Representative Publications

 

Developing Bioinformatics Methods

Mangul, Serghei; Mandric, Igor; Yang, Harry Taegyun; Strauli, Nicolas; Montoya, Dennis; Rotman, Jeremy; Wey, Will Van Der; Ronas, Jiem R; Statz, Benjamin; Zelikovsky, Alex; others,

Profiling adaptive immune repertoires across multiple human tissues by RNA Sequencing Journal Article Forthcoming

Nature Communications (accepted), Forthcoming.

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Mangul, Serghei; Yang, Harry Taegyun; Strauli, Nicolas; Gruhl, Franziska; Porath, Hagit T; Hsieh, Kevin; Chen, Linus; Daley, Timothy; Christenson, Stephanie; Wesolowska-Andersen, Agata; others,

ROP: dumpster diving in RNA-sequencing to find the source of 1 trillion reads across diverse adult human tissues Journal Article

Genome Biology, 19 (1), pp. 36, 2018.

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

Accurate viral population assembly from ultra-deep sequencing data Journal Article

Bioinformatics, 30 (12), pp. i329–i337, 2014.

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Benchmarking Omics Computational Tools

Mitchell, Keith; Mandric, Igor; Martin, Lana S; Pop, Mihai; Mangul, Serghei

Benchmarking of computational error-correction methods for next-generation sequencing via unique molecular identifiers Journal Article

bioRxiv, pp. 642843, 2019.

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Mangul, Serghei; Martin, Lana S; Hill, Brian L; Lam, Angela Ka-Mei; Distler, Margaret G; Zelikovsky, Alex; Eskin, Eleazar; Flint, Jonathan

Systematic benchmarking of omics computational tools Journal Article

Nature Communications, 10 (1393), pp. 1-11, 2019.

Abstract | Links | BibTeX | Altmetric

 

Improving Bioinformatics Software and Databases

Loeffler, Caitlin; Karlsberg, Aaron; Martin, Lana S; Eskin, Eleazar; Koslicki, David; Mangul, Serghei

Analysis of multiple fungal sequence repositories highlights shortcomings in microbial databases Journal Article

bioRxiv, pp. 497867, 2019.

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Mangul, Serghei; Mosqueiro, Thiago; Abdill, Richard J; Duong, Dat; Mitchell, Keith; Sarwal, Varuni; Hill, Brian; Brito, Jaqueline; Littman, Russell Jared; Statz, Benjamin; others,

Challenges and recommendations to improve the installability and archival stability of omics computational tools Journal Article

PLoS Biology, 17 (6), pp. e3000333, 2019.

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Mangul, Serghei; Martin, Lana S; Eskin, Eleazar; Blekhman, Ran

Improving the usability and archival stability of bioinformatics software Journal Article

Genome Biology, 20 (47), pp. 1-3, 2019.

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Expanding Bioinformatics Education

Mangul, Serghei

Interpreting and integrating big data in the life sciences Journal Article

Emerging Topics in Life Sciences, 3 (4), pp. 335–341, 2019.

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Mangul, Serghei; Martin, Lana S; Langmead, Ben; Sanchez-Galan, Javier E; Toma, Ian; Hormozdiari, Fereydoun; Pevzner, Pavel; Eskin, Eleazar

How bioinformatics and open data can boost basic science in countries and universities with limited resources Journal Article

Nature Biotechnology, 37 (3), pp. 324, 2019.

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Mangul, Serghei; Martin, Lana S; Eskin, Eleazar

Involving undergraduates in genomics research to narrow the education--research gap Journal Article

Nature Biotechnology, 36 (4), pp. 369, 2018.

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Mangul, Serghei; Martin, Lana S; Hoffmann, Alexander; Pellegrini, Matteo; Eskin, Eleazar

Addressing the digital divide in contemporary biology: lessons from teaching UNIX Journal Article

Trends in Biotechnology, 35 (10), pp. 901–903, 2017.

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Preprints

These works are available on the open-access preprint server bioRxiv.

He, Yuan; Chhetri, Surya B; Arvanitis, Marios; Srinivasan, Kaushik; c c, Fran; Ardlie, Kristin G; Barbeira, Alvaro N; Bonazzola, Rodrigo; Im, Hae Kyung; and Brown, Christopher D; Battle, Alexis

Mechanisms of tissue-specific genetic regulation revealed by latent factors across eQTLs Journal Article

bioRxiv, 2019.

