Research

VISTA: an integrated framework for structural variant discovery

Varuni Sarwal, Seungmo Lee, Jianzhi Yang, Sriram Sankararaman, Mark Chaisson, Eleazar Eskin, Serghei Mangul

Briefings in Bioinformatics · 19 Sep 2024

CAMP: A modular metagenomics analysis system for integrated multi-step data exploration

Lauren Mak, Braden Tierney, Cynthia Ronkowski, Rodolfo Brizola Toscan, Berk Turhan, Michael Toomey, Juan Sebastian Andrade Martinez, Chenlian Fu, Alexander G Lucaci, Arthur Henrique Barrios Solano, João Carlos Setubal, James R Henriksen, Sam Zimmerman, Malika Kopbayeva, Anna Noyvert, Zana Iwan, Shraman Kar, Nikita Nakazawa, Dmitry Meleshko, Dmytro Horyslavets, Valeriia Kantsypa, Alina Frolova, Andre Kahles, David Danko, Eran Elhaik, Pawel Labaj, Serghei Mangul, The International MetaSUB Consortium, Christopher E. Mason, Iman Hajirasouliha

bioRxiv · 14 Sep 2024

Community Structure and Temporal Dynamics of Viral Epistatic Networks Allow for Early Detection of Emerging Variants with Altered Phenotypes

Realistic assortment of novel metagenomics benchmarks with diverse biological and technological characteristics

N K Sharma, K Chhugani, Viorel Munteanu, Pavel Skums, Alexander Zelikovsky, Serghei Mangul

Biopolymers & Cell · 09 Sep 2024

Good software development practices improve citations of RNA seq tools

S Sharma, K Chhugani, D Deshpande, Serghei Mangul

Biopolymers & Cell · 08 Sep 2024

Assessing microbial genome representation across various reference databases: A comprehensive evaluation

G Boldirev, N K Sharma, Viorel Munteanu, A Bhavatharini, D Koslicki, Alexander Zelikovsky, Serghei Mangul

Biopolymers & Cell · 07 Sep 2024

A blended genome and exome sequencing method captures genetic variation in an unbiased, high-quality, and cost-effective manner

Toni A Boltz, Benjamin B Chu, Calwing Liao, Julia M Sealock, Robert Ye, Lerato Majara, Jack M Fu, Susan Service, Lingyu Zhan, Sarah E Medland, Sinead B Chapman, Simone Rubinacci, Matthew DeFelice, Jonna L Grimsby, Tamrat Abebe, Melkam Alemayehu, Fred K Ashaba, Elizabeth G Atkinson, Tim Bigdeli, Amanda B Bradway, Harrison Brand, Lori B Chibnik, Abebaw Fekadu, Michael Gatzen, Bizu Gelaye, Stella Gichuru, Marissa L Gildea, Toni C Hill, Hailiang Huang, Kalyn M Hubbard, Wilfred E. Injera, Roxanne James, Moses Joloba, Christopher Kachulis, Phillip R Kalmbach, Rogers Kamulegeya, Gabriel Kigen, Soyeon Kim, Nastassja Koen, Edith K. Kwobah, Joseph Kyebuzibwa, Seungmo Lee, Niall J Lennon, Penelope A Lind, Esteban A Lopera-Maya, Johnstone Makale, Serghei Mangul, Justin McMahon, Pierre Mowlem, Henry Musinguzi, Rehema M. Mwema, Noeline Nakasujja, Carter P Newman, Lethukuthula L Nkambule, Conor R O’Neil, Ana Maria Olivares, Catherine M. Olsen, Linnet Ongeri, Sophie J Parsa, Adele Pretorius, Raj Ramesar, Faye L Reagan, Chiara Sabatti, Jacquelyn A Schneider, Welelta Shiferaw, Anne Stevenson, Erik Stricker, Rocky E. Stroud II, Jessie Tang, David Whiteman, Mary T Yohannes, Mingrui Yu, Kai Yuan, NeuroGAP Psychosis, Dickens Akena, Lukoye Atwoli, Symon M. Kariuki, Karestan C. Koenen, Charles R. J. C. Newton, Dan J. Stein, Solomon Teferra, Zukiswa Zingela, Carlos N Pato, Michele T Pato, Carlos Lopez-Jaramillo, Nelson Freimer, Roel A Ophoff, Loes M Olde Loohuis, Michael E Talkowski, Benjamin M Neale, Daniel P Howrigan, Alicia R Martin

bioRxiv · 06 Sep 2024

The evolution of computational research in a data-centric world

Dhrithi Deshpande, Karishma Chhugani, Tejasvene Ramesh, Matteo Pellegrini, Sagiv Shiffman, Malak S. Abedalthagafi, Saleh Alqahtani, Jimmie Ye, Xiaole Shirley Liu, Jeffrey T. Leek, Alvis Brazma, Roel A. Ophoff, Gauri Rao, Atul J. Butte, Jason H. Moore, Vsevolod Katritch, Serghei Mangul

Cell · 22 Aug 2024

Genomic reproducibility in the bioinformatics era

Pelin Icer Baykal, Paweł P Łabaj, Florian Markowetz, Lynn M. Schriml, Daniel J. Stekhoven, Serghei Mangul, Niko Beerenwinkel

Springer · 09 Aug 2024

Analytical code sharing practices in biomedical research

Nitesh Kumar Sharma, Ram Ayyala, Dhrithi Deshpande, Yesha Patel, Viorel Munteanu, Dumitru Ciorba, Viorel Bostan, Andrada Fiscutean, Mohammad Vahed, Aditya Sarkar, Ruiwei Guo, Andrew Moore, Nicholas Darci-Mahed, Nicole Nogoy, Malak Abedalthagafi, Serghei Mangul

PeerJ Computer Science · 28 Jun 2024

Estimating Enzyme Expression and Metabolic Pathway Activity in Borreliella-Infected and Uninfected Mice

Filipp Martin Rondel, Hafsa Farooq, Roya Hosseini, Akshay Juyal, Sergey Knyazev, Serghei Mangul, Artem Rogovskyy, Alexander Zelikovsky

Journal of Computational Biology · 27 Jun 2024

Diversity and Distinctive Traits of the Global RNA Virome in Urban Environments

Zihao Gao, Jun Wu, Alexander G. Lucaci, Jian Ouyang, Lan Wang, Krista Ryon, Eran Elhaik, Alexander J. Probst, Xavier Rodó, Thirumalaisamy Velavan, Anastasia Chasapi, Christos A. Ouzounis, Manuela Oliveira, Emmanuel Dias-Neto, Olayinka O. Osuolale, Michael Poulsen, Dmitry Meleshko, Malay Bhattacharyya, Juan A. Ugalde, Maria A. Sierra, Braden T. Tierney, Bharath Prithiviraj, Nitesh Kumar Sharma, Viorel Munteanu, Serghei Mangul, Masayuki Ushio, Paweł P. Łabaj, Rodolfo Toscan, Balakrishnan Subramanian, Alina Frolova, Joshua Burkhart, Youping Deng, Klas I. Udekwu, Lynn M. Schriml, Nur Hazlin Hazrin-Chong, Haruo Suzuki, Patrick K. H. Lee, Lin Fa Wang, Christopher E. Mason, Tieliu Shi

Cell · 24 Jun 2024

The DNA methylation landscape across the TCR loci in patients with acute myeloid leukemia

