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Submissions from 2022

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Manifestations of Alzheimer's disease genetic risk in the blood are evident in a multiomic analysis in healthy adults aged 18 to 90., Laura M Heath, John C Earls, Andrew T Magis, Sergey A Kornilov, Jennifer C Lovejoy, Cory C Funk, Noa Rappaport, Benjamin A Logsdon, Lara M Mangravite, Brian W Kunkle, Eden R Martin, Adam C Naj, Nilüfer Ertekin-Taner, Todd E Golde, Leroy Hood, Nathan D Price, and Alzheimer’s Disease Genetics Consortium

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From telomere to telomere: The transcriptional and epigenetic state of human repeat elements., Savannah J Hoyt, Jessica Storer, Gabrielle A Hartley, Patrick G S Grady, Ariel Gershman, Leonardo G de Lima, Charles Limouse, Reza Halabian, Luke Wojenski, Matias Rodriguez, Nicolas Altemose, Arang Rhie, Leighton J Core, Jennifer L Gerton, Wojciech Makalowski, Daniel Olson, Jeb Rosen, Arian F A Smit, Aaron F Straight, Mitchell R Vollger, Travis J Wheeler, Michael C Schatz, Evan E Eichler, Adam M Phillippy, Winston Timp, Karen H Miga, and Rachel J O'Neill

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A Wipe-Based Stool Collection and Preservation Kit for Microbiome Community Profiling., Hui Hua, Cem Meydan, Evan E Afshin, Loukia N Lili, Christopher R D'Adamo, Nate Rickard, Joel T Dudley, Nathan D Price, Bodi Zhang, and Christopher E Mason

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Towards a unification of the 2 meanings of "epigenetics"., Sui Huang

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Accuracy of multiple sequence alignment methods in the reconstruction of transposable element families., Robert Hubley, Travis J Wheeler, and Arian F A Smit

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Development and Validation of a Breast Cancer Polygenic Risk Score on the Basis of Genetic Ancestry Composition., Elisha Hughes, Susanne Wagner, Dmitry Pruss, Ryan Bernhisel, Braden Probst, Victor Abkevich, Timothy Simmons, Brooke Hullinger, Thaddeus Judkins, Eric Rosenthal, Benjamin Roa, Susan M Domchek, Charis Eng, Judy Garber, Monique Gary, Jennifer Klemp, Semanti Mukherjee, Kenneth Offit, Olufunmilayo I Olopade, Joseph Vijai, Jeffrey N Weitzel, Pat Whitworth, Lamis Yehia, Ora K Gordon, Holly Pederson, Allison Kurian, Thomas P Slavin, Alexander Gutin, and Jerry S Lanchbury

Proteogenomic Characterization of Head and Neck Squamous Cell Cancer Immunopeptidomes to Detect Non Canonical Protein Targets for Cancer Immunotherapy., N Iwamoto, Richard Bryan Bell, Carlo Bifulco, Walter Urba, Rom Leidner, Brian D. Piening, Bernard A Fox, and See full author list in comments

Mid-pregnancy immune dysregulation and its association with maternal metabolic and genetic factors in those with preterm birth: Insights using artificial intelligence., L Jelliffe-Pawlowski, Brian D. Piening, and See full list of authors in comments

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PCM1-JAK2 Fusion Tyrosine Kinase Gene-Related Neoplasia: A Systematic Review of the Clinical Literature., Henry G Kaplan, Ruyun Jin, Carlo Bifulco, James M Scanlan, and David R Corwin

Multiomic Analyses Of Two Pig Kidney To Human Xenotransplants, B Keating, Brian Piening, M Mangiola, J Stern, W Zhang, A Griesemer, B Lonze, M Snyder, J Boeke, and R Montgomery

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Genomic Amplification of, Yuta Kobayashi, Matias A Bustos, Yoshiaki Shoji, Ron D Jachimowicz, Yosef Shiloh, and Dave S B Hoon

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Factors impacting genomic testing rates among epithelial ovarian cancer patients across a large community-based healthcare system (595), Nicole Kretzer, Christopher J. Darus, Nancy Biery, Roshanthi Weerasinghe, Hsin-Fang Li, Ann Vita, Shwetha Pindikuri, Amy Parrish, Charles Drescher, and Fernanda Musa

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Factors impacting genomic testing rates among epithelial ovarian cancer patients across a large community-based healthcare system, Nicole M. Kretzer, Christopher J. Darus, Nancy Biery, Roshanthi Weerasinghe, Grace Li, Ann Vita, Shwetha Pindikuri, Amy S. Parrish, Charles W Drescher, and Fernanda B. Musa

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Patterns of genomic testing for epithelial ovarian cancer across a large community-based health care network- a real world experience, Nicole M. Kretzer, Fernanda B. Musa, Christopher Darus, Nancy Biery, Roshanthi Weerasinghe, Grace Li, Ann Vita, Shwetha Pindikuri, Amy S. Parrish, and Charles W Drescher

Factors Impacting Genomic Testing Rates Among Epithelial Ovarian Cancer Patients ​Across a Large Community-Based Healthcare System, NM Kretzer, HF Li, and See all authors in comments

Frequency of Homologous Recombination Deficiency (HRD) in a Large Community Based Cohort of Epithelial Ovarian Cancer Cases (EOC), NM Kretzer, HF Li, and See all authors in comments

Patterns of Genomic Testing for Epithelial Ovarian Cancer (EOC) Across a Large Community-Based Health Care Network- A Real World Experience, NM Kretzer, HF Li, and See all authors in comments

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Proteomics Standards Initiative's ProForma 2.0: Unifying the Encoding of Proteoforms and Peptidoforms., Richard D LeDuc, Eric W Deutsch, Pierre-Alain Binz, Ryan T Fellers, Anthony J Cesnik, Joshua A Klein, Tim Van Den Bossche, Ralf Gabriels, Arshika Yalavarthi, Yasset Perez-Riverol, Jeremy Carver, Wout Bittremieux, Shin Kawano, Benjamin Pullman, Nuno Bandeira, Neil L Kelleher, Paul M Thomas, and Juan Antonio Vizcaíno

