Representative publications

Developing Bioinformatics Methods

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

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.

Abstract | Links | BibTeX | Altmetric

Mangul, Serghei; Mandric, Igor; Yang, Harry Taegyun; Strauli, Nicolas; Montoya, Dennis; Rotman, Jeremy; der Lay, Will Van; Ronas, Jiem R; Statz, Benjamin; Yao, Douglas; Zelikovsky, Alex; Spreafico, Roberto; Shifman, Sagiv; Zaitlen, Noah; Rossetti, Maura; Ansel, Mark K; Eskin, Eleazar

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

Nature Communications, Forthcoming.

Abstract | Links | BibTeX | Altmetric

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.

Abstract | Links | BibTeX | Altmetric

Benchmarking Omics Computational Tools

Mitchell, Keith; Brito, Jaqueline J; Mandric, Igor; Wu, Qiaozhen; Knyazev, Sergey; Chang, Sei; Martin, Lana S; Karlsberg, Aaron; Gerasimov, Ekaterina; Littman, Russell Jared; Hill, Brian L; Wu, Nicholas C; Yang, Harry Taegyun; Hsieh, Kevin; Chen, Linus; Littman, Eli; Shabani, Taylor; Shabanets, German; Yao, Douglas; Sun, Ren; Schroeder, Jan; Eskin, Eleazar; Zelikovsky, Alex; Skums, Pavel; Pop, Mihai; Mangul, Serghei

Benchmarking of computational error-correction methods for next-generation sequencing data Journal Article

Genome Biology, 21 (71), 2020.

Abstract | Links | BibTeX | Altmetric

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

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

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

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

Abstract | Links | BibTeX | Altmetric

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

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

Improving the usability and comprehensiveness of microbial databases Journal Article Forthcoming

BMC Biology, Forthcoming.

Abstract | Links | BibTeX | Altmetric

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.

Abstract | Links | BibTeX | Altmetric

Mangul, Serghei; Martin, Lana S; Langmead, Ben; Sanchez-Galan, Javier E; Toma, Ian V; 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.

Abstract | Links | BibTeX | Altmetric

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.

Abstract | Links | BibTeX | Altmetric

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.

Abstract | Links | BibTeX | Altmetric

Preprints

These works are available on open-access preprint servers, such as bioRxiv and aRxiv.

Alser, Mohammed; Rotman, Jeremy; Taraszka, Kodi; Shi, Huwenbo; Baykal, Pelin Icer; Yang, Harry Taegyun; Xue, Victor; Knyazev, Sergey; Singer, Benjamin D; Balliu, Brunilda; Koslicki, David; Pavel Skums, Alex Zelikovsky ; Alkan, Can; Mutlu, Onur; Mangul, Serghei

Technology dictates algorithms: Recent developments in read alignment Journal Article

arXiv, 2020.

Abstract | Links | BibTeX | Altmetric

Johnson, Ruth; Mangul, Serghei

Refining the conference experience for junior scientists in the wake of climate change Journal Article

arXiv, 2020.

Abstract | Links | BibTeX

LaPierre, Nathan; Alser, Mohammed; Eskin, Eleazar; Koslicki, David; Mangul, Serghei

Metalign: Efficient alignment-based metagenomic profiling via containment min hash Journal Article

bioRxiv, 2020.

Abstract | Links | BibTeX | Altmetric

Brito, Jaqueline J; Li, Jun; Moore, Jason H; Greene, Casey S; Nogoy, Nicole A; Garmire, Lana X; Mangul, Serghei

Enhancing rigor and reproducibility by improving software availability, usability, and archival stability Journal Article

arXiv, 2020.

Abstract | Links | BibTeX | Altmetric

Loeffler, Caitlin; Gibson, Keylie M; Martin, Lana S; Chang, Yutong; Rotman, Jeremy; Toma, Ian V; Mason, Christopher E; Eskin, Eleazar; Zackular, Joseph P; Crandall, Keith A; Koslicki, David; Mangul, Serghei

Unlocking the diagnostic and therapeutic potential of metagenomics Journal Article

arXiv, 2019.