Mateusz Pospiech, John Beckford, Advaith Maya Sanjeev Kumar, Mukund Tamizharasan, Jaqueline Brito, Gangning Liang, Serghei Mangul, Houda Alachkar

International Immunopharmacology · 28 May 2024

Fatemeh Mohebbi, Alex Zelikovsky, Serghei Mangul, Gerardo Chowell, Pavel Skums

Springer · 20 May 2024

Community Structure and Temporal Dynamics of Viral Epistatic Networks Allow for Early Detection of Emerging Variants with Altered Phenotypes

Fatemeh Mohebbi, Alexander Zelikovsky, Serghei Mangul, Gerardo Chowell, Pavel Skums

Springer · 17 May 2024

Packaging and containerization of computational methods

Mohammed Alser, Brendan Lawlor, Richard J. Abdill, Sharon Waymost, Ram Ayyala, Neha Rajkumar, Nathan LaPierre, Jaqueline Brito, Andre M. Ribeiro-dos-Santos, Nour Almadhoun, Varuni Sarwal, Can Firtina, Tomasz Osinski, Eleazar Eskin, Qiyang Hu, Derek Strong, Byoung-Do Kim, Malak S. Abedalthagafi, Onur Mutlu, Serghei Mangul

Nature Protocols · 02 Apr 2024

Early detection of emerging viral variants through analysis of community structure of coordinated substitution networks

Fatemeh Mohebbi, Alex Zelikovsky, Serghei Mangul, Gerardo Chowell, Pavel Skums

Nature Communications · 02 Apr 2024

The knowns and unknowns of long COVID-19: from mechanisms to therapeutical approaches

Roxana Gheorghita, Iuliana Soldanescu, Andrei Lobiuc, Olga Adriana Caliman-Sturdza, Roxana Filip, Adela Constantinescu – Bercu, Mihai Dimian, Serghei Mangul, Mihai Covasa

Frontiers in Immunology · 04 Mar 2024

Climate warming, environmental degradation and pollution as drivers of antibiotic resistance

Piotr Rzymski, Willis Gwenzi, Barbara Poniedziałek, Serghei Mangul, Andrzej Fal

Environmental Pollution · 23 Feb 2024

Large-scale integrative analysis of juvenile idiopathic arthritis for new insight into its pathogenesis

Daeun Kim, Jaeseung Song, Serghei Mangul, Nicholas Mancuso, Junghyun Jung, Wonhee Jang

Arthritis Research & Therapy · 10 Feb 2024

2023

BioLLMBench: A Comprehensive Benchmarking of Large Language Models in Bioinformatics

Varuni Sarwal, Viorel Munteanu, Timur Suhodolschi, Dumitru Ciorba, Eleazar Eskin, Wei Wang, Serghei Mangul

bioRxiv · 20 Dec 2023

Fasting-Mimicking Diet Inhibits Autophagy and Synergizes with Chemotherapy to Promote T-Cell-Dependent Leukemia-Free Survival

Roberta Buono, Jonathan Tucci, Raffaello Cutri, Novella Guidi, Serghei Mangul, Franca Raucci, Matteo Pellegrini, Steven D. Mittelman, Valter D. Longo

Cancers · 16 Dec 2023

Whole blood transcriptomics identifies subclasses of pediatric septic shock

Jamie O. Yang, Matt S. Zinter, Matteo Pellegrini, Man Yee Wong, Kinisha Gala, Daniela Markovic, Brian Nadel, Kerui Peng, Nguyen Do, Serghei Mangul, Vinay M. Nadkarni, Aaron Karlsberg, Dhrithi Deshpande, Manish J. Butte, Lisa Asaro, Michael Agus, Anil Sapru

Critical Care · 08 Dec 2023

Pioneering computational culture within pharmacy schools by empowering students with data science and bioinformatics skills

Cynthia Ronkowski, Nitesh Sharma, Mohammad Vahed, Yesha M. Patel, Dhrithi Deshpande, Hovhannes J. Gukasyan, Maryann Wu, Kerui Peng, Terry David Church, Rory E. Kim, Edith Mirzaian, William Vincent Padula, Daniel Tomaszewski, Tien M.H. Ng, Annie Wong-Beringer, Jennica Zaro, Dima M. Qato, Daryl L. Davies, Vassilios Papadopoulos, Serghei Mangul

Center for Open Science · 23 Nov 2023

Perceptual and technical barriers in sharing and formatting metadata accompanying omics studies

Yu-Ning Huang, Michael I. Love, Cynthia Flaire Ronkowski, Dhrithi Deshpande, Lynn M. Schriml, Annie Wong-Beringer, Barend Mons, Russell Corbett-Detig, Christopher I Hunter, Jason H. Moore, Lana X. Garmire, T.B.K. Reddy, Winston A. Hide, Atul J. Butte, Mark D. Robinson, Serghei Mangul

arXiv · 22 Nov 2023

MetaFast: Enabling Fast Metagenomic Classification via Seed Counting and Edit Distance Approximation

Arvid E. Gollwitzer, Mohammed Alser, Joel Bergtholdt, Joel Lindegger, Maximilian-David Rumpf, Can Firtina, Serghei Mangul, Onur Mutlu

arXiv · 03 Nov 2023

SequenceLab: A Comprehensive Benchmark of Computational Methods for Comparing Genomic Sequences

Maximilian-David Rumpf, Mohammed Alser, Arvid E. Gollwitzer, Joel Lindegger, Nour Almadhoun, Can Firtina, Serghei Mangul, Onur Mutlu

arXiv · 25 Oct 2023

A rigorous benchmarking of methods for SARS-CoV-2 lineage abundance estimation in wastewater

Viorel Munteanu, Victor Gordeev, Justin Maine Su, Khooshbu Kantibhai Patel, Nicolae Drabcinski, Oksana Zlenko, Maryna Kit, Yidian Xu, Pooja Jaiswal, Alex Zelikovsky, Serghei Mangul

arXiv · 29 Sep 2023

SARS-CoV-2 Wastewater Genomic Surveillance: Approaches, Challenges, and Opportunities

Viorel Munteanu, Michael Saldana, Nitesh Kumar Sharma, Wenhao O. Ouyang, Eva Aßmann, Victor Gordeev, Nadiia Kasianchuk, Braden T Tierney, Alexander G Lucaci, Sergey Knyazev, Dumitru Ciorba, Viorel Bostan, Christopher Mason, Pavel Skums, Nicholas C. Wu, Piotr Rzymski, Martin Hölzer, Alex Zelikovsky, Adam Smith, Serghei Mangul

arXiv · 23 Sep 2023

The Genomic Landscape of Colorectal Cancer in the Saudi Arabian Population Using a Comprehensive Genomic Panel

Ebtehal Alsolme, Saleh Alqahtani, Musa Fageeh, Duna Barakeh, Nitesh K. Sharma, Serghei Mangul, Heather A. Robinson, Amany Fathaddin, Charlotte Hauser, Malak Abedalthagafi

Diagnostics · 19 Sep 2023

Scientists without borders: lessons from Ukraine

Walter Wolfsberger, Karishma Chhugani, Khrystyna Shchubelka, Alina Frolova, Yuriy Salyha, Oksana Zlenko, Mykhailo Arych, Dmytro Dziuba, Andrii Parkhomenko, Volodymyr Smolanka, Zeynep H Gümüş, Efe Sezgin, Alondra Diaz-Lameiro, Viktor R Toth, Megi Maci, Eric Bortz, Fyodor Kondrashov, Patricia M Morton, Paweł P Łabaj, Veronika Romero, Jakub Hlávka, Serghei Mangul, Taras K Oleksyk

