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Rob Patro
259 New Computer Science BuildingStony Brook UniversityStony Brook, NY 11794T (631) – 632 – 8457
B [email protected]://www.robpatro.com
https://github.com/COMBINE-lab (lab GitHub page)
Current Research InterestsScalable Algorithms and Data Structures for Indexing, Searching and Analyzing High-throughput Genomic DataAlgorithms for Inferring and Comparing Biological NetworksNetwork Evolution & Systems Biology
Education2006-2012 Ph.D, University of Maryland at College Park, College Park, MD, GPA 4.0.
Advisor – Prof. Carl Kingsford2003-2006 BS, University of Maryland at College Park, College Park, MD, GPA 3.95.
Cum Laude and Departmental Honors2002 Attended, Worcester Polytechnic Institute, Worcester, MA, GPA 3.92.
Employment2014–present Assistant Professor, Department of Computer Science, Stony Brook University.
2012–2014 Postdoctoral Research Associate, Lane Center for Computational Biology, Carnegie Mellon University.2007–2012 Graduate Research Assistant, Department of Computer Science, University of Maryland.2006–2007 Graduate Teaching Assistant, Department of Computer Science, University of Maryland.2004–2006 Software Engineering Intern, NOAA, Silver Spring, MD.
2005 Undergraduate Teaching Assistant, Department of Computer Science, University of Maryland.1998 Software Development Intern, Honeywell, Columbia, MD.
PublicationsPapers & Theses (any pre-prints marked as such)Guillaume Marçais, Brad Solomon, Rob Patro, and Carl Kingsford. Sketching and sublinear data structures ingenomics. Annual Review of Biomedical Data Science, 2(1), apr 2019.
Sarkar,Hirak and Srivastava, Avi and Patro, Rob. Minnow: A principled framework for rapid simulation ofdscRNA-seq data at the read level. ISMB 2019, 2019. (to appear).
Charlotte Soneson, Michael I Love, Rob Patro, Shobbir Hussain, Dheeraj Malhotra, and Mark D Robinson. Ajunction coverage compatibility score to quantify the reliability of transcript abundance estimates and annotationcatalogs. Life science alliance, 2(1):e201800175, 2019.
Avi Srivastava, Laraib Malik, Tom Smith, Ian Sudbery, and Rob Patro. Alevin efficiently estimates accurategene abundances from dscrna-seq data. Genome biology, 20(1):65, 2019.
Anqi Zhu, Avi Srivastava, Joseph G Ibrahim, Rob Patro, and Michael I Love. Nonparametric expression analysisusing inferential replicate counts. bioRxiv, 2019. pre-print.
Michael I. Love, Charlotte Soneson, and Rob Patro. Swimming downstream: statistical analysis of differentialtranscript usage following Salmon quantification. F1000Research, 7:952, Oct. 2018.
Fatemeh Almodaresi, Prashant Pandey, Michael Ferdman, Rob Johnson, and Rob Patro. An Efficient, Scalableand Exact Representation of High-Dimensional Color Information Enabled via de Bruijn Graph Search. BioRxiv,2018. pre-print (to appear at RECOMB 2019).
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Fatemeh Almodaresi, Hirak Sarkar, Avi Srivastava, and Rob Patro. A space and time-efficient index for thecompacted colored de Bruijn graph. Bioinformatics, 34(13):i169–i177, 2018. (appeared at ISMB 2018).
Moriah L Jacobson, Lydia A Kim, Robert Patro, Barbara Rosati, and David McKinnon. Common and differentialtranscriptional responses to different models of traumatic stress exposure in rats. Translational Psychiatry,8(1):165, 2018.
Laraib Malik, Fatemeh Almodaresi, and Rob Patro. Grouper: graph-based clustering and annotation forimproved de novo transcriptome analysis. Bioinformatics, 34(19):3265–3272, 2018.
Laraib Malik and Rob Patro. Rich Chromatin Structure Prediction from Hi-C Data. IEEE/ACM Transactionson Computational Biology and Bioinformatics, pages 1–12, 2018. Journal version of ACM-BCB paper.
Prashant Pandey, Fatemeh Almodaresi, Michael A. Bender, Michael Ferdman, Rob Johnson, and Rob Patro.Mantis: A Fast, Small, and Exact Large-Scale Sequence Search Index. volume 10812 of Lecture Notes inComputer Science, pages 271–273. Springer, 2018. (Proceedings of RECOMB 2018).
Prashant Pandey, Fatemeh Almodaresi, Michael A. Bender, Michael Ferdman, Rob Johnson, and Rob Patro.Mantis: A Fast, Small, and Exact Large-Scale Sequence-Search Index. Cell Systems, 2018. Journal version ofRECOMB 2018 paper.
Hirak Sarkar, Mohsen Zakeri, Laraib Malik, and Rob Patro. Towards Selective-Alignment: Bridging theAccuracy Gap Between Alignment-Based and Alignment-Free Transcript Quantification. In Proceedings of the2018 ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics, BCB’18, pages 27–36, New York, NY, USA, 2018. ACM.
Charlotte Soneson, Michael I Love, Rob Patro, Shobbir Hussain, Dheeraj Malhotra, and Mark D Robinson. Ajunction coverage compatibility score to quantify the reliability of transcript abundance estimates and annotationcatalogs. BioRxiv, 2018. (pre-print).
Koen Van Den Berge, Katharina Hembach, Charlotte Soneson, Simone Tiberi, Lieven Clement, Michael I Love,Rob Patro, and Mark Robinson. RNA sequencing data: hitchhiker’s guide to expression analysis. PeerJPreprints, 6:e27283v1, 2018. pre-print (to appear in Annual Reviews).
Rob Patro, Geet Duggal, Michael I Love, Rafael A Irizarry, and Carl Kingsford. Salmon provides fast andbias-aware quantification of transcript expression. Nature Methods, 14(4):417–419, March 2017.
Fatemeh Almodaresi, Prashant Pandey, and Rob Patro. Rainbowfish: A Succinct Colored de Bruijn GraphRepresentation. In Russell Schwartz and Knut Reinert, editors, 17th International Workshop on Algorithms inBioinformatics (WABI 2017), volume 88 of Leibniz International Proceedings in Informatics (LIPIcs), pages18:1–18:15, Dagstuhl, Germany, 2017. Schloss Dagstuhl–Leibniz-Zentrum fuer Informatik.
Laraib Malik and Rob Patro. Rich chromatin structure prediction from Hi-C data. In Proceedings of the8th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics, pages184–193. ACM, 2017. (won best paper award.).
Prashant Pandey, Michael A. Bender, Rob Johnson, and Rob Patro. A General-Purpose Counting Filter: MakingEvery Bit Count. In Proceedings of the 2017 ACM International Conference on Management of Data, SIGMOD’17, pages 775–787, New York, NY, USA, 2017. ACM.
Prashant Pandey, Michael A Bender, Rob Johnson, and Rob Patro. deBGR: an efficient and near-exactrepresentation of the weighted de bruijn graph. Bioinformatics, 33(14):i133–i141, 2017. Proceedings of ISMB2017.
Hirak Sarkar and Rob Patro. Quark enables semi-reference-based compression of RNA-seq data. Bioinformatics,33(21):3380–3386, 2017.
Mohsen Zakeri, Avi Srivastava, Fatemeh Almodaresi, and Rob Patro. Improved data-driven likelihood factor-izations for transcript abundance estimation. Bioinformatics, 33(14):i142–i151, 2017. Proceedings of ISMB2017.
Avi Srivastava, Hirak Sarkar, Nitish Gupta, and Rob Patro. RapMap: a rapid, sensitive and accurate tool formapping RNA-seq reads to transcriptomes. Bioinformatics, 32(12):i192–i200, June 2016. Proceedings of ISMB2016.
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Komal Sanjeev, Nitish Gupta, Tim Wall, Carl Kingsford, and Rob Patro. Efficient Index Maintenance UnderDynamic Genome Modification. Proceedings of RECOMB-Seq 2016, April 2016.
Avi Srivastava, Larib Malik, and Rob Patro. Accurate, Fast and Lightweight Clustering of de novo Transcriptomesusing Fragment Equivalence Classes. Proceedings of RECOMB-Seq 2016, April 2016.