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Neoantigen T-Cell Receptor Gene Therapy in Pancreatic Cancer., Rom Leidner, Nelson Sanjuan Silva, Huayu Huang, David Sprott, Chunhong Zheng, Yi-Ping Shih, Amy Leung, Roxanne Payne, Kim Sutcliffe, Julie Cramer, Steven A Rosenberg, Bernard A Fox, Walter Urba, and Eric Tran

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The epigenetic impact of adverse childhood experiences through the lens of personalized medicine., Sheldon Levy and John Muench

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Systematic review of transcriptome and microRNAome associations with gestational diabetes mellitus., Kimberly A Lewis, Lisa Chang, Julinna Cheung, Bradley E Aouizerat, Laura L Jelliffe-Pawlowski, Monica R McLemore, Brian Piening, Larry Rand, Kelli K Ryckman, and Elena Flowers

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Addendum: Transcriptomics and proteomics reveal two waves of translational repression during the maturation of malaria parasite sporozoites., Scott E Lindner, Kristian E Swearingen, Melanie J Shears, Aswathy Sebastian, Michael P Walker, Erin N Vrana, Kevin J Hart, Allen M Minns, Istvan Albert, Photini Sinnis, Robert L Moritz, and Stefan H I Kappe

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Genome-wide interaction analysis identified low-frequency variants with sex disparity in lung cancer risk., Yafang Li, Xiangjun Xiao, Jianrong Li, Jinyoung Byun, Chao Cheng, Yohan Bossé, James McKay, Demetrios Albanes, Stephen Lam, Adonina Tardon, Chu Chen, Stig E Bojesen, Maria T Landi, Mattias Johansson, Angela Risch, Heike Bickeböller, H-Erich Wichmann, David C Christiani, Gad Rennert, Susanne Arnold, Gary E Goodman, John K Field, Michael P A Davies, Sanjay S Shete, Loic Le Marchand, Olle Melander, Hans Brunnström, Geoffrey Liu, Rayjean J Hung, Angeline S Andrew, Lambertus A Kiemeney, Hongbing Shen, Ryan Sun, Shan Zienolddiny, Kjell Grankvist, Mikael Johansson, Neil Caporaso, Dawn M Teare, Yun-Chul Hong, Philip Lazarus, Matthew B Schabath, Melinda C Aldrich, Ann G Schwartz, Ivan Gorlov, Kristen Purrington, Ping Yang, Yanhong Liu, Younghun Han, Joan E Bailey-Wilson, Susan M Pinney, Diptasri Mandal, James C Willey, Colette Gaba, Paul Brennan, Christopher I Amos, and INTEGRAL-ILCCO lung cancer consortium

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Author Correction: Comparative and demographic analysis of orang-utan genomes., Devin P Locke, LaDeana W Hillier, Wesley C Warren, Kim C Worley, Lynne V Nazareth, Donna M Muzny, Shiaw-Pyng Yang, Zhengyuan Wang, Asif T Chinwalla, Pat Minx, Makedonka Mitreva, Lisa Cook, Kim D Delehaunty, Catrina Fronick, Heather Schmidt, Lucinda A Fulton, Robert S Fulton, Joanne O Nelson, Vincent Magrini, Craig Pohl, Tina A Graves, Chris Markovic, Andy Cree, Huyen H Dinh, Jennifer Hume, Christie L Kovar, Gerald R Fowler, Gerton Lunter, Stephen Meader, Andreas Heger, Chris P Ponting, Tomas Marques-Bonet, Can Alkan, Lin Chen, Ze Cheng, Jeffrey M Kidd, Evan E Eichler, Simon White, Stephen Searle, Albert J Vilella, Yuan Chen, Paul Flicek, Jian Ma, Brian Raney, Bernard Suh, Richard Burhans, Javier Herrero, David Haussler, Rui Faria, Olga Fernando, Fleur Darré, Domènec Farré, Elodie Gazave, Meritxell Oliva, Arcadi Navarro, Roberta Roberto, Oronzo Capozzi, Nicoletta Archidiacono, Giuliano Della Valle, Stefania Purgato, Mariano Rocchi, Miriam K Konkel, Jerilyn A Walker, Brygg Ullmer, Mark A Batzer, Arian F A Smit, Robert Hubley, Claudio Casola, Daniel R Schrider, Matthew W Hahn, Victor Quesada, Xose S Puente, Gonzalo R Ordoñez, Carlos López-Otín, Tomas Vinar, Brona Brejova, Aakrosh Ratan, Robert S Harris, Webb Miller, Carolin Kosiol, Heather A Lawson, Vikas Taliwal, André L Martins, Adam Siepel, Arindam RoyChoudhury, Xin Ma, Jeremiah Degenhardt, Carlos D Bustamante, Ryan N Gutenkunst, Thomas Mailund, Julien Y Dutheil, Asger Hobolth, Mikkel H Schierup, Oliver A Ryder, Yuko Yoshinaga, Pieter J de Jong, George M Weinstock, Jeffrey Rogers, Elaine R Mardis, Richard A Gibbs, and Richard K Wilson

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A Comprehensive Evaluation of Consensus Spectrum Generation Methods in Proteomics., Xiyang Luo, Wout Bittremieux, Johannes Griss, Eric W Deutsch, Timo Sachsenberg, Lev I Levitsky, Mark V Ivanov, Julia A Bubis, Ralf Gabriels, Henry Webel, Aniel Sanchez, Mingze Bai, Lukas Käll, and Yasset Perez-Riverol