GigaScience · 27 Jul 2023

Rigorous benchmarking of T-cell receptor repertoire profiling methods for cancer RNA sequencing

Kerui Peng, Theodore Scott Nowicki, Katie Campbell, Mohammad Vahed, Dandan Peng, Yiting Meng, Anish Nagareddy, Yu-Ning Huang, Aaron Karlsberg, Zachary Miller, Jaqueline Brito, Brian Nadel, Victoria M. Pak, Malak S. Abedalthagafi, Amanda M. Burkhardt, Houda Alachkar, Antoni Ribas, Serghei Mangul

Briefings in Bioinformatics · 08 Jun 2023

A Rigorous Benchmarking of alignment-based HLA callers for RNA-seq data

Dottie Yu, Ram Ayyala, Serghei Mangul

bioRxiv · 24 May 2023

Meta-analysis of (single-cell method) benchmarks reveals the need for extensibility and interoperability

Anthony Sonrel, Almut Luetge, Charlotte Soneson, Izaskun Mallona, Pierre-Luc Germain, Sergey Knyazev, Jeroen Gilis, Reto Gerber, Ruth Seurinck, Dominique Paul, Emanuel Sonder, Helena L. Crowell, Imran Fanaswala, Ahmad Al-Ajami, Elyas Heidari, Stephan Schmeing, Stefan Milosavljevic, Yvan Saeys, Serghei Mangul, Mark D. Robinson

Genome Biology · 17 May 2023

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

Dhrithi Deshpande, Karishma Chhugani, Yutong Chang, Aaron Karlsberg, Caitlin Loeffler, Jinyang Zhang, Agata Muszyńska, Viorel Munteanu, Harry Yang, Jeremy Rotman, Laura Tao, Brunilda Balliu, Elizabeth Tseng, Eleazar Eskin, Fangqing Zhao, Pejman Mohammadi, Paweł P. Łabaj, Serghei Mangul

Frontiers in Genetics · 13 Mar 2023

TAMPA: interpretable analysis and visualization of metagenomics-based taxon abundance profiles

Varuni Sarwal, Jaqueline Brito, Serghei Mangul, David Koslicki

GigaScience · 28 Feb 2023

pyTCR: A comprehensive and scalable solution for TCR-Seq data analysis to facilitate reproducibility and rigor of immunogenomics research

2022

Remote opportunities for scholars in Ukraine

Karishma Chhugani, Alina Frolova, Yuriy Salyha, Andrada Fiscutean, Oksana Zlenko, Sanita Reinsone, Walter W. Wolfsberger, Oleksandra V. Ivashchenko, Megi Maci, Dmytro Dziuba, Andrii Parkhomenko, Eric Bortz, Fyodor Kondrashov, Paweł P. Łabaj, Veronika Romero, Jakub Hlávka, Taras K. Oleksyk, Serghei Mangul

Science · 23 Dec 2022

Exome-wide association study to identify rare variants influencing COVID-19 outcomes: Results from the Host Genetics Initiative

Guillaume Butler-Laporte, Gundula Povysil, Jack A. Kosmicki, Elizabeth T. Cirulli, Theodore Drivas, Simone Furini, Chadi Saad, Axel Schmidt, Pawel Olszewski, Urszula Korotko, Mathieu Quinodoz, Elifnaz Çelik, Kousik Kundu, Klaudia Walter, Junghyun Jung, Amy D. Stockwell, Laura G. Sloofman, Daniel M. Jordan, Ryan C. Thompson, Diane Del Valle, Nicole Simons, Esther Cheng, Robert Sebra, Eric E. Schadt, Seunghee Kim-Schulze, Sacha Gnjatic, Miriam Merad, Joseph D. Buxbaum, Noam D. Beckmann, Alexander W. Charney, Bartlomiej Przychodzen, Timothy Chang, Tess D. Pottinger, Ning Shang, Fabian Brand, Francesca Fava, Francesca Mari, Karolina Chwialkowska, Magdalena Niemira, Szymon Pula, J Kenneth Baillie, Alex Stuckey, Antonio Salas, Xabier Bello, Jacobo Pardo-Seco, Alberto Gómez-Carballa, Irene Rivero-Calle, Federico Martinón-Torres, Andrea Ganna, Konrad J. Karczewski, Kumar Veerapen, Mathieu Bourgey, Guillaume Bourque, Robert JM Eveleigh, Vincenzo Forgetta, David Morrison, David Langlais, Mark Lathrop, Vincent Mooser, Tomoko Nakanishi, Robert Frithiof, Michael Hultström, Miklos Lipcsey, Yanara Marincevic-Zuniga, Jessica Nordlund, Kelly M. Schiabor Barrett, William Lee, Alexandre Bolze, Simon White, Stephen Riffle, Francisco Tanudjaja, Efren Sandoval, Iva Neveux, Shaun Dabe, Nicolas Casadei, Susanne Motameny, Manal Alaamery, Salam Massadeh, Nora Aljawini, Mansour S. Almutairi, Yaseen M. Arabi, Saleh A. Alqahtani, Fawz S. Al Harthi, Amal Almutairi, Fatima Alqubaishi, Sarah Alotaibi, Albandari Binowayn, Ebtehal A. Alsolm, Hadeel El Bardisy, Mohammad Fawzy, Fang Cai, Nicole Soranzo, Adam Butterworth, Daniel H. Geschwind, Stephanie Arteaga, Alexis Stephens, Manish J. Butte, Paul C. Boutros, Takafumi N. Yamaguchi, Shu Tao, Stefan Eng, Timothy Sanders, Paul J. Tung, Michael E. Broudy, Yu Pan, Alfredo Gonzalez, Nikhil Chavan, Ruth Johnson, Bogdan Pasaniuc, Brian Yaspan, Sandra Smieszek, Carlo Rivolta, Stephanie Bibert, Pierre-Yves Bochud, Maciej Dabrowski, Pawel Zawadzki, Mateusz Sypniewski, Elżbieta Kaja, Pajaree Chariyavilaskul, Voraphoj Nilaratanakul, Nattiya Hirankarn, Vorasuk Shotelersuk, Monnat Pongpanich, Chureerat Phokaew, Wanna Chetruengchai, Katsushi Tokunaga, Masaya Sugiyama, Yosuke Kawai, Takanori Hasegawa, Tatsuhiko Naito, Ho Namkoong, Ryuya Edahiro, Akinori Kimura, Seishi Ogawa, Takanori Kanai, Koichi Fukunaga, Yukinori Okada, Seiya Imoto, Satoru Miyano, Serghei Mangul, Malak S. Abedalthagafi, Hugo Zeberg, Joseph J. Grzymski, Nicole L. Washington, Stephan Ossowski, Kerstin U. Ludwig, Eva C. Schulte, Olaf Riess, Marcin Moniuszko, Miroslaw Kwasniewski, Hamdi Mbarek, Said I. Ismail, Anurag Verma, David B. Goldstein, Krzysztof Kiryluk, Alessandra Renieri, Manuel A. R. Ferreira, J Brent Richards

PLOS Genetics · 03 Nov 2022

Kerui Peng, Jaden Moore, Mohammad Vahed, Jaqueline Brito, Guoyun Kao, Amanda M. Burkhardt, Houda Alachkar, Serghei Mangul

