Serghei Mangul

According to our database, Serghei Mangul authored at least 35 papers between 2011 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2024

Perceptual and technical barriers in sharing and formatting metadata accompanying omics studies.

Yu-Ning Huang, Michael I. Love, Cynthia Flaire Ronkowski, Dhrithi Deshpande, Lynn M. Schriml, Annie Wong-Beringer, Barend Mons, Russell Corbett-Detig, Christopher I Hunter, Jason H. Moore, Lana X. Garmire, T. B. K. Reddy, Winston A. Hide, Atul J. Butte, Mark D. Robinson, Serghei Mangul

CoRR, 2024

2023

Response to 'comment on rigorous benchmarking of T cell receptor repertoire profiling methods for cancer RNA sequencing' by Davydov A.N.; Bolotin D.A.; Poslavsky S. V. and Chudakov D.M.

Yu-Ning Huang, Mohammad Vahed, Kerui Peng, Houda Alachkar, Serghei Mangul

Briefings Bioinform., September, 2023

Rigorous benchmarking of T-cell receptor repertoire profiling methods for cancer RNA sequencing.

Kerui Peng, Theodore S. Nowicki, Katie Campbell, Mohammad Vahed, Dandan Peng, Yiting Meng, Anish Nagareddy, Yu-Ning Huang, Aaron Karlsberg, Zachary Miller, Jaqueline J. Brito, Brian B. Nadel, Victoria M. Pak, Malak S. Abedalthagafi, Amanda M. Burkhardt, Houda Alachkar, Antoni Ribas, Serghei Mangul

Briefings Bioinform., July, 2023

MetaFast: Enabling Fast Metagenomic Classification via Seed Counting and Edit Distance Approximation.

Arvid E. Gollwitzer, Mohammed Alser, Joel Bergtholdt, Joël Lindegger, Maximilian-David Rumpf, Can Firtina, Serghei Mangul, Onur Mutlu

CoRR, 2023

SequenceLab: A Comprehensive Benchmark of Computational Methods for Comparing Genomic Sequences.

Maximilian-David Rumpf, Mohammed Alser, Arvid E. Gollwitzer, Joël Lindegger, Nour Almadhoun, Can Firtina, Serghei Mangul, Onur Mutlu

CoRR, 2023

2022

Packaging, containerization, and virtualization of computational omics methods: Advances, challenges, and opportunities.

Mohammed Alser, Sharon Waymost, Ram Ayyala, Brendan Lawlor, Richard J. Abdill, Neha Rajkumar, Nathan LaPierre, Jaqueline J. Brito, Andre M. Ribeiro-dos-Santos, Can Firtina, Nour Almadhoun, Varuni Sarwal, Eleazar Eskin, Qiyang Hu, Derek Strong, Byoung-Do Kim, Malak S. Abedalthagafi, Onur Mutlu, Serghei Mangul

CoRR, 2022

A comprehensive benchmarking of WGS-based deletion structural variant callers.

Varuni Sarwal, Sebastian Niehus, Ram Ayyala, Minyoung Kim, Aditya Sarkar, Sei Chang, Angela Lu, Neha Rajkumar, Nicholas Darfci-Maher, Russell Littman, Karishma Chhugani, Arda Soylev, Zoia Comarova, Emily Wesel, Jacqueline Castellanos, Rahul Chikka, Margaret G. Distler, Eleazar Eskin, Jonathan Flint, Serghei Mangul

Briefings Bioinform., 2022

TAMPA: interpretable analysis and visualization of metagenomics-based taxon abundance profiles.

Varuni Sarwal, Serghei Mangul, David Koslicki

Proceedings of the IEEE International Parallel and Distributed Processing Symposium, 2022

Reproducibility of Bioinformatics Tools.

Pelin Icer Baykal, Niko Beerenwinkel, Serghei Mangul

Proceedings of the IEEE International Parallel and Distributed Processing Symposium, 2022

2021

Systematic evaluation of transcriptomics-based deconvolution methods and references using thousands of clinical samples.

Brian B. Nadel, Meritxell Oliva, Benjamin L. Shou, Keith Mitchell, Feiyang Ma, Dennis J. Montoya, Alice Mouton, Sarah Kim-Hellmuth, Barbara E. Stranger, Matteo Pellegrini, Serghei Mangul

Briefings Bioinform., 2021

A Novel Network Representation of SARS-CoV-2 Sequencing Data.

Sergey Knyazev, Daniel Novikov, Mark Grinshpon, Harman Singh, Ram Ayyala, Varuni Sarwal, Roya Hosseini, Pelin Icer Baykal, Pavel Skums, Ellsworth Campbell, Serghei Mangul, Alex Zelikovsky

Proceedings of the Bioinformatics Research and Applications - 17th International Symposium, 2021

2020

Benchmarking of computational error-correction methods for next-generation sequencing data.