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The risk of COVID-19 death is much greater and age dependent with type I IFN autoantibodies., Jérémy Manry, Paul Bastard, Adrian Gervais, Tom Le Voyer, Jérémie Rosain, Quentin Philippot, Eleftherios Michailidis, Hans-Heinrich Hoffmann, Shohei Eto, Marina Garcia-Prat, Lucy Bizien, Alba Parra-Martínez, Rui Yang, Liis Haljasmägi, Mélanie Migaud, Karita Särekannu, Julia Maslovskaja, Nicolas de Prost, Yacine Tandjaoui-Lambiotte, Charles-Edouard Luyt, Blanca Amador-Borrero, Alexandre Gaudet, Julien Poissy, Pascal Morel, Pascale Richard, Fabrice Cognasse, Jesús Troya, Sophie Trouillet-Assant, Alexandre Belot, Kahina Saker, Pierre Garçon, Jacques G Rivière, Jean-Christophe Lagier, Stéphanie Gentile, Lindsey B Rosen, Elana Shaw, Tomohiro Morio, Junko Tanaka, David Dalmau, Pierre-Louis Tharaux, Damien Sene, Alain Stepanian, Bruno Mégarbane, Vasiliki Triantafyllia, Arnaud Fekkar, James R Heath, José Luis Franco, Juan-Manuel Anaya, Jordi Solé-Violán, Luisa Imberti, Andrea Biondi, Paolo Bonfanti, Riccardo Castagnoli, Ottavia M Delmonte, Yu Zhang, Andrew L Snow, Steven M Holland, Catherine M Biggs, Marcela Moncada-Vélez, Andrés Augusto Arias, Lazaro Lorenzo, Soraya Boucherit, Dany Anglicheau, Anna M Planas, Filomeen Haerynck, Sotirija Duvlis, Tayfun Ozcelik, Sevgi Keles, Ahmed A Bousfiha, Jalila El Bakkouri, Carolina Ramirez-Santana, Stéphane Paul, Qiang Pan-Hammarström, Lennart Hammarström, Annabelle Dupont, Alina Kurolap, Christine N Metz, Alessandro Aiuti, Giorgio Casari, Vito Lampasona, Fabio Ciceri, Lucila A Barreiros, Elena Dominguez-Garrido, Mateus Vidigal, Mayana Zatz, Diederik van de Beek, Sabina Sahanic, Ivan Tancevski, Yurii Stepanovskyy, Oksana Boyarchuk, Yoko Nukui, Miyuki Tsumura, Loreto Vidaur, Stuart G Tangye, Sonia Burrel, Darragh Duffy, Lluis Quintana-Murci, Adam Klocperk, Nelli Y Kann, Anna Shcherbina, Yu-Lung Lau, Daniel Leung, Matthieu Coulongeat, Julien Marlet, Rutger Koning, Luis Felipe Reyes, Angélique Chauvineau-Grenier, Fabienne Venet, Guillaume Monneret, Michel C Nussenzweig, Romain Arrestier, Idris Boudhabhay, Hagit Baris-Feldman, David Hagin, Joost Wauters, Isabelle Meyts, Adam H Dyer, Sean P Kennelly, Nollaig M Bourke, Rabih Halwani, Fatemeh Saheb Sharif-Askari, Karim Dorgham, Jérôme Sallette, Souad Mehlal Sedkaoui, Suzan AlKhater, Raúl Rigo-Bonnin, Francisco Morandeira, Lucie Roussel, Donald C Vinh, Christian Erikstrup, Antonio Condino-Neto, Carolina Prando, Anastasiia Bondarenko, András N Spaan, Laurent Gilardin, Jacques Fellay, Stanislas Lyonnet, Kaya Bilguvar, Richard P Lifton, Shrikant Mane, Mark S Anderson, Bertrand Boisson, Vivien Béziat, Shen-Ying Zhang, Evangelos Andreakos, Olivier Hermine, Aurora Pujol, Pärt Peterson, Trine H Mogensen, Lee Rowen, James Mond, Stéphanie Debette, Xavier de Lamballerie, Charles Burdet, Lila Bouadma, Marie Zins, Pere Soler-Palacin, Roger Colobran, Guy Gorochov, Xavier Solanich, Sophie Susen, Javier Martinez-Picado, Didier Raoult, Marc Vasse, Peter K Gregersen, Lorenzo Piemonti, Carlos Rodríguez-Gallego, Luigi D Notarangelo, Helen C Su, Kai Kisand, Satoshi Okada, Anne Puel, Emmanuelle Jouanguy, Charles M Rice, Pierre Tiberghien, Qian Zhang, Jean-Laurent Casanova, Laurent Abel, and Aurélie Cobat

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Hypoxia induces HIF1α-dependent epigenetic vulnerability in triple negative breast cancer to confer immune effector dysfunction and resistance to anti-PD-1 immunotherapy., Shijun Ma, Yue Zhao, Wee Chyan Lee, Li-Teng Ong, Puay Leng Lee, Zemin Jiang, Gokce Oguz, Zhitong Niu, Min Liu, Jian Yuan Goh, Wenyu Wang, Matias A Bustos, Sidse Ehmsen, Adaikalavan Ramasamy, Dave Hoon, Henrik J Ditzel, Ern Yu Tan, Qingfeng Chen, and Qiang Yu

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Comparative genomic analysis of vertebrate mitochondrial reveals a differential of rearrangements rate between taxonomic class., Paula Montaña-Lozano, Manuela Moreno-Carmona, Mauricio Ochoa-Capera, Natalia S Medina, Jeffrey L Boore, and Carlos F Prada

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Standardized annotation of translated open reading frames., Jonathan M Mudge, Jorge Ruiz-Orera, John R Prensner, Marie A Brunet, Ferriol Calvet, Irwin Jungreis, Jose Manuel Gonzalez, Michele Magrane, Thomas F Martinez, Jana Felicitas Schulz, Yucheng T Yang, M Mar Albà, Julie L Aspden, Pavel V Baranov, Ariel A Bazzini, Elspeth Bruford, Maria Jesus Martin, Lorenzo Calviello, Anne-Ruxandra Carvunis, Jin Chen, Juan Pablo Couso, Eric W Deutsch, Paul Flicek, Adam Frankish, Mark Gerstein, Norbert Hubner, Nicholas T Ingolia, Manolis Kellis, Gerben Menschaert, Robert L Moritz, Uwe Ohler, Xavier Roucou, Alan Saghatelian, Jonathan S Weissman, and Sebastiaan van Heesch

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Constraint-Based Reconstruction and Analyses of Metabolic Models: Open-Source Python Tools and Applications to Cancer., Rachel H Ng, Jihoon W Lee, Priyanka Baloni, Christian Diener, James R Heath, and Yapeng Su