Frontiers in Immunology · 27 Oct 2022

A first update on mapping the human genetic architecture of COVID-19

Gita A. Pathak, Juha Karjalainen, Christine Stevens, Benjamin M. Neale, Mark Daly, Andrea Ganna, Shea J. Andrews, Masahiro Kanai, Mattia Cordioli, Renato Polimanti, Nadia Harerimana, Matti Pirinen, Rachel G. Liao, Karolina Chwialkowska, Amy Trankiem, Mary K. Balaconis, Huy Nguyen, Matthew Solomonson, Kumar Veerapen, Brooke Wolford, Genevieve Roberts, Danny Park, Catherine A. Ball, Marie Coignet, Shannon McCurdy, Spencer Knight, Raghavendran Partha, Brooke Rhead, Miao Zhang, Nathan Berkowitz, Michael Gaddis, Keith Noto, Luong Ruiz, Milos Pavlovic, Eurie L. Hong, Kristin Rand, Ahna Girshick, Harendra Guturu, Asher Haug Baltzell, Mari E. K. Niemi, Souad Rahmouni, Julien Guntz, Yves Beguin, Mattia Cordioli, Sara Pigazzini, Lindokuhle Nkambule, Michel Georges, Michel Moutschen, Benoit Misset, Gilles Darcis, Julien Guiot, Samira Azarzar, Stéphanie Gofflot, Sabine Claassen, Olivier Malaise, Pascale Huynen, Christelle Meuris, Marie Thys, Jessica Jacques, Philippe Léonard, Frederic Frippiat, Jean-Baptiste Giot, Anne-Sophie Sauvage, Christian Von Frenckell, Yasmine Belhaj, Bernard Lambermont, Tomoko Nakanishi, David R. Morrison, Vincent Mooser, J. Brent Richards, Guillaume Butler-Laporte, Vincenzo Forgetta, Rui Li, Biswarup Ghosh, Laetitia Laurent, Alexandre Belisle, Danielle Henry, Tala Abdullah, Olumide Adeleye, Noor Mamlouk, Nofar Kimchi, Zaman Afrasiabi, Nardin Rezk, Branka Vulesevic, Meriem Bouab, Charlotte Guzman, Louis Petitjean, Chris Tselios, Xiaoqing Xue, Jonathan Afilalo, Marc Afilalo, Maureen Oliveira, Bluma Brenner, Nathalie Brassard, Madeleine Durand, Erwin Schurr, Pierre Lepage, Jiannis Ragoussis, Daniel Auld, Michaël Chassé, Daniel E. Kaufmann, G. Mark Lathrop, Darin Adra, Caroline Hayward, Joseph T. Glessner, Douglas M. Shaw, Archie Campbell, Marcela Morris, Hakon Hakonarson, David J. Porteous, Jennifer Below, Anne Richmond, Xiao Chang, Hannah Polikowski, Petty E. Lauren, Hung-Hsin Chen, Zhu Wanying, Chloe Fawns-Ritchie, Kari North, Joseph B. McCormick, Xiao Chang, Joseph R. Glessner, Hakon Hakonarson, Christopher R. Gignoux, Stephen J. Wicks, Kristy Crooks, Kathleen C. Barnes, Michelle Daya, Jonathan Shortt, Nicholas Rafaels, Sameer Chavan, Paul R. H. J. Timmers, James F. Wilson, Albert Tenesa, Shona M. Kerr, Kenton D’Mellow, Doaa Shahin, Yasser M. El-Sherbiny, Kathrin Aprile von Hohenstaufen, Ali Sobh, Madonna M. Eltoukhy, Lindokuhle Nkambul, Tamer A. Elhadidy, Mohamed S. Abd Elghafar, Jehan J. El-Jawhari, Attia A. S. Mohamed, Marwa H. Elnagdy, Amr Samir, Mahmoud Abdel-Aziz, Walid T. Khafaga, Walaa M. El-Lawaty, Mohamed S. Torky, Mohamed R. El-shanshory, Amr M. Yassen, Mohamed A. F. Hegazy, Kamal Okasha, Mohammed A. Eid, Hanteera S. Moahmed, Carolina Medina-Gomez, M. Arfan Ikram, Andre G. Uitterlinden, Reedik Mägi, Lili Milani, Andres Metspalu, Triin Laisk, Kristi Läll, Maarja Lepamets, Tõnu Esko, Ene Reimann, Paul Naaber, Edward Laane, Jaana Pesukova, Pärt Peterson, Kai Kisand, Jekaterina Tabri, Raili Allos, Kati Hensen, Joel Starkopf, Inge Ringmets, Anu Tamm, Anne Kallaste, Helene Alavere, Kristjan Metsalu, Mairo Puusepp, Chiara Batini, Martin D. Tobin, Laura D. Venn, Paul H. Lee, Nick Shrine, Alexander T. Williams, Anna L. Guyatt, Catherine John, Richard J. Packer, Altaf Ali, Robert C. Free, Xueyang Wang, Louise V. Wain, Edward J. Hollox, Catherine E. Bee, Emma L. Adams, Aarno Palotie, Samuli Ripatti, Sanni Ruotsalainen, Kati Kristiansson, Sami Koskelainen, Markus Perola, Kati Donner, Katja Kivinen, Aarno Palotie, Mari Kaunisto, Carlo Rivolta, Pierre-Yves Bochud, Stéphanie Bibert, Noémie Boillat, Semira Gonseth Nussle, Werner Albrich, Mathieu Quinodoz, Dhryata Kamdar, Noémie Suh, Dionysios Neofytos, Véronique Erard, Cathy Voide, Pierre-Yves Bochud, Carlo Rivolta, Stéphanie Bibert, Mathieu Quinodoz, Dhryata Kamdar, Dionysios Neofytos, Véronique Erard, Cathy Voide, R. Friolet, P. Vollenweider, J. L. Pagani, M. Oddo, F. Meyer zu Bentrup, A. Conen, O. Clerc, O. Marchetti, A. Guillet, C. Guyat-Jacques, S. Foucras, M. Rime, J. Chassot, M. Jaquet, R. Merlet Viollet, Y. Lannepoudenx, L. Portopena, P. Y. Bochud, P. Vollenweider, J. L. Pagani, F. Desgranges, P. Filippidis, B. Guéry, D. Haefliger, E. E. Kampouri, O. Manuel, A. Munting, M. Papadimitriou-Olivgeris, J. Regina, L. Rochat-Stettler, V. Suttels, E. Tadini, J. Tschopp, M. Van Singer, B. Viala, N. Boillat-Blanco, T. Brahier, O. Hügli, J. Y. Meuwly, O. Pantet, S. Gonseth Nussle, M. Bochud, V. D’Acremont, S. Estoppey Younes, W. C. Albrich, N. Suh, A. Cerny, L. O’Mahony, C. von Mering, P. Y. Bochud, M. Frischknecht, G-R. Kleger, M. Filipovic, C. R. Kahlert, H. Wozniak, T. Rochat Negro, J. Pugin, K. Bouras, C. Knapp, T. Egger, A. Perret, P. Montillier, C. di Bartolomeo, B. Barda, Rafael de Cid, Anna Carreras, Victor Moreno, Manolis Kogevinas, Iván Galván-Femenía, Natalia Blay, Xavier Farré, Lauro Sumoy, Beatriz Cortés, Josep Maria Mercader, Marta Guindo-Martinez, David Torrents, Judith Garcia-Aymerich, Gemma Castaño-Vinyals, Carlota Dobaño, Marco Gori, Alessandra Renieri, Francesca Mari, Mario Umberto Mondelli, Francesco Castelli, Massimo Vaghi, Stefano Rusconi, Francesca Montagnani, Elena Bargagli, Federico Franchi, Maria Antonietta Mazzei, Luca Cantarini, Danilo Tacconi, Marco Feri, Raffaele Scala, Genni Spargi, Cesira Nencioni, Maria Bandini, Gian Piero Caldarelli, Anna Canaccini, Agostino Ognibene, Antonella D’Arminio Monforte, Massimo Girardis, Andrea Antinori, Daniela Francisci, Elisabetta Schiaroli, Pier Giorgio Scotton, Sandro Panese, Renzo Scaggiante, Matteo Della Monica, Mario Capasso, Giuseppe Fiorentino, Marco Castori, Filippo Aucella, Antonio Di Biagio, Luca Masucci, Serafina Valente, Marco Mandalà, Patrizia Zucchi, Ferdinando Giannattasio, Domenico A. 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2022 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW) · 01 May 2022

