Sairam Behera

Post-doctoral Research Fellow
Human Genome Sequencing Center
Baylor College of Medicine

Bio

Sairam Behera's research interests are in the areas of graph theory, algorithms, bioinformatics, next-generation sequencing NGS) data analysis and population genomics. In particular, he has been working on the development and analysis of algorithms for computational biology. He received his B.Tech in Computer Science and Engineering from NIT Rourkela (India), M.S. from University of Texas at Dallas and Ph.D. from University of Nebraska-Lincoln.

Publications

DBLP
Google Scholar

Journals:

S. Behera, S. Catreux, M. Rossi, S. Truong, Z. Huang, M. Ruehle, A. Visvanath, G. Parnaby, C. Roddey, V. Onuchic, D. L. Cameron, A. English, S. Mehtalia, J. Han, R. Mehio, F. J. Sedlazeck; Comprehensive and accurate genome analysis at scale using DRAGEN accelerated algorithms; Nature Biotechnology (2024); doi: 10.1038/s41587-024-02382-1
S. Behera, J. Belyeu, X. Chen, L. F Paulin, N. Q. Nguyen, E. Newman, M. Mahmoud, V. K. Menon, Q. Qi, P. Joshi, S. Marcovina, M. Rossi, E. Roller, J. Han, V. Onuchic, C. L Avery, C. M Ballantyne, C. J Rodriguez, R. C. Kaplan, D. M. Muzny, G. A. Metcalf, R. Gibbs, B. Yu, E. Boerwinkle, M. A. Eberle, F. J. Sedlazeck; Identification of allele-specific KIV-2 repeats and impact on Lp (a) measurements for cardiovascular disease risk; BMC Medical Genomics (2024); doi: 10.1186/s12920-024-02024-0
E. Kalef-Ezra, Z. G. Turan, D. Perez-Rodriguez, I. Bomann, S. Behera, C. Morley, S. W. Scholz, Z. Jaunmuktane, J. Demeulemeester, F. J. Sedlazeck, C. Proukakis; Single-cell somatic copy number variants in brain using different amplification methods and reference genomes; Nature Communications Biology (2024); doi: 10.1038/s42003-024-06940-w
M. Smolka, L. F. Paulin, C. M. Grochowski, M. Mahmoud, S. Behera, M. Gandhi, K. Hong, D. Pehlivan, S. W. Scholz, C. MB Carvalho, C. Proukakis, F. J. Sedlazeck; Comprehensive structural variant detection: from mosaic to population-level; Nature Biotechnology (2024); doi: 10.1038/s41587-023-02024-y
Kolmogorov M, Billingsley KJ, Mastoras M...S. Behera. Scalable nanopore sequencing of human genomes provides a comprehensive view of haplotype-resolved variation and methylation. Nature Methods (2023); doi: doi:10.1038/s41592-023-01993-x
C. Chin, S. Behera, A. Khalak, F. J. Sedlazeck, J. Wagner, J. M. Zook; Multiscale Analysis of Pangenome Enables Improved Representation of Genomic Diversity For Repetitive And Clinical Relevant Genes; Nature Methods (2023); doi: 10.1038/s41592-023-01914-y
S. Behera, J. LeFaive, P. Orchard, M. Mahmoud, L. F. Paulin, J. Farek, D. C. Soto, S. C. J. Parker, A. V. Smith, M. Y. Dennis, J. M. Zook, F. J. Sedlazeck; FixItFelix: improving genomic analysis by fixing reference errors; Genome Biology, Volume 24, Issue 31 (2023); doi: 10.1186/s13059-023-02863-7
L. Gan, K. Park, J. Chai, E. M. Updike, H. Kim, A. Voshall, S. Behera, X. Yu, Y. Cai, C. Zhang, M. A. Wilson, J. P. Mower, E. N. Moriyama, C. Zhang, S. Kaewsuwan, Q. Liu, J. Shanklin, E. B. Cahoon; Divergent evolution of extreme production of variant plant monounsaturated fatty acids; PNAS, Volume 119, Issue 30 (2022); doi: 10.1073/pnas.2201160119
A. Voshall, S. Behera, X. Li, X. Yu, K. Kapil, J. S. Deogun, J. Shanklin, E. B Cahoon, E. N. Moriyama; A consensus-based ensemble approach to improve transcriptome assembly; BMC Bioinformatics 22, 513 (2021); doi: 10.1186/s12859-021-04434-8
X. Lai*, S. Behera* , Z. Liang, Y. Lu, J. S. Deogun, J. C. Schnable; STAG-CNS: An Order-Aware Conserved Noncoding Sequences Discovery Tool for Arbitrary Numbers of Species; Molecular Plant, Volume 10, Issue 7 (2017); doi: 10.1016/j.molp.2017.05.010 [*joint first author]

Priprints:

