Steffen Heber Curriculum Vitae July 30 · 2019. 8. 5. · Steffen Heber – Curriculum Vitae July 30, 2019 Contact Department of Computer Science and Bioinformatics Research Center

Steffen Heber – Curriculum Vitae July 30, 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

email: [email protected]

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

https://people.engr.ncsu.edu/sheber

Personal Statement

Since his time in high school, Dr. Heber has been fascinated by the beauty and complexity at the intersection of computer science, mathematics, and 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 2450 citations; his h-index is 19, and his i10-index is 25. Dr. Heber has graduated 7 PhD and 6 MS students, and he has supervised one postdoctoral research associate. In addition, he has been awarded approximately $4.2M in funding.

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, A.N. Stepanova and J.M. 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.L. 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, K.R. 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 analysis

of the Xylella fastidiosa genome.” Nucleic Acids Research, 28(16), 3100-3104, 2000. [J29] S. Heber, J. Stoye, M. Frohme, J. Hoheisel and M. Vingron. “Contig Selection in Physical Mapping.”

Journal Computational Biology, 7(3/4), 395-408, 2000. [J30] K. Mayer, C. Schuller, R. Wambutt,…, S. Heber,..., (more than 100 authors). “Sequence and analysis of

chromosome 4 of the plant Arabidopsis thaliana.” Nature 402(6763), 769-777, 1999. [J31] P. Scholler, S. Heber and J. Hoheisel. “Optimization and automation of fluorescence-based DNA

hybridization for high-throughput clone mapping.” Electrophoresis 19(4), 504-508, 1998.

Conference & Workshop Papers

[C1] P. Perkins and S. Heber. “Using a Novel Negative Selection Inspired Anomaly Detection Algorithm to

Identify Corrupted Ribo-seq and RNA-seq Samples.” The 10th ACM Conference on Bioinformatics,

Computational Biology, and Health Informatics, ACM BCB 2019, accepted.

[C2] C. Wimberly and S. Heber. “PeakPass: A Machine Learning Approach for ChIP-Seq Blacklisting.” 15th

International Symposium, Bioinformatics Research and Applications, ISBRA 2019, accepted.

[C3] P. Perkins and S. Heber. "Identification of Ribosome Pause Sites Using a Z-Score Based Peak Detection

Algorithm." In 2018 IEEE 8th International Conference on Computational Advances in Bio and Medical

Sciences (ICCABS), pp. 1-6. IEEE, 2018.

[C4] S. Ebert, E. Farhana and S. Heber. “A parallel island model for biogeography-based classification rule

mining in julia.” In Proceedings of the Genetic and Evolutionary Computation Conference Companion

(GECCO '18), 1284-1291. Kyoto, Japan, July 15 - 19, 2018.

[C5] Q. Hu and S. Heber. “UORFseq: Identifying Translated uORFs based on Sequence Features via Tree-based

Algorithms.” In Proceedings of the 10th International Conference on Bioinformatics and Computational

Biology (BiCOB 2018), pp. 136 - 141, Las Vegas, Nevada, 19 - 21 March 2018.

[C6] E. Farhanah and S. Heber. “Biogeography-Based Rule Mining for Classification.” GECCO 2017,

Proceedings of the Genetic and Evolutionary Computation Conference, Berlin, Germany, pp. 417-424,

July 15-19, 2017.

[C7] Q. Hu, K. Merchante, A.N. Stepanova, J.M. Alonso and S. Heber. "Mining transcript features related to

translation in Arabidopsis using LASSO and random forest." IEEE 5th International Conference on

Computational Advances in Bio and Medical Sciences (ICCABS 2015), pp. 1-6, 15-17 Oct. 2015.

[C8] Q. Hu, K. Merchante, A.N. Stepanova, J.M. Alonso and S. Heber. "A Stacking-based Approach to Identify

Translated Upstream Open Reading Frames in Arabidopsis thaliana." ISBRA 2015, Lecture Notes in

Computer Science, Vol 9096, pp. 138, 49, June 7-10, 2015.

[C9] K. Merchante, Q. Hu, A.N. Stepanova, J.M. Alonso and S. Heber. "Deep sequencing of ribosomal

footprints for studying genome-wide mRNA translation in plants." IEEE 3rd International Conference on

Computational Advances in Bio and Medical Sciences (ICCABS 2013), pp. 1,1, 12-14 June 2013.

[C10] B.E. Howard, P. Veronese and S. Heber. "Improved RNA-Seq Partitions in Linear Models for Isoform

Quantification", IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2011), 151-

154, 2011.

[C11] B.E. Howard, X. Tan, P. Veronese and S. Heber. "Workshop: Using a transcript catalog and paired-end

RNA-Seq data to identify differential alternative splicing", IEEE 1st International Conference on

Computational Advances in Bio and Medical Sciences (ICCABS 2011), 270, 2011.

[C12] B.E. Howard and S. Heber. “Towards Reliable Splice Variant Quantification using RNA-Seq Data.” IEEE

International Conference on Bioinformatics & Biomedicine (BIBM 2009), 130-135, 2009.

[C13] J. Kim, S. Zhao and S. Heber. “Mining of Cis-regulatory Motifs Associated with Tissue-specific Alternative

Splicing.” 5th International Symposium, Bioinformatics Research and Applications, ISBRA 2009, Lecture

Notes in Bioinformatics, 260-271, 2009.

[C14] S. Zhao, J. Kim and S. Heber. “Analysis of Cis-regulatory Motifs in Cassette Exons by Incorporating Exon

Skipping Rates.” 5th International Symposium, Bioinformatics Research and Applications, ISBRA 2009,

Lecture Notes in Bioinformatics, 272-283, 2009.

[C15] B. Howard, B. Sick and S. Heber. “Practical Quality Assessment of Microarray Data by Simulation of

Differential Gene Expression.” 5th International Symposium, Bioinformatics Research and Applications,

ISBRA 2009, Lecture Notes in Bioinformatics, 18-27, 2009.

[C16] B. Howard, I. Perera, Y.J. Im, H. Winter-Sederoff, B. Sick and S. Heber. “Quality Assessment of Affymetrix

GeneChip Data using the EM Algorithm and a Naive Bayes Classifier.” Proceedings of the 7th IEEE

International Conference on Bioinformatics and Bioengineering (BIBE 2007), 232-237, 2007.