Abstract | Links | BibTeX | Altmetric

Oliva, Meritxell; Muñoz-Aguirre, Manuel; Kim-Hellmuth, Sarah; Wucher, Valentin; Gewirtz, Ariel DH; Cotter, Daniel J; Parsana, Princy; Kasela, Silva; Balliu, Brunilda; Viñuela, Ana; Castel, Stephane E; Mohammadi, Pejman; ç, Fran; Zou, Yuxin; Khramtsova, Ekaterina A; Skol, Andrew D; Garrido-Martín, Diego; Reverter, Ferran; Brown, Andrew; Evans, Patrick; Gamazon, Eric R; Payne, Anthony; Bonazzola, Rodrigo; Barbeira, Alvaro N; Hamel, Andrew R; Martinez-Perez, Angel; Soria, José Manuel; Consortium, The GTEx; Pierce, Brandon L; Stephens, Matthew; Eskin, Eleazar; Dermitzakis, Emmanouil T; Segrè, Ayellet V; Im, Hae Kyung; Engelhardt, Barbara E; Ardlie, Kristin G; Montgomery, Stephen B; Battle, Alexis; Lappalainen, Tuuli; Guigó, Roderic; Stranger, Barbara E

The impact of sex on gene expression and its genetic regulation across human tissues Journal Article

2019.

Abstract | BibTeX

Pividori, Milton D; Rajagopal, Padma S; Barbeira, Alvaro N; Liang, Yanyu; Melia, Owen; Bastarache, Lisa; Park, YoSon; Consortium, The GTEx; Wen, Xiaoquan; Im, Hae Kyung

PhenomeXcan: Mapping the genome to the phenome through the transcriptome Journal Article

bioRxiv, 2019.

Abstract | Links | BibTeX | Altmetric

Barbeira, Alvaro N; Bonazzola, Rodrigo; Gamazon, Eric R; Liang, Yanyu; Park, YoSon; Kim-Hellmuth, Sarah; Wang, Gao; Jiang, Zhuoxun; Zhou, Dan; Hormozdiari, Farhad; Liu, Boxiang; Rao, Abhiram; Hamel, Andrew R; Pividori, Milton D; ç, Fran; Group, The GTEx GWAS Working; Bastarache, Lisa; Jordan, Daniel M; Verbanck, Marie; Do, Ron; Consortium, The GTEx; Stephens, Matthew; Ardlie, Kristin G; McCarthy, Mark; Montgomery, Stephen B; Segrè, Ayellet V; Brown, Christopher D; Lappalainen, Tuuli; Wen, Xiaoquan; Im, Hae Kyung

Widespread dose-dependent effects of RNA expression and splicing on complex diseases and traits Journal Article

bioRxiv, 2019.

Abstract | Links | BibTeX | Altmetric

Chen, Yuhua; Quick, Corbin; Yu, Ketian; Barbeira, Alvaro N; Luca, Francesca; Pique-Regi, Roger; Im, Hae Kyung; Wen, Xiaoquan; Consortium, The GTEx

Investigating tissue-relevant causal molecular mechanisms of complex traits using probabilistic TWAS analysis Journal Article

bioRxiv, pp. 808295, 2019.

Abstract | Links | BibTeX | Altmetric

Kim-Hellmuth, Sarah; ç, Fran; Oliva, Meritxell; Munoz-Aguirre, Manuel; Wucher, Valentin; Kasela, Silva; Castel, Stephane E; Hamel, Andrew R; Vinuela, Ana; Roberts, Amy L

Cell type specific genetic regulation of gene expression across human tissues Journal Article

bioRxiv, pp. 806117, 2019.

Abstract | Links | BibTeX | Altmetric

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

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

bioRxiv, 2019.