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Organ-Based Proteome and Post-Translational Modification Profiling of a Widely Cultivated Tropical Water Fish, Labeo rohita, Mehar Un Nissa, Nevil Pinto, Arijit Mukherjee, Panga Jaipal Reddy, Biplab Ghosh, Zhi Sun, Saicharan Ghantasala, Chetanya Chetanya, Sanjyot Vinayak Shenoy, Robert L Moritz, Mukunda Goswami, and Sanjeeva Srivastava

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The complete sequence of a human genome., Sergey Nurk, Sergey Koren, Arang Rhie, Mikko Rautiainen, Andrey V Bzikadze, Alla Mikheenko, Mitchell R Vollger, Nicolas Altemose, Lev Uralsky, Ariel Gershman, Sergey Aganezov, Savannah J Hoyt, Mark Diekhans, Glennis A Logsdon, Michael Alonge, Stylianos E Antonarakis, Matthew Borchers, Gerard G Bouffard, Shelise Y Brooks, Gina V Caldas, Nae-Chyun Chen, Haoyu Cheng, Chen-Shan Chin, William Chow, Leonardo G de Lima, Philip C Dishuck, Richard Durbin, Tatiana Dvorkina, Ian T Fiddes, Giulio Formenti, Robert S Fulton, Arkarachai Fungtammasan, Erik Garrison, Patrick G S Grady, Tina A Graves-Lindsay, Ira M Hall, Nancy F Hansen, Gabrielle A Hartley, Marina Haukness, Kerstin Howe, Michael W Hunkapiller, Chirag Jain, Miten Jain, Erich D Jarvis, Peter Kerpedjiev, Melanie Kirsche, Mikhail Kolmogorov, Jonas Korlach, Milinn Kremitzki, Heng Li, Valerie V Maduro, Tobias Marschall, Ann M McCartney, Jennifer McDaniel, Danny E Miller, James C Mullikin, Eugene W Myers, Nathan D Olson, Benedict Paten, Paul Peluso, Pavel A Pevzner, David Porubsky, Tamara Potapova, Evgeny I Rogaev, Jeffrey A Rosenfeld, Steven L Salzberg, Valerie A Schneider, Fritz J Sedlazeck, Kishwar Shafin, Colin J Shew, Alaina Shumate, Ying Sims, Arian F A Smit, Daniela C Soto, Ivan Sović, Jessica Storer, Aaron Streets, Beth A Sullivan, Françoise Thibaud-Nissen, James Torrance, Justin Wagner, Brian P Walenz, Aaron Wenger, Jonathan M D Wood, Chunlin Xiao, Stephanie M Yan, Alice C Young, Samantha Zarate, Urvashi Surti, Rajiv C McCoy, Megan Y Dennis, Ivan A Alexandrov, Jennifer L Gerton, Rachel J O'Neill, Winston Timp, Justin M Zook, Michael C Schatz, Evan E Eichler, Karen H Miga, and Adam M Phillippy

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The 2022 Report on the Human Proteome from the HUPO Human Proteome Project., Gilbert S Omenn, Lydie Lane, Christopher M Overall, Charles Pineau, Nicolle H Packer, Ileana M Cristea, Cecilia Lindskog, Susan T Weintraub, Sandra Orchard, Michael H A Roehrl, Edouard Nice, Siqi Liu, Nuno Bandeira, Yu-Ju Chen, Tiannan Guo, Ruedi Aebersold, Robert L Moritz, and Eric W Deutsch

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Personal Dense Dynamic Data Clouds Connect Systems Biomedicine to Scientific Wellness., Gilbert S Omenn, Andrew T Magis, Nathan D Price, and Leroy Hood

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The Human Tumor Atlas Network's beginning steps toward the future of collaborative multi-omic discovery., David B Page

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Molecular alterations associated with improved outcome in patients with glioblastoma treated with Tumor-Treating Fields., Manjari Pandey, Joanne Xiu, Sandeep Mittal, Jia Zeng, Michelle Saul, Santosh Kesari, Amir Azadi, Herbert Newton, Karina Deniz, Katherine Ladner, Ashley Sumrall, W Michael Korn, and Emil Lou

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Associations between SARS-CoV-2 variants and risk of COVID-19 hospitalization among confirmed cases in Washington State: a retrospective cohort study., Miguel I Paredes, Stephanie M Lunn, Michael Famulare, Lauren A Frisbie, Ian Painter, Roy Burstein, Pavitra Roychoudhury, Hong Xie, Shah A Mohamed Bakhash, Ricardo Perez, Maria Lukes, Sean Ellis, Saraswathi Sathees, Patrick C Mathias, Alexander Greninger, Lea M Starita, Chris D Frazar, Erica Ryke, Weizhi Zhong, Luis Gamboa, Machiko Threlkeld, Jover Lee, Evan McDermot, Melissa Truong, Deborah A Nickerson, Daniel L Bates, Matthew E Hartman, Eric Haugen, Truong N Nguyen, Joshua D Richards, Jacob L Rodriguez, John A Stamatoyannopoulos, Eric Thorland, Geoff Melly, Philip E Dykema, Drew C MacKellar, Hannah K Gray, Avi Singh, JohnAric M Peterson, Denny Russell, Laura Marcela Torres, Scott Lindquist, Trevor Bedford, Krisandra J Allen, and Hanna N Oltean

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Genetic polymorphisms and correlation with treatment induced cardiotoxicity and prognosis in breast cancer patients., Parvin Peddi, Peter A Fasching, Duan Liu, Emmanuel Quinaux, Nicholas J Robert, Vicente Valero, John Crown, Carla Falkson, Adam Brufsky, Julie M Cunningham, Richard M Weinshilboum, Tadeusz Pienkowski, Wolfgang Eiermann, Miguel Martín, Valerie Bee, Xiaoyan Wang, Liewei Wang, Eric Yang, Dennis J Slamon, and Sara A Hurvitz

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Pathogenic fusion detection in solid malignancies utilizing RNA-DNA based comprehensive genomic profiling (CGP) testing., Brian D. Piening, Alexa K Dowdell, Ryan Meng, Ann Vita, Roshanthi Weerasinghe, Alisha Stein, Bela Bapat, Brock Shroeder, Shu-Ching Chang, Lauren Harold, Mark Schmidt, Thomas R. Ward, Josiah T Wagner, Stanley Piotrowski, Phillip G. Febbo, and Carlo Bifulco