[C17] L. Li, S. Heber, Q. Zhang and M. Andersen. “Statistical Approaches to Identifying Androgen Response

Elements.” IEEE ICDM Workshop on Mining and Management of Biological Data, October 28, 95-100,

2007.

[C18] S. Zhao, J. Kim and S. Heber. “Large-scale Discovery of Regulatory Motifs Involved in Alternative Splicing.”

Proceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering (BIBE 2007),

1399-1403, 2007.

[C19] J. Kim, S. Zhao and 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.

[C20] S. Heber and B. Sick. “Automatic Quality Assessment of Affymetrix GeneChip Data.” ACMSE 2006: The

44th ACM Southeast Conference, Melbourne, Florida, 411-416, March 2006.

[C21] Bergeron, S. Heber and 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.

[C22] S. Heber, M. Alekseyev, S.H. Sze, H. Tang and 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.

[C23] S. Heber and J. Stoye. “Algorithms for finding gene clusters.” Proceedings of the 1st Workshop on

Algorithms in BioInformatics (WABI 2001), Lecture Notes in Computer Science 2149, 254-265, 2001.

[C24] S. Heber and J. Stoye. “Finding All Common Intervals of k Permutations.” Proceedings of the 12th Annual

Symposium on Combinatorial Pattern (CPM 2000), Lecture Notes in Computer Science 2089, 207-218,

2001.

[C25] S. Heber, J. Stoye, J. Hoheisel and M. Vingron. “Contig Selection in Physical Mapping.” Proc. of the Fourth

Annual International Conference on Computational Molecular Biology (RECOMB 2000), 155–164, 2000.

[C26] S. Heber, J. Stoye, M. Frohme, J. Hoheisel and 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.

Posters and Abstracts

[P1] D. Schreiner, J. Simicevic, G. Russo, S. Heber, A. Schmidt, P. Scheiffele. “Deciphering the neurexin code

in neuronal circuitry.” 10th Göttingen Meeting of the German Neuroscience Society, Göttingen,

Germany, March 13-16, 2013.

[P2] B.E. Howard, S. Heber. “One gene, many transcripts: quantifying splice variants with RNA-Sequencing.”

Symposium on RNA Biology VIII: RNA, Tool and Target, Raleigh, NC, October 16-17, 2009.

[P3] S. Kumar, B. Weehler, S. Heber, T.Lomax, H. Sederoff. “Small RNAs in Arabidopsis Roots and their

Differential Regulation in Response to Gravity.” 26th Annual Interdisciplinary Plant Group Symposium,

Columbia, Missouri, May 27-29, 2009.

[P4] S. Heber, P. Veronese. “Role of pre-mRNA splicing in plant response to the environment.” Abstract Book

of the XXII Annual Plant Molecular Biology Retreat, North Carolina Arboretum, Asheville, NC, September

26-28, 2008.

[P5] H. Sederoff, S. Heber, B. Howard, H. Myburg-Nichols, R. Hammond, R. Salinas-Mondragon, C.S. Brown.

“Gravity-Induced Gene Expression in Plants.” 37th COSPAR Scientific Assembly, Montréal, Canada, July

13-20, 2008.

[P6] L. Li, S. Heber, Q. Zhang, M. Andersen. “In Silico Identification of Androgen Response Elements.”

International Conference on Advances in Interdisciplinary Statistics and Combinatorics, Greensboro, NC,

USA October 12-14, 2007.

[P7] J. Frahm, A. Hawkridge, B. Howard, S. Heber, D.C. Muddiman, W.M. Keck. “Forbidden Zones in

Proteomics and Ramifications and Possibilities for Label-Free Proteomics Assessment of Retention Time

Reproducibility and Normalization Strategies.” 54th ASMS Conference on Mass Spectrometry and Allied

Topics, Seattle, WA, May 2006.

[P8] S. Heber, S. Saha. “Evolutionary Conservation and Selection of Alternatively Spliced Human Genes.”

RECOMB 2005, Cambridge, May 2005.

[P9] S. Zhao, J. Kim, S. Heber. “Discovery of tissue-specific Motifs regulating Alternative Splicing in Mouse.”

RNA Society of NC Seminar Series, August 2005.

[P10] J. Leipzig, S. Heber. “The Alternative Splicing Gallery (ASG): Visualizing Gene Structure and Alternative

Splicing.” RECOMB 2004, San Diego, 530-531, May 2004.

[P11] S. Heber. “Bootstrap Techniques in Physical Mapping.” German Cancer Research Center (DKFZ),

Heidelberg, Germany, December 2000. Best Poster Award Winner.

Book Chapters

[BC1] S. Heber, B.E. Howard. “Genome Rearrangements.” In Bioinformatics for Biologists textbook, edited by

P.A. Pevzner and R. Shamir. University Press, 167-187, 2011.

Other Publications

[O1] C. Chauve, Y. Diekmann, S. Heber, J. Mixtacki, S. Rahmann, J. Stoye. “On Common Intervals with Errors.”

Report 2006-02, University of Bielefeld, ISSN 0946-7831

[O2] S. Heber. “Algorithms for Physical Mapping.” Ph.D. thesis, IWR/SFB preprint, 2001.

[O3] Book review: “Instant Notes in Bioinformatics.” by D.R. Westhead, J.H. Parish, and RM. Twyman, BIOS

Scientific Publisher, 2005.

Patents

• “Splicing graph assembler,” U.S. provisional patent application: (PR2179)51293/276515

Software

• The Alternative Splicing Gallery (ASG, https://brcwebportal.cos.ncsu.edu/asg/) is an annotated splicing

graph database of all human genes. The database is especially known for its useful user interface. The ASG

provides basic gene information and allows users to interactively assemble transcripts, to download

transcript catalogs, and to compare the results with predictions of other databases.

• The Remote Analysis Computation for gene Expression data server (RACE, http://race.unil.ch) is a collection

of web tools designed to assist with the analysis of DNA microarray data and results. RACE performs probe

https://brcwebportal.cos.ncsu.edu/asg/

http://race.unil.ch/

level data preprocessing, quality checks, normalization, and visualization for Affymetrix GeneChips as well

as clustering and differential analysis of normalized expression levels or ratios for arbitrary platforms. The

user can customize each analysis request, and upon submission the analysis is executed in a fully automated

way.

• Bioinformatics in Motion (http://statgen.ncsu.edu/slse/animations/) is an a library of interactive

animations for Bioinformatics algorithms and applications. The site also provides an online resource portal

of freely available educational resources for Bioinformatics and Life Science topics. The library was

supported by an Education Enhancement grant of the North Carolina Biotechnology Center.

