Submissions from 2023
Integrated unbiased multiomics defines disease-independent placental clusters in common obstetrical syndromes., Oren Barak, Tyler Lovelace, Samantha Piekos, Tianjiao Chu, Zhishen Cao, Elena Sadovsky, Jean-Francois Mouillet, Yingshi Ouyang, W Tony Parks, Leroy Hood, Nathan D Price, Panayiotis V Benos, and Yoel Sadovsky
spongEffects: ceRNA modules offer patient-specific insights into the miRNA regulatory landscape., Fabio Boniolo, Markus Hoffmann, Norman Roggendorf, Bahar Tercan, Jan Baumbach, Mauro A A Castro, A Gordon Robertson, Dieter Saur, and Markus List
Trans-Proteomic Pipeline: Robust Mass Spectrometry-Based Proteomics Data Analysis Suite., Eric W Deutsch, Luis Mendoza, David D Shteynberg, Michael R Hoopmann, Zhi Sun, Jimmy K Eng, and Robert L Moritz
Proteomics Standards Initiative at Twenty Years: Current Activities and Future Work., Eric W Deutsch, Juan Antonio Vizcaíno, Andrew R Jones, Pierre-Alain Binz, Henry Lam, Joshua Klein, Wout Bittremieux, Yasset Perez-Riverol, David L Tabb, Mathias Walzer, Sylvie Ricard-Blum, Henning Hermjakob, Steffen Neumann, Tytus D Mak, Shin Kawano, Luis Mendoza, Tim Van Den Bossche, Ralf Gabriels, Nuno Bandeira, Jeremy Carver, Benjamin Pullman, Zhi Sun, Nils Hoffmann, Jim Shofstahl, Yunping Zhu, Luana Licata, Federica Quaglia, Silvio C E Tosatto, and Sandra E Orchard
Pembrolizumab in Patients With Tumors With High Tumor Mutational Burden: Results From the Targeted Agent and Profiling Utilization Registry Study., Herbert L Duvivier, Michael Rothe, Pam K Mangat, Elizabeth Garrett-Mayer, Eugene R Ahn, Tareq Al Baghdadi, Ajjai S Alva, Stephanie A Dublis, Timothy L Cannon, Carmen J Calfa, Rui Li, Deepti Behl, Vi K Chiu, Philip J Gold, Alissa S Marr, Kathryn F Mileham, Steven Francis Powell, Jordi Rodon, Ramya Thota, Gina N Grantham, Abigail Gregory, Dominique C Hinshaw, Susan Halabi, and Richard L Schilsky
Editorial: Translational phenomics and its applications in immunotherapy., Hai Fang, Liye Chen, Leroy Hood, and Qiang Tian
Effects of HLA single chain trimer design on peptide presentation and stability., Kathryn A K Finton, Peter B Rupert, Della J Friend, Ana Dinca, Erica S Lovelace, