Research

2021

Virtual meetings promise to eliminate the geographical and administrative barriers and increase accessibility, diversity, and inclusivity

Juncheng Wu, Anushka Rajesh, Yu-Ning Huang, Karishma Chhugani, Rajesh Acharya, Kerui Peng, Ruth D. Johnson, Andrada Fiscutean, Carla Daniela Robles-Espinoza, Francisco M. De La Vega, Riyue Bao, Serghei Mangul

Cold Spring Harbor Laboratory  ·  08 Jul 2021

Accurate assembly of minority viral haplotypes from next-generation sequencing through efficient noise reduction

Sergey Knyazev, Viachaslau Tsyvina, Anupama Shankar, Andrew Melnyk, Alexander Artyomenko, Tatiana Malygina, Yuri B Porozov, Ellsworth M Campbell, William M Switzer, Pavel Skums, Serghei Mangul, Alex Zelikovsky

Nucleic Acids Research  ·  02 Jul 2021

Dietary Supplements and Nutraceuticals under Investigation for COVID-19 Prevention and Treatment

Ronan Lordan, Halie M. Rando, Casey S. Greene,

mSystems  ·  29 Jun 2021

Unlocking capacities of viral genomics for the COVID-19 pandemic response

Sergey Knyazev, Karishma Chhugani, Varuni Sarwal, Ram Ayyala, Harman Singh, Smruthi Karthikeyan, Dhrithi Deshpande, Zoia Comarova, Angela Lu, Yuri Porozov, Aiping Wu, Malak Abedalthagafi, Shivashankar Nagaraj, Adam Smith, Pavel Skums, Jason Ladner, Tommy Tsan-Yuk Lam, Nicholas Wu, Alex Zelikovsky, Rob Knight, Keith Crandall, Serghei Mangul

arXiv:2104.14005 [q-bio]  ·  04 Jun 2021

Seeing beyond the target: Leveraging off-target reads in targeted clinical tumor sequencing to identify prognostic biomarkers

Serghei Mangul, Jaqueline J Brito, Stefan Groha, Noah Zaitlen, Alexander Gusev

Cold Spring Harbor Laboratory  ·  29 May 2021

Rare loss-of-function variants in type I IFN immunity genes are not associated with severe COVID-19

Gundula Povysil, Guillaume Butler-Laporte, Ning Shang, Chen Wang, Atlas Khan, Manal Alaamery, Tomoko Nakanishi, Sirui Zhou, Vincenzo Forgetta, Robert J. M. Eveleigh, Mathieu Bourgey, Naveed Aziz, Steven J.M. Jones, Bartha Knoppers, Stephen W. Scherer, Lisa J. Strug, Pierre Lepage, Jiannis Ragoussis, Guillaume Bourque, Jahad Alghamdi, Nora Aljawini, Nour Albesher, Hani M. Al-Afghani, Bader Alghamdi, Mansour S. Almutair, Ebrahim Sabri Mahmoud, Leen Abu-Safieh, Hadeel El Bardisy, Fawz S. Al Harthi, Abdulraheem Alshareef, Bandar Ali Suliman, Saleh A. Alqahtani, Abdulaziz Almalik, May M. Alrashed, Salam Massadeh, Vincent Mooser, Mark Lathrop, Mohamed Fawzy, Yaseen M. Arabi, Hamdi Mbarek, Chadi Saad, Wadha Al-Muftah, Junghyun Jung, Serghei Mangul, Radja Badji, Asma Al Thani, Said I. Ismail, Ali G. Gharavi, Malak S. Abedalthagafi, J Brent Richards, David B. Goldstein, Krzysztof Kiryluk

Journal of Clinical Investigation  ·  27 May 2021

Detection of viral gene expression in risk‐stratified biopsies reveals no active HPV in cutaneous squamous cell carcinoma

Amy R. Vandiver, Brandon J. Thomas, Mohammad Karimzada, Byron C. Knowles, Giovanni A. Botten, Roberto Spreafico, Jeremy N. Rotman, Nima M Gharavi, Cameron Chesnut, Kevin Wesel, Serghei Mangul, Teresa Soriano, Philip O. Scumpia

Experimental Dermatology  ·  25 May 2021

Diversity in immunogenomics: the value and the challenge

Kerui Peng, Yana Safonova, Mikhail Shugay, Alice B. Popejoy, Oscar L. Rodriguez, Felix Breden, Petter Brodin, Amanda M. Burkhardt, Carlos Bustamante, Van-Mai Cao-Lormeau, Martin M. Corcoran, Darragh Duffy, Macarena Fuentes-Guajardo, Ricardo Fujita, Victor Greiff, Vanessa D. Jönsson, Xiao Liu, Lluis Quintana-Murci, Maura Rossetti, Jianming Xie, Gur Yaari, Wei Zhang, Malak S. Abedalthagafi, Khalid O. Adekoya, Rahaman A. Ahmed, Wei-Chiao Chang, Clive Gray, Yusuke Nakamura, William D. Lees, Purvesh Khatri, Houda Alachkar, Cathrine Scheepers, Corey T. Watson, Gunilla B. Karlsson Hedestam, Serghei Mangul

