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Steffen Heber – Curriculum Vitae June 28, 2019

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Steffen Heber – Curriculum Vitae June 28, 2019 Steffen Heber – Curriculum Vitae June 28, 2019 Contact Department of Computer Science and Bioinformatics Research Center North Carolina State University Campus Box 7566 Raleigh, NC 27695 office: 2260 EB2 and 347 Ricks Hall phone: 919-513-1118 and 919-513-2726 fax: 919-515-7315 web page: https://people.engr.ncsu.edu/sheber Education • Ph.D. in Mathematics, University of Heidelberg, Heidelberg, Germany, 2001 Dissertation title: Algorithms for Physical Mapping. Major Professor: Martin Vingron • Staatsexamen in Mathematics and Biology, University of Heidelberg, Heidelberg, Germany, 1998 • Diploma (US equivalent: MS) in Mathematics, University of Heidelberg, Heidelberg, Germany, 1995 Employment NC State University, NC • August 2010-present: Associate Professor, Department of Computer Science Joint appointment with College of Sciences • October 2003-July 2010: Assistant Professor, Department of Computer Science Joint appointment with College of Physical and Mathematical Sciences University of California, San Diego, CA • May 2001-May 2003: Postdoctoral Fellow, Department of Computer Science and Engineering German Cancer Research Center (DKFZ), Heidelberg, Germany • February 1997-April 2001: Predoctoral Fellow, Functional Genome Analysis & Theoretical Bioinformatics Group Personal Statement Since his time in high school, Dr. Heber has been fascinated by the intersection of technology and modern biology. He has studied mathematics and biology at the University of Heidelberg in Germany. While working at the German Cancer Research Center (DKFZ), he received his PhD under the guidance of Martin Vingron and Joerg Hoheisel for investigating algorithmic problems that originate during physical mapping of complex genomes. After postdoctoral research on EST-assembly algorithms with Pavel Pevzner at UCSD, Dr. Heber joined NCSU in 2003. He is an associate professor in the Department of Computer Science. He holds a joint appointment between the Department of Computer Science and the College of Sciences to support the Bioinformatics Research Center (BRC) at NCSU. Part of his effort is devoted to service for the BRC, including collaborative research with faculty from other NCSU colleges and mentoring Computer Science oriented Bioinformatics graduate students. His research focuses on bioinformatics and computational biology. In most of his work Dr. Heber uses algorithms as tools for analyzing biological data. Recently however, he has started a complementary research thrust that investigates how nature can be used to inspire algorithm design. His research interests include data-driven storytelling, gene transcription and alternative splicing, translation, nature-inspired computation, and common intervals. His academic activities so far have yielded 72 publications with approximately 2400 citations, and 46 research presentations. Honors and Awards • Carol Miller Graduate Lecturer Award, 2018 and 2013 • Thank a Teacher Recognition Letter Fall 2016 (2 nominations), Spring 2015 (3 nominations), Fall 2014, Fall 2013, Spring 2013 • IBM faculty award, 2008 • One of the “RASS” Top Ten Papers Advancing the Science of Risk Assessment, 2007 • Best Paper Award, ACMSE, 2007 • Faculty Research and Professional Development Award, NC State University, 2006 • Travel Award, ISCB, 2002 • Best Poster Award, DKFZ Poster Presentation, 2000 • Diploma passed with distinction, 1995 • Baccalaureate exam passed with distinction, 1987 • 1st Place, Baden-Wuerttemberg Mathematics Contest, 1986 Publications and Presentations Journal Articles [J0] C. Wimberly and S. Heber. “PeakPass: A Machine Learning Approach for ChIP-Seq Blacklisting”. Journal of Computational Biology, ISBRA 2019 special issue, invited, in preparation. [J1] P. Perkins, S. Mazzoni-Putman, A. Stepanova, J. Alonso and S. Heber. “riboStreamR: A Web Application for Quality Control, Analysis, and Visualization of Ribo-seq Data”. BMC Genomics. 2019 Jun 6;20(Suppl 5):422. [J2] D.A. Tokarz, K.A. Heffelfinger, D.D. Jima, J. Gerlach, R.N. Shah, I. Rodriguez-Nunez, A.N. Kortum, A.A. Fletcher, S.K. Nordone, J.M. Law, S. Heber and J.A. Yoder. “Disruption of Trim9 function abrogates macrophage motility in vivo.” J Leukoc Biol. 2017 Dec;102(6):1371-1380. [J3] C. Merchante, Q. Hu, S. Heber, AN. Stepanova and JM. Alonso. “A Ribosome Footprinting Protocoll in Plants.” Bio-protocol Vol 6, Iss 21, Nov 05, 2016 DOI:10.21769/BioProtoc.1985 [J4] G. Villarino, M. Flores-Vergara, Q. Hu, B. Sehra, A. de Luis Balaguer, S. Manrique, L. Robles, J. Brumos, A. Stepanova, J. Alonso, E. Sundberg, S. Heber and R.G. Franks. “Transcriptomic Signature of the SHATTERPROOF2 Expression Domain Reveals the Meristematic Nature of Arabidopsis Gynoecial Medial Domain.” Plant Physiol. 