Serghei Mangul

Publication Activity (10 Years)

Years Active: 2010-2024
Publications (10 Years): 22

Top Topics

Influenza Virus

Genomic Sequences

Closely Related

Top Venues

Briefings Bioinform.

Publications

Fatemeh Mohebbi, Alexander Zelikovsky, Serghei Mangul, Gerardo Chowell, Pavel Skums
Community Structure and Temporal Dynamics of Viral Epistatic Networks Allow for Early Detection of Emerging Variants with Altered Phenotypes. RECOMB (2024)
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
Perceptual and technical barriers in sharing and formatting metadata accompanying omics studies. CoRR (2024)
Nitesh Kumar Sharma, Ram Ayyala, Dhrithi Deshpande, Yesha Patel, Viorel Munteanu, Dumitru Ciorba, Viorel Bostan, Andrada Fiscutean, Mohammad Vahed, Aditya Sarkar, Ruiwei Guo, Andrew Moore, Nicholas Darci-Maher, Nicole Nogoy, Malak S. Abedalthagafi, Serghei Mangul
Analytical code sharing practices in biomedical research. PeerJ Comput. Sci. 10 (2024)
Yu-Ning Huang, Mohammad Vahed, Kerui Peng, Houda Alachkar, Serghei Mangul
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. Briefings Bioinform. 24 (6) (2023)
Arvid E. Gollwitzer, Mohammed Alser, Joel Bergtholdt, Joël Lindegger, Maximilian-David Rumpf, Can Firtina, Serghei Mangul, Onur Mutlu
MetaFast: Enabling Fast Metagenomic Classification via Seed Counting and Edit Distance Approximation. CoRR (2023)
Maximilian-David Rumpf, Mohammed Alser, Arvid E. Gollwitzer, Joël Lindegger, Nour Almadhoun, Can Firtina, Serghei Mangul, Onur Mutlu
SequenceLab: A Comprehensive Benchmark of Computational Methods for Comparing Genomic Sequences. CoRR (2023)
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
Rigorous benchmarking of T-cell receptor repertoire profiling methods for cancer RNA sequencing. Briefings Bioinform. 24 (4) (2023)
Pelin Icer Baykal, Niko Beerenwinkel, Serghei Mangul
Reproducibility of Bioinformatics Tools. IPDPS Workshops (2022)
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
Packaging, containerization, and virtualization of computational omics methods: Advances, challenges, and opportunities. CoRR (2022)
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
A comprehensive benchmarking of WGS-based deletion structural variant callers. Briefings Bioinform. 23 (4) (2022)
Varuni Sarwal, Serghei Mangul, David Koslicki
TAMPA: interpretable analysis and visualization of metagenomics-based taxon abundance profiles. IPDPS Workshops (2022)
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
Systematic evaluation of transcriptomics-based deconvolution methods and references using thousands of clinical samples. Briefings Bioinform. 22 (6) (2021)
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
A Novel Network Representation of SARS-CoV-2 Sequencing Data. ISBRA (2021)
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
Benchmarking of computational error-correction methods for next-generation sequencing data. BCB (2020)
Jaqueline J. Brito, Thiago Mosqueiro, Douglas J. Chapski, Juan De la Hoz, Paulo Matias, Lana S. Martin, Matteo Pellegrinni, Serghei Mangul
Telescope: an interactive tool for managing large scale analysis from mobile devices. CoRR (2019)
Serghei Mangul, Harry (Taegyun) Yang, Noah Zaitlen
ROP: Dumpster Diving in RNA-sequencing to Find the Source of 1 Trillion Reads Across Diverse Adult Human Tissues. BCB (2018)
Alexander Artyomenko, Nicholas C. Wu, Serghei Mangul, Eleazar Eskin, Ren Sun, Alex Zelikovsky
Long Single-Molecule Reads Can Resolve the Complexity of the Influenza Virus Composed of Rare, Closely Related Mutant Variants. J. Comput. Biol. 24 (6) (2017)
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 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
The impact of rare variation on gene expression across tissues. Nat. 550 (7675) (2017)
Serghei Mangul, David Koslicki
Reference-free comparison of microbial communities via de Bruijn graphs. BCB (2016)