Nature Methods  ·  17 May 2021

Population-scale tissue transcriptomics maps long non-coding RNAs to complex disease

Olivia M. de Goede, Daniel C. Nachun, Nicole M. Ferraro, Michael J. Gloudemans, Abhiram S. Rao, Craig Smail, Tiffany Y. Eulalio, François Aguet, Bernard Ng, Jishu Xu, Alvaro N. Barbeira, Stephane E. Castel, Sarah Kim-Hellmuth, YoSon Park, Alexandra J. Scott, Benjamin J. Strober, Christopher D. Brown, Xiaoquan Wen, Ira M. Hall, Alexis Battle, Tuuli Lappalainen, Hae Kyung Im, Kristin G. Ardlie, Sara Mostafavi, Thomas Quertermous, Karla Kirkegaard, Stephen B. Montgomery, Shankara Anand, Stacey Gabriel, Gad A. Getz, Aaron Graubert, Kane Hadley, Robert E. Handsaker, Katherine H. Huang, Xiao Li, Daniel G. MacArthur, Samuel R. Meier, Jared L. Nedzel, Duyen T. Nguyen, Ayellet V. Segrè, Ellen Todres, Brunilda Balliu, Rodrigo Bonazzola, Andrew Brown, Donald F. Conrad, Daniel J. Cotter, Nancy Cox, Sayantan Das, Emmanouil T. Dermitzakis, Jonah Einson, Barbara E. Engelhardt, Eleazar Eskin, Elise D. Flynn, Laure Fresard, Eric R. Gamazon, Diego Garrido-Martín, Nicole R. Gay, Roderic Guigó, Andrew R. Hamel, Yuan He, Paul J. Hoffman, Farhad Hormozdiari, Lei Hou, Brian Jo, Silva Kasela, Seva Kashin, Manolis Kellis, Alan Kwong, Xin Li, Yanyu Liang, Serghei Mangul, Pejman Mohammadi, Manuel Muñoz-Aguirre, Andrew B. Nobel, Meritxell Oliva, Yongjin Park, Princy Parsana, Ferran Reverter, John M. Rouhana, Chiara Sabatti, Ashis Saha, Matthew Stephens, Barbara E. Stranger, Nicole A. Teran, Ana Viñuela, Gao Wang, Fred Wright, Valentin Wucher, Yuxin Zou, Pedro G. Ferreira, Gen Li, Marta Melé, Esti Yeger-Lotem, Debra Bradbury, Tanya Krubit, Jeffrey A. McLean, Liqun Qi, Karna Robinson, Nancy V. Roche, Anna M. Smith, David E. Tabor, Anita Undale, Jason Bridge, Lori E. Brigham, Barbara A. Foster, Bryan M. Gillard, Richard Hasz, Marcus Hunter, Christopher Johns, Mark Johnson, Ellen Karasik, Gene Kopen, William F. Leinweber, Alisa McDonald, Michael T. Moser, Kevin Myer, Kimberley D. Ramsey, Brian Roe, Saboor Shad, Jeffrey A. Thomas, Gary Walters, Michael Washington, Joseph Wheeler, Scott D. Jewell, Daniel C. Rohrer, Dana R. Valley, David A. Davis, Deborah C. Mash, Mary E. Barcus, Philip A. Branton, Leslie Sobin, Laura K. Barker, Heather M. Gardiner, Maghboeba Mosavel, Laura A. Siminoff, Paul Flicek, Maximilian Haeussler, Thomas Juettemann, W. James Kent, Christopher M. Lee, Conner C. Powell, Kate R. Rosenbloom, Magali Ruffier, Dan Sheppard, Kieron Taylor, Stephen J. Trevanion, Daniel R. Zerbino, Nathan S. Abell, Joshua Akey, Lin Chen, Kathryn Demanelis, Jennifer A. Doherty, Andrew P. Feinberg, Kasper D. Hansen, Peter F. Hickey, Farzana Jasmine, Lihua Jiang, Rajinder Kaul, Muhammad G. Kibriya, Jin Billy Li, Qin Li, Shin Lin, Sandra E. Linder, Brandon L. Pierce, Lindsay F. Rizzardi, Andrew D. Skol, Kevin S. Smith, Michael Snyder, John Stamatoyannopoulos, Hua Tang, Meng Wang, Latarsha J. Carithers, Ping Guan, Susan E. Koester, A. Roger Little, Helen M. Moore, Concepcion R. Nierras, Abhi K. Rao, Jimmie B. Vaught, Simona Volpi

Cell  ·  01 May 2021

Improving the completeness of public metadata accompanying omics studies

Anushka Rajesh, Yutong Chang, Malak S. Abedalthagafi, Annie Wong-Beringer, Michael I. Love, Serghei Mangul