• riboStreamR (http://uhura.cos.ncsu.edu:3842/) is a comprehensive Ribo-seq quality control platform in the

form of an R Shiny web application. RiboStreamR provides visualization and analysis tools for various Ribo-

seq QC metrics, including read length distribution, read periodicity, and translational efficiency.

Invited Presentations

[P1] “Identifying the Signatures of Missing Transcripts.” 2017 IEEE 8th International Conference on

Computational Advances in Bio and Medical Sciences (ICCABS) Workshop on Computational Advances

for Next Generation Sequencing (CANGS 2018), Las Vegas, Nevada, 18-20 Oct. 2018.

[P2] “riboStreamR: A Web Application for Quality Control, Analysis, and Visualization of Ribo-seq Data.” 2017

IEEE 7th International Conference on Computational Advances in Bio and Medical Sciences (ICCABS)

Workshop on Computational Advances for Next Generation Sequencing (CANGS 2017), Orlando, Florida,

19-21 Oct. 2017.

[P3] “From Alternative Splicing to Biogeography-Based Optimization – Using Computer Science to Learn

about Biology and Vice Versa.” Plant & Microbial Biology Seminar, NC State University, Raleigh, March

21, 2017.

[P4] “Using PacBio Long-read Sequencing to Investigate Genes with Complex Splicing Behavior.” 5th

Workshop on Computational Advances for Next Generation Sequencing (CANGS 2016), Miami, Florida,

October 16, 2015.

[P5] “Hidden Transcriptome Complexity in Pseudomonas-Infected Arabidopsis.” Plant and Animal Genomes

XXII Conference, San Diego, California, January 12, 2014.

[P6] "Deep sequencing of ribosomal footprints for studying genome-wide mRNA translation in plants." 3rd

Workshop on Computational Advances for Next Generation Sequencing (CANGS 2013), New Orleans,

Louisiana, June 12, 2013.

[P7] “Using a Transcript Catalog and Paired-End RNA-Seq Data to Identify Differential Alternative Splicing.”

Workshop on Computational Advances for Next Generation Sequencing (CANGS 2011), Orlando, Florida,

February 4,2011.

[P8] “Investigating the role of alternative splicing in plant immune response with quantitative RNA-Seq.” Plant

and Animal Genomes XIX Conference, San Diego, California, January 15, 2011.

[P9] “Genome-wide analysis of alternative splicing in Arabidopsis stress response.” Zurich University of

Applied Sciences, Zurich, Switzerland, August 14, 2009.

[P10] “Bioinformatics in Motion: Animations for Teaching Bioinformatics.” Symposium on Life Science

Education, Raleigh, North Carolina, May 26, 2009.

[P11] “Replacing the Expert – An Unsupervised Classification Approach for Quality Assessment of Affymetrix

GeneChip Data.” Environmental Protection Agency - National Health and Environmental Effects

Research Laboratory, Raleigh, North Carolina, March 2007.

http://statgen.ncsu.edu/slse/animations/

http://uhura.cos.ncsu.edu:3842/

[P12] “Automatic Quality Assessment of Affymetrix GeneChip Data.” Second Annual Conference on

Computational Biology, NIEHS, Raleigh, North Carolina, September 2006.

[P13] “Computational Prediction of Alternatively Spliced Transcripts.” Intramural Computational Biology and

Bioinformatics Conference, NIEHS, Raleigh, North Carolina, September 2005.

[P14] “Notes on Common Intervals of Trees.” General Theory of Information Transfer and Combinatorics,

Bielefeld, Germany, April 2004.

[P15] “Algorithms for sequence analysis.” Pan-American Advanced Studies Institute, Montevideo, Uruguay,

February 2004.

[P16] “Text Mining in Bioinformatics.” Pan-American Advanced Studies Institute, Montevideo, Uruguay,

February 2004.

[P17] “The Alternative Splicing Gallery: Investigating Gene Structure and Alternative Splicing.” Department of

Genetics, NCSU, Raleigh, North Carolina, March 2004.

[P18] “Reliability in Physical Mapping.” Exploratory Workshop Functional Genomics, Paris, France, 1999.

Regular Presentations

[P19] “PeakPass: A Machine Learning Approach for ChIP-Seq Blacklisting.” 15th International Symposium,

Bioinformatics Research and Applications, ISBRA 2019, Barcelona, Spain, June 3–6, 2019.

[P20] “Tell me and I will forget, teach me and I may remember, involve me and I learn.” DELTA summer short

workshop session on student engagement, August 15, 2018.

[P21] “A parallel island model for biogeography-based classification rule mining in julia.” The Genetic and

Evolutionary Computation Conference (GECCO 2018), Kyoto, Japan — July 15 - 19, 2018.

[P22] “Biogeography-Based Rule Mining for Classification.” The Genetic and Evolutionary Computation

Conference (GECCO 2017), Berlin, Germany July 15th-19th, 2017.

[P23] "Mining transcript features related to translation in Arabidopsis using LASSO and random forest." IEEE

5th International Conference on Computational Advances in Bio and Medical Sciences (ICCABS 2015),

Miami, Florida, October 15-17, 2015.

[P24] "A Stacking-based Approach to Identify Translated Upstream Open Reading Frames in Arabidopsis

thaliana." 11th International Symposium, Bioinformatics Research and Applications, ISBRA 2015,

Norfolk, Virginia, June 7-10, 2015.

[P25] "Deep sequencing of ribosomal footprints for studying genome-wide mRNA translation in plants." IEEE

International Conference on Computational Advances in Bio and Medical Sciences (ICCABS 2013), New

Orleans, Louisiana, June 12-14, 2013.

[P26] "Improved RNA-Seq Partitions in Linear Models for Isoform Quantification.", IEEE International

Conference on Bioinformatics and Biomedicine (BIBM 2011), Atlanta, Georgia, November 12-15, 2011.

[P27] “Using a transcript catalog and paired-end RNA-Seq data to identify differential alternative splicing.",

IEEE 1st International Conference on Computational Advances in Bio and Medical Sciences (ICCABS

2011), Orlando, Florida, February 3-5, 2011.

[P28] “The Hidden Transcriptome in Plant Microbe Interactions.” Plant and Animal Genomes XIX Conference,

San Diego, California, January 15-19, 2011.