Rob Patro, Raquel Norel, Robert J. Prill, Julio Saez-Rodriguez, Peter Lorenz, Felix Steinbeck, Bjoern Ziems,Mitja Luštrek, Nicola Barbarini, Alessandra Tiengo, Riccardo Bellazzi, Hans-Jürgen Thiesen, Gustavo Stolovitzky,and Carl Kingsford. A computational method for designing diverse linear epitopes including citrullinatedpeptides with desired binding affinities to intravenous immunoglobulin. BMC Bioinformatics, 17(1):1–13, 2016.
Richard Smith-Unna, Chris Boursnell, Rob Patro, Julian M Hibberd, and Steven Kelly. TransRate: reference-freequality assessment of de novo transcriptome assemblies. Genome Research, 26(8):1134–1144, 2016.
Carl Kingsford and Rob Patro. Reference-based compression of short-read sequences using path encoding.Bioinformatics, 31(12):1920–1928, 2015.
Mikhail Lipatov, Komal Sanjeev, Rob Patro, and Krishna Veeramah. Maximum Likelihood Estimation ofBiological Relatedness from Low Coverage Sequencing Data. BioRxiv, 2015. pre-print, (under revision).
Rob Patro and Carl Kingsford. Data-dependent bucketing improves reference-free compression of sequencingreads. Bioinformatics, 31(17):2770–2777, 2015.
Zhong Sichen, Lu Zhao, Yan Liang, Mohammadzaman Zamani, Rob Patro, Rezaul Chowdhury, Esther M Arkin,Joseph SB Mitchell, and Steven Skiena. Optimizing Read Reversals for Sequence Compression. In Algorithmsin Bioinformatics, pages 189–202. Springer, 2015.
Runxuan Zhang, Cristiane PG Calixto, Nikoleta A Tzioutziou, Allan B James, Craig G Simpson, WenbinGuo, Yamile Marquez, Maria Kalyna, Rob Patro, Eduardo Eyras, et al. AtRTD–a comprehensive referencetranscript dataset resource for accurate quantification of transcript-specific expression in arabidopsis thaliana.New Phytologist, 2015.
Darya Filippova†, Rob Patro†, Geet Duggal†, and Carl Kingsford. Identification of Alternative TopologicalDomains in Chromatin. Algorithms for Molecular Biology, 9(1):1, 2014. (†denotes equal contribution).
Rob Patro, Stephen M Mount, and Carl Kingsford. Sailfish enables alignment-free isoform quantification fromRNA-seq reads using lightweight algorithms. Nature Biotechnology, 32(5):462–464, 2014.
Geet Duggal, Rob Patro, Emre Sefer, Hao Wang, Darya Filippova, Samir Khuller, and Carl Kingsford. Resolvingspatial inconsistencies in chromosome conformation measurements. Algorithms for Molecular Biology, 8(1):8,2013. (extended journal version of WABI 2012 paper which is not listed here).
Darya Filippova†, Rob Patro†, Geet Duggal†, and Carl Kingsford. Multiscale Identification of TopologicalDomains in Chromatin. In Algorithms in Bioinformatics, pages 300–312. Springer, 2013. (†denotes equalcontribution).
Rob Patro and Carl Kingsford. Predicting protein interactions via parsimonious network history inference.Bioinformatics, 29(13):i237–i246, 2013. (ISMB/ECCB 2013).
Hao Wang, Geet Duggal, Rob Patro, Michelle Girvan, Sridhar Hannenhalli, and Carl Kingsford. TopologicalProperties of Chromosome Conformation Graphs Reflect Spatial Proximities Within Chromatin. In Proceedingsof the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics, BCB’13,pages 306:306–306:315, New York, NY, USA, 2013. ACM.
Rob Patro. Computationally Comparing Biological Networks and Reconstructing Their Evolution. PhD thesis,University of Maryland, College Park, College Park, MD, 20742, 2012.
Rob Patro, John Dickerson, Sujal Bista, Satyandra Gupta, and Amitabh Varshney. Speeding Up ParticleTrajectory Simulations under Moving Force Fields using GPUs. ASME Journal of Computing and InformationScience in Engineering, 12(2), 2012.
