RNA-Seq based discovery and reconstruction of unannotated transcripts in partially annotated genomes. - Serghei Mangul; Adrian Caciula; Ion I. Mandoiu; Alexander Zelikovsky (BIBM Workshops, 2011)

Poster: ViSpA: Viral spectrum assembling method. - Irina Astrovskaya; Bassam Tork; Serghei Mangul; Kelly Westbrooks; Ion I. Mandoiu; Peter Balfe; Alexander Zelikovsky (ICCABS, 2011)

Poster: Haplotype discovery from high-throughput sequencing data. - Serghei Mangul; Alexander Zelikovsky (ICCABS, 2011)

Maximum Likelihood Estimation of Incomplete Genomic Spectrum from HTS Data. - Serghei Mangul; Irina Astrovskaya; Marius Nicolae; Bassam Tork; Ion I. Mandoiu; Alexander Zelikovsky (WABI, 2011)

Estimation of alternative splicing isoform frequencies from RNA-Seq data. - Marius Nicolae; Serghei Mangul; Ion I. Mandoiu; Alex Zelikovsky (Algorithms Mol. Biol., 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)

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 (BCB, 2012)

Workshop: Novel transcript reconstruction from paired-end RNA-Seq reads using fragment length distribution. - Serghei Mangul; Adrian Caciula; Ion I. Mandoiu; Alexander Zelikovsky (ICCABS, 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)

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)

Monte-Carlo Regression algorithm for isoform frequency estimation from RNA-Seq data. - Adrian Caciula; Alex Zelikovsky; Serghei Mangul; James Lindsay; Ion I. Mandoiu (ICCABS, 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 (ICCABS, 2013)

Reconstruction of influenza a virus variants from PacBio reads. - Alexander Artyomenko; Serghei Mangul; Nicholas C. Wu; Eleazar Eskin; Ren Sun; Alex Zelikovsky (ICCABS, 2014)

Deterministic regression algorithm for transcriptome frequency estimation. - Adrian Caciula; Olga Glebova; Alexander Artyomenko; Serghei Mangul; James Lindsay; Ion I. Mandoiu; Alex Zelikovsky (ICCABS, 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 (ICCABS, 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)

2SNV: Quasispecies reconstruction from PacBio reads. - Alexander Artyomenko; Nicholas C. Wu; Serghei Mangul; Eleazar Eskin; Ren Sun; Alex Zelikovsky (ICCABS, 2015)

Reference-free comparison of microbial communities via de Bruijn graphs. - Serghei Mangul; David Koslicki (BCB, 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 (ISBRA, 2016)

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)

The impact of rare variation on gene expression across tissues. - Xin Li 130; 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; et al. (Nat., 2017)

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 (BCB, 2018)

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)

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; et al. (BCB, 2020)

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 (ISBRA, 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)

Reproducibility of Bioinformatics Tools. - Pelin Icer Baykal; Niko Beerenwinkel; Serghei Mangul (IPDPS Workshops, 2022)

TAMPA: interpretable analysis and visualization of metagenomics-based taxon abundance profiles. - Varuni Sarwal; Serghei Mangul; David Koslicki (IPDPS Workshops, 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 Darci-Maher; Russell Littman; Karishma Chhugani; Arda Soylev; et al. (Briefings Bioinform., 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; et al. (CoRR, 2022)

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)

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)

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; et al. (Briefings Bioinform., 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., 2023)

Community Structure and Temporal Dynamics of Viral Epistatic Networks Allow for Early Detection of Emerging Variants with Altered Phenotypes. - Fatemeh Mohebbi; Alexander Zelikovsky; Serghei Mangul; Gerardo Chowell; Pavel Skums (RECOMB, 2024)

VISTA: an integrated framework for structural variant discovery. - Varuni Sarwal; Seungmo Lee; Jianzhi Yang; Sriram Sankararaman; Mark Chaisson; Eleazar Eskin; Serghei Mangul (Briefings Bioinform., 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; et al. (CoRR, 2024)

Analytical code sharing practices in biomedical research. - 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; et al. (PeerJ Comput. Sci., 2024)

Estimating Enzyme Expression and Metabolic Pathway Activity in Borreliella-Infected and Uninfected Mice. - Filipp Rondel; Hafsa Farooq; Roya Hosseini; Akshay Juyal; Sergey Knyazev; Serghei Mangul; Artem S. Rogovskyy; Alexander Zelikovsky (J. Comput. Biol., 2025)