Keith Mitchell, Jaqueline J. Brito, Igor Mandric, Qiaozhen Wu, Sergey Knyazev, Sei Chang, Lana S. Martin, Aaron Karlsberg, Ekaterina Gerasimov, Russell Littman, Brian L. Hill, Nicholas C. Wu, Harry (Taegyun) Yang, Kevin Hsieh, Linus Chen, Eli Littman, Taylor Shabani, German Enik, Douglas Yao, Ren Sun, Jan Schroeder, Eleazar Eskin, Alex Zelikovsky, Pavel Skums, Mihai Pop, Serghei Mangul

Proceedings of the BCB '20: 11th ACM International Conference on Bioinformatics, 2020

2019

Telescope: an interactive tool for managing large scale analysis from mobile devices.

Jaqueline J. Brito, Thiago Mosqueiro, Douglas J. Chapski, Juan De la Hoz, Paulo Matias, Lana S. Martin, Matteo Pellegrinni, Serghei Mangul

CoRR, 2019

2018

ROP: Dumpster Diving in RNA-sequencing to Find the Source of 1 Trillion Reads Across Diverse Adult Human Tissues.

Serghei Mangul, Harry (Taegyun) Yang, Noah Zaitlen

Proceedings of the 2018 ACM International Conference on Bioinformatics, 2018

2017

The impact of rare variation on gene expression across tissues.

Xin Li, Yungil Kim, Emily K. Tsang, Joe R. Davis, Farhan N. Damani, Colby Chiang, Gaelen T. Hess, Zachary Zappala, Benjamin J. Strober, Alexandra J. Scott, Amy Li, Andrea Ganna, Michael C. Bassik, Jason D. Merker, François Aguet, Kristin G. Ardlie, Beryl B. Cummings, Ellen T. Gelfand, Gad Getz, Kane Hadley, Robert E. Handsaker, Katherine H. Huang, Seva Kashin, Konrad J. Karczewski, Monkol Lek, Xiao Li, Daniel G. MacArthur, Jared L. Nedzel, Duyen T. Nguyen, Michael S. Noble, Ayellet V. Segrè, Casandra A. Trowbridge, Taru Tukiainen, Nathan S. Abell, Brunilda Balliu, Ruth Barshir, Omer Basha, Alexis J. Battle, Gireesh K. Bogu, Andrew Brown, Christopher D. Brown, Stephane E. Castel, Lin S. Chen, Donald F. Conrad, Nancy J. Cox, Olivier Delaneau, Emmanouil T. Dermitzakis, Barbara E. Engelhardt, Eleazar Eskin, Pedro G. Ferreira, Laure Frésard, Eric R. Gamazon, Diego Garrido-Martín, Ariel D. H. Gewirtz, Genna Gliner, Michael J. Gloudemans, Roderic Guigó, Ira M. Hall, Buhm Han, Yuan He, Farhad Hormozdiari, Cedric Howald, Hae Kyung Im, Brian Jo, Eun Yong Kang, Sarah Kim-Hellmuth, Tuuli Lappalainen, Gen Li, Boxiang Liu, Serghei Mangul, Mark I. McCarthy, Ian C. McDowell, Pejman Mohammadi, Jean Monlong, Stephen B. Montgomery

Nat., 2017

Long Single-Molecule Reads Can Resolve the Complexity of the Influenza Virus Composed of Rare, Closely Related Mutant Variants.

Alexander Artyomenko, Nicholas C. Wu, Serghei Mangul, Eleazar Eskin, Ren Sun, Alex Zelikovsky

J. Comput. Biol., 2017

2016

HapIso: An Accurate Method for the Haplotype-Specific Isoforms Reconstruction from Long Single-Molecule Reads.

Serghei Mangul, Harry (Taegyun) Yang, Farhad Hormozdiari, Elizabeth Tseng, Alex Zelikovsky, Eleazar Eskin

Proceedings of the Bioinformatics Research and Applications - 12th International Symposium, 2016

Reference-free comparison of microbial communities via de Bruijn graphs.

Serghei Mangul, David Koslicki

Proceedings of the 7th ACM International Conference on Bioinformatics, 2016

2015

2SNV: Quasispecies reconstruction from PacBio reads.

Alexander Artyomenko, Nicholas C. Wu, Serghei Mangul, Eleazar Eskin, Ren Sun, Alex Zelikovsky

Proceedings of the 5th IEEE International Conference on Computational Advances in Bio and Medical Sciences, 2015

2014

Accurate viral population assembly from ultra-deep sequencing data.