Rob Patro and Carl Kingsford. Global network alignment using multiscale spectral signatures. Bioinformatics,28(23):3105–3114, 2012.
Rob Patro, Emre Sefer, Justin Malin, Guillaume Marçais, Saket Navlakha, and Carl Kingsford. Parsimoniousreconstruction of network evolution. Algorithms for Molecular Biology, 7(1):25, 2012. (extended journal versionof WABI 2011 paper below).
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Robert Patro†, Geet Duggal†, Emre Sefer, Hao Wang, Darya Filippova, and Carl Kingsford. The missing models:a data-driven approach for learning how networks grow. In Proceedings of the 18th ACM SIGKDD internationalconference on Knowledge discovery and data mining, pages 42–50. ACM, 2012. (†denotes equal contribution).
Youngmin Kim, Rob Patro, Cheuk Yiu Ip, Dianne P. O’Leary, and Andriy Anishkin. Salient Frame Detectionfor Molecular Dynamics Simulations. In Scientific Visualization: Interactions, Features, Metaphors, volume 2 ofDagstuhl Follow-Ups, pages 160–175. Schloss Dagstuhl–Leibniz-Zentrum fuer Informatik, Dagstuhl, Germany,2011.
Andre Maximo, Rob Patro, Amitabh Varshney, and Ricardo Farias. A Robust and Rotationally Invariant LocalSurface Descriptor with Applications to Non-local Mesh Processing. Graphical Models, 73(5):231–242, 2011.
Rob Patro, Cheuk Yiu Ip, Sujal Bista, Samuel Cho, Dave Thirumalai, and Amitabh Varshney. MDMap : Asystem for data-driven layout and exploration of molecular dynamics simulations. In Proceedings of the 1st
IEEE symposium on biological data visualization, pages 111–118, Providence, RI, USA, 2011.
Rob Patro, Cheuk Yiu Ip, Sujal Bista, and Amitabh Varshney. Social Snapshot: A System for TemporallyCoupled Social Photography. Computer Graphics and Applications, IEEE, 31(1):74–84, 2011.
Rob Patro, Emre Sefer, Justin Malin, Guillaume Marçais, Saket Navlakha, and Carl Kingsford. ParsimoniousReconstruction of Network Evolution. In Teresa Przytycka and Marie-France Sagot, editors, Algorithms inBioinformatics, volume 6833 of Lecture Notes in Computer Science, pages 237–249. Springer Berlin / Heidelberg,2011.
Rob Patro, Cheuk Yiu Ip, and Amitabh Varshney. Saliency Guided Summarization of Molecular DynamicsSimulations. In Scientific Visualization: Advanced Concepts, volume 1 of Dagstuhl Follow-Ups, pages 321–335.Schloss Dagstuhl–Leibniz-Zentrum fuer Informatik, Dagstuhl, Germany, 2010.
Aswin C. Sankaranarayanan, Rob Patro, PavanTuraga, Amitabh Varshney, and Rama Chellappa. Modeling and Visualization of Human Activities forMulticamera Networks. EURASIP Journal on Image and Video Processing, vol. 2009(Article ID 259860), 2009.
Invited Talks
Rob Patro. Improving Computational Methods for Single-Cell Gene Expression Analysis. Gloria and MarkSnyder Symposium on Cancer Medicine, 2019.
Rob Patro. The past, present and future of transcript quantification: recent progress & some remainingchallenges. Invited talk at EMBL-EBI Industry Workshop: The past, present and future of RNA-seq technologyand its application to drug discovery, November 2018.
Rob Patro. Drinking from the firehose: lightweight methods and data structures for indexing, searching andanalyzing genomic data. Invited talk at UMD (Computational Biology Seminar), October 2018.
Rob Patro. Drinking from the firehose: lightweight methods and data structures for indexing, searching andanalyzing genomic data. Invited talk at USC (Computational Biology Seminar), October 2018.
Rob Patro. Deconvolution, dictionaries and de Bruijn graphs : algorithm and data structure design for moderngenomics. Invited talk at Penn State Workshop on Emerging Methods for Sequence Analysis, June 2018.
