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ORCIDSerghei Mangul
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2020 – today
- 2024
[j12]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: e2066 (2024)- [c22]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: 356-359 - [i6]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 abs/2401.02965 (2024) - 2023
- [j11]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) - [j10]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) - [e2]Xuan Guo, Serghei Mangul, Murray Patterson, Alexander Zelikovsky:
Bioinformatics Research and Applications - 19th International Symposium, ISBRA 2023, Wrocław, Poland, October 9-12, 2023, Proceedings. Lecture Notes in Computer Science 14248, Springer 2023, ISBN 978-981-99-7073-5 [contents] - [i5]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 abs/2310.16908 (2023) - [i4]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 abs/2311.02029 (2023) - 2022
- [j9]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:
A comprehensive benchmarking of WGS-based deletion structural variant callers. Briefings Bioinform. 23(4) (2022) - [c21]Pelin Icer Baykal, Niko Beerenwinkel, Serghei Mangul:
Reproducibility of Bioinformatics Tools. IPDPS Workshops 2022: 216 - [c20]Varuni Sarwal, Serghei Mangul, David Koslicki:
TAMPA: interpretable analysis and visualization of metagenomics-based taxon abundance profiles. IPDPS Workshops 2022: 217 - [e1]Mukul S. Bansal, Zhipeng Cai, Serghei Mangul:
Bioinformatics Research and Applications - 18th International Symposium, ISBRA 2022, Haifa, Israel, November 14-17, 2022, Proceedings. Lecture Notes in Computer Science 13760, Springer 2022, ISBN 978-3-031-23197-1 [contents] - [i3]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 abs/2203.16261 (2022) - 2021
- [j8]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) - [c19]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: 165-175 - 2020
- [c18]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: 63:1
2010 – 2019
- 2019
- [i2]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 abs/1909.12469 (2019) - 2018
- [c17]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: 573 - 2017
- [j7]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): 558-570 (2017) - [j6]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:
The impact of rare variation on gene expression across tissues. Nat. 550(7675): 239-243 (2017) - 2016
- [c16]Serghei Mangul, David Koslicki:
Reference-free comparison of microbial communities via de Bruijn graphs. BCB 2016: 68-77 - [c15]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: 80-92 - [c14]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: 164-175 - 2015
- [c13]Alexander Artyomenko, Nicholas C. Wu, Serghei Mangul, Eleazar Eskin, Ren Sun, Alex Zelikovsky:
2SNV: Quasispecies reconstruction from PacBio reads. ICCABS 2015: 1 - 2014
- [j5]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): 329-337 (2014) - [c12]Alexander Artyomenko, Serghei Mangul, Nicholas C. Wu, Eleazar Eskin, Ren Sun, Alex Zelikovsky:
Reconstruction of influenza a virus variants from PacBio reads. ICCABS 2014: 1 - [c11]Adrian Caciula, Olga Glebova, Alexander Artyomenko, Serghei Mangul, James Lindsay, Ion I. Mandoiu, Alex Zelikovsky:
Deterministic regression algorithm for transcriptome frequency estimation. ICCABS 2014: 1 - [c10]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: 1 - 2013
- [c9]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: 1 - [c8]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: 1 - 2012
- [j4]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): A11 (2012) - [j3]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): 251-261 (2012) - [c7]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: 369-376 - [c6]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: 1 - 2011
- [j2]Marius Nicolae, Serghei Mangul, Ion I. Mandoiu, Alex Zelikovsky:
Estimation of alternative splicing isoform frequencies from RNA-Seq data. Algorithms Mol. Biol. 6: 9 (2011) - [j1]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): S1 (2011) - [c5]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: 118-123 - [c4]Irina Astrovskaya, Bassam Tork, Serghei Mangul, Kelly Westbrooks, Ion I. Mandoiu, Peter Balfe, Alexander Zelikovsky:
Poster: ViSpA: Viral spectrum assembling method. ICCABS 2011: 234 - [c3]Serghei Mangul, Alexander Zelikovsky:
Poster: Haplotype discovery from high-throughput sequencing data. ICCABS 2011: 255 - [c2]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: 213-224 - 2010
- [c1]Marius Nicolae, Serghei Mangul, Ion I. Mandoiu, Alexander Zelikovsky:
Estimation of Alternative Splicing isoform Frequencies from RNA-Seq Data. WABI 2010: 202-214 - [i1]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
Coauthor Index
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last updated on 2024-10-07 22:10 CEST by the dblp team
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