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Nature Methods · 01 Apr 2022

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L. Jones, Tara McHugh, Hamza Meghari, Lauran O’Neill, Mark J. Peters, Samiran Ray, Ana Luisa Tomas, Iona Burn, Geraldine Hambrook, Katarina Manso, Ruth Penn, Pradeep Shanmugasundaram, Julie Tebbutt, Danielle Thornton, Jade Cole, Michelle Davies, Rhys Davies, Donna Duffin, Helen Hill, Ben Player, Emma Thomas, Angharad Williams, Denise Griffin, Nycola Muchenje, Mcdonald Mupudzi, Richard Partridge, Jo-Anna Conyngham, Rachel Thomas, Mary Wright, Maria Alvarez Corral, Reni Jacob, Cathy Jones, Craig Denmade, Sarah Beavis, Katie Dale, Rachel Gascoyne, Joanne Hawes, Kelly Pritchard, Lesley Stevenson, Amanda Whileman, Patricia Doble, Joanne Hutter, Corinne Pawley, Charmaine Shovelton, Marius Vaida, Deborah Butcher, Susie O’Sullivan, Nicola Butterworth-Cowin, Norfaizan Ahmad, Joann Barker, Kris Bauchmuller, Sarah Bird, Kay Cawthron, Kate Harrington, Yvonne Jackson, Faith Kibutu, Becky Lenagh, Shamiso Masuko, Gary H. 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Suttichet, Vorasuk Shotelersuk, Monnat Pongpanich, Chureerat Phokaew, Wanna Chetruengchai, Watsamon Jantarabenjakul, Opass Putchareon, Pattama Torvorapanit, Thanyawee Puthanakit, Pintip Suchartlikitwong, Nattiya Hirankarn, Voraphoj Nilaratanakul, Pimpayao Sodsai, Ben M. Brumpton, Kristian Hveem, Cristen Willer, Wei Zhou, Tormod Rogne, Erik Solligard, Bjørn Olav Åsvold, Malak Abedalthagafi, Manal Alaamery, Saleh Alqahtani, Duna Barakeh, Fawz Al Harthi, Ebtehal Alsolm, Leen Abu Safieh, Albandary M. Alowayn, Fatimah Alqubaishi, Amal Al Mutairi, Serghei Mangul, Abdulraheem Alshareef, Mona Sawaji, Mansour Almutairi, Nora Aljawini, Nour Albesher, Yaseen M. Arabi, Ebrahim S. Mahmoud, Amin K. Khattab, Roaa T. Halawani, Ziab Z. Alahmadey, Jehad K. Albakri, Walaa A. Felemban, Bandar A. 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Nature · 07 Mar 2022

SARS-CoV-2 Respiratory distress syndrome Genome-wide association studies

The Pioneer Advantage: Filling the blank spots on the map of genome diversity in Europe

Taras K Oleksyk, Walter W Wolfsberger, Khrystyna Schubelka, Serghei Mangul, Stephen J O’Brien

GigaScience · 01 Jan 2022

2021

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

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Nature Biotechnology · 29 Dec 2021

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Ludwig, Selina Rolker, Markus M. Nöthen, Julia Fazaal, Verena Keitel, Björn Jensen, Torsten Feldt, Lisa Knopp, Julia Schröder, Carlo Maj, Fabian Brand, Marc M. Berger, Thorsten Brenner, Anke Hinney, Oliver Witzke, Robert Bals, Christian Herr, Nicole Ludwig, Jörn Walter, Jochen Schneider, Johanna Erber, Christoph D. Spinner, Clemens M. Wendtner, Christof Winter, Ulrike Protzer, Nicolas Casadei, Stephan Ossowski, Olaf H. Riess, Eva C. Schulte, J. Brent Richards, Guillaume Butler-Laporte, Mirosław Kwasniewski, Urszula Korotko, Karolina Chwialkowska, Magdalena Niemira, Jerzy Jaroszewicz, Barbara Sobala-Szczygiel, Beata Puzanowska, Anna Parfieniuk-Kowerda, Diana Martonik, Anna Moniuszko-Malinowska, Sławomir Pancewicz, Dorota Zarębska-Michaluk, Krzysztof Simon, Monika Pazgan-Simon, Iwona Mozer-Lisewska, Maciej Bura, Agnieszka Adamek, Krzysztof Tomasiewicz Małgorzata Pawłowska, Anna Piekarska, Aleksandra Berkan-Kawinska, Andrzej Horban, Justyna Kowalska, Regina Podlasin, Piotr Wasilewski, Arsalin Azzadin, Miroslaw Czuczwar, Slawomir Czaban, Paweł Olszewski, Jacek Bogocz, Magdalena Ochab, Anna Kruk, Sandra Uszok, Agnieszka Bielska, Anna Szałkowska, Justyna Raczkowska, Gabriela Sokołowska, Joanna Chorostowska-Wynimko, Aleksandra Jezela-Stanek, Adriana Roży, Urszula Lechowicz, Urszula Polowianiuk, Kamil Grubczak, Aleksandra Starosz, Andrzej Eljaszewicz, Wiktoria Izdebska, Adam Krętowski, Robert Flisiak, Marcin Moniuszko, Malak Abedalthaga Alaamery, Salam Massadeh, Mohamed Fawzy, Hadeel AlBardis, Nora Aljawini, Moneera Alsuwailm, Faisal Almalki, Serghei Mangul, Junghyun Jung, Hamdi Mbarek, Chadi Saad, Yaser Al-Sarraj, Wadha Al-Muftah, Radja Badji, Asma Al Thani, Said I. Ismail, Francesca Mari, Alessandra Renieri, Simone Furini

Human Genetics · 10 Dec 2021

A comprehensive analysis of code and data availability in biomedical research

Dhrithi Deshpande, Aditya Sarkar, Ruiwei Guo, Andrew Moore, Nicholas Darci-Maher, SERGHEI MANGUL

Center for Open Science · 27 Nov 2021

The systematic assessment of completeness of public metadata accompanying omics studies

Yu-Ning Huang, Anushka Rajesh, Ram Ayyala, Aditya Sarkar, Ruiwei Guo, Elizabeth Ling, Irina Nakashidze, Man Yee Wong, Jieting Hu, Dottie Yu, Qiushi Peng, Grace Scheg, Khooshbu Kantibhai Patel, Tejasvene Ramesh, Ke Wang, Anushka Yadav, Fangyun Liu, Jay Himanshu Mehta, Grigore Boldirev, Alexey Nosov, Yutong Chang, Malak S. Abedalthagafi, Serghei Mangul