[P29] “Towards Reliable Splice Variant Quantification using RNA-Seq Data.” IEEE International Conference on

Bioinformatics & Biomedicine, BIBM 2009, Washington D.C., November 1-4, 2009.

[P30] “Alternative splicing in plant-microbe interactions.” The 2009 American Phytopathological Society (APS)

Annual Meeting, APS 2009, Portland, Oregon, August 1-5, 2009.

[P31] “Mining of Cis-regulatory Motifs Associated with Tissue-specific Alternative Splicing.” 5th International

Symposium, Bioinformatics Research and Applications, ISBRA 2009, Nova Southeastern University, Ft.

Lauderdale, Florida, May 13-16, 2009.

[P32] “Analysis of Cis-regulatory Motifs in Cassette Exons by Incorporating Exon Skipping Rates.” 5th

International Symposium, Bioinformatics Research and Applications, ISBRA 2009, Nova Southeastern

University, Ft. Lauderdale, Florida, May 13-16, 2009.

[P33] “Practical Quality Assessment of Microarray Data by Simulation of Differential Gene Expression.” 5th

International Symposium, Bioinformatics Research and Applications, ISBRA 2009, Nova Southeastern

University, Ft. Lauderdale, Florida, May 13-16, 2009.

[P34] “The Bioinformatics in Motion Project.” First RECOMB Satellite Conference on Bioinformatics Education.

University of California, San Diego, CA, March 14-15, 2009.

[P35] “Statistical Approaches to Identifying Androgen Response Elements.” IEEE ICDM Workshop on Mining

and Management of Biological Data, Omaha, Nebraska, October 28, 2007.

[P36] “Quality Assessment of Affymetrix GeneChip Data using the EM Algorithm and a Naive Bayes Classifier.”

7th IEEE International Conference on Bioinformatics and Bioengineering (BIBE 2007), Harvard Medical

School, Boston, Massachusetts, October 14-17, 2007.

[P37] “Large-scale Discovery of Regulatory Motifs Involved in Alternative Splicing.” 7th IEEE International

Conference on Bioinformatics and Bioengineering (BIBE 2007), Harvard Medical School, Boston,

Massachusetts, October 14-17, 2007.

[P38] “Finding association rules of cis-regulatory elements involved in alternative splicing.” The 45th ACM

Southeast Conference (ACMSE 2007), Winston-Salem, NC, March 23-24, 2007.

[P39] “Automatic Quality Assessment of Affymetrix GeneChip Data.” The 44th ACM Southeast Conference

(ACMSE 2006), Melbourne, Florida, March 10-12, 2006.

[P40] “In Silico Prediction of Yeast Deletion Phenotypes.” X-meeting, 1st international conference of the

Brazilian Association for Bioinformatics and Computational Biology AB3C, Caxambu, MG, Brazil, October

4-7, 2005.

[P41] “Common Intervals of Graphs.” DIMACS Workshop on Detecting and Processing Regularities in High

Throughput Biological Data, Rutgers University, NJ, June 20-22, 2005.

[P42] “Splicing Graphs and EST Assembly Problem.” 10th International Conference on Intelligent Systems for

Molecular Biology (ISMB 2002), Edmonton, Canada, August 3-7, 2002.

[P43] “Common Intervals and Sorting by Reversals: A Marriage of Necessity.” European Conference on

Computational Biology 2002 (ECCB 2002), Saarbrucken, Germany, October 6-9, 2002.

[P44] “Algorithms for finding gene clusters.” 1st Workshop on Algorithms in BioInformatics (WABI 2001),

University of Aarhus, Denmark, August 28-31, 2001.

[P45] “Finding All Common Intervals of k Permutations.” 12th Annual Symposium on Combinatorial Pattern

(CPM 2000), Jerusalem, Israel, July 1-4, 2001.

[P46] “Contig Selection in Physical Mapping.” Fourth Annual International Conference on Computational

Molecular Biology (RECOMB 2000), Tokyo, Japan, April 8-11, 2000.

[P47] “Resampling Methods in Physical Mapping.” 24th Annual Conference of the GfKl, University of Passau,

Germany, March 15-17, 2000.

Funding

I have been awarded approximately $4.2M (extramural: $4.1M, intramural&donations: $120k) in funding.

Extramural

• Identification of Translational Hormone-Response Gene Networks and Cis-Regulatory Elements, NSF, PI: J.

Alonso, Co-PI: S. Heber, A. Stepanova, C. Williams. $2,675,026, 8/2015-7/2021.

• Transcriptional Nodes Coordinate Patterning and Cellular Proliferation During Carpel Margin Meristem

Development, NSF, PI: R. Franks, Co-PI: S. Heber, $819,507, 03/2014-02/2019.

• Role of Alternative Splicing in Arabidopsis Immune Response, NSF, PI: S. Heber, Co-PI: P. Veronese, $299,420,

12/2009-11/2012.

• Enhancing Bioinformatics Education, North Carolina Biotechnology Center, PI: S. Heber, $98,018 including

$17,882 matching funds, 5/16/2008-5/15/2010.

• A Bioinformatics Computing Cluster for NC State University, North Carolina Biotechnology Center, PI: S.

Heber, $283,783, 2/2007-1/2008.

Intramural

• Multimodal Storytelling for Data Analysis and Quality Control in RNA Sequencing, NCSU Research and

Innovation Seed Funding Program, PI: S. Heber, Co-PI: A. Jhala, D. Aylor, F. Right, $31,250 including $6,250

matching funds, 7/2019-6/2020.

• Bio-Inspired Computation with Julia, NCSU Innovative Summer Course Development, PI: S. Heber, $9,701, FY

2016-17.

• Development of Analytical Tools to Study Genome-Wide mRNA Translation in Plants at a Single-Codon

Resolution, NCSU Research and Innovation Seed Funding Program, PIs: S. Heber, J. Alonso, $29,268 including

$7,317 matching funds, 5/2011-4/2012.

• An Intelligent User-Guided Microarray Analysis Server, NCSU CBI/RNA Inter-College Research Fund, PIs: S.

Heber, H. W. Sederoff, $10,500, 11/06-10/08.

• Integrating Algorithm Visualization into CSC 505, NCSU LITRE, PI: S. Heber, $6,300, 1/2006-6/2007.

Donations

• $3,000 from ePartners LabCore and Merck to support the Symposium on Storytelling with Data, 2018.

• $2,000 from SAS/JMP to support the Symposium on Life Science Education, 2009.

• One-year assistantship (amount in kind: $26,000) from the Environmental Protection Agency for my PhD

student Brian Howard to support our research, 2006.