Genome Biology  ·  15 Apr 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

Cold Spring Harbor Laboratory  ·  10 Mar 2021

Identification and Development of Therapeutics for COVID-19

Halie M. Rando, Nils Wellhausen, Soumita Ghosh, Alexandra J. Lee, Anna Ada Dattoli, Fengling Hu, James Brian Byrd, Diane N. Rafizadeh, Yanjun Qi, Yuchen Sun, Jeffrey M. Field, Marouen Ben Guebila, Nafisa M. Jadavji, Ronan Lordan, Ashwin N. Skelly, Bharath Ramsundar, Christian Brueffer, Jinhui Wang, Rishi Raj Goel, YoSon Park, COVID-19 Review Consortium, Simina M. Boca, Anthony Gitter, Casey S. Greene

arXiv:2103.02723 [q-bio]  ·  03 Mar 2021

Lack of diversity in T cell receptor sequencing studies

Yu-Ning Huang, Kerui Peng, Alice B. Popejoy, Jieting Hu, Theodore Scott Nowicki, Stefan M. Gold, Lluis Quintana-Murci, Macarena Fuentes-Guajardo, Mikhail Shugay, Victor Greiff, Amanda M. Burkhardt, Houda Alachkar, SERGHEI MANGUL

Center for Open Science  ·  01 Mar 2021

The Gene Expression Deconvolution Interactive Tool (GEDIT): accurate cell type quantification from gene expression data

Brian B Nadel, David Lopez, Dennis J Montoya, Feiyang Ma, Hannah Waddel, Misha M Khan, Serghei Mangul, Matteo Pellegrini

GigaScience  ·  16 Feb 2021

RNA-seq data science: From raw data to effective interpretation

Dhrithi Deshpande, Karishma Chhugani, Yutong Chang, Aaron Karlsberg, Caitlin Loeffler, Jinyang Zhang, Agata Muszynska, Jeremy Rotman, Laura Tao, Brunilda Balliu, Elizabeth Tseng, Eleazar Eskin, Fangqing Zhao, Pejman Mohammadi, Pawel P. Labaj, Serghei Mangul

arXiv:2010.02391 [q-bio]  ·  16 Feb 2021

Pathogenesis, Symptomatology, and Transmission of SARS-CoV-2 through analysis of Viral Genomics and Structure

Halie M. Rando, Adam L. MacLean, Alexandra J. Lee, Sandipan Ray, Vikas Bansal, Ashwin N. Skelly, Elizabeth Sell, John J. Dziak, Lamonica Shinholster, Lucy D’Agostino McGowan, Marouen Ben Guebila, Nils Wellhausen, Sergey Knyazev, Simina M. Boca, Stephen Capone, Yanjun Qi, YoSon Park, Yuchen Sun, David Mai, Christian Brueffer, James Brian Byrd, Jinhui Wang, Ronan Lordan, Ryan Velazquez, Gregory L. Szeto, John P. Barton, Rishi Raj Goel, Serghei Mangul, Tiago Lubiana, COVID-19 Review Consortium, Anthony Gitter, Casey S. Greene

arXiv:2102.01521 [q-bio]  ·  12 Feb 2021

Exploiting the GTEx resources to decipher the mechanisms at GWAS loci

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

Genome Biology  ·  26 Jan 2021

cancer single cell ovarian cancer

2020

Path to independence: Overview of challenges and opportunities of computational data-driven research in biology

Karishma Chhugani, Vanessa Jönsson, SERGHEI MANGUL

Center for Open Science  ·  25 Nov 2020

cancer single cell ovarian cancer
A comprehensive benchmarking of WGS-based structural variant callers

Varuni Sarwal, Sebastian Niehus, Ram Ayyala, Sei Chang, Angela Lu, Nicholas Darci-Maher, Russell Littman, Karishma Chhugani, Arda Soylev, Zoia Comarova, Emily Wesel, Jacqueline Castellanos, Rahul Chikka, Margaret G. Distler, Eleazar Eskin, Jonathan Flint, Serghei Mangul

Cold Spring Harbor Laboratory  ·  17 Sep 2020

cancer machine learning
Transcriptomic signatures across human tissues identify functional rare genetic variation

Nicole M. Ferraro, Benjamin J. Strober, Jonah Einson, Nathan S. Abell, Francois Aguet, Alvaro N. Barbeira, Margot Brandt, Maja Bucan, Stephane E. Castel, Joe R. Davis, Emily Greenwald, Gaelen T. Hess, Austin T. Hilliard, Rachel L. Kember, Bence Kotis, YoSon Park, Gina Peloso, Shweta Ramdas, Alexandra J. Scott, Craig Smail, Emily K. Tsang, Seyedeh M. Zekavat, Marcello Ziosi, Aradhana, Kristin G. Ardlie, Themistocles L. Assimes, Michael C. Bassik, Christopher D. Brown, Adolfo Correa, Ira Hall, Hae Kyung Im, Xin Li, Pradeep Natarajan, Tuuli Lappalainen, Pejman Mohammadi, Stephen B. Montgomery, Alexis Battle, ,

