol 4, no. 1 (January 2008): e21. https://doi.org/10.1371/journal.pcbi.0040021.
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    • Gottwein, Eva, Neelanjan Mukherjee, Christoph Sachse, Corina Frenzel, William H. Majoros, Jen-Tsan A. Chi, Ravi Braich, et al. “A viral microRNA functions as an orthologue of cellular miR-155.” Nature 450, no. 7172 (December 13, 2007): 1096–99. https://doi.org/10.1038/nature05992.
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    • Majoras, W. H., and U. Ohler. “Advancing the state of the art in computational gene prediction.” Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) 4366 LNBI (December 1, 2007): 81–106.
    • Brady, Siobhan M., David A. Orlando, Ji-Young Lee, Jean Y. Wang, Jeremy Koch, José R. Dinneny, Daniel Mace, Uwe Ohler, and Philip N. Benfey. “A high-resolution root spatiotemporal map reveals dominant expression patterns.” Science 318, no. 5851 (November 2, 2007): 801–6. https://doi.org/10.1126/science.1146265.
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    • Majoros, William H., and Uwe Ohler. “Spatial preferences of microRNA targets in 3' untranslated regions.” Bmc Genomics 8 (June 7, 2007): 152. https://doi.org/10.1186/1471-2164-8-152.
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    • Ruvinsky, Ilya, Uwe Ohler, Christopher B. Burge, and Gary Ruvkun. “Detection of broadly expressed neuronal genes in C. elegans.” Dev Biol 302, no. 2 (February 15, 2007): 617–26. https://doi.org/10.1016/j.ydbio.2006.09.014.
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    • Huang, Weichun, Joseph R. Nevins, and Uwe Ohler. “Phylogenetic simulation of promoter evolution: estimation and modeling of binding site turnover events and assessment of their impact on alignment tools.” Genome Biol 8, no. 10 (2007): R225. https://doi.org/10.1186/gb-2007-8-10-r225.
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    • Mace, Daniel L., Ji-Young Lee, Richard W. Twigg, Juliette Colinas, Philip N. Benfey, and Uwe Ohler. “Quantification of transcription factor expression from Arabidopsis images.” Bioinformatics 22, no. 14 (July 15, 2006): e323–31. https://doi.org/10.1093/bioinformatics/btl228.
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    • Narlikar, Leelavati, Raluca Gordân, Uwe Ohler, and Alexander J. Hartemink. “Informative priors based on transcription factor structural class improve de novo motif discovery.” Bioinformatics 22, no. 14 (July 15, 2006): e384–92. https://doi.org/10.1093/bioinformatics/btl251.
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    • Huang, Weichun, David M. Umbach, Uwe Ohler, and Leping Li. “Optimized mixed Markov models for motif identification.” Bmc Bioinformatics 7 (June 2, 2006): 279. https://doi.org/10.1186/1471-2105-7-279.
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    • Lee, Ji-Young, Juliette Colinas, Jean Y. Wang, Daniel Mace, Uwe Ohler, and Philip N. Benfey. “Transcriptional and posttranscriptional regulation of transcription factor expression in Arabidopsis roots.” Proc Natl Acad Sci U S A 103, no. 15 (April 11, 2006): 6055–60. https://doi.org/10.1073/pnas.0510607103.
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    • Ohler, Uwe. “Identification of core promoter modules in Drosophila and their application in accurate transcription start site prediction.” Nucleic Acids Res 34, no. 20 (2006): 5943–50. https://doi.org/10.1093/nar/gkl608.
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    • Bajic, Vladimir B., Michael R. Brent, Randall H. Brown, Adam Frankish, Jennifer Harrow, Uwe Ohler, Victor V. Solovyev, and Sin Lam Tan. “Performance assessment of promoter predictions on ENCODE regions in the EGASP experiment.” Genome Biol 7 Suppl 1, no. Suppl 1 (2006): S3.1-S313. https://doi.org/10.1186/gb-2006-7-s1-s3.
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    • Ohler, Uwe, Noam Shomron, and Christopher B. Burge. “Recognition of unknown conserved alternatively spliced exons.” Plos Comput Biol 1, no. 2 (July 2005): 113–22. https://doi.org/10.1371/journal.pcbi.0010015.
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    • Ohler, Uwe, Soraya Yekta, Lee P. Lim, David P. Bartel, and Christopher B. Burge. “Patterns of flanking sequence conservation and a characteristic upstream motif for microRNA gene identification.” Rna 10, no. 9 (September 2004): 1309–22. https://doi.org/10.1261/rna.5206304.
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    • Lim, Chin Yan, Buyung Santoso, Thomas Boulay, Emily Dong, Uwe Ohler, and James T. Kadonaga. “The MTE, a new core promoter element for transcription by RNA polymerase II.” Genes Dev 18, no. 13 (July 1, 2004): 1606–17. https://doi.org/10.1101/gad.1193404.
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    • Ohler, Uwe, Guo-chun Liao, Heinrich Niemann, and Gerald M. Rubin. “Computational analysis of core promoters in the Drosophila genome.” Genome Biol 3, no. 12 (2002): RESEARCH0087. https://doi.org/10.1186/gb-2002-3-12-research0087.
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    • Ohler, U., and H. Niemann. “Identification and analysis of eukaryotic promoters: recent computational approaches.” Trends Genet 17, no. 2 (February 2001): 56–60. https://doi.org/10.1016/s0168-9525(00)02174-0.
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    • Ohler, U., H. Niemann, H. Liao Gc, and G. M. Rubin. “Joint modeling of DNA sequence and physical properties to improve eukaryotic promoter recognition.” Bioinformatics 17 Suppl 1 (2001): S199–206. https://doi.org/10.1093/bioinformatics/17.suppl_1.s199.
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    • Ohler, U. “Promoter prediction on a genomic scale--the Adh experience.” Genome Res 10, no. 4 (April 2000): 539–42. https://doi.org/10.1101/gr.10.4.539.
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    • Reese, M. G., G. Hartzell, N. L. Harris, U. Ohler, J. F. Abril, and S. E. Lewis. “Genome annotation assessment in Drosophila melanogaster.” Genome Res 10, no. 4 (April 2000): 483–501. https://doi.org/10.1101/gr.10.4.483.
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    • Ohler, U., G. Stemmer, S. Harbeck, and H. Niemann. “Stochastic segment models of eukaryotic promoter regions.” Pac Symp Biocomput, 2000, 380–91. https://doi.org/10.1142/9789814447331_0036.
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    • Ohler, U., S. Harbeck, H. Niemann, E. Nöth, and M. G. Reese. “Interpolated markov chains for eukaryotic promoter recognition.” Bioinformatics 15, no. 5 (May 1999): 362–69. https://doi.org/10.1093/bioinformatics/15.5.362.
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  • Book Sections

    • Kavanaugh, L. A., and U. Ohler. “Predicting non-coding RNA transcripts.” In Bioinformatics: Tools and Applications, 65–97, 2007. https://doi.org/10.1007/978-0-387-92738-1_4.
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    • Majoros, W. H., I. Korf, and U. Ohler. “Gene prediction methods.” In Bioinformatics: Tools and Applications, 99–119, 2007. https://doi.org/10.1007/978-0-387-92738-1_5.
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  • Conference Papers

    • Ding, Jiandong, Danqing Li, Uwe Ohler, Jihong Guan, and Shuigeng Zhou. “Genome-wide search for miRNA-target interactions in Arabidopsis thaliana with an integrated approach.” In Bmc Genomics, 13 Suppl 3:S3, 2012. https://doi.org/10.1186/1471-2164-13-S3-S3.
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