Serghei Mangul, Nicholas C. Wu, Nicholas Mancuso, Alex Zelikovsky, Ren Sun, Eleazar Eskin

Bioinform., 2014

VGA: A method for viral quasispecies assembly from ultra-deep sequencing data.

Serghei Mangul, Nicholas C. Wu, Nicholas Mancuso, Alex Zelikovsky, Ren Sun, Eleazar Eskin

Proceedings of the IEEE 4th International Conference on Computational Advances in Bio and Medical Sciences, 2014

Deterministic regression algorithm for transcriptome frequency estimation.

Adrian Caciula, Olga Glebova, Alexander Artyomenko, Serghei Mangul, James Lindsay, Ion I. Mandoiu, Alex Zelikovsky

Proceedings of the IEEE 4th International Conference on Computational Advances in Bio and Medical Sciences, 2014

Reconstruction of influenza a virus variants from PacBio reads.

Alexander Artyomenko, Serghei Mangul, Nicholas C. Wu, Eleazar Eskin, Ren Sun, Alex Zelikovsky

Proceedings of the IEEE 4th International Conference on Computational Advances in Bio and Medical Sciences, 2014

2013

Transcriptome assembly and quantification from Ion Torrent RNA-Seq data.

Serghei Mangul, Sahar Al Seesi, Ion I. Mandoiu, Adrian Caciula, Alex Zelikovsky, Dumitru Brinza

Proceedings of the IEEE 3rd International Conference on Computational Advances in Bio and Medical Sciences, 2013

Monte-Carlo Regression algorithm for isoform frequency estimation from RNA-Seq data.

Adrian Caciula, Alex Zelikovsky, Serghei Mangul, James Lindsay, Ion I. Mandoiu

Proceedings of the IEEE 3rd International Conference on Computational Advances in Bio and Medical Sciences, 2013

2012

Improved transcriptome quantification and reconstruction from RNA-Seq reads using partial annotations.

Serghei Mangul, Adrian Caciula, Olga Glebova, Ion I. Mandoiu, Alex Zelikovsky

Silico Biol., 2012

TRIP: a method for novel transcript reconstruction from paired-end RNA-seq reads.

Serghei Mangul, Adrian Caciula, Dumitru Brinza, Ion I. Mandoiu, Alex Zelikovsky

BMC Bioinform., 2012

Workshop: Novel transcript reconstruction from paired-end RNA-Seq reads using fragment length distribution.

Serghei Mangul, Adrian Caciula, Ion I. Mandoiu, Alexander Zelikovsky

Proceedings of the IEEE 2nd International Conference on Computational Advances in Bio and Medical Sciences, 2012

An integer programming approach to novel transcript reconstruction from paired-end RNA-Seq reads.

Serghei Mangul, Adrian Caciula, Sahar Al Seesi, Dumitru Brinza, Abdul Rouf Banday, Rahul Kanadia

Proceedings of the ACM International Conference on Bioinformatics, 2012

2011

Inferring viral quasispecies spectra from 454 pyrosequencing reads.

Irina Astrovskaya, Bassam Tork, Serghei Mangul, Kelly Westbrooks, Ion I. Mandoiu, Peter Balfe, Alex Zelikovsky

BMC Bioinform., 2011

Estimation of alternative splicing isoform frequencies from RNA-Seq data.

Marius Nicolae, Serghei Mangul, Ion I. Mandoiu, Alex Zelikovsky

Algorithms Mol. Biol., 2011

Maximum Likelihood Estimation of Incomplete Genomic Spectrum from HTS Data.

Serghei Mangul, Irina Astrovskaya, Marius Nicolae, Bassam Tork, Ion I. Mandoiu, Alexander Zelikovsky

Proceedings of the Algorithms in Bioinformatics - 11th International Workshop, 2011

Poster: Haplotype discovery from high-throughput sequencing data.

Serghei Mangul, Alexander Zelikovsky

Proceedings of the IEEE 1st International Conference on Computational Advances in Bio and Medical Sciences, 2011

Poster: ViSpA: Viral spectrum assembling method.

Irina Astrovskaya, Bassam Tork, Serghei Mangul, Kelly Westbrooks, Ion I. Mandoiu, Peter Balfe, Alexander Zelikovsky

Proceedings of the IEEE 1st International Conference on Computational Advances in Bio and Medical Sciences, 2011

RNA-Seq based discovery and reconstruction of unannotated transcripts in partially annotated genomes.

Serghei Mangul, Adrian Caciula, Ion I. Mandoiu, Alexander Zelikovsky

Proceedings of the 2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, 2011