Science  ·  11 Sep 2020

cancer single cell ovarian cancer
Cell type–specific genetic regulation of gene expression across human tissues

Sarah Kim-Hellmuth, François Aguet, Meritxell Oliva, Manuel Muñoz-Aguirre, Silva Kasela, Valentin Wucher, Stephane E. Castel, Andrew R. Hamel, Ana Viñuela, Amy L. Roberts, Serghei Mangul, Xiaoquan Wen, Gao Wang, Alvaro N. Barbeira, Diego Garrido-Martín, Brian B. Nadel, Yuxin Zou, Rodrigo Bonazzola, Jie Quan, Andrew Brown, Angel Martinez-Perez, José Manuel Soria, Gad Getz, Emmanouil T. Dermitzakis, Kerrin S. Small, Matthew Stephens, Hualin S. Xi, Hae Kyung Im, Roderic Guigó, Ayellet V. Segrè, Barbara E. Stranger, Kristin G. Ardlie, Tuuli Lappalainen,

Science  ·  11 Sep 2020

cancer single cell ovarian cancer
The GTEx Consortium atlas of genetic regulatory effects across human tissues

Science  ·  11 Sep 2020

cancer single cell ovarian cancer
A vast resource of allelic expression data spanning human tissues

Stephane E. Castel, François Aguet, Pejman Mohammadi, Kristin G. Ardlie, Tuuli Lappalainen,

Genome Biology  ·  11 Sep 2020

cancer single cell ovarian cancer
Impact of admixture and ancestry on eQTL analysis and GWAS colocalization in GTEx

Nicole R. Gay, Michael Gloudemans, Margaret L. Antonio, Nathan S. Abell, Brunilda Balliu, YoSon Park, Alicia R. Martin, Shaila Musharoff, Abhiram S. Rao, François Aguet, Alvaro N. Barbeira, Rodrigo Bonazzola, Farhad Hormozdiari, Kristin G. Ardlie, Christopher D. Brown, Hae Kyung Im, Tuuli Lappalainen, Xiaoquan Wen, Stephen B. Montgomery,

Genome Biology  ·  11 Sep 2020

cancer single cell ovarian cancer
sn-spMF: matrix factorization informs tissue-specific genetic regulation of gene expression

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

Genome Biology  ·  11 Sep 2020

cancer single cell ovarian cancer
PTWAS: investigating tissue-relevant causal molecular mechanisms of complex traits using probabilistic TWAS analysis

Yuhua Zhang, Corbin Quick, Ketian Yu, Alvaro Barbeira, Francesca Luca, Roger Pique-Regi, Hae Kyung Im, Xiaoquan Wen,

Genome Biology  ·  11 Sep 2020

cancer single cell ovarian cancer
Determinants of telomere length across human tissues

Kathryn Demanelis, Farzana Jasmine, Lin S. Chen, Meytal Chernoff, Lin Tong, Dayana Delgado, Chenan Zhang, Justin Shinkle, Mekala Sabarinathan, Hannah Lin, Eduardo Ramirez, Meritxell Oliva, Sarah Kim-Hellmuth, Barbara E. Stranger, Tsung-Po Lai, Abraham Aviv, Kristin G. Ardlie, François Aguet, Habibul Ahsan, Jennifer A. Doherty, Muhammad G. Kibriya, Brandon L. Pierce,

Science  ·  10 Sep 2020

cancer single cell ovarian cancer
The impact of sex on gene expression across human tissues

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

Science  ·  10 Sep 2020

cancer single cell ovarian cancer
Metalign: efficient alignment-based metagenomic profiling via containment min hash

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

Genome Biology  ·  10 Sep 2020

cancer single cell ovarian cancer
PhenomeXcan: Mapping the genome to the phenome through the transcriptome

Milton Pividori, Padma S. Rajagopal, Alvaro Barbeira, Yanyu Liang, Owen Melia, Lisa Bastarache, YoSon Park, GTEx Consortium, Xiaoquan Wen, Hae K. Im

Science Advances  ·  01 Sep 2020

Metagenomics for clinical diagnostics: technologies and informatics

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

arXiv:1911.11304 [q-bio]  ·  07 Aug 2020

cancer machine learning
Technology dictates algorithms: Recent developments in read alignment

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

arXiv:2003.00110 [q-bio]  ·  09 Jul 2020

Profiling immunoglobulin repertoires across multiple human tissues using RNA sequencing

Igor Mandric, Jeremy Rotman, Harry Taegyun Yang, Nicolas Strauli, Dennis J. Montoya, William Van Der Wey, Jiem R. Ronas, Benjamin Statz, Douglas Yao, Velislava Petrova, Alex Zelikovsky, Roberto Spreafico, Sagiv Shifman, Noah Zaitlen, Maura Rossetti, K. Mark Ansel, Eleazar Eskin, Serghei Mangul