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Elucidating Diversity in Obesity-Related Phenotypes Using Longitudinal and Multi-omic Approaches, Brian D. Piening, Alexa K Dowdell, and Michael P. Snyder

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Whole transcriptome profiling of prospective endomyocardial biopsies reveals prognostic and diagnostic signatures of cardiac allograft rejection., Brian D. Piening, Alexa K Dowdell, Mengqi Zhang, Bao-Li Loza, David Walls, Hui Gao, Maede Mohebnasab, Yun Rose Li, Eric Elftmann, Eric Wei, Divya Gandla, Hetal Lad, Hassan Chaib, Nancy K Sweitzer, Mario Deng, Alexandre C Pereira, Martin Cadeiras, Abraham Shaked, Michael P Snyder, and Brendan J Keating

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PTPRD and CNTNAP2 as markers of tumor aggressiveness in oligodendrogliomas., Kirsi J Rautajoki, Serafiina Jaatinen, Aliisa M Tiihonen, Matti Annala, Elisa M Vuorinen, Anni Kivinen, Minna J Rauhala, Kendra K Maass, Kristian W Pajtler, Olli Yli-Harja, Pauli Helén, Joonas Haapasalo, Hannu Haapasalo, Wei Zhang, and Matti Nykter

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Discovery and Visualization of Uncharacterized Drug-Protein Adducts Using Mass Spectrometry., Michael Riffle, Michael R Hoopmann, Daniel Jaschob, Guo Zhong, Robert L Moritz, Michael J MacCoss, Trisha N Davis, Nina Isoherranen, and Alex Zelter

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Quality control of large genome datasets., Max Robinson, Arpita Joshi, Ansh Vidyarthi, Mary Maccoun, Sanjay Rangavajjhala, and Gustavo Glusman

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Gene-gene interaction of AhRwith and within the Wntcascade affects susceptibility to lung cancer., Albert Rosenberger, Nils Muttray, Rayjean J Hung, David C Christiani, Neil E Caporaso, Geoffrey Liu, Stig E Bojesen, Loic Le Marchand, Demetrios Albanes, Melinda C Aldrich, Adonina Tardon, Guillermo Fernández-Tardón, Gad Rennert, John K Field, Michael P A Davies, Triantafillos Liloglou, Lambertus A Kiemeney, Philip Lazarus, Bernadette Wendel, Aage Haugen, Shanbeh Zienolddiny, Stephen Lam, Matthew B Schabath, Angeline S Andrew, Eric J Duell, Susanne M Arnold, Gary E Goodman, Chu Chen, Jennifer A Doherty, Fiona Taylor, Angela Cox, Penella J Woll, Angela Risch, Thomas R Muley, Mikael Johansson, Paul Brennan, Maria Teresa Landi, Sanjay S Shete, Christopher I Amos, and Heike Bickeböller

Candidate antigens for a ductal carcinoma in situ vaccine, essential for breast cancer cell survival across multiple subtypes, are immunogenic in DCIS and IBC, SE Sanborn

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Analytic pipelines to assess the relationship between immune response and germline genetics in human tumors., Rosalyn W Sayaman, Mohamad Saad, Carolina Heimann, Donglei Hu, Khalid Kunji, Jessica Roelands, Denise M Wolf, Scott Huntsman, Michele Ceccarelli, Vésteinn Thorsson, Elad Ziv, and Davide Bedognetti

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The immune landscape of solid pediatric tumors., Shimaa Sherif, Jessica Roelands, William Mifsud, Eiman I Ahmed, Christophe M Raynaud, Darawan Rinchai, Abbirami Sathappan, Ata Maaz, Ayman Saleh, Erdener Ozer, Khalid A Fakhro, Borbala Mifsud, Vésteinn Thorsson, Davide Bedognetti, and Wouter R L Hendrickx

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Methodologies for the De novo Discovery of Transposable Element Families, Jessica Storer, Robert Hubley, Jeb Rosen, and Arian F A Smit

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Cebidae, Jessica M Storer, Jerilyn A Walker, Morgan A Brown, and Mark A Batzer

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Recently Integrated Alu Elements in Capuchin Monkeys: A Resource for Cebus/ Sapajus Genomics, Jessica Storer, Jerilyn A Walker, Catherine E Rockwell, Grayce Mores, Thomas O Beckstrom, Joseph D Orkin, Amanda D Melin, Kimberley A Phillips, Christian Roos, and Mark A Batzer

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SL-Cloud: A Cloud-based resource to support synthetic lethal interaction discovery., Bahar Tercan, Guangrong Qin, Taek-Kyun Kim, Boris Aguilar, John Phan, William Longabaugh, David Pot, Christopher J Kemp, Nyasha Chambwe, and Ilya Shmulevich

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Molecular states during acute COVID-19 reveal distinct etiologies of long-term sequelae., Ryan C Thompson, Nicole W Simons, Lillian Wilkins, Esther Cheng, Diane Marie Del Valle, Gabriel E Hoffman, Carlo Cervia, Brian Fennessy, Konstantinos Mouskas, Nancy J Francoeur, Jessica S Johnson, Lauren Lepow, Jessica Le Berichel, Christie Chang, Aviva G Beckmann, Ying-Chih Wang, Kai Nie, Nicholas Zaki, Kevin Tuballes, Vanessa Barcessat, Mario A Cedillo, Dan Yuan, Laura Huckins, Panos Roussos, Thomas U Marron, Mount Sinai COVID-19 Biobank Team, Benjamin S Glicksberg, Girish Nadkarni, James R Heath, Edgar Gonzalez-Kozlova, Onur Boyman, Seunghee Kim-Schulze, Robert Sebra, Miriam Merad, Sacha Gnjatic, Eric E Schadt, Alexander W Charney, and Noam D Beckmann

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Neoantigen T-Cell Receptor Gene Therapy in Pancreatic Cancer. Reply., Eric Tran, Walter Urba, and Rom Leidner

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Attractor-Specific and Common Expression Values in Random Boolean Network Models (with a Preliminary Look at Single-Cell Data)., Marco Villani, Gianluca D'Addese, Stuart A Kauffman, and Roberto Serra