Rob Patro. When less enables more: making models and methods for modern genomics. Invited talk at MIT(Computational Biology Seminar), March 2018.
Rob Patro. Faster, Smaller, Better : How improved methods can facilitate better biology. Invited talk at theUniversity of Basel (Computational Biology Seminar), November 2017.
Rob Patro. Algorithmic advances in high-throughput transcriptome analysis. Invited talk at Calico, July 2017.
Rob Patro. Algorithmic advances in high-throughput transcriptome analysis. Invited talk at GRAIL, July 2017.
Rob Patro. Don’t count on it: Pragmatic and theoretical concerns and best practices for mapping and quantifyingRNA-seq data. Invited talk at DIBSI 2017 training, July 2017.
Rob Patro. Algorithmic advances in transcript quantification. Invited talk at HiCOMB 2017 (IEEE InternationalWorkshop on High Performance Computational Biology), May 2017.
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Rob Patro. Accurate, fast and bias-aware transcript quantification with Salmon. Biostatistics & MedicalInformatics Seminar Series, University of Wisconsin, Madison, September 2016.
Rob Patro. A New Deal for Transcriptomics: Better Biology through Better Algorithms. Laufer Center forQuantitative Biology Seminar, 2016.
Rob Patro. Fast Algorithms for Improved Transcriptome Analysis. Genomics JHU seminar series, JohnsHopkins University, 2016.
Rob Patro. Rethinking the big BAM: Analysis-efficient computing for improved transcriptome analysis. WeillCornell Medical School, 2016.
Rob Patro. Rethinking the big BAM: Fast algorithms for improved transcriptome analysis. Personal GenomDiagnostics, 2016.
Komal Sanjeev, Nitish Gupta, Tim Wall, Carl Kingsford, and Rob Patro. Efficient Index Maintenance UnderDynamic Genome Modification. RECOMB-Seq 2016, 2016.
Avi Srivastava, Larib Malik, and Rob Patro. Accurate, Fast and Lightweight Clustering of de novo Transcrip-tomes using Fragment Equivalence Classes. RECOMB-Seq 2016, 2016.
Rob Patro. The wait is over: lightweight methods for accurate, fast and scalable analysis of transcriptomes.New York Genome Center, invited talk, September 2015.
Rob Patro, Stephen Mount, and Carl Kingsford. Sailfish and Salmon enable alignment-free isoform quantificationfrom RNA-seq reads using lightweight algorithms. RECOMB 2015 Highlight Talk, April 2015.
Rob Patro, Stephen Mount, and Carl Kingsford. Salmon spawns the next the next generation of RNAseqanalysis with versatile and ultrafast transcript quantification. Simons Center for Quantitative Biology Seminar,March 2015.
Darya Filippova, Rob Patro, Geet Duggal, and Carl Kingsford. Identification of alternative topological domainsin chromatin. ACM Conference on Bioinformatics, Computational Biology, and Health Informatics, 2015.(highlight talk, presented by Filippova).
Rob Patro, Stephen Mount, and Carl Kingsford. Sailfish — RNA-seq Expression Estimates Need Not TakeLonger Than a Cup of Coffee. Genome Informatics, October 2013.
Rob Patro and Carl Kingsford. Global Network Alignment Using Multiscale Spectral Signatures. GLBIOConference, May 2013.
Rob Patro, Stephen Mount, and Carl Kingsford. Sailfish: Expression Estimates Shouldn’t Take Longer than aCup of Coffee. Automated Personal Genome Analysis for Clinical Advisors, 2013.
Rob Patro and Carl Kingsford. Learning from Diversity: Epitope Prediction with Sequence and StructureFeatures using an Ensemble of Support Vector Machines, 2010. Winner, DREAM5 Challenge 1 Competition.Presented at RECOMB Systems Biology Satellite Conference.
Posters
Fatemeh Almodaresi, Prashant Pandey, and Rob Patro. Rainbowfish: A Succinct Colored de Bruijn GraphRepresentation. Workshop on Algorithms in Bioinformatics, August 2017.
Fatemeh Almodaresi, Hirak Sarkar, and Rob Patro. A space and time-efficient index for the compacted coloredde Bruijn graph. ACM BCB, August 2017.