Nature Communications  ·  19 Jun 2020

cancer machine learning
Refining the conference experience for junior scientists in the wake of climate change

Ruth Johnson, Andrada Fiscutean, Serghei Mangul

arXiv:2002.12268 [physics]  ·  17 Jun 2020

cancer machine learning
Intratumoral CD4+ T Cells Mediate Anti-tumor Cytotoxicity in Human Bladder Cancer

David Y. Oh, Serena S. Kwek, Siddharth S. Raju, Tony Li, Elizabeth McCarthy, Eric Chow, Dvir Aran, Arielle Ilano, Chien-Chun Steven Pai, Chiara Rancan, Kathryn Allaire, Arun Burra, Yang Sun, Matthew H. Spitzer, Serghei Mangul, Sima Porten, Maxwell V. Meng, Terence W. Friedlander, Chun Jimmie Ye, Lawrence Fong

Cell  ·  01 Jun 2020

Exploiting the GTEx resources to decipher the mechanisms at GWAS loci

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

Cold Spring Harbor Laboratory  ·  23 May 2020

Improving the usability and comprehensiveness of microbial databases

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

BMC Biology  ·  07 Apr 2020

cancer machine learning
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, 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

Genome Biology  ·  17 Mar 2020

cancer single cell ovarian cancer
PhenomeXcan: Mapping the genome to the phenome through the transcriptome

Milton Pividori, Padma S. Rajagopal, Alvaro Barbeira, Yanyu Liang, Owen Melia, Lisa Bastarache, YoSon Park, Xiaoquan Wen, Hae K. Im,

Cold Spring Harbor Laboratory  ·  13 Mar 2020

cancer machine learning
Metalign: Efficient alignment-based metagenomic profiling via containment min hash

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

Cold Spring Harbor Laboratory  ·  18 Jan 2020

cancer machine learning
Telescope: an interactive tool for managing large-scale analysis from mobile devices

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

GigaScience  ·  01 Jan 2020

2019

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

Yuhua Zhang, Corbin Quick, Ketian Yu, Alvaro Barbeira, Francesca Luca, Roger Pique-Regi, Hae Kyung Im, Xiaoquan Wen,

Cold Spring Harbor Laboratory  ·  17 Oct 2019

cancer machine learning
Mechanisms of tissue-specific genetic regulation revealed by latent factors across eQTLs

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

Cold Spring Harbor Laboratory  ·  06 Oct 2019

cancer machine learning
A vast resource of allelic expression data spanning human tissues

Stephane E. Castel, François Aguet, Pejman Mohammadi, Kristin G. Ardlie, Tuuli Lappalainen,

Cold Spring Harbor Laboratory  ·  03 Oct 2019

cancer machine learning
Diverse transcriptomic signatures across human tissues identify functional rare genetic variation

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

Cold Spring Harbor Laboratory  ·  03 Oct 2019

cancer machine learning
Long non-coding RNA gene regulation and trait associations across human tissues

O. M. de Goede, N. M. Ferraro, D. C. Nachun, A. S. Rao, F. Aguet, A. N. Barbeira, S. E. Castel, S. Kim-Hellmuth, Y. Park, A. J. Scott, B. J. Strober, C. D. Brown, X. Wen, I. M. Hall, A. Battle, T. Lappalainen, H. K. Im, K. G. Ardlie, T. Quertermous, K. Kirkegaard, S. B. Montgomery,

Cold Spring Harbor Laboratory  ·  03 Oct 2019

cancer machine learning
Transcriptional profiling of single fiber cells in a transgenic paradigm of an inherited childhood cataract reveals absence of molecular heterogeneity

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

Journal of Biological Chemistry  ·  01 Sep 2019

cancer single cell ovarian cancer
Interpreting and integrating big data in the life sciences

Serghei Mangul

Emerging Topics in Life Sciences  ·  16 Aug 2019

cancer machine learning
Challenges and recommendations to improve the installability and archival stability of omics computational tools

Serghei Mangul, Thiago Mosqueiro, Richard J. Abdill, Dat Duong, Keith Mitchell, Varuni Sarwal, Brian Hill, Jaqueline Brito, Russell Jared Littman, Benjamin Statz, Angela Ka-Mei Lam, Gargi Dayama, Laura Grieneisen, Lana S. Martin, Jonathan Flint, Eleazar Eskin, Ran Blekhman

PLOS Biology  ·  20 Jun 2019

cancer single cell ovarian cancer
MiCoP: microbial community profiling method for detecting viral and fungal organisms in metagenomic samples

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

BMC Genomics  ·  06 Jun 2019

Systematic benchmarking of omics computational tools

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

Nature Communications  ·  27 Mar 2019

cancer single cell ovarian cancer
How bioinformatics and open data can boost basic science in countries and universities with limited resources

