- Ph.D., Mathematics, University of Heidelberg, Germany, 2001
Title: Algorithms for Physical Mapping. Major Professor: Martin Vingron
- Staatsexamen, Mathematics and Biology, University of Heidelberg, Germany, 1998
- Diploma (US equivalent: MS), Mathematics, University of Heidelberg, Germany, 1995
- October 2003-present: Assistant Professor, NC State University, Department of Computer Science, NC
- May 2001-May 2003: Postdoctoral Fellow, University of California, San Diego, Department of Computer Science and Engineering, CA
- January 2000-April 2001: Lecturer, Heidelberg Life Science Lab, Heidelberg, Germany
- February 1997- April 2001: Predoctoral Fellow, German Cancer Research Center (DKFZ), Functional Genome Analysis & Theoretical Bioinformatics Group, Heidelberg, Germany
- March 1994-December 1996: Research Assistant, University of Heidelberg, Department of Mathematics, Heidelberg, Germany
- 1992(summer), 1993(summer): Research Assistant, Robert Bosch GmbH, Stuttgart, Germany
Scholarly and Professional Awards
Refereed Journal Publications
B.E.Howard, B.Sick, 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.
S.Heber, R.Mayr, J.Stoye. Common Intervals of Multiple Permutations. Algorithmica, online first, DOI 10.1007/s00453-009-9332-1, 2009.
T.Wang, T.Furey, J.J.Connelly, S.Ji, S.Nelson, S.Heber, S.G.Gregory, E.R. Hauser. A general integrative genomic feature transcription factor binding site prediction method applied to analysis of USF1 binding in cardiovascular disease. Human Genomics, 3(3), 221-35, 2009.
B.M.Wheeler, A.M.Heimberg, V.N.Moy, E.A.Sperling, T.W.Holstein, S.Heber, K.J.Peterson. The deep evolution of metazoan microRNAs. Evol Dev. 360(6), 573-87,2009.
L.Li, M.E.Andersen, S.Heber, 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.
D.Zhi, U.Keich, P.Pevzner, S.Heber, H.Tang. Correcting Base-assignment Errors in Repeat Regions of Shotgun Assembly. IEEE/ACM TCBB, 4(1), 54-64, 2007.
S.Heber, B.Sick. Quality Assessment of Affymetrix GeneChip data. OMICS: A Journal of Integrative Biology, 10(3):358-68, 2006.
S.Saha, S.Heber. In Silico Prediction of Yeast Deletion Phenotypes. Genet. Mol. Res., 5(1):224-32, 2006.
J.L. Frahm, BE. Howard, 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.
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.
S.Heber and C.Savage. Common Intervals of Trees. Information Processing Letters, Vol. 93, Issue 2, 69-74, 2005.
J.Leipzig, P.Pevzner and S.Heber. The Alternative Splicing Gallery (ASG): Bridging the Gap Between Genome and Transcriptome. Nucleic Acids Research, 32, 3977-3983, 2004.
J.Leipzig, D.Nielsen and S.Heber. The Splicing Graph: A tool for Visualizing Gene Structure and Alternative Splicing. Future Drug Discovery, Mar., 62-65, 2004.
S.Heber, J.Stoye. The European Conference on Computational Biology (ECCB 2002). Drug Discovery Today, Vol. 8, No. 3, 113-114, 2003.
R.Wambutt, G.Murphy, G.Volckaert,…, S. Heber,..., et al.. Progress in Arabidopsis genome sequencing and functional genomics. J. Biotechnology 78, 81-292, 2000.
S.Heber, J.Hoheisel, M.Vingron. Applications of Bootstrap Techniques to Physical Mapping. GENOMICS, 69(2), 235-241, 2000.
M.Frohme, A.Camargo, S.Heber, C.Czink, A.Simpson, J.Hoheisel, A.deSouza. Mapping analysis of the Xylella fastidiosa genome. Nucleic Acids Res., 28(16), 3100-3104, 2000.