Teaching and Mentoring

During my time at NCSU, I have been teaching classes in Bioinformatics, and Algorithms for students in Computer

Science, Functional Genomics, and Bioinformatics, and I have been a Bioinformatics lecturer at NCSU’s Science

House (K12) and in various Summer Schools. I have received the Carol Miller Graduate Lecturer Award two times

and my teaching evaluations have been consistently high and above department average.

Courses Taught

• CSC 316 - Data Structures for Computer Scientists (Fall 2006, Spring 2010 (buyout), Spring 2011)

• CSC 422/522 - Automated Learning and Data Analysis (Fall 2010 (2 sections), Fall 2013 (2 sections), Spring

2015)

• CSC 505 - Design and Analysis of Algorithms (Fall 2004, Spring 2006, Spring 2008, Spring 2009, Fall 2009, Fall

2011, Spring 2013-15, Fall 2015 (3 sections), Summer 2017, Fall 2017 (3 sections), Summer 2018, Fall 2018

(3 sections), Summer 2019)

• CSC 530 - Computational Methods for Molecular Biology (Spring 2007-10, Fall 2011, Spring 2013, Fall 2014-

18)

• CSC 591 - Special Topics in Computer Science: Comparative Genomics (Fall 2007, Spring 2008)

• CSC 591 - Special Topics in Computer Science: Modern Topics in Bioinformatics (Spring 2004)

• CSC 791 - Advanced Topics in Computer Science: Computational Genomics (Fall 2010)

• BI/GS 811 temporary number PP 810/610G - Genomic Science Journal Club (Fall 2004 (2 sections), Spring

2005 (3 sections), Fall 2005 (3 sections), Spring 2006 (3 sections))

Other Teaching

• Summer CSC 495 Special Topics Course

Nature-Inspired Computation with Julia, 5 weeks Summer course, 2018

Bio-Inspired Computation with Julia, 5 weeks Summer course, 2017

• Summer Short Course in Bioinformatics

Expression Analysis, 2 days course, Raleigh, June 2016

• Summer Institute in Statistical Genetics

Introduction to Bioinformatics, 2.5 days course, Raleigh, May 2003-2005, and Faro, July 2004

• Lecturer, Pan-American Advanced Studies Institute

Hands on training – Searching biological databases, Montevideo, February 2004

• CSC 499 Independent Study projects

Summary of Student Evaluations (2014-2019)

Students rate the effectiveness of their teachers on a scale of 1-5, where 1 is poor and 5 is outstanding.

Format: Instructor average/Department average, scores above department average are labeled by ‘*’.

Course Enrollment Semester

Instructor

explained

material well

Overall,

instructor was

an effective

teacher

This course

improved my

knowledge of

the subject

Overall, the

course was

excellent

CSC 505 (001) 80 Fall 2018 4.5*/3.9 4.6*/4.0 4.6*/4.1 4.5*/3.9

CSC 505 (002) 116 Fall 2018 4.4*/3.9 4.4*/4.0 4.6*/4.1 4.4*/3.9

CSC 505 (601) 13 Fall 2018 3.8/4.1 3.8/4.2 4.3/4.6 3.5/4.1

CSC 530 14 Fall 2018 4.9*/3.9 4.6*/4.0 4.6*/4.1 4.4*/3.9

CSC 505 (651) 23 Sum10 2018 4.3/4.4 4.3/4.3 4.4/4.4 3.9/3.9

CSC 505 (001) 81 Fall 2017 4.2*/4.1 4.3*/4.2 4.4*/4.3 4.3*/4.2

CSC 505 (002) 115 Fall 2017 4.5*/4.1 4.5*/4.2 4.5*/4.3 4.5*/4.2

CSC 505 (601) 18 Fall 2017 4.2*/4.0 4.2*/4.0 4.2/4.4 3.3/3.9

CSC 530 10 Fall 2017 4.7*/4.1 4.7*/4.2 5.0*/4.3 4.7*/4.2

CSC 505 (651) 15 Sum10 2017 4.4/4.5 4.3/4.3 4.4/4.6 3.9/4.2

CSC 505 (601) 21 Spring 2017 4.1/4.4 4.6*/4.5 4.9*/4.6 4.4/4.4

CSC 505 (002) 71 Fall 2016 4.4*/4.0 4.6*/4.1 4.4*/4.3 4.4*/4.1

CSC 505 (003) 73 Fall 2016 4.3*/4.0 4.4*/4.1 4.4*/4.3 4.3*/4.1

CSC 505 (601) 29 Fall 2016 4.7*/4.0 4.6*/4.1 4.8*/4.3 4.6*/4.1

CSC 530 16 Fall 2016 4.3*/4.0 4.3*/4.1 4.5*/4.3 3.8/4.1

CSC 505 (651) 17 Sum10 2016 4.4*/3.3 4.4*/3.8 4.8*/4.3 4.2*/4.0

CSC 530 6 Fall 2015 5*/4.0 5*/4.1 5*/4.3 5*/4.1

CSC 505 (001) 98 Fall 2015 4.2*/4.0 4.4*/4.1 4.6*/4.3 4.4*/4.1

CSC 505 (002) 82 Fall 2015 4.2*/4.0 4.4*/4.1 4.5*/4.3 4.4*/4.1

CSC 505 (601) 27 Fall 2015 4.2*/4.0 4.3*/4.1 4.2/4.3 4.1/4.1

CSC 530 12 Fall 2014 4.4*/3.9 4.2*/4.0 4.4*/4.3 4.2*/4.0

CSC 505 119 Spring 2014 4.3*/4.1 4.3*/4.2 4.5*/4.4 4.3*/4.2

Anonymous Students’ Feedback (selected): CSC 505, Fall 2015

• “very enthusiastic professor”

• “Excellent course. One of the best courses I have ever taken.”

• “Im glad I took this course, really enjoyed the teaching and developed an interest in this subject.”

• “The course was really awesome. I would like the course to be a bit more programming oriented if

possible. The assignments were well defined and interesting. Dr. Heber's way of teaching the course is

remarkable.”

Summary of Peer Evaluations

For evaluation details, please see the corresponding reports.

• CSC 505 - Design and Analysis of Algorithms, reviewers: Dr. R. Dutta and Dr. R. Vatsavai, Fall 2018: ”In

summary, Dr. Heber is highly knowledgeable on his subject matter, projected his enthusiasm for it, and

effectively communicated this topic to the students. We find him an excellent teacher.”