Cold Spring Harbor Laboratory · 23 Nov 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, Ronan Lordan, 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, David Mai, Yuchen Sun, Joel D. Boerckel, Christian Brueffer, James Brian Byrd, Jeremy P. Kamil, Jinhui Wang, Ryan Velazquez, Gregory L. Szeto, John P. Barton, Rishi Raj Goel, Serghei Mangul, Tiago Lubiana, Anthony Gitter, Casey S. Greene

mSystems · 26 Oct 2021

Systematic evaluation of transcriptomics-based deconvolution methods and references using thousands of clinical samples

Brian B. Nadel, Meritxell Oliva, Benjamin L. Shou, Keith Mitchell, Feiyang Ma, Dennis J. Montoya, Alice Mouton, Sarah Kim-Hellmuth, Barbara E. Stranger, Matteo Pellegrini, Serghei Mangul

Briefings in Bioinformatics · 03 Oct 2021

Ancestral diversity is limited in published 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

Immunity · 01 Oct 2021

Integrating big data computational skills in education to facilitate reproducibility and transparency in pharmaceutical sciences

Kerui Peng, Yu Ning Huang, Varuni Sarwal, Houda Alachkar, Annie Wong‐Beringer, Serghei Mangul

JACCP: JOURNAL OF THE AMERICAN COLLEGE OF CLINICAL PHARMACY · 01 Oct 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 Albes, Hani M. Al-Afghani, Bader Alghamdi, Mansour S. Almutairi, 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 · 15 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

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

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

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 · 29 Jan 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

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, Ronan Lordan, Yanjun Qi, Yuchen Sun, Christian Brueffer, Jeffrey M. Field, Marouen Ben Guebila, Nafisa M. Jadavji, Ashwin N. Skelly, Bharath Ramsundar, Jinhui Wang, Rishi Raj Goel, YoSon Park, the COVID-19 Review Consortium, Simina M. Boca, Anthony Gitter, Casey S. Greene

arXiv · 01 Jan 2021

A Novel Network Representation of SARS-CoV-2 Sequencing Data

Sergey Knyazev, Daniel Novikov, Mark Grinshpon, Harman Singh, Ram Ayyala, Varuni Sarwal, Roya Hosseini, Pelin Icer Baykal, Pavel Skums, Ellsworth Campbell, Serghei Mangul, Alex Zelikovsky

Bioinformatics Research and Applications · 01 Jan 2021

Minimal spanning network Genetic relatedness SARS-CoV-2

2020

Systematic overview of challenges and opportunities of computational data-driven research in biology

Tejasvene Ramesh, Karishma Chhugani, Vanessa Jönsson, SERGHEI MANGUL

Center for Open Science · 25 Nov 2020

cancer single cell ovarian cancer

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

Genome Biology · 26 Oct 2020

PUMAA: A Platform for Accessible Microbiome Analysis in the Undergraduate Classroom

Keith Mitchell, Jiem Ronas, Christopher Dao, Amanda C. Freise, Serghei Mangul, Casey Shapiro, Jordan Moberg Parker

Frontiers in Microbiology · 06 Oct 2020

A Quantitative Proteome Map of the Human Body

Lihua Jiang, Meng Wang, Shin Lin, Ruiqi Jian, Xiao Li, Joanne Chan, Guanlan Dong, Huaying Fang, Aaron E. Robinson, Michael P. Snyder, François Aguet, Shankara Anand, Kristin G. Ardlie, Stacey Gabriel, Gad Getz, Aaron Graubert, Kane Hadley, Robert E. Handsaker, Katherine H. Huang, Seva Kashin, Daniel G. MacArthur, Samuel R. Meier, Jared L. Nedzel, Duyen Y. Nguyen, Ayellet V. Segrè, Ellen Todres, Brunilda Balliu, Alvaro N. Barbeira, Alexis Battle, Rodrigo Bonazzola, Andrew Brown, Christopher D. Brown, Stephane E. Castel, Don Conrad, Daniel J. Cotter, Nancy Cox, Sayantan Das, Olivia M. de Goede, Emmanouil T. Dermitzakis, Barbara E. Engelhardt, Eleazar Eskin, Tiffany Y. Eulalio, Nicole M. Ferraro, Elise 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, Hae Kyung Im, Brian Jo, Silva Kasela, Manolis Kellis, Sarah Kim-Hellmuth, Alan Kwong, Tuuli Lappalainen, Xin Li, Yanyu Liang, Serghei Mangul, Pejman Mohammadi, Stephen B. Montgomery, Manuel Muñoz-Aguirre, Daniel C. Nachun, Andrew B. Nobel, Meritxell Oliva, YoSon Park, Yongjin Park, Princy Parsana, Ferran Reverter, John M. Rouhana, Chiara Sabatti, Ashis Saha, Andrew D. Skol, Matthew Stephens, Barbara E. Stranger, Benjamin J. Strober, Nicole A. Teran, Ana Viñuela, Gao Wang, Xiaoquan Wen, Fred Wright, Valentin Wucher, Yuxin Zou, Pedro G. Ferreira, Gen Li, Marta Melé, Esti Yeger-Lotem, Mary E. Barcus, Debra Bradbury, Tanya Krubit, Jeffrey A. McLean, Liqun Qi, Karna Robinson, Nancy V. Roche, Anna M. Smith, Leslie Sobin, 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, Philip A. Branton, 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, Rajinder Kaul, Muhammad G. Kibriya, Jin Billy Li, Qin Li, Sandra E. Linder, Brandon L. Pierce, Lindsay F. Rizzardi, Kevin S. Smith, John Stamatoyannopoulos, Hua Tang, 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 Oct 2020

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, François Aguet, Shankara Anand, Kristin G. Ardlie, Stacey Gabriel, Gad A. Getz, Aaron Graubert, Kane Hadley, Robert E. Handsaker, Katherine H. Huang, Seva Kashin, Xiao Li, Daniel G. MacArthur, Samuel R. Meier, Jared L. Nedzel, Duyen T. Nguyen, Ayellet V. Segrè, Ellen Todres, Brunilda Balliu, Alvaro N. Barbeira, Alexis Battle, Rodrigo Bonazzola, Andrew Brown, Christopher D. Brown, Stephane E. Castel, Donald F. Conrad, Daniel J. Cotter, Nancy Cox, Sayantan Das, Olivia M. de Goede, Emmanouil T. Dermitzakis, Jonah Einson, Barbara E. Engelhardt, Eleazar Eskin, Tiffany Y. Eulalio, Nicole M. Ferraro, Elise D. Flynn, Laure Fresard, Eric R. Gamazon, Diego Garrido-Martín, Nicole R. Gay, Michael J. Gloudemans, Roderic Guigó, Andrew R. Hame, Yuan He, Paul J. Hoffman, Farhad Hormozdiari, Lei Hou, Hae Kyung Im, Brian Jo, Silva Kasela, Manolis Kellis, Sarah Kim-Hellmuth, Alan Kwong, Tuuli Lappalainen, Xin Li, Yanyu Liang, Serghei Mangul, Pejman Mohammadi, Stephen B. Montgomery, Manuel Muñoz-Aguirre, Daniel C. Nachun, Andrew B. Nobel, Meritxell Oliva, YoSon Park, Yongjin Park, Princy Parsana, Abhiram S. Rao, Ferran Reverter, John M. Rouhana, Chiara Sabatti, Ashis Saha, Matthew Stephens, Barbara E. Stranger, Benjamin J. Strober, Nicole A. Teran, Ana Viñuela, Gao Wang, Xiaoquan Wen, Fred Wright, Valentin Wucher, Yuxin Zou, Pedro G. Ferreira, Gen Li, Marta Melé, Esti Yeger-Lotem, Mary E. Barcus, Debra Bradbury, Tanya Krubit, Jeffrey A. McLean, Liqun Qi, Karna Robinson, Nancy V. Roche, Anna M. Smith, Leslie Sobin, 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, Philip A. Branton, 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

