Serghei Mangul

Publication Activity (10 Years)

Years Active: 2020-2024
Publications (10 Years): 32

Top Topics

Gene Expression

Respiratory Syndrome Coronavirus

Top Venues

Nature communications

Briefings in bioinformatics

This page only lists publications with an associated author ORCID identifier.

Publications

Pelin Icer Baykal, Paweł Piotr Łabaj, Florian Markowetz, Lynn M Schriml, Daniel Johannes Stekhoven, Serghei Mangul, Niko Beerenwinkel
Genomic reproducibility in the bioinformatics era. Genome biology 25 (1) (2024)
Mohammed Alser, Brendan Lawlor, Richard J Abdill, Sharon Waymost, Ram Ayyala, Neha Rajkumar, Nathan LaPierre, Jaqueline Brito, André M Ribeiro-Dos-Santos, Nour Almadhoun, Varuni Sarwal, Can Firtina, Tomasz Osinski, Eleazar Eskin, Qiyang Hu, Derek Strong, Byoung-Do B D Kim, Malak S Abedalthagafi, Onur Mutlu, Serghei Mangul
Packaging and containerization of computational methods. Nature protocols (2024)
Pelin Icer Baykal, Paweł Piotr Łabaj, Florian Markowetz, Lynn M Schriml, Daniel Johannes Stekhoven, Serghei Mangul, Niko Beerenwinkel
Genomic reproducibility in the bioinformatics era. Genome biology 25 (1) (2024)
Varuni Sarwal, Seungmo Lee, Jianzhi Yang, Sriram Sankararaman, Mark Chaisson, Eleazar Eskin, Serghei Mangul
VISTA: an integrated framework for structural variant discovery. Briefings in bioinformatics 25 (5) (2024)
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, Sinéad B Chapman, Simone Rubinacci, Matthew DeFelice, Jonna L Grimsby, Tamrat Abebe, Melkam Alemayehu, Fred K Ashaba, Elizabeth G Atkinson, Tim B 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, Kamulegeya Rogers, Gabriel Kigen, Soyeon Kim, Nastassja Koen, Edith Kamaru 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, Jessie Tang, David C Whiteman, Mary T Yohannes, Mingrui Yu, Kai Yuan, null null, 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 López-Jaramillo, Nelson Freimer, Roel A Ophoff, Loes M Olde Loohuis, Michael E Talkowski, Benjamin M Neale, Daniel P Howrigan, Alicia R Martin
A blended genome and exome sequencing method captures genetic variation in an unbiased, high-quality, and cost-effective manner. bioRxiv : the preprint server for biology (2024)
Dottie Yu, Ram Ayyala, Sarah Hany Sadek, Likhitha Chittampalli, Hafsa Farooq, Junghyun Jung, Abdullah Al Nahid, Grigore Boldirev, Mina Jung, Sungmin Park, Austin Nguyen, Alex Zelikovsky, Nicholas Mancuso, Jong Wha J Joo, Reid F Thompson, Houda Alachkar, Serghei Mangul
A rigorous benchmarking of alignment-based HLA typing algorithms for RNA-seq data. bioRxiv : the preprint server for biology (2024)
Pelin Icer Baykal, Paweł Piotr Łabaj, Florian Markowetz, Lynn M Schriml, Daniel Johannes Stekhoven, Serghei Mangul, Niko Beerenwinkel
Genomic reproducibility in the bioinformatics era. Genome biology 25 (1) (2024)
Fatemeh Mohebbi, Alex Zelikovsky, Serghei Mangul, Gerardo Chowell, Pavel Skums
Early detection of emerging viral variants through analysis of community structure of coordinated substitution networks. Nature communications 15 (1) (2024)
Fatemeh Mohebbi, Alex Zelikovsky, Serghei Mangul, Gerardo Chowell, Pavel Skums
Early detection of emerging viral variants through analysis of community structure of coordinated substitution networks. Nature communications 15 (1) (2024)
Fatemeh Mohebbi, Alex Zelikovsky, Serghei Mangul, Gerardo Chowell, Pavel Skums
Early detection of emerging viral variants through analysis of community structure of coordinated substitution networks. Nature communications 15 (1) (2024)
Dottie Yu, Ram Ayyala, Sarah Hany Sadek, Likhitha Chittampalli, Hafsa Farooq, Junghyun Jung, Abdullah Al Nahid, Grigore Boldirev, Mina Jung, Sungmin Park, Austin Nguyen, Alex Zelikovsky, Nicholas Mancuso, Jong Wha J Joo, Reid F Thompson, Houda Alachkar, Serghei Mangul