• CSC 505 - Design and Analysis of Algorithms, reviewers: Dr. R. St. Amant and Dr. M. Stallmann, Fall 2015:

“Dr. Heber is a competent and diligent teacher.”

• CSC 505 - Design and Analysis of Algorithms, reviewers: Dr. J. Lester and Dr. M. Stallmann, Spring 2009: “Dr.

Heber’s lecture was excellent in every respect. He is knowledgeable of the subject matter, projected his

enthusiasm for it, and effectively delivered his expertise to the students.”

• CSC 505 - Design and Analysis of Algorithms, reviewers: Dr. C. Savage and Dr. N. Samatova, Spring 2008:

“Prof. Heber is a knowledgeable and competent teacher, offering a well-designed, relevant, and challenging

class.”

• CSC 591 - Comparative Genomics, reviewers: Dr. R. Mayr and Dr. M. Stallmann, Fall 2007: “Dr. Heber is

knowledgeable in the subject, appears to do an excellent job of presenting it (based on our observations)

and is able to motivate and actively involve the students.”

• CSC 316 - Data Structures, reviewers: Dr. R. Mayr and Dr. D. Bahler, Fall 2006: The observers found “Dr.

Heber’s teaching to be very good, making it highly likely that students could absorb the main points of the

material.”

• PP 610/810G - Genomic Science Journal Club, reviewers: Dr. C. Savage and Dr. J. Kang, Fall 2005: “Dr. Heber

a well organized, well-informed teacher, offering a stimulating and challenging course of great value to the

graduate students.”

• CSC 505 - Design and Analysis of Algorithms, reviewers: Dr. R. Funderlic and Dr. M. Stallmann, Fall 2004: “Dr.

Heber appears to be doing an excellent job as a first-time teacher of a difficult course.”

Instructional Development

• Together with Dr. Heckmann I have organized and taught a DELTA summer short workshop session “Tell me

and I will forget, teach me and I may remember, involve me and I learn” on student engagement in August

15, 2018. The session summarizes the different aspects of student engagement and discusses popular

methods and misconceptions about how to promote student engagement for both, in class and online

teaching.

• I have organized the Symposium on Life Sciences Education. The discussed topics include educational

technology and resources for Biology, Biochemistry, Bioinformatics, Genetics, Functional Genomics, and

related fields. The North Carolina Biotechnology Center in Research Triangle Park hosted the event on May

26, 2009. The symposium was a forum for researchers, K12 educators, and students to meet, discuss and

exchange ideas about modern technologies and resources in Life Science education. The symposium was

sponsored by the NC Biotechnology Center, and SAS, JMP.

Educational Technology

• The Bioinformatics in Motion project (http://statgen.ncsu.edu/slse/animations/) is a publicly available library of Flash animations for Bioinformatics Education. The animations target especially Bioinformatics instructors, Distance Education, and independent student learning.

Interactive educational resources can bring scientific concepts to life, and that is certainly the case with the animated modules presented on the Bioinformatics in Motion website. The website includes six modules that teach key concepts in bioinformatics: sequence alignment, database search, motif discovery, genome rearrangements, fragment assembly, and hidden Markov Models. Information is presented clearly within the modules as both narration and printed text, and the user can adjust display options such as the size of the printed text. Beyond passive animations, the modules also include simulations and other interactive elements to engage learners. The website includes links to resources related to the modules (such as primary literature), and there is also a small collection of links to other online teaching resources. Overall this is a very useful site to educators and students alike. Taralyn Tan, Best of The Web, Genetic Engineering & Biotechnology News, June 15, 2016 (Vol. 36, No. 12).

• The Learning in a Technology Rich Environment (LITRE) project Integrating Algorithm Visualization into CSC 505 project (http://litre.ncsu.edu/dfiles/proposals_2005/heber.pdf) is a library of dynamic animations and interactive visual representations of abstract algorithm design and analysis concepts.

Course Development for the Bioinformatics Graduate Program

• As a member of the Bioinformatics / CSC Course Sequence Committee I have participated in developing and updating the core courses of the NCSU Graduate Program in Bioinformatics.

• I have developed and taught a Module for the Short Course Expression Analysis offered by the Bioinformatics Research Center in June 13-14, 2016. The two-day short course covers basic concepts of gene expression, including analyses of microarrays and of transcriptomic sequencing, as well as basic principles of differential expression testing, multiple hypotheses, and false discoveries.

• CSC 530 Computational Methods for Molecular Biology: The course is an integral part of the Bioinformatics Master/PhD degrees. I completely revised the format and content of this class. The course introduces students to basic algorithmic principles used in Bioinformatics. The course consists of a set of lectures complementing topics covered in Bioinformatics I (ST 590A), Bioinformatics II (ST 590C), as well as a team project, where student teams propose, conduct, and describe a small research problem. The teams present

their results in a public poster presentation at the end of class. The class contains an introduction into the R software environment for statistical computing and graphics, as well as a guest lecture by Margaret Heil about poster preparation and presentation.

• CSC 591Q Special topics: Comparative Genomics: The course integrates computational aspects of Genome Rearrangements, Motif Discovery, and Comparative Genomics with hands-on experience. The course includes an introduction to the R/Bioconductor software environment, in-class R demonstrations, as well as student presentations of research papers.

• PP 610/810G Genomic Science Journal Club: a weekly journal club mandatory for bioinformatics and functional genomics students. Students present and critique papers from research journals. The papers discussed are solicited from our NCSU faculty. David Bird and I revised the outline and format of this course and created several web pages, including a web forum for students.

• CSC 591Q Special topics: Modern Topics in Bioinformatics: The course covers modern bioinformatics topics including text mining, ontologies, Systems Biology, and mRNA structure. The course contains a lab component and emphasizes student presentations of research papers.

• Spencer Muse (Department of Statistics) and I have developed the Bioinformatics Module for the NCSU Summer Institute in Statistical Genetics. The 2.5-day module comprises a lab component and eight (two hour) theory blocks.

Course Development for the Department of Computer Science

• CSC 495 Nature-Inspired Computation with Julia: This course teaches students how computational processes can be derived from natural models, and how to implement and evaluate such algorithms using the recently developed high-performance programming language Julia. The course focuses on major nature-inspired algorithmic approaches, including evolutionary computing (genetic algorithms, evolution strategies, genetic programming, differential evolution, etc.), social computing (for example particle swarm algorithms, ant colony optimization, etc.), and artificial immune systems. The course includes an introduction to the julia software environment, in-class julia demonstrations, student presentations, and an implementation project.