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

Nature Biotechnology  ·  04 Mar 2019

cancer machine learning
Improving the usability and archival stability of bioinformatics software

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

Genome Biology  ·  27 Feb 2019

cancer machine learning
Porcine Viruses: From Pathogenesis to Strategies for Control

Caister Academic Press  ·  01 Jan 2019

Hidden Treasures in Contemporary RNA Sequencing

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

SpringerBriefs in Computer Science  ·  01 Jan 2019

cancer single cell ovarian cancer

2018

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

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

iScience  ·  01 Dec 2018

cancer single cell ovarian cancer
A Comprehensive Map of Genetic Variation in the World’s Largest Ethnic Group—Han Chinese

Charleston W K Chiang, Serghei Mangul, Christopher Robles, Sriram Sankararaman

Molecular Biology and Evolution  ·  01 Nov 2018

cancer machine learning
AIRR Community Standardized Representations for Annotated Immune Repertoires

Jason Anthony Vander Heiden, Susanna Marquez, Nishanth Marthandan, Syed Ahmad Chan Bukhari, Christian E. Busse, Brian Corrie, Uri Hershberg, Steven H. Kleinstein, Frederick A. Matsen IV, Duncan K. Ralph, Aaron M. Rosenfeld, Chaim A. Schramm, Scott Christley, Uri Laserson,

Frontiers in Immunology  ·  28 Sep 2018

cancer machine learning
Abstract 4688: Single-cell discrimination of altered human T cell states in the bladder tumor microenvironment

David Yoonsuk Oh, Serena S. Kwek, Serghei Mangul, Siddharth S. Raju, Sasha Targ, Arun Burra, Eric Chow, Dvir Aran, Sima Porten, Maxwell V. Meng, Terence W. Friedlander, Chun Jimmie Ye, Lawrence Fong

American Association for Cancer Research (AACR)  ·  01 Jul 2018

Transcriptome analysis in whole blood reveals increased microbial diversity in schizophrenia

Loes M. Olde Loohuis, Serghei Mangul, Anil P. S. Ori, Guillaume Jospin, David Koslicki, Harry Taegyun Yang, Timothy Wu, Marco P. Boks, Catherine Lomen-Hoerth, Martina Wiedau-Pazos, Rita M. Cantor, Willem M. de Vos, René S. Kahn, Eleazar Eskin, Roel A. Ophoff

Translational Psychiatry  ·  10 May 2018

cancer machine learning
Involving undergraduates in genomics research to narrow the education–research gap

Serghei Mangul, Lana S Martin, Eleazar Eskin

Nature Biotechnology  ·  01 Apr 2018

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

Serghei Mangul, Harry Taegyun Yang, Nicolas Strauli, Franziska Gruhl, Hagit T. Porath, Kevin Hsieh, Linus Chen, Timothy Daley, Stephanie Christenson, Agata Wesolowska-Andersen, Roberto Spreafico, Cydney Rios, Celeste Eng, Andrew D. Smith, Ryan D. Hernandez, Roel A. Ophoff, Jose Rodriguez Santana, Erez Y. Levanon, Prescott G. Woodruff, Esteban Burchard, Max A. Seibold, Sagiv Shifman, Eleazar Eskin, Noah Zaitlen

Genome Biology  ·  15 Feb 2018

cancer single cell ovarian cancer
Single Cell Heterogeneity is Absent in the Transgenic Paradigm of an Inherited Cataract

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

SSRN Electronic Journal  ·  01 Jan 2018

2017

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

Ashis Saha, Yungil Kim, Ariel D.H. Gewirtz, Brian Jo, Chuan Gao, Ian C. McDowell, Barbara E. Engelhardt, Alexis Battle,

Genome Research  ·  01 Nov 2017

cancer machine learning
Identifying cis-mediators for trans-eQTLs across many human tissues using genomic mediation analysis