Geno4ME: establishment of an equitable whole-genome sequencing-based platform for clinical screening in a large healthcare system, Josiah Wagner, I A. Lucas-Beckett, K R. Emery, B A. Cosgrove, John T. Welle, K Jade, N D. Wagner, J Rinaldi, Lindsay Dickey, K G. Jones, L Yuan, E M. Shull, J Clemens, Keri Vartanian, A T. Magis, M B. Campbell, Brian Piening, Carlo Bifulco, and Ora K. Gordon

Clinical Performance of Comprehensive Genomic Profiling Using a Wide Range of Input Quantities and Solid Tumor Tissue Types, Josiah Wagner, S Reynolds, A Dowdell, E Shull, J Welle, M Pukay, R Rattray, C Moung-Wen, T Ward, M Campbell, C Bifulco, and B Piening

Streamlining Solid Tumor Comprehensive Genomic Profiling Workflows Using Learned Variant and Sequencing Noise Autoclassification, Thomas Ward, S Reynolds, J Wagner, N Naidoo, E Shull, John Welle, R Rattray, C Moung-Wen, Mary Campbell, Brian Piening, and Carlo Bifulco

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Identification of clinically actionable biomarkers via routine comprehensive genomic profiling across a large community health system, Roshanthi Weerasinghe, Ryan Meng, Alexa K Dowdell, Bela Bapat, Ann Vita, Brock Schroeder, Alisha Stein, Lauren Harold, Mark Schmidt, Shu-Ching Chang, Thomas R. Ward, Josiah T Wagner, Stanley Piotrowski, Phillip G. Febbo, Carlo Bifulco, and Brian D. Piening

Design and Validation of a Whole-Genome SequencingBased Assay for Population Health, John Welle, Brian Piening, Josiah Wagner, I Lucas-Beckett, Thomas Ward, B Cosgrove, Eric Shull, R Rattray, Marina Pukay, Milena Ricks, K Childers, J Linehan, M Campbell, Ora Gordon, and Carlo Bifulco

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Heterogeneity in statin responses explained by variation in the human gut microbiome., Tomasz Wilmanski, Sergey A Kornilov, Christian Diener, Matthew P Conomos, Jennifer C Lovejoy, Paola Sebastiani, Eric S Orwoll, Leroy Hood, Nathan D Price, Noa Rappaport, Andrew T Magis, and Sean M Gibbons

Submissions from 2021

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Transition Therapy: Tackling the Ecology of Tumor Phenotypic Plasticity., Guim Aguadé-Gorgorió, Stuart Kauffman, and Ricard Solé

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iNetModels 2.0: an interactive visualization and database of multi-omics data., Muhammad Arif, Cheng Zhang, Xiangyu Li, Cem Güngör, Buğra Çakmak, Metin Arslantürk, Abdellah Tebani, Berkay Özcan, Oğuzhan Subaş, Wenyu Zhou, Brian Piening, Hasan Turkez, Linn Fagerberg, Nathan Price, Leroy Hood, Michael Snyder, Jens Nielsen, Mathias Uhlen, and Adil Mardinoglu

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Systems modeling of metabolic dysregulation in neurodegenerative diseases., Priyanka Baloni, Cory C Funk, Ben Readhead, and Nathan D Price

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Evaluation of FKBP5 as a cortisol activity biomarker in patients with ACTH-dependent Cushing syndrome., Irina Bancos, Betul Ayse Hatipoglu, Kevin C J Yuen, Lakshmi Chandramohan, Sandeep Chaudhari, and Andreas G Moraitis

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Data management of sensitive human proteomics data: current practices, recommendations and perspectives for the future., Nuno Bandeira, Eric W Deutsch, Oliver Kohlbacher, Lennart Martens, and Juan Antonio Vizcaíno

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mzMLb: A Future-Proof Raw Mass Spectrometry Data Format Based on Standards-Compliant mzML and Optimized for Speed and Storage Requirements., Ranjeet S Bhamber, Andris Jankevics, Eric W Deutsch, Andrew R Jones, and Andrew W Dowsey

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Implications of Selection Bias Due to Delayed Study Entry in Clinical Genomic Studies., Samantha Brown, Jessica A Lavery, Ronglai Shen, Axel S Martin, Kenneth L Kehl, Shawn M Sweeney, Eva M Lepisto, Hira Rizvi, Caroline G McCarthy, Nikolaus Schultz, Jeremy L Warner, Ben Ho Park, Philippe L Bedard, Gregory J Riely, Deborah Schrag, Katherine S Panageas, AACR Project GENIE Consortium, Walter Urba, Brady Bernard, Brian D. Piening, and Carlo Bifulco

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TE Hub: A community-oriented space for sharing and connecting tools, data, resources, and methods for transposable element annotation., TE Hub Consortium, Tyler A Elliott, Tony Heitkam, Robert Hubley, Hadi Quesneville, Alexander Suh, and Travis J Wheeler

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Editorial: Personal Genomes: Accessing, Sharing, and Interpretation., Manuel Corpas, Stephan Beck, Gustavo Glusman, and Mahsa Shabani

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A proteomics sample metadata representation for multiomics integration and big data analysis., Chengxin Dai, Anja Füllgrabe, Julianus Pfeuffer, Elizaveta M Solovyeva, Jingwen Deng, Pablo Moreno, Selvakumar Kamatchinathan, Deepti Jaiswal Kundu, Nancy George, Silvie Fexova, Björn Grüning, Melanie Christine Föll, Johannes Griss, Marc Vaudel, Enrique Audain, Marie Locard-Paulet, Michael Turewicz, Martin Eisenacher, Julian Uszkoreit, Tim Van Den Bossche, Veit Schwämmle, Henry Webel, Stefan Schulze, David Bouyssié, Savita Jayaram, Vinay Kumar Duggineni, Patroklos Samaras, Mathias Wilhelm, Meena Choi, Mingxun Wang, Oliver Kohlbacher, Alvis Brazma, Irene Papatheodorou, Nuno Bandeira, Eric W Deutsch, Juan Antonio Vizcaíno, Mingze Bai, Timo Sachsenberg, Lev I Levitsky, and Yasset Perez-Riverol