A rigorous benchmarking of alignment-based HLA typing algorithms for RNA-seq data. bioRxiv : the preprint server for biology (2024)
Varuni Sarwal, Jaqueline Brito, Serghei Mangul, David Koslicki
TAMPA: interpretable analysis and visualization of metagenomics-based taxon abundance profiles. GigaScience 12 (2023)
Varuni Sarwal, Jaqueline Brito, Serghei Mangul, David Koslicki
TAMPA: interpretable analysis and visualization of metagenomics-based taxon abundance profiles. GigaScience 12 (2023)
Varuni Sarwal, Jaqueline Brito, Serghei Mangul, David Koslicki
TAMPA: interpretable analysis and visualization of metagenomics-based taxon abundance profiles. GigaScience 12 (2023)
Nitesh Kumar Sharma, Ram Ayyala, Dhrithi Deshpande, Yesha M Patel, Viorel Munteanu, Dumitru Ciorba, Andrada Fiscutean, Mohammad Vahed, Aditya Sarkar, Ruiwei Guo, Andrew Moore, Nicholas Darci-Maher, Nicole A Nogoy, Malak S Abedalthagafi, Serghei Mangul
Analytical code sharing practices in biomedical research. bioRxiv : the preprint server for biology (2023)
Kerui Peng, Theodore S 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
Rigorous benchmarking of T-cell receptor repertoire profiling methods for cancer RNA sequencing. Briefings in bioinformatics (2023)
Walter W Wolfsberger, Karishma Chhugani, Khrystyna Shchubelka, Alina Frolova, Yuriy Salyha, Oksana Zlenko, Mykhailo Arych, Dmytro Dziuba, Andrii Parkhomenko, Volodymyr Smolanka, Zeynep Hülya Gümüş, Efe Sezgin, Alondra Diaz-Lameiro, Viktor R Toth, Megi Maci, Eric Bortz, Fyodor A Kondrashov, Patricia M Morton, Paweł Piotr Łabaj, Veronika Romero, Jakub P Hlávka, Serghei Mangul, Tarás K Oleksyk
Scientists without borders: lessons from Ukraine. GigaScience 12 (2023)
Halie M Rando, Adam L MacLean, Alexandra J Lee, Ronan Lordan, Sandipan Ray, Vikas Bansal, Ashwin N Skelly, Elizabeth A 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 Lee Szeto, John P Barton, Rishi Raj Goel, Serghei Mangul, Tiago Lubiana Alves, null null, Anthony Gitter, Casey S Greene
Correction for Rando et al., "Pathogenesis, Symptomatology, and Transmission of SARS-CoV-2 through Analysis of Viral Genomics and Structure". mSystems 7 (1) (2022)
Varuni Sarwal, Sebastian Niehus, Ram Ayyala, Minyoung Kim, Aditya Sarkar, Sei Chang, Angela Lu, Neha Rajkumar, Nicholas Darfci-Maher, Russell Littman, Karishma Chhugani, Arda Soylev, Zoia Comarova, Emily Wesel, Jacqueline Castellanos, Rahul Chikka, Margaret G Distler, Eleazar Eskin, Jonathan Flint, Serghei Mangul
A comprehensive benchmarking of WGS-based deletion structural variant callers. Briefings in bioinformatics 23 (4) (2022)
Brian B Nadel, Meritxell Oliva, Benjamin L Shou, Keith Mitchell, Feiyang Ma, Dennis J Montoya, Alice Mouton, Sarah Kim-Hellmuth, Barbara E Stranger, Matteo Pellegrini, Serghei Mangul
Systematic evaluation of transcriptomics-based deconvolution methods and references using thousands of clinical samples. Briefings in bioinformatics 22 (6) (2022)
Sergey Knyazev, Karishma Chhugani, Varuni Sarwal, Ram Ayyala, Harman Singh, Smruthi Karthikeyan, Dhrithi Deshpande, Pelin Icer Baykal, Zoia Comarova, Angela Lu, Yuri B Porozov, Tetyana I Vasylyeva, Joel O Wertheim, Braden T Tierney, Charles Y Chiu, Ren Sun, Aiping Wu, Malak S Abedalthagafi, Victoria M Pak, Shivashankar H Nagaraj, Adam L Smith, Pavel Skums, Bogdan Pasaniuc, Andrey Komissarov, Christopher E Mason, Eric Bortz, Philippe Lemey, Fyodor Kondrashov, Niko Beerenwinkel, Tommy Tsan-Yuk Lam, Nicholas C Wu, Alex Zelikovsky, Rob Knight, Keith A Crandall, Serghei Mangul
Unlocking capacities of genomics for the COVID-19 response and future pandemics. Nature methods 19 (4) (2022)
Tarás K Oleksyk, Walter W Wolfsberger, Khrystyna Schubelka, Serghei Mangul, Stephen J O'Brien
The Pioneer Advantage: Filling the blank spots on the map of genome diversity in Europe. GigaScience 11 (2022)