Rob Patro and Carl Kingsford. Global Network Alignment Using Multiscale Spectral Signatures. GLBIOConference, May 2013.
Rob Patro and Carl Kingsford. Global Network Alignment Using Multiscale Spectral Signatures. SystemsBiology: Networks, March 2013.
Rob Patro and Carl Kingsford. Global Network Alignment Using Multiscale Spectral Signatures. 20th AnnualInternational Conference on Intelligent Systems for Molecular Biology, July 2012.
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Rob Patro and Carl Kingsford. Learning from Diversity: Epitope Prediction with Sequence and StructureFeatures using an Ensemble of Support Vector Machines, 2010. Winner, DREAM5 Challenge 1 Competition.Presented at RECOMB Systems Biology Satellite Conference.
Adam Phillippy, Michael Schatz, Timur Chabuk, Bo Liu, Rob Patro, and Steven Salzberg. Improving theGenome Sequence of D. simulans via Co-assembly of Multiple Strains. Biology of Genomes, May 2009.
Contract and Grant SupportTitle: A Modular Framework for Accurate, Efficient, and Reproducible Analysis of RNA-seq DataPI/PD: Robert Patro (co-PI: Michael Love)Agency: NIHAward Number: R01 HG009937Duration: 08/18/2018 – 6/30/2023Amount: $1,538,195
Title: CSR: Medium: Approximate Membership Query Data Structures in Computational Biology and StoragePI: Robert Patro (co-PIs: Michael Bender, Michael Ferdman)Agency: NSFAward Number: 1763680Duration: 08/15/2018 – 7/31/2022Amount: $1,999,995
Title: Efficient tools for quantifying and simulating transcript-level abundance in single-cell RNA-seqPI: Robert PatroAgency: SVCFAward Number: 182752Duration: 03/01/2018 – 02/28/2019Amount: $132,708.00
Title: CAREER: A Comprehensive and Lightweight Framework for Transcriptome AnalysisPI: Robert PatroAgency: NSFAward Number: 1750472Duration: 02/01/2018 – 01/31/2023Amount: $625,000.00
Title: Bilateral BBSRC-NSF/BIO: ABI Innovation: Data-driven hierarchical analysis of de novo transcriptomesPI: Robert Patro (co-PI: Julian Hibberd)Agency: NSFAward Number: 1564917Duration: 07/01/2016 – 06/30/2018Amount: $639,767.80 ($310,627 at Stony Brook, £205,713 at Cambridge University)
Open Source Softwarepufferfish Pufferfish: A space and time-efficient index for the compacted colored de Bruijn graph, https:
//github.com/COMBINE-lab/pufferfish .mantis mantis: A Fast, Small, and Exact Large-Scale Sequence-Search Index, https://github.com/
splatlab/mantis .Salmon Accurate, Fast and Model-aware Transcript-level Expression Estimation, https://github.com/
COMBINE-lab/salmon .Sailfish Rapid Mapping-based Isoform Quantification from RNA-Seq Reads, https://github.com/
kingsfordgroup/sailfish .Squeakr An Exact and Approximate k-mer Counting System, https://github.com/splatlab/squeakr .
Rainbowfish A tool for succinct colored de Bruijn Graph representation, https://github.com/COMBINE-lab/rainbowfish .
RapMap Rapid Sensitive and Accurate Read Mapping via Quasi-mapping, https://github.com/COMBINE-lab/RapMap .
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deBGR deBGR: An Efficient and Near-Exact Representation of the weighted de Bruijn Graph, https://github.com/splatlab/debgr .
RapClust Accurate, Lightweight Clustering of de novo Transcriptomes using Fragment Equivalence Classes,https://github.com/COMBINE-lab/RapClust .
Matryoshka Methods for the Automated Discovery of Hierarchically-Structured Chromatin Domains, https://github.com/COMBINE-lab/matryoshka .
Quark Semi-reference-based compression of RNA-seq data, https://github.com/COMBINE-lab/quark .SkipPatch Efficient Index Maintenance Under Dynamic Genome Modification, https://github.com/
COMBINE-lab/SkipPatch .Mince Data-dependent Bucketing for Reference-free Compression of Sequencing Reads, https://github.
com/Kingsford-Group/mince .GHOST Biological Network Alignment using Multiscale Spectral Signatures, https://github.com/
Kingsford-Group/ghost2.PARANA2 Parsimonious Ancestral Network History Inference, https://github.com/kingsfordgroup/parana2.