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Advances and Utility of the Human Plasma Proteome., Eric W Deutsch, Gilbert S Omenn, Zhi Sun, Michal Maes, Maria Pernemalm, Krishnan K Palaniappan, Natasha Letunica, Yves Vandenbrouck, Virginie Brun, Sheng-Ce Tao, Xiaobo Yu, Philipp E Geyer, Vera Ignjatovic, Robert L Moritz, and Jochen M Schwenk

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Universal Spectrum Identifier for mass spectra., Eric W Deutsch, Yasset Perez-Riverol, Jeremy Carver, Shin Kawano, Luis Mendoza, Tim Van Den Bossche, Ralf Gabriels, Pierre-Alain Binz, Benjamin Pullman, Zhi Sun, Jim Shofstahl, Wout Bittremieux, Tytus D Mak, Joshua Klein, Yunping Zhu, Henry Lam, Juan Antonio Vizcaíno, and Nuno Bandeira

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Neoadjuvant anti-OX40 (MEDI6469) therapy in patients with head and neck squamous cell carcinoma activates and expands antigen-specific tumor-infiltrating T cells., Rebekka Duhen, Carmen Ballesteros-Merino, Alexandra K Frye, Eric Tran, Venkatesh Rajamanickam, Shu-Ching Chang, Yoshinobu Koguchi, Carlo Bifulco, Brady Bernard, Rom Leidner, Brendan Curti, Bernard A Fox, Walter Urba, Richard Bryan Bell, and Andrew D Weinberg

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Are There Limits in Explainability of Prognostic Biomarkers? Scrutinizing Biological Utility of Established Signatures., Frank Emmert-Streib, Kalifa Manjang, Matthias Dehmer, Olli Yli-Harja, and Anssi Auvinen

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Current Triple-Negative Breast Cancer Subtypes: Dissecting the Most Aggressive Form of Breast Cancer., Miquel Ensenyat-Mendez, Pere Llinàs-Arias, Javier I J Orozco, Sandra Íñiguez-Muñoz, Matthew P Salomon, Borja Sesé, Maggie L DiNome, and Diego M Marzese

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Challenges and Errors in Genetic Testing: The Fifth Case Series., Meagan B Farmer, Danielle C Bonadies, Holly J Pederson, Kathryn A Mraz, Julie W Whatley, Deanna R Darnes, Jessica Johnson Denton, Diana De Rosa, Alexis Heatherly, Jessica Kenney, Kimberly Lane, Deborah Paul, Renée C Pelletier, Kristen Shannon, Danielle Williams, and Ellen T Matloff

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Identification of kidney disease diagnoses in patients with diabetes by biopsies and electronic health records, Eva Fast, Cami R Jones, Kenn Daratha, Susanne B. Nicholas, Radica Alicic, Cynthia C. Nast, Jonathan E. Zuckerman, Sarthak Patel, Ken Allison, Adam Tebbe, Michelle Penny, Keith C. Norris, and Katherine Tuttle

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Molluscan mitochondrial genomes break the rules., Fabrizio Ghiselli, André Gomes-Dos-Santos, Coen M Adema, Manuel Lopes-Lima, Joel Sharbrough, and Jeffrey L Boore

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Elevated rates of horizontal gene transfer in the industrialized human microbiome., Mathieu Groussin, Mathilde Poyet, Ainara Sistiaga, Sean M Kearney, Katya Moniz, Mary Noel, Jeff Hooker, Sean M Gibbons, Laure Segurel, Alain Froment, Rihlat Said Mohamed, Alain Fezeu, Vanessa A Juimo, Sophie Lafosse, Francis E Tabe, Catherine Girard, Deborah Iqaluk, Le Thanh Tu Nguyen, B Jesse Shapiro, Jenni Lehtimäki, Lasse Ruokolainen, Pinja P Kettunen, Tommi Vatanen, Shani Sigwazi, Audax Mabulla, Manuel Domínguez-Rodrigo, Yvonne A Nartey, Adwoa Agyei-Nkansah, Amoako Duah, Yaw A Awuku, Kenneth A Valles, Shadrack O Asibey, Mary Y Afihene, Lewis R Roberts, Amelie Plymoth, Charles A Onyekwere, Roger E Summons, Ramnik J Xavier, and Eric J Alm

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Single-Cell Profiling of Fatty Acid Uptake Using Surface-Immobilized Dendrimers., Zhili Guo, Hanjun Cheng, Zhonghan Li, Shiqun Shao, Priyanka Sarkar, Siwen Wang, Rohit Chaudhuri, Nicole G Perkins, Fei Ji, Wei Wei, and Min Xue

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Correction to: Physician-directed genetic screening to evaluate personal risk for medically actionable disorders: a large multi-center cohort study., Eden V Haverfield, Edward D Esplin, Sienna J Aguilar, Kathryn E Hatchell, Kelly E Ormond, Andrea Hanson-Kahn, Paldeep S Atwal, Sarah Macklin-Mantia, Stephanie Hines, Caron W-M Sak, Steven Tucker, Steven B Bleyl, Peter J Hulick, Ora K Gordon, Lea Velsher, Jessica Y J Gu, Scott M Weissman, Teresa Kruisselbrink, Christopher Abel, Michele Kettles, Anne Slavotinek, Bryce A Mendelsohn, Robert C Green, Swaroop Aradhya, and Robert L Nussbaum

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Physician-directed genetic screening to evaluate personal risk for medically actionable disorders: a large multi-center cohort study., Eden V Haverfield, Edward D Esplin, Sienna J Aguilar, Kathryn E Hatchell, Kelly E Ormond, Andrea Hanson-Kahn, Paldeep S Atwal, Sarah Macklin-Mantia, Stephanie Hines, Caron W-M Sak, Steven Tucker, Steven B Bleyl, Peter J Hulick, Ora K Gordon, Lea Velsher, Jessica Y J Gu, Scott M Weissman, Teresa Kruisselbrink, Christopher Abel, Michele Kettles, Anne Slavotinek, Bryce A Mendelsohn, Robert C Green, Swaroop Aradhya, and Robert L Nussbaum

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Integrated genetic and metabolic landscapes predict vulnerabilities of temozolomide resistant glioblastoma cells., Selva Rupa Christinal Immanuel, Avinash D Ghanate, Dharmeshkumar S Parmar, Ritu Yadav, Riya Uthup, Venkateswarlu Panchagnula, and Anu Raghunathan