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de Goede, Olivia M; Ferraro, Nicole M; Nachun, Daniel C; Rao, Abhiram; c c, Fran; Barbeira, Alvaro N; Castel, Stephane E; Kim-Hellmuth, Sarah; Park, YoSon; Scott, Alexandra J; Strober, Benjamin J; and Brown, Christopher D; Wen, Xiaoquan; Hall, Ira M; Battle, Alexis; Lappalainen, Tuuli; Im, Hae Kyung; Ardlie, Kristin G; Quertermous, Thomas; Kirkegaard, Karla; Montgomery, Stephen B

Long non-coding RNA gene regulation and trait associations across human tissues Journal Article

bioRxiv, 2019.

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Ferraro, Nicole M; Strober, Benjamin J; Einson, Jonah; Li, Xin; Aguet, Francois; Barbeira, Alvaro N; Castel, Stephane E; Davis, Joe R; Hilliard, Austin T; Kotis, Bence; Park, YoSon; Scott, Alexandra J; Smail, Craig; Tsang, Emily K; Ardlie, Kristin G; Assimes, Themistocles L; Hall, Ira; Im, Hae Kyung; and Lappalainen, Tuuli; Mohammadi, Pejman; Montgomery, Stephen B; Battle, Alexis

Diverse transcriptomic signatures across human tissues identify functional rare genetic variation Journal Article

bioRxiv, 2019.

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Castel, Stephane E; Aguet, Francois; Mohammadi, Pejman; and Ardlie, Kristin; Lappalainen, Tuuli

A vast resource of allelic expression data spanning human tissues Journal Article

bioRxiv, 2019.

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c c, Fran; Barbeira, Alvaro N; Bonazzola, Rodrigo; Brown, Andrew; Castel, Stephane E; Jo, Brian; Kasela, Silva; Kim-Hellmuth, Sarah; Liang, Yanyu; Oliva, Meritxell; Parsana, Princy E; Flynn, Elise; Fresard, Laure; Gaamzon, Eric R; Hamel, Andrew R; He, Yuan; Hormozdiari, Farhad; Mohammadi, Pejman; ~n, Manuel Mu; Park, YoSon; Saha, Ashis; 'c, Ayellet Segr V; Strober, Benjamin J; Wen, Xiaoquan; Wucher, Valentin; Das, Sayantan; 'i, Diego Garrido-Mart; Gay, Nicole R; Handsaker, Robert E; Hoffman, Paul J; Kashin, Seva; Kwong, Alan; Li, Xiao; MacArthur, Daniel; Rouhana, John M; Stephens, Matthew; Todres, Ellen; ~n, Ana Vi; Wang, Gao; Zou, Yuxin; and Brown, Christopher D; Cox, Nancy; Dermitzakis, Emmanouil; Engelhardt, Barbara E; Getz, Gad; Guigo, Roderic; Montgomery, Stephen B; Stranger, Barbara E; Im, Hae Kyung; Battle, Alexis; Ardlie, Kristin G; Lappalainen, Tuuli

The GTEx Consortium atlas of genetic regulatory effects across human tissues Journal Article

bioRxiv, 2019.

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

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

arXiv, (1909.12469), 2019.

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Loeffler, Caitlin; Karlsberg, Aaron; Martin, Lana S; Eskin, Eleazar; Koslicki, David; Mangul, Serghei

Analysis of multiple fungal sequence repositories highlights shortcomings in microbial databases Journal Article

bioRxiv, pp. 497867, 2019.

Links | BibTeX | Altmetric

Mitchell, Keith; Mandric, Igor; Martin, Lana S; Pop, Mihai; Mangul, Serghei

Benchmarking of computational error-correction methods for next-generation sequencing via unique molecular identifiers Journal Article

bioRxiv, pp. 642843, 2019.

Links | BibTeX | Altmetric

Mitchell, Keith; Dao, Chris; Freise, Amanda; Mangul, Serghei; Parker, Jordan Moberg

PUMA: A tool for processing 16S rRNA taxonomy data for analysis and visualization Journal Article

bioRxiv, pp. 482380, 2018.

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Bhat, Suraj; Gangalum, Rajendra K; Kim, Dongjae; Mangul, Serghei; Kashyap, Raj K; Xinxai, Zhou; Elashoff, David

Single Cell Heterogeneity is Absent in the Transgenic Paradigm of an Inherited Cataract Journal Article

Available at SSRN 3244893, 2018.