Honors2018 Dean’s Millionaires Club, (raising over $1,000,000 in external funding as PI in the preceding year).2017 Best Paper Award, ACM BCB ’17, Rich chromatin structure prediction from Hi-C data.2013 ISMB travel fellowship.2012 ISMB Student travel fellowship.2010 1st Place, DREAM 5 Challenge 1.2010 Goldhaber Travel Grant.2009 i3D Student Stipend Award.
2007-–2008 Verizon Fellowship Recipient.2006-–2008 Block Fellowship, Department of Computer Science, University of Maryland.
2006 Computer Science Departmental Honors, University of Maryland.2006 CMPS Honors Graduate, University of Maryland.
2003—2006 Deans List, University of Maryland.2002 Charles O. Thompson Scholar, Worcester Polytechnic Institute.
Upsilon Pi Epsilon Honor Society for the Computing Sciences.Phi Sigma Pi National Honors Fraternity.National Society of Collegiate Scholars.
Memberships in Professional Societies2012–2014,2016–2018
International Society for Computational Biology (ISCB).
2016, 2017 ACM SigBIO.
Professional Activities2019 PLOS Computational Biology, Guest Editor.2019 Genome Informatics, Discussion Leader (transcriptomics).2019 RECOMB 2019, Posters Chair.2019 RECOMB 2019, Program Committee Member.2019 ISMB 2019, Program Committee Member.2018 IPDPS 2019, Program Committee Member.2019 Oxford Bioinformatics, Reviewer.2019 Nature Communications, Reviewer.2018 ISMB 2018, Program Committee Member (Comparative and Functional Genomics)).2018 WABI 2018, Program Committee Member.2018 BCB 2018, Program Committee Member.
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2018 RECOMB SEQ 2018, Program Committee Member.2018 HICOMB 2018, Program Committee Member.2018 Genome Biology, Reviewer.2018 Genome Research, Reviewer.2018 Bioinformatics, Reviewer.2018 BMC Genomics, Reviewer.2018 PeerJ, Reviewer.2017 ISMB 2017, Program Committee Member (Abstracts).2017 WABI 2017, Program Committee Member.2017 BCB 2017, Program Committee Member.2017 HICOMB 2017, Program Committee Member.2017 RECOMB-Seq 2017, Program Committee Member.2017 Asia Pacific Bioinformatics Conference (APBC) 2017, Program Committee Member.2017 Nucleic Acids Research, Reviewer.2017 Genome Biology, Reviewer.2017 Cell Systems, Reviewer.2017 PlOS Computational Biology, Reviewer.2017 Bioinformatics, Reviewer.2017 IEEE/ACM Transactions on Computational Biology and Bioinformatics, Reviewer.2016 Nature Methods & Nature Genetics, Reviewer.2016 Cell Systems, Reviewer.2016 PeerJ, Reviewer.2016 RECOMB-seq and RECOMB-CCB, Program Committee Member.2016 Genome Biology, Reviewer.2016 Nucleic Acids Research, Reviewer.2016 Bioinformatics, Reviewer.2016 Journal of Bioinformatics and Computational Biology, Reviewer.2016 F1000, Reviewer.2015 F1000, Reviewer.2015 Algorithms, Reviewer.2015 Genome Research, Reviewer.2015 Asia Pacific Bioinformatics Conference (APBC) 2016, Program Committee Member.2015 Bioinformatics, Reviewer.2015 PLoS ONE, Reviewer.2015 BMC Bioinformatics, Reviewer.2015 IEEE Transactions on Computational Biology and Bioinformatics, Reviewer.2014 BMC Bioinformatics, Reviewer.2014 RECOMB, Poster Selection Committee.2014 Nucleic Acids Research, Reviewer.2014 ISMB, Reviewer.2013 BMC Bioinformatics, Reviewer.2012 PLOS Computational Biology & PLOS One, Reviewer.2011 Workshop for Algorithms in Bioinformatics & Intelligent Systems for Molecular Biology, Reviewer.2010 ACM SIGGRAPH Symposium on Interactive 3D Graphics and Games (i3D), Publicity Co-Chair.