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Chromatin-Associated Protein Complexes Link DNA Base J and Transcription Termination in, Bryan C Jensen, Isabelle Q Phan, Jacquelyn R McDonald, Aakash Sur, Mark A Gillespie, Jeffrey A Ranish, Marilyn Parsons, and Peter J Myler

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Integrative functional genomic analysis of intron retention in human and mouse brain with Alzheimer's disease., Hong-Dong Li, Cory C Funk, Karen McFarland, Eric B Dammer, Mariet Allen, Minerva M Carrasquillo, Yona Levites, Paramita Chakrabarty, Jeremy D Burgess, Xue Wang, Dennis Dickson, Nicholas T Seyfried, Duc M Duong, James J Lah, Steven G Younkin, Allan I Levey, Gilbert S Omenn, Nilüfer Ertekin-Taner, Todd E Golde, and Nathan D Price

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Epigenetic Regulation of Immunotherapy Response in Triple-Negative Breast Cancer., Pere Llinàs-Arias, Sandra Íñiguez-Muñoz, Kelly McCann, Leonie Voorwerk, Javier I J Orozco, Miquel Ensenyat-Mendez, Borja Sesé, Maggie L DiNome, and Diego M Marzese

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Prognostic gene expression signatures of breast cancer are lacking a sensible biological meaning., Kalifa Manjang, Shailesh Tripathi, Olli Yli-Harja, Matthias Dehmer, Galina Glazko, and Frank Emmert-Streib

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Limitations of Explainability for Established Prognostic Biomarkers of Prostate Cancer., Kalifa Manjang, Olli Yli-Harja, Matthias Dehmer, and Frank Emmert-Streib

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A high-quality bonobo genome refines the analysis of hominid evolution., Yafei Mao, Claudia R Catacchio, LaDeana W Hillier, David Porubsky, Ruiyang Li, Arvis Sulovari, Jason D Fernandes, Francesco Montinaro, David S Gordon, Jessica M Storer, Marina Haukness, Ian T Fiddes, Shwetha Canchi Murali, Philip C Dishuck, PingHsun Hsieh, William T Harvey, Peter A Audano, Ludovica Mercuri, Ilaria Piccolo, Francesca Antonacci, Katherine M Munson, Alexandra P Lewis, Carl Baker, Jason G Underwood, Kendra Hoekzema, Tzu-Hsueh Huang, Melanie Sorensen, Jerilyn A Walker, Jinna Hoffman, Françoise Thibaud-Nissen, Sofie R Salama, Andy W C Pang, Joyce Lee, Alex R Hastie, Benedict Paten, Mark A Batzer, Mark Diekhans, Mario Ventura, and Evan E Eichler

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Asexuality associated with marked genomic expansion of tandemly repeated rRNA and histone genes., Kyle E McElroy, Stefan Müller, Dunja Lamatsch, Laura Bankers, Peter D Fields, Joseph R Jalinsky, Joel Sharbrough, Jeffrey L Boore, John M Logsdon, and Maurine Neiman

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Progress Identifying and Analyzing the Human Proteome: 2021 Metrics from the HUPO Human Proteome Project., Gilbert S Omenn, Lydie Lane, Christopher M Overall, Young-Ki Paik, Ileana M Cristea, Fernando J Corrales, Cecilia Lindskog, Susan Weintraub, Michael H A Roehrl, Siqi Liu, Nuno Bandeira, Sudhir Srivastava, Yu-Ju Chen, Ruedi Aebersold, Robert L Moritz, and Eric W Deutsch

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miRNome and Functional Network Analysis of PGRMC1 Regulated miRNA Target Genes Identify Pathways and Biological Functions Associated With Triple Negative Breast Cancer., Diego A Pedroza, Matthew Ramirez, Venkatesh Rajamanickam, Ramadevi Subramani, Victoria Margolis, Tugba Gurbuz, Adriana Estrada, and Rajkumar Lakshmanaswamy

Multi-Omics at Providence, Brian D. Piening

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Targeted genomic analysis of 364 adrenocortical carcinomas., Nikita Pozdeyev, Lauren Fishbein, Laurie M Gay, Ethan S Sokol, Ryan Hartmaier, Jeffrey S Ross, Sourat Darabi, Michael J Demeure, Adwitiya Kar, Lindsey J Foust, Katrina Koc, Daniel W Bowles, Stephen Leong, Margaret E Wierman, and Katja Kiseljak-Vassiliades

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A Curriculum for Genomic Education of Molecular Genetic Pathology Fellows:A Report of the Association for Molecular Pathology Training and Education Committee., Jason N Rosenbaum, Anna B Berry, Alanna J Church, Kristy Crooks, Jeffrey R Gagan, Dolores López-Terrada, John D Pfeifer, Hanna Rennert, Iris Schrijver, Anthony N Snow, David Wu, and Mark D Ewalt

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Universal Spectrum Explorer: A Standalone (Web-)Application for Cross-Resource Spectrum Comparison., Tobias Schmidt, Patroklos Samaras, Viktoria Dorfer, Christian Panse, Tobias Kockmann, Leon Bichmann, Bart van Puyvelde, Yasset Perez-Riverol, Eric W Deutsch, Bernhard Kuster, and Mathias Wilhelm

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Genomic and Molecular Profiling of Human Papillomavirus Associated Head and Neck Squamous Cell Carcinoma Treated with Immune Checkpoint Blockade Compared to Survival Outcomes., Hira Shaikh, Julie E McGrath, Brittany Hughes, Joanne Xiu, Pavel Brodskiy, Ammar Sukari, Sourat Darabi, Chukwuemeka Ikpeazu, Chadi Nabhan, Wolfgang Michael Korn, and Trisha M Wise-Draper

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Curation Guidelines for de novo Generated Transposable Element Families., Jessica Storer, Robert Hubley, Jeb Rosen, and Arian F A Smit

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The Dfam community resource of transposable element families, sequence models, and genome annotations., Jessica Storer, Robert Hubley, Jeb Rosen, Travis J Wheeler, and Arian F Smit