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Mangul, Serghei; Driesche, Sarah Van; Martin, Lana S; Martin, Kelsey C; Eskin, Eleazar

UMI-Reducer: Collapsing duplicate sequencing reads via Unique Molecular Identifiers Journal Article

bioRxiv, pp. 103267, 2017.

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All Publications

Find us on Google Scholar or Pubmed.

Lees, William; Busse, Christian E; Corcoran, Martin; Ohlin, Mats; Scheepers, Cathrine; A, IV Matsen Frederick; Yaari, Gur; Watson, Corey T; Community, The AIRR; Collins, Andrew; Shepherd, Adrian J

OGRDB: a reference database of inferred immune receptor genes Journal Article

Nucleic Acids Research, 2019, ISSN: 0305-1048, (gkz822).

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Bhat, Suraj P; Gangalum, Rajendra K; Kim, Dongjae; Mangul, Serghei; Kashyap, Raj K; Zhou, Xinkai; Elashoff, David

Transcriptional profiling of single fiber cells in a transgenic paradigm of an inherited childhood cataract reveals absence of molecular heterogeneity Journal Article

Journal of Biological Chemistry, 294 , pp. 13530-13544, 2019.

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Mangul, Serghei

Interpreting and integrating big data in the life sciences Journal Article

Emerging Topics in Life Sciences, 3 (4), pp. 335–341, 2019.

Links | BibTeX | Altmetric

Mangul, Serghei; Mosqueiro, Thiago; Abdill, Richard J; Duong, Dat; Mitchell, Keith; Sarwal, Varuni; Hill, Brian; Brito, Jaqueline; Littman, Russell Jared; Statz, Benjamin; others,

Challenges and recommendations to improve the installability and archival stability of omics computational tools Journal Article

PLoS Biology, 17 (6), pp. e3000333, 2019.

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LaPierre, Nathan; Mangul, Serghei; Alser, Mohammed; Mandric, Igor; Wu, Nicholas C; Koslicki, David; Eskin, Eleazar

MiCoP: microbial community profiling method for detecting viral and fungal organisms in metagenomic samples Journal Article

BMC Genomics, 20 (5), pp. 423, 2019.

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Mangul, Serghei; Martin, Lana S; Hill, Brian L; Lam, Angela Ka-Mei; Distler, Margaret G; Zelikovsky, Alex; Eskin, Eleazar; Flint, Jonathan

Systematic benchmarking of omics computational tools Journal Article

Nature Communications, 10 (1393), pp. 1-11, 2019.

Abstract | Links | BibTeX | Altmetric

Mangul, Serghei; Martin, Lana S; Langmead, Ben; Sanchez-Galan, Javier E; Toma, Ian; Hormozdiari, Fereydoun; Pevzner, Pavel; Eskin, Eleazar

How bioinformatics and open data can boost basic science in countries and universities with limited resources Journal Article

Nature Biotechnology, 37 (3), pp. 324, 2019.

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Mangul, Serghei; Yang, Harry Taegyun; Eskin, Eleazar; Zaitlen, Noah

Hidden Treasures in Contemporary RNA Sequencing Book Chapter

Hidden Treasures in Contemporary RNA Sequencing. SpringerBriefs in Computer Science., pp. 1–93, Springer, 2019.

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Mangul, Serghei; Martin, Lana S; Eskin, Eleazar; Blekhman, Ran

Improving the usability and archival stability of bioinformatics software Journal Article

Genome Biology, 20 (47), pp. 1-3, 2019.

Abstract | Links | BibTeX | Altmetric

Mangul, Serghei; Mandric, Igor; Yang, Harry Taegyun; Strauli, Nicolas; Montoya, Dennis; Rotman, Jeremy; Wey, Will Van Der; Ronas, Jiem R; Statz, Benjamin; Zelikovsky, Alex; others,

Profiling adaptive immune repertoires across multiple human tissues by RNA Sequencing Journal Article Forthcoming

Nature Communications (accepted), Forthcoming.

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Bhat, Suraj P; Gangalum, Rajendra K; Kim, Dongjae; Mangul, Serghei; Kashyap, Raj K; Zhou, Xinkai; Elashoff, David

Absence of Single Cell Transcriptional Heterogeneity in the transgenic paradigm of the inherited Lamellar cataract Journal Article

Investigative Ophthalmology & Visual Science, 60 (9), pp. 1381–1381, 2019.