Serghei Mangul, Harry (Taegyun) Yang, Farhad Hormozdiari, Elizabeth Tseng, Alex Zelikovsky, Eleazar Eskin
HapIso: An Accurate Method for the Haplotype-Specific Isoforms Reconstruction from Long Single-Molecule Reads. ISBRA (2016)
Alexander Artyomenko, Nicholas C. Wu, Serghei Mangul, Eleazar Eskin, Ren Sun, Alex Zelikovsky
Long Single-Molecule Reads Can Resolve the Complexity of the Influenza Virus Composed of Rare, Closely Related Mutant Variants. RECOMB (2016)
Alexander Artyomenko, Nicholas C. Wu, Serghei Mangul, Eleazar Eskin, Ren Sun, Alex Zelikovsky
2SNV: Quasispecies reconstruction from PacBio reads. ICCABS (2015)
Serghei Mangul, Nicholas C. Wu, Nicholas Mancuso, Alex Zelikovsky, Ren Sun, Eleazar Eskin
Accurate viral population assembly from ultra-deep sequencing data. Bioinform. 30 (12) (2014)
Alexander Artyomenko, Serghei Mangul, Nicholas C. Wu, Eleazar Eskin, Ren Sun, Alex Zelikovsky
Reconstruction of influenza a virus variants from PacBio reads. ICCABS (2014)
Adrian Caciula, Olga Glebova, Alexander Artyomenko, Serghei Mangul, James Lindsay, Ion I. Mandoiu, Alex Zelikovsky
Deterministic regression algorithm for transcriptome frequency estimation. ICCABS (2014)
Serghei Mangul, Nicholas C. Wu, Nicholas Mancuso, Alex Zelikovsky, Ren Sun, Eleazar Eskin
VGA: A method for viral quasispecies assembly from ultra-deep sequencing data. ICCABS (2014)
Serghei Mangul, Sahar Al Seesi, Ion I. Mandoiu, Adrian Caciula, Alex Zelikovsky, Dumitru Brinza
Transcriptome assembly and quantification from Ion Torrent RNA-Seq data. ICCABS (2013)
Adrian Caciula, Alex Zelikovsky, Serghei Mangul, James Lindsay, Ion I. Mandoiu
Monte-Carlo Regression algorithm for isoform frequency estimation from RNA-Seq data. ICCABS (2013)
Serghei Mangul, Adrian Caciula, Ion I. Mandoiu, Alexander Zelikovsky
Workshop: Novel transcript reconstruction from paired-end RNA-Seq reads using fragment length distribution. ICCABS (2012)
Serghei Mangul, Adrian Caciula, Dumitru Brinza, Ion I. Mandoiu, Alex Zelikovsky
TRIP: a method for novel transcript reconstruction from paired-end RNA-seq reads. BMC Bioinform. 13 (S-18) (2012)
Serghei Mangul, Adrian Caciula, Sahar Al Seesi, Dumitru Brinza, Abdul Rouf Banday, Rahul Kanadia
An integer programming approach to novel transcript reconstruction from paired-end RNA-Seq reads. BCB (2012)
Serghei Mangul, Adrian Caciula, Olga Glebova, Ion I. Mandoiu, Alex Zelikovsky
Improved transcriptome quantification and reconstruction from RNA-Seq reads using partial annotations. Silico Biol. 11 (5-6) (2012)
Serghei Mangul, Alexander Zelikovsky
Poster: Haplotype discovery from high-throughput sequencing data. ICCABS (2011)
Marius Nicolae, Serghei Mangul, Ion I. Mandoiu, Alex Zelikovsky
Estimation of alternative splicing isoform frequencies from RNA-Seq data. Algorithms Mol. Biol. 6 (2011)
Irina Astrovskaya, Bassam Tork, Serghei Mangul, Kelly Westbrooks, Ion I. Mandoiu, Peter Balfe, Alex Zelikovsky
Inferring viral quasispecies spectra from 454 pyrosequencing reads. BMC Bioinform. 12 (S-6) (2011)
Serghei Mangul, Adrian Caciula, Ion I. Mandoiu, Alexander Zelikovsky
RNA-Seq based discovery and reconstruction of unannotated transcripts in partially annotated genomes. BIBM Workshops (2011)
Serghei Mangul, Irina Astrovskaya, Marius Nicolae, Bassam Tork, Ion I. Mandoiu, Alexander Zelikovsky
Maximum Likelihood Estimation of Incomplete Genomic Spectrum from HTS Data. WABI (2011)
Irina Astrovskaya, Bassam Tork, Serghei Mangul, Kelly Westbrooks, Ion I. Mandoiu, Peter Balfe, Alexander Zelikovsky
Poster: ViSpA: Viral spectrum assembling method. ICCABS (2011)
Marius Nicolae, Serghei Mangul, Ion I. Mandoiu, Alex Zelikovsky
Estimation of alternative splicing isoform frequencies from RNA-Seq data. Structure Discovery in Biology: Motifs, Networks & Phylogenies (2010)
Marius Nicolae, Serghei Mangul, Ion I. Mandoiu, Alexander Zelikovsky
Estimation of Alternative Splicing isoform Frequencies from RNA-Seq Data. WABI (2010)