S.Heber, J.Stoye, M.Frohme, J.Hoheisel, M.Vingron. Contig Selection in Physical Mapping. J. Comp. Bio., 7(3/4), 395-408, 2000.
K.Mayer, C.Schuller, R.Wambutt,…, S.Heber,..., et al.. Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana. Nature 402, 769-777, 1999.
P.Scholler, S.Heber, J.Hoheisel. Optimization and automation of fluorescence-based DNA hybridizatrion for high-throughput clone mapping. Electrophoresis 19, 504-508, 1998.
Refereed Conference and Workshop Publications
Brian Howard, Steffen Heber. Towards Reliable Splice Variant Quantification using RNA-Seq Data. IEEE International Conference on Bioinformatics & Biomedicine (BIBM 2009), (accepted).
Jihye Kim, Sihui Zhao and Steffen Heber. Mining of Cis-regulatory Motifs Associated with Tissue-specific Alternative Splicing. 5th International Symposium, Bioinformatics Research and Applications, ISBRA2009, Lecture Notes in Bioinformatics, 260-71, 2009.
Sihui Zhao, Jihye Kim and Steffen Heber. Analysis of Cis-regulatory Motifs in Cassette Exons by Incorporating Exon Skipping Rates. 5th International Symposium, Bioinformatics Research and Applications, ISBRA2009, Lecture Notes in Bioinformatics, 272-83, 2009.
B.Howard, Beate Sick and Steffen Heber. Practical Quality Assessment of Microarray Data by Simulation of Differential Gene Expression. 5th International Symposium, Bioinformatics Research and Applications, ISBRA2009, Lecture Notes in Bioinformatics, 18-27, 2009.
B.Howard, I.Perera, Y.J.Im, H.Winter-Sederoff, B.Sick, S.Heber. Quality Assessment of Affymetrix GeneChip Data using the EM Algorithm and a Naive Bayes Classifier. BIBE 2007, 232-237.
L.Li, S.Heber, Q.Zhang, M.Andersen. Statistical Approaches to Identifying Androgen Response Elements. IEEE ICDM Workshop on Mining and Management of Biological Data. October 28, 2007.
S.Zhao, J.Kim, S.Heber. Large-scale Discovery of Regulatory Motifs Involved in Alternative Splicing. BIBE 2007: 1399-1403.
J.Kim, S.Zhao, S.Heber. Finding association rules of cis-regulatory elements involved in alternative splicing. ACMSE 2007: The 45th ACM Southeast Conference, Winston-Salem, North Carolina, 232-237, March 2007. Best Regular Paper Award Winner.
S.Heber, B.Sick. Automatic Quality Assessment of Affymetrix GeneChip Data. ACMSE 2006: The 44th ACM Southeast Conference, Melbourne, Florida, 411-416, March 2006.
Bergeron, S. Heber, J. Stoye. Common Intervals and Sorting by Reversals: A Marriage of Necessity. European Conference on Computational Biology 2002 (ECCB 2002), Bioinformatics, Suppl. 2, 54-61, 2002.
S.Heber, M.Alekseyev, S.H.Sze, H.Tang, P.Pevzner. Splicing Graphs and EST Assembly Problem. The 10th International Conference on Intelligent Systems for Molecular Biology (ISMB 2002), Bioinformatics, Suppl. 1, 181-188, 2002.
S.Heber, J.Stoye. Algorithms for finding gene clusters. Proceedings of WABI 2001, Lecture Notes in Computer Science 2149, 254-265, 2001.
S.Heber, J.Stoye, J.Hoheisel, M.Vingron. Contig Selection in Physical Mapping. Proc. of the Fourth Annual International Conference on Computational Molecular Biology (RECOMB 2000), journal version, 155–164, 2000.
S. Heber, J. Stoye, M. Frohme, J. Hoheisel, M. Vingron. Resampling Methods in Physical Mapping, In W. Gaul, G. Ritter (Eds.): Classification, Automation, and New Media: Proc. 24th Annual Conference of the GfKl, 2000. Volume 20 of Studies in Classification, Data Analysis, and Knowledge Organization (Springer Verlag), 437-444, 2000.
