Serghei Mangul

47 papers B 2C 2Journal 21Unranked 19
YearRankTypeTitle / Venue / Authors
2026 — ed.
Computational Advances in Bio and Medical Sciences - 13th International Conference, ICCABS 2025, Atlanta, GA, USA, January 12-14, 2025, Revised Selected Papers
ICCABS
Mohammed Alser, Mukul S. Bansal, Yury Khudyakov, Serghei Mangul, Ion I. Mandoiu, Marmar Moussa, Murray Patterson, Sanguthevar Rajasekaran, Pavel Skums, Shibu Yooseph, Alexander Zelikovsky
2026 J jnl
FASTR: Reimagining FASTQ via Compact Image-inspired Representation.
CoRR
Adrian Tkachenko, Sepehr Salem, Ayotomiwa Ezekiel Adeniyi, Zülal Bingöl, Mohammed Nayeem Uddin, Akshat Prasanna, Alexander Zelikovsky, Serghei Mangul, Can Alkan, Mohammed Alser
2025 J jnl
A decentralized future for the open-science databases.
CoRR
Gaurav Sharma, Viorel Munteanu, Nika Mansouri-Ghiasi, Jineta Banerjee, Susheel Varma, Luca Foschini, Kyle Ellrott, Onur Mutlu, Dumitru Ciorba, Roel A. Ophoff, Viorel Bostan, Christopher E. Mason, Jason H. Moore, Despoina Sousoni, Arunkumar Krishnan, Mihai Dimian, Gustavo Stolovitzky, Fabio G. Liberante, Taras K. Oleksyk, Serghei Mangul
2025 J jnl
Estimating Enzyme Expression and Metabolic Pathway Activity in
J. Comput. Biol.
Filipp Rondel, Hafsa Farooq, Roya Hosseini, Akshay Juyal, Sergey Knyazev, Serghei Mangul, Artem S. Rogovskyy, Alexander Zelikovsky
2024 J jnl
Analytical code sharing practices in biomedical research.
PeerJ Comput. Sci.
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
2024 B conf
Community Structure and Temporal Dynamics of Viral Epistatic Networks Allow for Early Detection of Emerging Variants with Altered Phenotypes.
RECOMB
Fatemeh Mohebbi, Alexander Zelikovsky, Serghei Mangul, Gerardo Chowell, Pavel Skums
2024 J jnl
Perceptual and technical barriers in sharing and formatting metadata accompanying omics studies.
CoRR
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
2024 J jnl
VISTA: an integrated framework for structural variant discovery.
Briefings Bioinform.
Varuni Sarwal, Seungmo Lee, Jianzhi Yang, Sriram Sankararaman, Mark Chaisson, Eleazar Eskin, Serghei Mangul
2023 — ed.
Bioinformatics Research and Applications - 19th International Symposium, ISBRA 2023, Wrocław, Poland, October 9-12, 2023, Proceedings
ISBRA
Xuan Guo, Serghei Mangul, Murray Patterson, Alexander Zelikovsky
2023 J jnl
MetaFast: Enabling Fast Metagenomic Classification via Seed Counting and Edit Distance Approximation.
CoRR
Arvid E. Gollwitzer, Mohammed Alser, Joel Bergtholdt, Joël Lindegger, Maximilian-David Rumpf, Can Firtina, Serghei Mangul, Onur Mutlu
2023 J jnl
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.
Yu-Ning Huang, Mohammad Vahed, Kerui Peng, Houda Alachkar, Serghei Mangul
2023 J jnl
Rigorous benchmarking of T-cell receptor repertoire profiling methods for cancer RNA sequencing.
Briefings Bioinform.
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
2023 J jnl
SequenceLab: A Comprehensive Benchmark of Computational Methods for Comparing Genomic Sequences.
CoRR
Maximilian-David Rumpf, Mohammed Alser, Arvid E. Gollwitzer, Joël Lindegger, Nour Almadhoun, Can Firtina, Serghei Mangul, Onur Mutlu
2022 J jnl
A comprehensive benchmarking of WGS-based deletion structural variant callers.