Fan Yang, Jiebiao Wang, The GTEx Consortium, Brandon L. Pierce, Lin S. Chen, 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 Battle, Gireesh K. Bogu, Andrew Brown, Christopher D. Brown, Stephane E. Castel, Lin S. Chen, Colby Chiang, Donald F. Conrad, Nancy J. Cox, Farhan N. Damani, Joe R. Davis, 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 Guigo, Ira M. Hall, Buhm Han, Yuan He, Farhad Hormozdiari, Cedric Howald, Hae Kyung Im, Brian Jo, Eun Yong Kang, Yungil Kim, Sarah Kim-Hellmuth, Tuuli Lappalainen, Gen Li, Xin Li, Boxiang Liu, Serghei Mangul, Mark I. McCarthy, Ian C. McDowell, Pejman Mohammadi, Jean Monlong, Stephen B. Montgomery, Manuel Muñoz-Aguirre, Anne W. Ndungu, Dan L. Nicolae, Andrew B. Nobel, Meritxell Oliva, Halit Ongen, John J. Palowitch, Nikolaos Panousis, Panagiotis Papasaikas, YoSon Park, Princy Parsana, Anthony J. Payne, Christine B. Peterson, Jie Quan, Ferran Reverter, Chiara Sabatti, Ashis Saha, Michael Sammeth, Alexandra J. Scott, Andrey A. Shabalin, Reza Sodaei, Matthew Stephens, Barbara E. Stranger, Benjamin J. Strober, Jae Hoon Sul, Emily K. Tsang, Sarah Urbut, Martijn Bunt, Gao Wang, Xiaoquan Wen, Fred A. Wright, Hualin S. Xi, Esti Yeger-Lotem, Zachary Zappala, Judith B. Zaugg, Yi-Hui Zhou, Joshua M. Akey, Daniel Bates, Joanne Chan, Lin S. Chen, Melina Claussnitzer, Kathryn Demanelis, Morgan Diegel, Jennifer A. Doherty, Andrew P. Feinberg, Marian S. Fernando, Jessica Halow, Kasper D. Hansen, Eric Haugen, Peter F. Hickey, Lei Hou, Farzana Jasmine, Ruiqi Jian, Lihua Jiang, Audra Johnson, Rajinder Kaul, Manolis Kellis, Muhammad G. Kibriya, Kristen Lee, Jin Billy Li, Qin Li, Xiao Li, Jessica Lin, Shin Lin, Sandra Linder, Caroline Linke, Yaping Liu, Matthew T. Maurano, Benoit Molinie, Stephen B. Montgomery, Jemma Nelson, Fidencio J. Neri, Meritxell Oliva, Yongjin Park, Brandon L. Pierce, Nicola J. Rinaldi, Lindsay F. Rizzardi, Richard Sandstrom, Andrew Skol, Kevin S. Smith, Michael P. Snyder, John Stamatoyannopoulos, Barbara E. Stranger, Hua Tang, Emily K. Tsang, Li Wang, Meng Wang, Nicholas Van Wittenberghe, Fan Wu, Rui Zhang, Concepcion R. Nierras, Philip A. Branton, Latarsha J. Carithers, Ping Guan, Helen M. Moore, Abhi Rao, Jimmie B. Vaught, Sarah E. Gould, Nicole C. Lockart, Casey Martin, Jeffery P. Struewing, Simona Volpi, Anjene M. Addington, Susan E. Koester, A. Roger Little, Lori E. Brigham, Richard Hasz, Marcus Hunter, Christopher Johns, Mark Johnson, Gene Kopen, William F. Leinweber, John T. Lonsdale, Alisa McDonald, Bernadette Mestichelli, Kevin Myer, Brian Roe, Michael Salvatore, Saboor Shad, Jeffrey A. Thomas, Gary Walters, Michael Washington, Joseph Wheeler, Jason Bridge, Barbara A. Foster, Bryan M. Gillard, Ellen Karasik, Rachna Kumar, Mark Miklos, Michael T. Moser, Scott D. Jewell, Robert G. Montroy, Daniel C. Rohrer, Dana R. Valley, David A. Davis, Deborah C. Mash, Anita H. Undale, Anna M. Smith, David E. Tabor, Nancy V. Roche, Jeffrey A. McLean, Negin Vatanian, Karna L. Robinson, Leslie Sobin, Mary E. Barcus, Kimberly M. Valentino, Liqun Qi, Steven Hunter, Pushpa Hariharan, Shilpi Singh, Ki Sung Um, Takunda Matose, Maria M. Tomaszewski, Laura K. Barker, Maghboeba Mosavel, Laura A. Siminoff, Heather M. Traino, Paul Flicek, Thomas Juettemann, Magali Ruffier, Dan Sheppard, Kieron Taylor, Stephen J. Trevanion, Daniel R. Zerbino, Brian Craft, Mary Goldman, Maximilian Haeussler, W. James Kent, Christopher M. Lee, Benedict Paten, Kate R. Rosenbloom, John Vivian, Jingchun Zhu

Genome Research  ·  01 Nov 2017

Dynamic landscape and regulation of RNA editing in mammals

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

Nature  ·  12 Oct 2017

cancer machine learning
Genetic effects on gene expression across human tissues

Nature  ·  12 Oct 2017

cancer machine learning
Addressing the Digital Divide in Contemporary Biology: Lessons from Teaching UNIX

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

Trends in Biotechnology  ·  01 Oct 2017

cancer single cell ovarian cancer
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

Journal of Computational Biology  ·  01 Jun 2017

HapIso: An Accurate Method for the Haplotype- Specific Isoforms Reconstruction From Long Single-Molecule Reads

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

IEEE Transactions on NanoBioscience  ·  01 Mar 2017

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

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

Cold Spring Harbor Laboratory  ·  25 Jan 2017

2016

Discovering Single Nucleotide Polymorphisms Regulating Human Gene Expression Using Allele Specific Expression from RNA-seq Data