2007–2009 IEEE Visualization Conference, Reviewer.2007, 2008,
2010SIGGRAPH Conference, Reviewer.
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Advising and TeachingDoctoral Students (alphabetical by last name)Fatemeh Almodaresi TS.Wasif Khan, (independent study).Laraib Malik.Hirak Sarkar.Avi Srivastava.Mohsen Zakeri.
Masters Students (alphabetical by last name)Srikant Aggarwal.Eshita Bheda.Anuja Bawaskar.Siddhartha Chhabra.Geoffrey Churchill, MS with thesis.Revati Damle.Komal Dhuri.Nitish Gupta, MS with thesis.Shreyas Harisha.Nikhil Junneti.Anand Kulkarni.Nikhil Mehta.Nikhil Mohan.Rasika Pohankar.Mridul Ranjan.Manu Rao.Komal Sanjeev, MS with thesis.Ayush Sengupta.Akshat Singhal.Aditya Srivastava.Alok Thatikunta.Shravya Rani Thatipally.
Undergraduate and High School Students (alphabetical by last name)Geoffrey Glass, Simons Summer Program Scholar, 2017.Lise Ho, practicum in teaching.Kyeongsoo Kim, practicum in teaching.Anjalie Kini, Simons Summer Program Scholar, 2018.Freeman Lou, practicum in teaching.Spiro Razis, Undergraduate Researcher.Matthew Weston, practicum in teaching.Ph.D. CommitteesLuiz Irber, Qualifying exam committee member.Fatemeh Almodaresi TS, RPE committee member (advisor).Laraib Malik, RPE committee member (advisor).Hirak Sarkar, RPE committee member (advisor).Avi Srivastava, RPE committee member (advisor).Mohsen Zakeri, RPE committee member (advisor).Mohammad Amin, RPE committee member and preliminary committee member.Keffy Kehrli, Preliminary exam committee member, Department of Genetics.
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Bihua Yu, Preliminary exam committee member, AMS Department.Dr. Hayan Lee, Ph.D. exam committee member, Graduated Summer 2015.Dr. Jason O’rawe, Preliminary Ph.D. exam committee member and defense committee member, Departmentof Genetics.Dr. Han Fang, Preliminary Ph.D. exam committee member and defense committee member, Department ofApplied Math and Statistics.Dr. Prashant Pandey, Preliminary Ph.D. exam committee member and defense committee member.Courses Taught
Spring 2019 CSE373, ∼ 110 students, Computational Biology.Fall 2018 CSE549, ∼ 65 students, Computational Biology.Fall 2018 CSE642, ∼ 45 students, Seminar in Algorithms.
Spring 2018 CSE373, ∼ 160 students, Analysis of Algorithms.Spring 2018 CSE642, ∼ 35 students, Seminar in Algorithms.
Fall 2017 CSE549, ∼ 100 students, Computational Biology.Fall 2017 CSE642, ∼ 26 students, Seminar in Algorithms.Fall 2016 CSE549, ∼ 60 students, Computational Biology.Fall 2015 CSE549, ∼ 75 students, Computational Biology.
Spring 2015 CSE548, ∼ 10 students, Graduate Analysis of Algorithms (Ph.D.).Fall 2014 CSE549, ∼ 60 students, Computational Biology.
Departmental Service2017, 2018 Graduate curriculum committee.2014, 2015,2016, 2017,
2018
Graduate admissions committee.
2014, 2015,2016, 2018
Faculty hiring committee.
University Service2019 Simons Summer Program admissions committee.2018 Simons Summer Program admissions committee.
Extramural Service2019 NSF, Panelist.2018 NSF, Panelist.2018 American Heart Association, Panelist.2016 NSF, Panelist.
SkillsExpert C/C++ (including C++11/14/17), CUDA, GLSL, Java, LATEX, OpenGL, Python, Ruby, Scala.Some
ExperienceHaskell, Matlab, OCaml, Perl, Prolog, R, Rust, Scheme.
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