Functional Genomics Center Zurich, ETH Zurich and the University of Zurich, Switzerland, August 14, 2009.
Genome-wide analysis of alternative splicing in Arabidopsis stress response.
- Symposium for Life Science Education, Raleigh, May 2009.
Bioinformatics in Motion: Animations for Teaching Bioinformatics
- First RECOMB Satellite Conference on Bioinformatics Education. University of California, San Diego, March, 2009.
The Bioinformatics in Motion Project.
- EnvironmentalProtection Agency - National Health and Environmental Effects Research Laboratory (NHEERL), Raleigh, March 2007.
Replacing the Expert – An Unsupervised Classification Approach for Quality Assessment of Affymetrix GeneChip Data
- Second Annual Conference on Computational Biology, NIEHS, September 2006.
Automatic Quality Assessment of Affymetrix GeneChip Data
- Intramural Computational Biology and Bioinformatics Conference, NIEHS, September 2005.
Computational Prediction of Alternatively Spliced Transcripts
- DIMACS Workshop on Detecting and Processing Regularities in High Throughput Biological Data, Rutgers University, June 2005.
Common Intervals of Graphs.
- General Theory of Information Transfer and Combinatorics, Bielefeld, April 2004
Notes on Common Intervals of Trees
- Pan-American Advanced Studies Institute, Montevideo, Uruguay, February 2004
Algorithms for sequence analysis
- Pan-American Advanced Studies Institute, Montevideo, Uruguay, February 2004
Text Mining in Bioinformatics
- NCSU, Department of Genetics, March 2004
The Alternative Splicing Gallery: Investigating Gene Structure and Alternative Splicing
- Exploratory Workshop Functional Genomics, Paris, France, 1999
Reliability in Physical Mapping
- Role of Alternative Splicing in Plant Immune Response
Agency: NSF, PI: S.Heber, CoPI: P.Veronese
- Enhancing Bioinformatics Education
Agency: NCBC, PI: S.Heber, Duration: 5/16/2008-5/15/2010
- High-Performance Data Analytics with Demonstrations to DOE-Mission Applications
Agency: NSF, PI: N.Samatova, Co-PI S.Heber, Duration: 10/2008-8/2009
- A Bioinformatics Computing Cluster for NC State University
Agency: North Carolina Biotechnology Center, PI: S.Heber, Duration: 2/2007-1/2008
- An Intelligent User-Guided Microarray Analysis Server
CBI/RNA Inter-College Research Proposal, PIs: HW.Sederoff, S.Heber, Duration: 11/06-10/08
- Integrating Algorithm Visualization into CSC 505
Agency: LITRE, PI: S.Heber, Duration: 1/2006-6/2007
- Alternative Splicing and Proteome Diversity
Agency: NCSU Faculty Research & Professional Development Fund, PI: S.Heber, Duration: 1/2006-12/2006
- Editorial Board: The Journal of Bioinformatics - Theory and Applications, 2005-present
- Founder and Chair of the Organizing Committee of the Symposium for Life Science Education, 2009
- Editor of the Symposium for Life Science Education proceedings, 2009
- Co-organizer of a special session "Mechanisms of post-transcriptional control of gene functions in plant-microbe interactions (AS, PTGS, sumoylation and more…)" in the American Phytopathological Society (APS) Annual Meeting, 2009
- Member of the Symposium for Life Science Education Program Committee, 2009
- Member of RECOMB Comparative Genomics Program Committee, 2007 and 2009
- Member of ACMSE Program Committee, 2007
- Member of Pacific Symposium on Biocomputing (PSB) Program Committee, 2004
- Grant reviewing: RFBR (2006), North Carolina Biotechnology Center (2005), NSF (2003)
- Book review: Instant Notes in Bioinformatics, 2005
- Selected Journal Reviewing: Journal of Computational Biology, Nucleic Acids Research, BMC Genomics, BMC Bioinformatics, Bioinformatics, PLOS Genetics, Molecular Biology and Evolution