Briefings Bioinform.
Varuni Sarwal, Sebastian Niehus, Ram Ayyala, Minyoung Kim, Aditya Sarkar, Sei Chang, Angela Lu, Neha Rajkumar, Nicholas Darci-Maher, Russell Littman, Karishma Chhugani, Arda Soylev, Zoia Comarova, Emily E. Wesel, Jacqueline Castellanos, Rahul Chikka, Margaret G. Distler, Eleazar Eskin, Jonathan Flint, Serghei Mangul
2022 — ed.
Bioinformatics Research and Applications - 18th International Symposium, ISBRA 2022, Haifa, Israel, November 14-17, 2022, Proceedings
ISBRA
Mukul S. Bansal, Zhipeng Cai, Serghei Mangul
2022 J jnl
Packaging, containerization, and virtualization of computational omics methods: Advances, challenges, and opportunities.
CoRR
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
2022 — conf
Reproducibility of Bioinformatics Tools.
IPDPS Workshops
Pelin Icer Baykal, Niko Beerenwinkel, Serghei Mangul
2022 — conf
TAMPA: interpretable analysis and visualization of metagenomics-based taxon abundance profiles.
IPDPS Workshops
Varuni Sarwal, Serghei Mangul, David Koslicki
2021 — conf
A Novel Network Representation of SARS-CoV-2 Sequencing Data.
ISBRA
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
2021 J jnl
Systematic evaluation of transcriptomics-based deconvolution methods and references using thousands of clinical samples.
Briefings Bioinform.
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
2020 — conf
Benchmarking of computational error-correction methods for next-generation sequencing data.
BCB
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
2019 J jnl
Telescope: an interactive tool for managing large scale analysis from mobile devices.
CoRR
Jaqueline J. Brito, Thiago Mosqueiro, Douglas J. Chapski, Juan De la Hoz, Paulo Matias, Lana S. Martin, Matteo Pellegrinni, Serghei Mangul
2018 — conf
ROP: Dumpster Diving in RNA-sequencing to Find the Source of 1 Trillion Reads Across Diverse Adult Human Tissues.
BCB
Serghei Mangul, Harry (Taegyun) Yang, Noah Zaitlen
2017 J jnl
Long Single-Molecule Reads Can Resolve the Complexity of the Influenza Virus Composed of Rare, Closely Related Mutant Variants.
J. Comput. Biol.
Alexander Artyomenko, Nicholas C. Wu, Serghei Mangul, Eleazar Eskin, Ren Sun, Alex Zelikovsky
2017 J jnl
The impact of rare variation on gene expression across tissues.
Nat.
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
2016 — conf
HapIso: An Accurate Method for the Haplotype-Specific Isoforms Reconstruction from Long Single-Molecule Reads.
ISBRA
Serghei Mangul, Harry (Taegyun) Yang, Farhad Hormozdiari, Elizabeth Tseng, Alex Zelikovsky, Eleazar Eskin
2016 B conf
Long Single-Molecule Reads Can Resolve the Complexity of the Influenza Virus Composed of Rare, Closely Related Mutant Variants.
RECOMB
Alexander Artyomenko, Nicholas C. Wu, Serghei Mangul, Eleazar Eskin, Ren Sun, Alex Zelikovsky
2016 — conf
Reference-free comparison of microbial communities via de Bruijn graphs.
BCB
Serghei Mangul, David Koslicki
2015 — conf
2SNV: Quasispecies reconstruction from PacBio reads.
ICCABS
Alexander Artyomenko, Nicholas C. Wu, Serghei Mangul, Eleazar Eskin, Ren Sun, Alex Zelikovsky
2014 J jnl
Accurate viral population assembly from ultra-deep sequencing data.
Bioinform.
Serghei Mangul, Nicholas C. Wu, Nicholas Mancuso, Alex Zelikovsky, Ren Sun, Eleazar Eskin
2014 — conf
Deterministic regression algorithm for transcriptome frequency estimation.