Abstract | Links | BibTeX | Altmetric

de Goede, Olivia M; Ferraro, Nicole M; Nachun, Daniel C; Rao, Abhiram; ç, Fran; Barbeira, Alvaro N; Castel, Stephane E; Kim-Hellmuth, Sarah; Park, YoSon; Scott, Alexandra J; Strober, Benjamin J; Consortium, The GTEx; 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.

Abstract | Links | BibTeX | Altmetric

Ferraro, Nicole M; Strober, Benjamin J; Einson, Jonah; Li, Xin; ç, Fran; 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 M; Im, Hae Kyung; Consortium, The GTEx; Lappalainen, Tuuli; Mohammadi, Pejman; Montgomery, Stephen B; Battle, Alexis

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

bioRxiv, 2019.

Abstract | Links | BibTeX | Altmetric

ç, 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; Gamazon, Eric R; Hamel, Andrew R; He, Yuan; Hormozdiari, Farhad; Mohammadi, Pejman; Muñoz-Aguirre, Manuel; Park, YoSon; Saha, Ashis; Segrè, Ayellet V; Strober, Benjamin J; Wen, Xiaoquan; Wucher, Valentin; Das, Sayantan; Garrido-Martín, Diego; Gay, Nicole R; Handsaker, Robert E; Hoffman, Paul J; Kashin, Seva; Kwong, Alan; Li, Xiao; MacArthur, Daniel; Rouhana, John M; Stephens, Matthew; Todres, Ellen; Viñuela, Ana; Wang, Gao; Zou, Yuxin; Consortium, The GTEx; Brown, Christopher D; Cox, Nancy; Dermitzakis, Emmanouil T; 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.

Abstract | Links | BibTeX | Altmetric

Castel, Stephane E; ç, Fran; Mohammadi, Pejman; Ardlie, Kristin G; Lappalainen, Tuuli; Consortium, The GTEx

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

bioRxiv, pp. 792911, 2019.

Abstract | 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.

Abstract | Links | BibTeX | Altmetric

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, 2017.

Abstract | Links | BibTeX | Altmetric

All publications

Find us on Google Scholar or Pubmed.

Mitchell, Keith; Brito, Jaqueline J; Mandric, Igor; Wu, Qiaozhen; Knyazev, Sergey; Chang, Sei; Martin, Lana S; Karlsberg, Aaron; Gerasimov, Ekaterina; Littman, Russell Jared; Hill, Brian L; Wu, Nicholas C; Yang, Harry Taegyun; Hsieh, Kevin; Chen, Linus; Littman, Eli; Shabani, Taylor; Shabanets, German; Yao, Douglas; Sun, Ren; Schroeder, Jan; Eskin, Eleazar; Zelikovsky, Alex; Skums, Pavel; Pop, Mihai; Mangul, Serghei

Benchmarking of computational error-correction methods for next-generation sequencing data Journal Article

Genome Biology, 21 (71), 2020.

Abstract | Links | BibTeX | Altmetric

Brito, Jaqueline J; Mosqueiro, Thiago; Rotman, Jeremy; Xue, Victor; Chapski, Douglas J; la Hoz, Juan De; Matias, Paulo; Martin, Lana S; Zelikovsky, Alex; Pellegrini, Matteo; Mangul, Serghei

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

GigaScience, 9 (1), pp. giz163, 2020.

Abstract | Links | BibTeX | Altmetric

Lees, William; Busse, Christian E; Corcoran, Martin; Ohlin, Mats; Scheepers, Cathrine; IV, Frederick Matsen A; 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, 48 (D1), pp. D964–D970, 2019, ISSN: 0305-1048.

Abstract | Links | BibTeX | Altmetric

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.

Abstract | Links | BibTeX | Altmetric

Mangul, Serghei

Interpreting and integrating big data in the life sciences Journal Article

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

Abstract | Links | BibTeX | Altmetric

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

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

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

Abstract | Links | BibTeX | Altmetric

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.