BibTeX

Gangalum, Rajendra K; Kim, Dongjae; Kashyap, Raj K; Mangul, Serghei; Zhou, Xinkai; Elashoff, David; Bhat, Suraj P

Spatial Analysis of Single Fiber Cells of the Developing Ocular Lens Reveals Regulated Heterogeneity of Gene Expression Journal Article

iScience, 10 , pp. 66–79, 2018.

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Heiden, Jason Anthony Vander; Marquez, Susanna; Marthandan, Nishanth; Bukhari, Syed Ahmad Chan; Busse, Christian E; Corrie, Brian; Hershberg, Uri; Kleinstein, Steven H; IV, Frederick Matsen A; Ralph, Duncan K; others,

AIRR Community Standardized Representations for Annotated Immune Repertoires Journal Article

Frontiers in Immunology, 9 , pp. 2206, 2018.

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Chiang, Charleston WK; Mangul, Serghei; Robles, Christopher; Sankararaman, Sriram

A comprehensive map of genetic variation in the world’s largest ethnic group—Han Chinese Journal Article

Molecular Biology and Evolution, 35 (11), pp. 2736–2750, 2018.

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Loohuis, Loes Olde M; Mangul, Serghei; Ori, Anil PS; Jospin, Guillaume; Koslicki, David; Yang, Harry Taegyun; Wu, Timothy; Boks, Marco P; Lomen-Hoerth, Catherine; Wiedau-Pazos, Martina; others,

Transcriptome analysis in whole blood reveals increased microbial diversity in schizophrenia Journal Article

Translational Psychiatry, 8 (1), pp. 96, 2018.

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Mangul, Serghei; Martin, Lana S; Eskin, Eleazar

Involving undergraduates in genomics research to narrow the education--research gap Journal Article

Nature Biotechnology, 36 (4), pp. 369, 2018.

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Mangul, Serghei; Yang, Harry Taegyun; Strauli, Nicolas; Gruhl, Franziska; Porath, Hagit T; Hsieh, Kevin; Chen, Linus; Daley, Timothy; Christenson, Stephanie; Wesolowska-Andersen, Agata; others,

ROP: dumpster diving in RNA-sequencing to find the source of 1 trillion reads across diverse adult human tissues Journal Article

Genome Biology, 19 (1), pp. 36, 2018.

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Consortium, GTEx; others,

Genetic effects on gene expression across human tissues Journal Article

Nature, 550 (7675), pp. 204, 2017.

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Tan, Meng How; Li, Qin; Shanmugam, Raghuvaran; Piskol, Robert; Kohler, Jennefer; Young, Amy N; Liu, Kaiwen Ivy; Zhang, Rui; Ramaswami, Gokul; Ariyoshi, Kentaro; others,

Dynamic landscape and regulation of RNA editing in mammals Journal Article

Nature, 550 (7675), pp. 249, 2017.

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Saha, Ashis; Kim, Yungil; Gewirtz, Ariel DH; Jo, Brian; Gao, Chuan; McDowell, Ian C; Engelhardt, Barbara E; Battle, Alexis; ç, Fran; Ardlie, Kristin G; others,

Co-expression networks reveal the tissue-specific regulation of transcription and splicing Journal Article

Genome Research, 27 (11), pp. 1843–1858, 2017.

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Mangul, Serghei; Martin, Lana S; Hoffmann, Alexander; Pellegrini, Matteo; Eskin, Eleazar

Addressing the digital divide in contemporary biology: lessons from teaching UNIX Journal Article

Trends in Biotechnology, 35 (10), pp. 901–903, 2017.

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

Long single-molecule reads can resolve the complexity of the influenza virus composed of rare, closely related mutant variants Journal Article

Journal of Computational Biology, 24 (6), pp. 558–570, 2017.

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Barbeira, Alvaro N; Dickinson, Scott P; Bonazzola, Rodrigo; Zheng, Jiamao; Wheeler, Heather E; Torres, Jason M; Torstenson, Eric S; Shah, Kaanan P; Garcia, Tzintzuni; Edwards, Todd L; others,

Exploring the phenotypic consequences of tissue specific gene expression variation inferred from GWAS summary statistics Journal Article

Nature Communications, 9 (1), pp. 1825, 2017.