Science · 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, François Aguet, Shankara Anand, Kristin G. Ardlie, Stacey Gabriel, Gad A. Getz, Aaron Graubert, Kane Hadley, Robert E. Handsaker, Katherine H. Huang, Seva Kashin, Xiao Li, Daniel G. MacArthur, Samuel R. Meier, Jared L. Nedzel, Duyen T. Nguyen, Ayellet V. Segrè, Ellen Todres, Brunilda Balliu, Alvaro N. Barbeira, Alexis Battle, Rodrigo Bonazzola, Andrew Brown, Christopher D. Brown, Stephane E. Castel, Donald F. Conrad, Daniel J. Cotter, Nancy Cox, Sayantan Das, Olivia M. de Goede, Emmanouil T. Dermitzakis, Jonah Einson, Barbara E. Engelhardt, Eleazar Eskin, Tiffany Y. Eulalio, Nicole M. Ferraro, Elise D. Flynn, Laure Fresard, Eric R. Gamazon, Diego Garrido-Martín, Nicole R. Gay, Michael J. Gloudemans, Roderic Guigó, Andrew R. Hame, Yuan He, Paul J. Hoffman, Farhad Hormozdiari, Lei Hou, Hae Kyung Im, Brian Jo, Silva Kasela, Manolis Kellis, Sarah Kim-Hellmuth, Alan Kwong, Tuuli Lappalainen, Xin Li, Yanyu Liang, Serghei Mangul, Pejman Mohammadi, Stephen B. Montgomery, Manuel Muñoz-Aguirre, Daniel C. Nachun, Andrew B. Nobel, Meritxell Oliva, YoSon Park, Yongjin Park, Princy Parsana, Abhiram S. Rao, Ferran Reverter, John M. Rouhana, Chiara Sabatti, Ashis Saha, Matthew Stephens, Barbara E. Stranger, Benjamin J. Strober, Nicole A. Teran, Ana Viñuela, Gao Wang, Xiaoquan Wen, Fred Wright, Valentin Wucher, Yuxin Zou, Pedro G. Ferreira, Gen Li, Marta Melé, Esti Yeger-Lotem, Mary E. Barcus, Debra Bradbury, Tanya Krubit, Jeffrey A. McLean, Liqun Qi, Karna Robinson, Nancy V. Roche, Anna M. Smith, Leslie Sobin, 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, Philip A. Branton, 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

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, François Aguet, Shankara Anand, Kristin G. Ardlie, Stacey Gabriel, Gad A. Getz, Aaron Graubert, Kane Hadley, Robert E. Handsaker, Katherine H. Huang, Seva Kashin, Xiao Li, Daniel G. MacArthur, Samuel R. Meier, Jared L. Nedzel, Duyen T. Nguyen, Ayellet V. Segrè, Ellen Todres, Brunilda Balliu, Alvaro N. Barbeira, Alexis Battle, Rodrigo Bonazzola, Andrew Brown, Christopher D. Brown, Stephane E. Castel, Donald F. Conrad, Daniel J. Cotter, Nancy Cox, Sayantan Das, Olivia M. de Goede, Emmanouil T. Dermitzakis, Jonah Einson, Barbara E. Engelhardt, Eleazar Eskin, Tiffany Y. Eulalio, Nicole M. Ferraro, Elise D. Flynn, Laure Fresard, Eric R. Gamazon, Diego Garrido-Martín, Nicole R. Gay, Michael J. Gloudemans, Roderic Guigó, Andrew R. Hame, Yuan He, Paul J. Hoffman, Farhad Hormozdiari, Lei Hou, Hae Kyung Im, Brian Jo, Silva Kasela, Manolis Kellis, Sarah Kim-Hellmuth, Alan Kwong, Tuuli Lappalainen, Xin Li, Yanyu Liang, Serghei Mangul, Pejman Mohammadi, Stephen B. Montgomery, Manuel Muñoz-Aguirre, Daniel C. Nachun, Andrew B. Nobel, Meritxell Oliva, YoSon Park, Yongjin Park, Princy Parsana, Abhiram S. Rao, Ferran Reverter, John M. Rouhana, Chiara Sabatti, Ashis Saha, Matthew Stephens, Barbara E. Stranger, Benjamin J. Strober, Nicole A. Teran, Ana Viñuela, Gao Wang, Xiaoquan Wen, Fred Wright, Valentin Wucher, Yuxin Zou, Pedro G. Ferreira, Gen Li, Marta Melé, Esti Yeger-Lotem, Mary E. Barcus, Debra Bradbury, Tanya Krubit, Jeffrey A. McLean, Liqun Qi, Karna Robinson, Nancy V. Roche, Anna M. Smith, Leslie Sobin, 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, Philip A. Branton, 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

Science · 11 Sep 2020

cancer single cell ovarian cancer

The GTEx Consortium atlas of genetic regulatory effects across human tissues

François Aguet, Shankara Anand, Kristin G. Ardlie, Stacey Gabriel, Gad A. Getz, Aaron Graubert, Kane Hadley, Robert E. Handsaker, Katherine H. Huang, Seva Kashin, Xiao Li, Daniel G. MacArthur, Samuel R. Meier, Jared L. Nedzel, Duyen T. Nguyen, Ayellet V. Segrè, Ellen Todres, Brunilda Balliu, Alvaro N. Barbeira, Alexis Battle, Rodrigo Bonazzola, Andrew Brown, Christopher D. Brown, Stephane E. Castel, Donald F. Conrad, Daniel J. Cotter, Nancy Cox, Sayantan Das, Olivia M. de Goede, Emmanouil T. Dermitzakis, Jonah Einson, Barbara E. Engelhardt, Eleazar Eskin, Tiffany Y. Eulalio, Nicole M. Ferraro, Elise D. Flynn, Laure Fresard, Eric R. Gamazon, Diego Garrido-Martín, Nicole R. Gay, Michael J. Gloudemans, Roderic Guigó, Andrew R. Hame, Yuan He, Paul J. Hoffman, Farhad Hormozdiari, Lei Hou, Hae Kyung Im, Brian Jo, Silva Kasela, Manolis Kellis, Sarah Kim-Hellmuth, Alan Kwong, Tuuli Lappalainen, Xin Li, Yanyu Liang, Serghei Mangul, Pejman Mohammadi, Stephen B. Montgomery, Manuel Muñoz-Aguirre, Daniel C. Nachun, Andrew B. Nobel, Meritxell Oliva, YoSon Park, Yongjin Park, Princy Parsana, Abhiram S. Rao, Ferran Reverter, John M. Rouhana, Chiara Sabatti, Ashis Saha, Matthew Stephens, Barbara E. Stranger, Benjamin J. Strober, Nicole A. Teran, Ana Viñuela, Gao Wang, Xiaoquan Wen, Fred Wright, Valentin Wucher, Yuxin Zou, Pedro G. Ferreira, Gen Li, Marta Melé, Esti Yeger-Lotem, Mary E. Barcus, Debra Bradbury, Tanya Krubit, Jeffrey A. McLean, Liqun Qi, Karna Robinson, Nancy V. Roche, Anna M. Smith, Leslie Sobin, 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, Philip A. Branton, 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