Abstract | Links | BibTeX | Altmetric

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 V; 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.

Abstract | Links | BibTeX | Altmetric

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.

Abstract | Links | BibTeX | Altmetric

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; der Lay, Will Van; Ronas, Jiem R; Statz, Benjamin; Yao, Douglas; Zelikovsky, Alex; Spreafico, Roberto; Shifman, Sagiv; Zaitlen, Noah; Rossetti, Maura; Ansel, Mark K; Eskin, Eleazar

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

Nature Communications, Forthcoming.

Abstract | Links | BibTeX | Altmetric

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.

Abstract | 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.

Abstract | Links | BibTeX | Altmetric

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; Rosenfeld, Aaron M; Schramm, Chaim A; Community, The AIRR; Christley, Scott; Laserson, Uri

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

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

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

Abstract | Links | BibTeX | Altmetric

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.

Abstract | Links | BibTeX | Altmetric

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

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.

Abstract | Links | BibTeX | Altmetric

Consortium, The GTEx

Genetic effects on gene expression across human tissues Journal Article

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

Abstract | Links | BibTeX | Altmetric

Tan, Meng How; Li, Qin; Shanmugam, Raghuvaran; Piskol, Robert; Kohler, Jennefer; Young, Amy N; Liu, Kaiwen Ivy; Zhang, Rui; Ramaswami, Gokul; Ariyoshi, Kentaro; Gupte, Ankita; Keegan, Liam P; George, Cyril X; Ramu, Avinash; Huang, Ni; Pollina, Elizabeth A; Leeman, Dena S; Rustighi, Alessandra; Goh, YP Sharon; Consortium, The GTEx; Chawla, Ajay; Sal, Giannino Del; Peltz, Gary; Brunet, Anne; Conrad, Donald F; Samuel, Charles E; O’Connell, Mary A; Walkley, Carl R; Nishikura, Kazuko; Li, Jin Billy

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; Consortium, The GTEx; Engelhardt, Barbara E; Battle, Alexis

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.

Abstract | Links | BibTeX | Altmetric

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; Stahl, Eli A; Huckins, Laura M; Consortium, The GTEx; Nicolae, Dan L; Cox, Nancy J; Im, Hae Kyung

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; Consortium, The GTEx; Pierce, Brandon L; Chen, Lin S

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, Harry Taegyun; 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, Brandon; Karimzada, Mohammed; Spreafico, Roberto; Mangul, Serghei; Botten, Jason W; Rotman, Jeremy; Wesel, Kevin; Binder, Pratibha S; Gharavi, Nima; Chesnut, Robert W

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.

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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

Bioinformatics, Computational Biology and Biomedicine 2016: Proceedings of the 7th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics, pp. 68-77, Association for Computing Machinery 2016.

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

Applications of High‐Fidelity Sequencing Protocol to RNA Viruses Book Chapter

Mӑndoiu, Ion I; Zelikovsky, Alex (Ed.): Computational Methods for Next Generation Sequencing Data Analysis, pp. 85-104, Wiley Online Library, 2016.

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

Transcriptome Quantification and Differential Expression from NGS Data Book Chapter

Mӑndoiu, Ion I; Zelikovsky, Alex (Ed.): Computational Methods for Next Generation Sequencing Data Analysis, pp. 301-327, Wiley Online Library, 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

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

Scientific Reports, 6 (29032), 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 I; 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; Mӑndoiu, Ion I; 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; Mӑndoiu, Ion I; 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; Mӑndoiu, Ion I; 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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Loeffler, Caitlin; Karlsberg, Aaron; Martin, Lana S; Eskin, Eleazar; Koslicki, David; Mangul, Serghei

Improving the usability and comprehensiveness of microbial databases Journal Article Forthcoming

BMC Biology, Forthcoming.

Abstract | Links | BibTeX | Altmetric