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Yang, Fan; Wang, Jiebiao; Pierce, Brandon L; Chen, Lin S; ç, Fran; Ardlie, Kristin G; Cummings, Beryl B; Gelfand, Ellen T; Getz, Gad; Hadley, Kane; others,

Identifying cis-mediators for trans-eQTLs across many human tissues using genomic mediation analysis Journal Article

Genome Research, 27 (11), pp. 1859–1871, 2017.

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Mangul, Serghei; Yang, Taegyun Harry; Hormozdiari, Farhad; Dainis, Alexandra Marie; Tseng, Elizabeth; Ashley, Euan A; Zelikovsky, Alex; Eskin, Eleazar

HapIso: an accurate method for the haplotype-specific isoforms reconstruction from long single-molecule reads Journal Article

IEEE Transactions on Nanobioscience, 16 (2), pp. 108–115, 2017.

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Thomas, B; Karimzada, M; Spreafico, R; Mangul, S; Botten, G; Rothman, J; Wesel, K; Binder, S; Gharavi, N; Chesnut, C; others,

104 Lack of human papilloma virus transcription in cutaneous squamous cell carcinoma stratified by histological grade and host immune status Journal Article

Journal of Investigative Dermatology, 137 (5), pp. S18, 2017.

BibTeX

Kang, Eun Yong; Martin, Lisa J; Mangul, Serghei; Isvilanonda, Warin; Zou, Jennifer; Ben-David, Eyal; Han, Buhm; Lusis, Aldons J; Shifman, Sagiv; Eskin, Eleazar

Discovering single nucleotide polymorphisms regulating human gene expression using allele specific expression from RNA-seq data Journal Article

Genetics, 204 (3), pp. 1057–1064, 2016.

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Mangul, Serghei; Koslicki, David

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

Proceedings of the 7th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics, pp. 68-77, ACM 2016.

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Mangul, Serghei; Wu, Nicholas C; Nenastyeva, Ekaterina; Mancuso, Nicholas; Zelikovsky, Alexander; Sun, Ren; Eskin, Eleazar

Applications of High‐Fidelity Sequencing Protocol to RNA Viruses Journal Article

Computational Methods for Next Generation Sequencing Data Analysis, pp. 85-104, 2016.

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Glebova, Olga; Temate-Tiagueu, Yvette; Caciula, Adrian; Seesi, Sahar Al; Artyomenko, Alexander; Mangul, Serghei; Lindsay, James; ă, Ion I M; Zelikovsky, Alexander

Transcriptome Quantification and Differential Expression from NGS Data Journal Article

Computational Methods for Next Generation Sequencing Data Analysis, pp. 301-327, 2016.

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Schokrpur, Shiruyeh; Hu, Junhui; Moughon, Diana L; Liu, Peijun; Lin, Lucia C; Hermann, Kip; Mangul, Serghei; Guan, Wei; Pellegrini, Matteo; Xu, Hua; others,

CRISPR-mediated VHL knockout generates an improved model for metastatic renal cell carcinoma Journal Article

Scientific Reports, 6 , pp. 29032, 2016.

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

VGA: a method for viral quasispecies assembly from ultra-deep sequencing data Inproceedings

2014 IEEE 4th International Conference on Computational Advances in Bio and Medical Sciences (ICCABS), pp. 1–1, IEEE 2014.

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Mangul, Serghei; Caciula, Adrian; Seesi, Sahar Al; Brinza, Dumitru; Mӑndoiu, Ion; Zelikovsky, Alex

Transcriptome assembly and quantification from Ion Torrent RNA-Seq data Journal Article

BMC Genomics, 15 (5), pp. S7, 2014.

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

Accurate viral population assembly from ultra-deep sequencing data Journal Article

Bioinformatics, 30 (12), pp. i329–i337, 2014.

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Mangul, Serghei; Caciula, Adrian; Glebova, Olga; Mandoiu, Ion; Zelikovsky, Alex

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

In Silico Biology, 11 (5, 6), pp. 251–261, 2011.

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Astrovskaya, Irina; Tork, Bassam; Mangul, Serghei; Westbrooks, Kelly; ă, Ion M; Balfe, Peter; Zelikovsky, Alex

Inferring viral quasispecies spectra from 454 pyrosequencing reads Inproceedings

BMC Bioinformatics, pp. S1, BioMed Central 2011.

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Nicolae, Marius; Mangul, Serghei; ă, Ion I M; Zelikovsky, Alex

Estimation of alternative splicing isoform frequencies from RNA-Seq data Journal Article

Algorithms for Molecular Biology, 6 (1), pp. 9, 2011.

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