Science · 11 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, François Aguet, Shankara Anand, Kristin G. Ardlie, Stacey Gabriel, Gad A. Getz, Aaron Graubert, Kane Hadley, Robert E. Handsaker, Katherine H. Huang, Seva Kashin, Xiao Li, Daniel G. MacArthur, Samuel R. Meier, Jared L. Nedzel, Duyen T. Nguyen, Ayellet V. Segrè, Ellen Todres, Brunilda Balliu, Alvaro N. Barbeira, Alexis Battle, Rodrigo Bonazzola, Andrew Brown, Christopher D. Brown, Stephane E. Castel, Donald F. Conrad, Daniel J. Cotter, Nancy Cox, Sayantan Das, Olivia M. de Goede, Emmanouil T. Dermitzakis, Jonah Einson, Barbara E. Engelhardt, Eleazar Eskin, Tiffany Y. Eulalio, Nicole M. Ferraro, Elise D. Flynn, Laure Fresard, Eric R. Gamazon, Diego Garrido-Martín, Nicole R. Gay, Michael J. Gloudemans, Roderic Guigó, Andrew R. Hame, Yuan He, Paul J. Hoffman, Farhad Hormozdiari, Lei Hou, Hae Kyung Im, Brian Jo, Silva Kasela, Manolis Kellis, Sarah Kim-Hellmuth, Alan Kwong, Tuuli Lappalainen, Xin Li, Yanyu Liang, Serghei Mangul, Pejman Mohammadi, Stephen B. Montgomery, Manuel Muñoz-Aguirre, Daniel C. Nachun, Andrew B. Nobel, Meritxell Oliva, YoSon Park, Yongjin Park, Princy Parsana, Abhiram S. Rao, Ferran Reverter, John M. Rouhana, Chiara Sabatti, Ashis Saha, Matthew Stephens, Barbara E. Stranger, Benjamin J. Strober, Nicole A. Teran, Ana Viñuela, Gao Wang, Xiaoquan Wen, Fred Wright, Valentin Wucher, Yuxin Zou, Pedro G. Ferreira, Gen Li, Marta Melé, Esti Yeger-Lotem, Mary E. Barcus, Debra Bradbury, Tanya Krubit, Jeffrey A. McLean, Liqun Qi, Karna Robinson, Nancy V. Roche, Anna M. Smith, Leslie Sobin, 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, Philip A. Branton, 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

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, François Aguet, Shankara Anand, Kristin G. Ardlie, Stacey Gabriel, Gad A. Getz, Aaron Graubert, Kane Hadley, Robert E. Handsaker, Katherine H. Huang, Seva Kashin, Xiao Li, Daniel G. MacArthur, Samuel R. Meier, Jared L. Nedzel, Duyen T. Nguyen, Ayellet V. Segrè, Ellen Todres, François Aguet, Shankara Anand, Kristin G. Ardlie, Brunilda Balliu, Alvaro N. Barbeira, Alexis Battle, Rodrigo Bonazzola, Andrew Brown, Christopher D. Brown, Stephane E. Castel, Donald F. Conrad, Daniel J. Cotter, Nancy Cox, Sayantan Das, Olivia M. de Goede, Emmanouil T. Dermitzakis, Jonah Einson, Barbara E. Engelhardt, Eleazar Eskin, Tiffany Y. Eulalio, Nicole M. Ferraro, Elise D. Flynn, Laure Fresard, Eric R. Gamazon, Diego Garrido-Martín, Nicole R. Gay, Gad A. Getz, Michael J. Gloudemans, Aaron Graubert, Roderic Guigó, Kane Hadley, Andrew R. Hame, Robert E. Handsaker, Yuan He, Paul J. Hoffman, Farhad Hormozdiari, Lei Hou, Katherine H. Huang, Hae Kyung Im, Brian Jo, Silva Kasela, Seva Kashin, Manolis Kellis, Sarah Kim-Hellmuth, Alan Kwong, Tuuli Lappalainen, Xiao Li, Xin Li, Yanyu Liang, Daniel G. MacArthur, Serghei Mangul, Samuel R. Meier, Pejman Mohammadi, Stephen B. Montgomery, Manuel Muñoz-Aguirre, Daniel C. Nachun, Jared L. Nedzel, Duyen T. Nguyen, Andrew B. Nobel, Meritxell Oliva, Yo Son Park, Yongjin Park, Princy Parsana, Abhiram S. Rao, Ferran Reverter, John M. Rouhana, Chiara Sabatti, Ashis Saha, Ayellet V. Segrè, Andrew D. Skol, Matthew Stephens, Barbara E. Stranger, Benjamin J. Strober, Nicole A. Teran, Ellen Todres, Ana Viñuela, Gao Wang, Xiaoquan Wen, Fred Wright, Valentin Wucher, Yuxin Zou, Pedro G. Ferreira, Gen Li, Marta Melé, Esti Yeger-Lotem, Mary E. Barcus, Debra Bradbury, Tanya Krubit, Jeffrey A. McLean, Liqun Qi, Karna Robinson, Nancy V. Roche, Anna M. Smith, Leslie Sobin, 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, Lei Hou, Farzana Jasmine, Lihua Jiang, Rajinder Kaul, Manolis Kellis, Muhammad G. Kibriya, Jin Billy Li, Qin Li, Shin Lin, Sandra E. Linder, Stephen B. Montgomery, Meritxell Oliva, Yongjin Park, Brandon L. Pierce, Lindsay F. Rizzardi, Andrew D. Skol, Kevin S. Smith, Michael Snyder, John Stamatoyannopoulos, Barbara E. Stranger, Hua Tang, Meng Wang, Philip A. Branton, 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, Kristin G. Ardlie, Tuuli Lappalainen

Genome Biology · 11 Sep 2020

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

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 · 11 Sep 2020

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

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 · 07 Aug 2020

cancer machine learning

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 · 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

Recommendations to enhance rigor and reproducibility in biomedical research

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

GigaScience · 01 Jun 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

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

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 · 04 Oct 2019

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

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

Interpreting and integrating big data in the life sciences

Serghei Mangul

Emerging Topics in Life Sciences · 26 Jun 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 · 01 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 · 01 Mar 2019

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

Hidden Treasures in Contemporary RNA Sequencing

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

Hidden Treasures in Contemporary RNA Sequencing · 01 Jan 2019

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

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

Keith Mitchell, Christopher Dao, Amanda Freise, Serghei Mangul, Jordan Moberg Parker

Cold Spring Harbor Laboratory · 29 Nov 2018

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 · 30 Aug 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

Involving undergraduates in genomics research to narrow the education–research gap

Serghei Mangul, Lana S Martin, Eleazar Eskin

Nature Biotechnology · 01 Apr 2018

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

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

Genetic effects on gene expression across human tissues

Nature · 12 Oct 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 · 11 Oct 2017

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

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

Reference-free comparison of microbial communities via de Bruijn graphs

Serghei Mangul, David Koslicki

Proceedings of the 7th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics · 02 Oct 2016