C. Chin, S. Behera, G. Metcalf, R. A. Gibbs, E. Boerwinkle, F. J. Sedlazeck; A pan-genome approach to decipher variants in the highly complex tandem repeat of LPA; bioRxiv; doi: 10.1101/2022.06.08.495395

Conferences:

S. Behera, J. S. Deogun, E. N. Moriyama; MinIsoClust: Isoform clustering using minhash and locality sensitive hashing; ACM-BCB 2020, pp. 1-7
S. Behera, S. Gayen, J. S. Deogun and N. V. Vinodchandran; KmerEstimate: A Streaming Algorithm for Estimating k-mer Counts with Optimal Space Usage; ACM-BCB 2018, pp. 438-447
S. Behera, J. S. Deogun, X. Lai and J. C. Schnable, DiCE: Discovery of Conserved Noncoding Sequences Efficiently; IEEE BIBM 2017, pp. 79-82
S. Behera , A. Voshall, J. S. Deogun and E. N. Moriyama, Performance comparison and an ensemble approach of transcriptome assembly; IEEE BIBM 2017, pp. 2207-2210
N. Pavlovikj, K. Begcy, S. Behera, M. Campbell, H. Walia, J. S. Deogun; Analysis of transcriptome assembly pipelines for wheat; IEEE BIBM 2016, pp. 137-140
N. Pavlovikj, K. Begcy, S. Behera, M. Campbell, H. Walia, J. S. Deogun; Comparing and optimizing transcriptome assembly pipeline for diploid wheat; ACM-BCB 2014, pp. 603-604
N. Pavlovikj, K. Begcy, S. Behera, M. Campbell, H. Walia, J. S. Deogun; A Comparison of a Campus Cluster and Open Science Grid Platforms for Protein-Guided Assembly Using Pegasus Workflow Management System; IPDPS 2014, pp. 546-555
N. Pavlovikj, K. Begcy, S. Behera , M. Campbell, H. Walia, J. S. Deogun; Evaluating Distributed Platforms for Protein-Guided Scientific Workflow XSEDE 2014, 38:1-38:8
S. Behera , O. Daescu, L. Papiez; Optimal delivery of volumetric modulated arc therapy (VMAT) for moving target; IEEE BIBM 2011, pp. 297-304

Book chapters:

S. Behera, A. Voshall, E. N. Moriyama; Plant transcriptome assembly: review and benchmarking; Bioinformatics, Exon Publications; Chapter 7, pp. 109-130 (2021); doi: 10.36255/exonpublications.bioinformatics.2021.ch7
S. Behera, J. S. Deogun, E. N. Moriyama; MinCNE: Identifying Conserved Noncoding Elements Using Min-Wise Hashing; Advances in Computer Vision and Computational Biology, Transactions on Computational Science and Computational Intelligence, Springer (2021); doi: 10.1007/978-3-030-71051-4_53

Softwares

KmerEstimate: A Streaming Algorithm for Estimating k-mer Counts with Optimal Space Usage. https://github.com/srbehera11/KmerEstimate
STAG_CNS: An order-aware conserved noncoding sequence discovery tool for arbitrary numbers of species. https://github.com/srbehera11/stag-cns/
DiCE: Finding CNS in similar species. https://github.com/srbehera11/DiCE

Posters

Fixing falsely duplicated and collapsed regions of the GRCh38 reference genome; [ASHG 2022, Reviewers' choice abstract]
Identification of allele-specific KIV-2 repeats among multi-ethnic groups and association with LP(a) measurements; ASHG 2021
Comprehensive genomics at scale using DRAGEN pipeline; CSHL Genome Informatics, 2021
Towards Improving Transcriptome Assemblies UNL Plant Science Retreat 2018
Performance comparison and an ensemble approach of transcriptome assembly; IEEE BIBM 2017
STAG-CNS: Conserved non-coding sequence discovery tool; UNL Plant Science Retreat 2016
Transcriptome analysis of drought responses in wheat; UNL Plant Science Retreat 2014

Talks

Bio-IT World Conference 2023
Labroots Genetic Week 2023
HGSC seminar talk: Towards fixing GRCh38 reference genome; Human Genome Sequencing Center, Baylor College of Medicine
PSI seminar talk: Towards Improving Transcriptome Assemblies; Center for plant science innovation, University of Nebraska-Lincoln

Teachings

I was an instructor or Teaching Assistant for the following courses at University of Nebraska-Lincoln

CSCE 924: Graph Algorithms
CSCE 923: Development and Analysis of Efficient Algorithms
CSCE 823: Design and Analysis of Algorithms
CSCE 251K: C Programming
CSCE 155H: Computer Science I Honors
CSCE 155E: Computer Science I

Contact

Email: Sairam[DOT]Behera[AT]bcm[DOT]edu

Baylor College of Medicine
1 Baylor Plaza, Houston, TX 77030

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