• CSC 422/522 Automated Learning and Data Analysis: I revised and updated the course to include a module about how to design and present a scientific poster. Teams of up to three students collaborate during the semester on a class related data mining project and present their results at the end of the semester in a public poster presentation.

• CSC 791 Advanced Topics in Computer Science: Computational Genomics: the course combines algorithmic aspects of next-generation sequencing data with hands-on experience. The course includes an introduction to the R/Bioconductor software environment, in-class R demonstrations, as well as student presentations of research papers.

• CSC 505 Design and Analysis of Algorithms: I revised and updated the course to include a new module about approximation algorithms, hands-on implementation and benchmarking exercises, educational videos, as well as algorithm animations developed in my LITRE project Integrating Algorithm Visualization into CSC 505.

• CSC 316 Data Structures: I revised and updated the course to include a new set of homework assignments, an expanded set of accompanying material, as well as algorithm animations developed in my LITRE project Integrating Algorithm Visualization into CSC 505.

Mentoring Activities

During my time at NCSU I have graduated 7 PhD students, 4 thesis Master students, and 2 non-thesis Master

students. I have participated in 66 graduate committees and mentored 17 undergraduate students. Currently, I

am directing Patrick Perkins (PhD Bioinformatics), and Sohail Shaikh (MS Computer Science), one visiting scholar

(Bhupinder Sehra) and 4 undergraduate students.

Undergraduate Advising

• Bella Samuelsson, REU Site: Socially Relevant Computing and Analytics, in progress

• Daniel Jeffries, REU Site: Socially Relevant Computing and Analytics, in progress

• Tushar Arora, Independent Research CSC 499, in progress

• Jaells Naranjo, Independent Research CSC 499, in progress

• Baris Akdogan, Independent Research CSC 499, Spring 2019

• David Wang, Independent Research CSC 499, Spring 2019

• Jack Kurtz, Independent Research CSC 499, Spring 2019

• Wenting Zheng, Independent Research CSC 499, Spring 2019

• Sam Ebert, Independent Research CSC 499 & Supervised Research, Fall 2017-Fall 2018

• Adam Davis, Independent Research CSC 499, Spring 2017

• Felix Kim, Independent Research CSC 499, Spring 2017

• Iain Dixon, Independent Research CSC 499, Spring 2017

• Luke Cunningham, Independent Research CSC 499, Spring 2017

• Stephen Williamson, Independent Research CSC 499, Fall 2010

• Andre van Schalkwyk, Independent Research CSC 499, Fall 2010

• Rasul Abduguev, Independent Research CSC 499, Fall 2010

• Joshua Ortiz, NSF Alliances for Graduate Education and the Professoriate (AGEP), Summer 2007

Independent Study Projects & Lab Rotations

• Debadeep Sen, PhD Computer Science, Spring 2018

• Andrew Trivette, PhD Bioinformatics, Spring 2016

• Patrick Perkins, PhD Bioinformatics, Fall 2015

• Guozhu Zhang, PhD Bioinformatics, Spring 2013

• Ravi Mathur, PhD Bioinformatics, Spring 2013

• Aravind Venkatesan, MS Computer Science, Spring 2010

• Haizhou Fu, PhD Computer Science, Spring 2008

• Jiangtian Li, PhD Computer Science, Spring 2005

• Jeremy Leipzig, MS Computer Science, Spring 2004

• Soma Saha, MS Computer Science, Spring 2004

Postdoctoral Researcher Advising

• Dr. Brian Howard, 11/2009-11/2011

PhD Students Advising

• Patrick Perkins, PhD Bioinformatics, passed prelim exam, in progress

• Qiwen Hu, PhD Bioinformatics, Chair, completed 5/25/2016

Title: Genome-wide Search for Elements that may Affect Translation in Arabidopsis thaliana

• Brian Howard, PhD Bioinformatics, Chair, completed 10/13/2009

Title: Methods for the Accurate Analysis of High-Throughput Transcriptome Data

• Jihye Kim, PhD Bioinformatics, Chair, completed 7/10/2009

Title: Mining of cis-Regulatory Motifs Associated with Tissue-Specific Alternative Splicing

• Pankaj Chopra, PhD Computer Science, Co-Chair with D. Bitzer, completed 4/9/2009.

Title: Data Mining Techniques to Enable Large-scale Exploratory Analysis of Heterogeneous Scientific Data

• Sihui Zhao, PhD Bioinformatics, Chair with Z. B. Zang, completed, 3/23/2009

Title: Analysis of Cis-acting Regulatory Motifs Involved in Alternative Splicing

• Wang, Tianyuan, PhD Bioinformatics, Chair with E. Hauser, completed 3/12/2009

Title: Identifying Transcription Factor Targets and Studying Human Complex Disease Genes

• Li Li, PhD Bioinformatics, Chair, completed 9/20/2007

Title: Computational Modeling of Dose Response Relationships for Steroid Hormone Receptor-Mediated

Gene Expression and Prediction of Androgen Response Element

MS Students Advising

• Sohail Shaikh, MS Computer Science, in progress

• Charles Wimberley, MS Computer Science, completed 3/1/2018

Title: PeakPass: A Machine Learning Approach for ChIP-Seq Blacklisting

• Sushamna Deodhar, MS Computer Science, Co-Chair with A. Motsinger-Reif, completed 10/28/2009

Title: Using Grammatical Evolution Decision Trees for Detecting Gene-Gene Interactions in Genetic

Epidemiology

• Benjamin Wheeler, MS Computer Science, Chair, completed 5/6/2008

Title: Automating the annotation and discovery of Micro RNA in multispecies high throughput 454

Sequencing

• Soma Saha, MS Computer Science, Chair, completed 1/4/2006

Title: Building an Essential Gene Classification Framework

Non-Thesis Master Directed

• Dhiral Phadke, MS Bioinformatics, Chair, completed 2005

• Hermonta Godwin, MS Bioinformatics, Chair, completed 2005

Graduate Committees

• During my time at NCSU I have participated in 66 graduate committees, 9 are in progress.

Professional Activities

I have been serving on multiple committees for the Department of Computer Science, for the Bioinformatics

Graduate Program, and at the university level. Off campus, I have been active in promoting Life Science

Education, and I have had a multi-faceted reviewer activity: I am a member of the editorial board of Network

Modeling Analysis in Health Informatics and Bioinformatics, I am an active book and journal reviewer, and I am

serving on multiple conference program committees. In addition, I have participated in 23 grant review panels

(mostly NSF).