2016 May;171(1):42-61. [J5] Q. Hu, C. Merchante, A. Stepanova, J. Alonso and S. Heber. “Genome-wide Search for Translated Upstream Open Reading Frames in Arabidopsis thaliana.” IEEE Trans Nanobioscience. 2016 Mar; 15(2):148-57. [J6] J. Merchante, J. Brumos, J. Yun, Q. Hu, KR. Spencer, P. Enriquez, B.M. Binder, S. Heber, A.N. Stepanova and J.M. Alonso. “Gene-specific translation regulation mediated by the hormone signaling molecule EIN2.” Cell. 2015 Oct 22;163(3):684-97. Recommended in F1000Prime as being of special significance in its field. [J7] D. Schreiner, T.M. Nguyen, G. Russo, S. Heber, A. Patrignani, E. Ahrné and P. Scheiffele. “Targeted combinatorial alternative splicing generates brain region-specific repertoires of neurexins.” Neuron. 2014 Oct 22;84(2):386-98. [J8] B.E. Howard, Q. Hu, A.C. Babaoglu, M. Chandra, M. Borghi, X. Tan, L. He, H. Winter-Sederoff, W. Gassmann, P. Veronese and S. Heber. “High-Throughput RNA Sequencing of Pseudomonas-Infected Arabidopsis Reveals Hidden Transcriptome Complexity and Novel Splice Variants.” PLoS One. 2013 Oct 1;8(10):e74183. [J9] B.E. Howard and S. Heber. “Towards Reliable Splice Variant Quantification using RNA-Seq Data.” BMC Bioinformatics, 11 Suppl 3:S6, 2010 Apr 29. Highly accessed. [J10] K.-Y. Chang, D. Georgianna, S. Heber, G. Payne and D. Muddiman. “Detection of Alternative Splicing on the Proteome Level in Aspergillus flavus.” Journal of Proteome Research, 9(3):1209-17, 2010. [J11] R. Shi, Y.-H. Sun, Q. Li, S. Heber, R. Sederoff and V. Chiang. “Towards a systems approach for lignin biosynthesis in Populus trichocarpa: abundance and specificity of transcripts and predictive power of promoter motifs in the monolignol biosynthetic genes.” Plant and Cell Physiology, 51(1):144-63. Epub 2009 Dec 8. [J12] S. Heber, R. Mayr and J. Stoye. “Common Intervals of Multiple Permutations.” Algorithmica, 60, 2, 175- 206, 2009. [J13] B.E. Howard, B. Sick and S. Heber. “Unsupervised Assessment of Microarray Data Quality Using a Gaussian Mixture Model.” BMC Bioinformatics, 10:191. DOI 10.1186/1471-2105-10-191, 2009. Highly accessed. [J14] T. Wang, T. Furey, J.J. Connelly, S. Ji, S. Nelson, S. Heber, S.G. Gregory and E.R. Hauser. “A novel genome- scale transcription factor binding site prediction method and its application to candidate gene identification in human disease.” Human Genomics, 3(3), 221-35, 2009. [J15] B.M. Wheeler, A.M. Heimberg, V.N. Moy, E.A. Sperling, T.W. Holstein, S. Heber and K.J. Peterson. “The deep evolution of metazoan microRNAs.” Evolution & Development 360(6), 573-87, 2009. [J16] L. Li, M.E. Andersen, S. Heber and Q. Zhang. “Non-monotonic dose response relationship in steroid hormone receptor-mediated gene expression.” Journal of Molecular Endocrinology, 38, 569-585, 2007. One of the 2007 “RASS” Top Ten Papers Advancing the Science of Risk Assessment. [J17] D. Zhi, U. Keich, P. Pevzner, S. Heber and H. Tang. “Correcting Base-assignment Errors in Repeat Regions of Shotgun Assembly.” IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB), 4(1), 54-64, 2007. [J18] S. Heber and B. Sick. “Quality Assessment of Affymetrix GeneChip data.” OMICS: A Journal of Integrative Biology, 10(3), 358-68, 2006. [J19] S. Saha and S. Heber. “In Silico Prediction of Yeast Deletion Phenotypes.” Genetics and Molecular Research, 5(1), 224-32, 2006. [J20] J.L. Frahm, B.E. Howard and S. Heber, D.C. Muddiman. “Accessible Proteomics Space and its Implications for Peak Capacity for Zero-, One- and Two- Dimensional Separations Coupled with FT-ICR and TOF Mass Spectrometry.” Journal of Mass Spectrometry, 41(3), 281-288, 2006. [J21] M. Psarros, S. Heber, M. Sick, K. Harshman and B. Sick. “RACE: Remote Analysis Computation for gene Expression data.” Nucleic Acids Research, 33(Web Server issue), W638-43, 2005. [J22] S. Heber and C. Savage. “Common Intervals of Trees.” Information Processing Letters, 93(2), 69-74, 2005. [J23] J. Leipzig, P. Pevzner and S. Heber. “The Alternative Splicing Gallery (ASG): Bridging the Gap Between Genome and Transcriptome.” Nucleic Acids Research, 32(13), 3977-3983, 2004. [J24] J. Leipzig, D. Nielsen and S. Heber. “The Splicing Graph: A tool for Visualizing Gene Structure and Alternative Splicing.” Future Drug Discovery, March, 62-65, 2004. [J25] S. Heber and J. Stoye. “The European Conference on Computational Biology (ECCB 2002).” Drug Discovery Today, 8(3), 113-114, 2003. [J26] R. Wambutt, G. Murphy, G. Volckaert,…, S. Heber,..., (more than 100 authors). “Progress in Arabidopsis genome sequencing and functional genomics.” Journal of Biotechnology, 78(3), 81-292, 2000. [J27] S. Heber, J. Hoheisel and M. Vingron. “Applications of Bootstrap Techniques to Physical Mapping.” GENOMICS, 69(2), 235-241, 2000. [J28] M. Frohme, A. Camargo, S. Heber, C. Czink, A. Simpson, J. Hoheisel and A. deSouza. “Mapping
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