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
Virtual meetings promise to eliminate geographical and administrative barriers and increase accessibility, diversity and inclusivity. Nature biotechnology 40 (1) (2022)
Guillaume Butler-Laporte, Gundula Povysil, Jack A Kosmicki, Elizabeth T Cirulli, Theodore G Drivas, Simone Furini, Chadi Saad, Axel Schmidt, Pawel Olszewski, Urszula Korotko, Mathieu Quinodoz, Elifnaz Celik, Kousik Kundu, Klaudia Walter, Junghyun Jung, Amy D Stockwell, Laura G Sloofman G Sloofman, Daniel M Jordan, Ryan C Thompson, Diane M Del Valle, Nicole W 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 S 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 R 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, null null, null null, null null, null null, null null, null null, null null, null null, Daniel H Geschwind, Stephanie A Arteaga, Alexis Stephens, Manish J Butte, Paul C Boutros, Takafumi N Yamaguchi, Shu Tao, Stefan E Eng, Timothy Sanders, Paul J Tung, Michael E Broudy, Yu Pan, Alfredo E Gonzalez, Nikhil Chavan, Ruth Johnson, Bogdan Pasaniuc, Brian L Yaspan, Christos M Polymeropoulos, Carlo Rivolta, Stephanie Bibert, Pierre-Yves Bochud, Maciej Dąbrowski, 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, John Brent Richards
Exome-wide association study to identify rare variants influencing COVID-19 outcomes: Results from the Host Genetics Initiative. PLoS genetics 18 (11) (2022)
Anushka Rajesh, Yutong Chang, Malak S Abedalthagafi, Annie Wong-Beringer, Michael I Love, Serghei Mangul
Improving the completeness of public metadata accompanying omics studies. Genome biology 22 (1) (2021)
Mohammed Alser, Jeremy Rotman, Dhrithi Deshpande, 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
Technology dictates algorithms: recent developments in read alignment. Genome biology 22 (1) (2021)
Halie M Rando, Adam L MacLean, Alexandra J Lee, Sandipan Ray, Vikas Bansal, Ashwin N Skelly, Elizabeth A 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 Lee Szeto, John P Barton, Rishi Raj Goel, Serghei Mangul, Tiago Lubiana Alves, null null, Anthony Gitter, Casey S Greene
Pathogenesis, Symptomatology, and Transmission of SARS-CoV-2 through analysis of Viral Genomics and Structure. ArXiv (2021)
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, Khalid Olajide Adekoya, 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
Diversity in immunogenomics: the value and the challenge. Nature methods 18 (6) (2021)
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, Alexander Zelikovsky, Roberto Spreafico, Sagiv Shifman, Noah A Zaitlen, Maura Rossetti, Karl Mark Ansel, Eleazar Eskin, Serghei Mangul
Profiling immunoglobulin repertoires across multiple human tissues using RNA sequencing. Nature communications 11 (1) (2020)
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, Alexander Zelikovsky, Roberto Spreafico, Sagiv Shifman, Noah A Zaitlen, Maura Rossetti, Karl Mark Ansel, Eleazar Eskin, Serghei Mangul
Author Correction: Profiling immunoglobulin repertoires across multiple human tissues using RNA sequencing. Nature communications 11 (1) (2020)
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 Anand Brown, Angel Martinez-Perez, José Manuel Soria, null null, Gad A Getz, Emmanouil T Dermitzakis, Kerrin S Small, Matthew Stephens, Hualin S Xi, Hae Kyung Im, Roderic Guigo, Ayellet V Segrè, Barbara E Stranger, Kristin G Ardlie, Tuuli Lappalainen
Cell type-specific genetic regulation of gene expression across human tissues. Science (New York, N.Y.) 369 (6509) (2020)
Nathan LaPierre, Mohammed Alser, Eleazar Eskin, David Koslicki, Serghei Mangul
Metalign: efficient alignment-based metagenomic profiling via containment min hash. Genome biology 21 (1) (2020)