Member of University Committees

• Faculty Well Being Committee, 2015-present

• Alternate Board Member, IRB Committee, 2015-present

• Advisory Board, Associate Professors’ Community, 2012-2017

• CFEP cluster hire/Bioinformatics search committee, 2012-2014

• Multiple Review Panels for Limited Submission Award Nominations (Pew, Beckman, and Searle), 2006-

2007

Member of Department Committees

• CSC Innovation Committee, 2017-2018

• CSC Graduate Program Oversight Committee, 2013-2016

• CSC Strategic Planning Committee, 2011-2015

• Assessment of CSC 226 Committee, 2013

• CSC Graduate Admissions Committee, 2006-2008, 2010-11

• Chair, Assessment of CSC 481 Committee, 2010

• Chair, CSC Minority Recruiting Committee, 2008-2009

• Bioinformatics/CSC Course Sequence Committee, 2004-present

• CSC Peer Evaluation Committee. Conducted teaching evaluations of 19 faculty members

• Bioinformatics Graduate Admissions Committee, 2005-2007

• CSC Minorities Committee, 2004-2005

• CSC Computer Steering Committee, 2004

Member of Editorial Boards

• Network Modeling Analysis in Health Informatics and Bioinformatics, 2017-present

• Dataset Papers in Biology, 2012-2017

• The Journal of Bioinformatics - Theory and Applications, 2005-2013

Events Organized or Chaired

• Organizer, Symposium on Storytelling with Data, NCSU, 2019

• Organizer, Symposium on Life Sciences Education, NC Biotechnology Center, 2009

• Co-Organizer, APS Annual Meeting special session "Mechanisms of post-transcriptional control of gene

functions in plant-microbe interactions (AS, PTGS, sumoylation and more…)", 2009

Service on Expert Panels

• Eleventh International Conference on Bioinformatics, Biocomputational Systems and Biotechnologies

(BIOTECHNO 2019) Industry/Research Advisory Committee, 2019

• Tenth International Conference on Bioinformatics, Biocomputational Systems and Biotechnologies


• Ninth International Conference on Bioinformatics, Biocomputational Systems and Biotechnologies


Tenure and Promotion Reviewing

• The tenure and promotion case of a faculty member at the University of Central Florida, 2013

Member of Program Committees

• International Symposium on Network Enabled Health Informatics, Biomedicine and Bioinformatics (HI-BI-

BI), 2019

• International Symposium on Bioinformatics Research and Applications (ISBRA), 2019

• Eleventh International Conference on Bioinformatics, Biocomputational Systems and Biotechnologies

(BIOTECHNO 2019), 2019



BI), 2018

• Tenth International Conference on Bioinformatics, Biocomputational Systems and Biotechnologies



BI), 2017

• Ninth International Conference on Bioinformatics, Biocomputational Systems and Biotechnologies


• International Conference on Computational Advances in Bio and medical Sciences (ICCABS), 2017




• Eighth International Conference on Bioinformatics, Biocomputational Systems and Biotechnologies



BI), 2016

• IEEE International Conference on Information Reuse and Integration (IEEE IRI 2015), 2015


• The Seventh International Conference on Bioinformatics, Biocomputational Systems and Biotechnologies



BI), 2015


• The Sixth International Conference on Bioinformatics, Biocomputational Systems and Biotechnologies



BI), 2014



BI), 2013

• International Symposium on Network Analysis and Mining for Health Informatics, Biomedicine and

Bioinformatics (Net-HI-BI-BI), 2013



• The Fifth International Conference on Bioinformatics, Biocomputational Systems and Biotechnologies


• The 23rd International Conference on Genome Informatics (GIW 2012), 2012


BI), 2012


• 2nd IEEE International Conference on Computational Advances in Bio and medical Sciences (ICCABS), 2012

• The Fourth International Conference on Bioinformatics, Biocomputational Systems and Biotechnologies


• 1st IEEE International Conference on Computational Advances in Bio and medical Sciences (ICCABS), 2011

• The Third International Conference on Bioinformatics, Biocomputational Systems and Biotechnologies


• 21st Annual Symposium on Combinatorial Pattern Matching (CPM 2010), 2010

• 1st International Conference on Advances in Bioinformatics and Applications (BIOINFO 2010), 2010

• RECOMB Comparative Genomics, 2009

• RECOMB Comparative Genomics, 2007

• ACMSE, 2007

• Ad-hoc Reviewer, Algebraic Biology, 2007

• Ad-hoc Reviewer, Pacific Symposium on Biocomputing (PSB), 2004

Grant Proposal Reviewing

• Panel Member, NSF SBIR/STTR Phase I, 2019, 2018, 2017 (2 panels), 2016, 2015 (2 panels), 2014 (2 panels),

2013, 2012

• Panel Member, NSF SBIR/STTR Phase II, 2018 (2 panels), 2017 (2 panels), 2016, 2015

• Panel Member, NSF CAREER, 2017

• Panel Member, NSF Postdoctoral Research Fellowships in Biology, 2016, 2015

• AAAS Reviewer for the Science Agency of Saudi Arabia, 2012

• Grant Reviewer for the Russian Foundation for Basic Research (RFBR), 2006

• Panel Member, North Carolina Biotechnology Center, 2005

Journal Submission Reviewing

BMC Bioinformatics, BMC Genomics, Bioinformatics, Database: The Journal of Biological Databases and

Curation, Nucleic Acids Research, PLOS Genetics, Journal of Computational Biology, Molecular Biology and

Evolution, International Journal of Bioinformatics Research and Applications, Network Modeling Analysis in

Health Informatics and Bioinformatics, Proceeding of the National Academy of Sciences of the United States of

America

Book Proposal Reviewing

• Instant Notes in Bioinformatics for BIOS Scientific Publishers, 2005

• Textbook on Nature-Inspired Computational Intelligence, Cambridge University Press, 2018

Member of Professional Organizations

• International Society of Computational Biology (ISCB)

• Institute of Electrical and Electronics Engineers (IEEE)

• Association for Computing Machinery (ACM)

Documents

Steffen Heber Curriculum Vitae July 30 · 2019. 8. 5. · Steffen Heber – Curriculum Vitae July 30, 2019 Contact Department of Computer Science and Bioinformatics Research Center