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

Genetics  ·  01 Nov 2016

Local genetic effects on gene expression across 44 human tissues

François Aguet, Andrew A. Brown, Stephane E. Castel, Joe R. Davis, Pejman Mohammadi, Ayellet V. Segrè, Zachary Zappala, Nathan S. Abell, Laure Frésard, Eric R. Gamazon, Ellen Gelfand, Michael J. Gloudemans, Yuan He, Farhad Hormozdiari, Xiao Li, Xin Li, Boxiang Liu, Diego Garrido-Martín, Halit Ongen, John J. Palowitch, YoSon Park, Christine B. Peterson, Gerald Quon, Stephan Ripke, Andrey A. Shabalin, Tyler C. Shimko, Benjamin J. Strober, Timothy J. Sullivan, Nicole A. Teran, Emily K. Tsang, Hailei Zhang, Yi-Hui Zhou, Alexis Battle, Carlos D. Bustamonte, Nancy J. Cox, Barbara E. Engelhardt, Eleazar Eskin, Gad Getz, Manolis Kellis, Gen Li, Daniel G. MacArthur, Andrew B. Nobel, Chiara Sabbati, Xiaoquan Wen, Fred A. Wright, Tuuli Lappalainen, Kristin G. Ardlie, Emmanouil T. Dermitzakis, Christopher D. Brown, Stephen B. Montgomery,

Cold Spring Harbor Laboratory  ·  09 Sep 2016

Applications of High-Fidelity Sequencing Protocol to RNA Viruses

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

Wiley  ·  26 Aug 2016

CRISPR-Mediated VHL Knockout Generates an Improved Model for Metastatic Renal Cell Carcinoma

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

Scientific Reports  ·  30 Jun 2016

2015

2SNV: Quasispecies reconstruction from PacBio reads

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

Institute of Electrical and Electronics Engineers (IEEE)  ·  01 Oct 2015

2014

Transcriptome assembly and quantification from Ion Torrent RNA-Seq data

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

BMC Genomics  ·  14 Jul 2014

Accurate viral population assembly from ultra-deep sequencing data

S. Mangul, N. C. Wu, N. Mancuso, A. Zelikovsky, R. Sun, E. Eskin

Bioinformatics  ·  15 Jun 2014

sequencing viral population assembly
Deterministic regression algorithm for transcriptome frequency estimation

Adrian Caciula, Olga Glebova, Alexander Artyomenko, Serghei Mangul, James Lindsay, Ion I. Mandoiu, Alex Zelikovsky

Institute of Electrical and Electronics Engineers (IEEE)  ·  01 Jun 2014

Reconstruction of influenza a virus variants from PacBio reads

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

Institute of Electrical and Electronics Engineers (IEEE)  ·  01 Jun 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

Institute of Electrical and Electronics Engineers (IEEE)  ·  01 Jun 2014

2013

Monte-Carlo Regression algorithm for isoform frequency estimation from RNA-Seq data

Adrian Caciula, Alex Zelikovsky, Serghei Mangul, James Lindsay, Ion Mandoiu

Institute of Electrical and Electronics Engineers (IEEE)  ·  01 Jun 2013

2012

Workshop: Novel transcript reconstruction from paired-end RNA-Seq reads using fragment length distribution

Serghei Mangul, Adrian Caciula, Ion Mandoiu, Alex Zelikovsky

Institute of Electrical and Electronics Engineers (IEEE)  ·  01 Feb 2012

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

Association for Computing Machinery (ACM)  ·  01 Jan 2012

2011

RNA-Seq based discovery and reconstruction of unannotated transcripts in partially annotated genomes

S. Mangul, A. Caciula, I. Mandoiu, A. Zelikovsky

Institute of Electrical and Electronics Engineers (IEEE)  ·  01 Nov 2011

Inferring viral quasispecies spectra from 454 pyrosequencing reads

Irina Astrovskaya, Bassam Tork, Serghei Mangul, Kelly Westbrooks, Ion Măndoiu, Peter Balfe, Alex Zelikovsky

BMC Bioinformatics  ·  28 Jul 2011

Estimation of alternative splicing isoform frequencies from RNA-Seq data

Marius Nicolae, Serghei Mangul, Ion I Măndoiu, Alex Zelikovsky

Algorithms for Molecular Biology  ·  19 Apr 2011

Maximum Likelihood Estimation of Incomplete Genomic Spectrum from HTS Data

Serghei Mangul, Irina Astrovskaya, Marius Nicolae, Bassam Tork, Ion Mandoiu, Alex Zelikovsky

Lecture Notes in Computer Science  ·  01 Jan 2011

2009

Simulation Of Emission Dispersion As The Method Of Air Quality Management

Z. Comarova, S. Mangul

NATO Science for Peace and Security Series C: Environmental Security  ·  01 Apr 2009

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The citations on this page were generated automatically from just identifiers using the Manubot cite utility developed in the Greene Lab!

California (CA), USA
California (CA), USA