ICCABS
Adrian Caciula, Olga Glebova, Alexander Artyomenko, Serghei Mangul, James Lindsay, Ion I. Mandoiu, Alex Zelikovsky
2014 — conf
Reconstruction of influenza a virus variants from PacBio reads.
ICCABS
Alexander Artyomenko, Serghei Mangul, Nicholas C. Wu, Eleazar Eskin, Ren Sun, Alex Zelikovsky
2014 — conf
VGA: A method for viral quasispecies assembly from ultra-deep sequencing data.
ICCABS
Serghei Mangul, Nicholas C. Wu, Nicholas Mancuso, Alex Zelikovsky, Ren Sun, Eleazar Eskin
2013 — conf
Monte-Carlo Regression algorithm for isoform frequency estimation from RNA-Seq data.
ICCABS
Adrian Caciula, Alex Zelikovsky, Serghei Mangul, James Lindsay, Ion I. Mandoiu
2013 — conf
Transcriptome assembly and quantification from Ion Torrent RNA-Seq data.
ICCABS
Serghei Mangul, Sahar Al Seesi, Ion I. Mandoiu, Adrian Caciula, Alex Zelikovsky, Dumitru Brinza
2012 — conf
An integer programming approach to novel transcript reconstruction from paired-end RNA-Seq reads.
BCB
Serghei Mangul, Adrian Caciula, Sahar Al Seesi, Dumitru Brinza, Abdul Rouf Banday, Rahul Kanadia
2012 J jnl
Improved transcriptome quantification and reconstruction from RNA-Seq reads using partial annotations.
Silico Biol.
Serghei Mangul, Adrian Caciula, Olga Glebova, Ion I. Mandoiu, Alex Zelikovsky
2012 J jnl
TRIP: a method for novel transcript reconstruction from paired-end RNA-seq reads.
BMC Bioinform.
Serghei Mangul, Adrian Caciula, Dumitru Brinza, Ion I. Mandoiu, Alex Zelikovsky
2012 — conf
Workshop: Novel transcript reconstruction from paired-end RNA-Seq reads using fragment length distribution.
ICCABS
Serghei Mangul, Adrian Caciula, Ion I. Mandoiu, Alexander Zelikovsky
2011 J jnl
Estimation of alternative splicing isoform frequencies from RNA-Seq data.
Algorithms Mol. Biol.
Marius Nicolae, Serghei Mangul, Ion I. Mandoiu, Alex Zelikovsky
2011 J jnl
Inferring viral quasispecies spectra from 454 pyrosequencing reads.
BMC Bioinform.
Irina Astrovskaya, Bassam Tork, Serghei Mangul, Kelly Westbrooks, Ion I. Mandoiu, Peter Balfe, Alex Zelikovsky
2011 C conf
Maximum Likelihood Estimation of Incomplete Genomic Spectrum from HTS Data.
WABI
Serghei Mangul, Irina Astrovskaya, Marius Nicolae, Bassam Tork, Ion I. Mandoiu, Alexander Zelikovsky
2011 — conf
Poster: Haplotype discovery from high-throughput sequencing data.
ICCABS
Serghei Mangul, Alexander Zelikovsky
2011 — conf
Poster: ViSpA: Viral spectrum assembling method.
ICCABS
Irina Astrovskaya, Bassam Tork, Serghei Mangul, Kelly Westbrooks, Ion I. Mandoiu, Peter Balfe, Alexander Zelikovsky
2011 — conf
RNA-Seq based discovery and reconstruction of unannotated transcripts in partially annotated genomes.
BIBM Workshops
Serghei Mangul, Adrian Caciula, Ion I. Mandoiu, Alexander Zelikovsky
2010 C conf
Estimation of Alternative Splicing isoform Frequencies from RNA-Seq Data.
WABI
Marius Nicolae, Serghei Mangul, Ion I. Mandoiu, Alexander Zelikovsky
2010 — conf
Estimation of alternative splicing isoform frequencies from RNA-Seq data.
Structure Discovery in Biology: Motifs, Networks & Phylogenies
Marius Nicolae, Serghei Mangul, Ion I. Mandoiu, Alex Zelikovsky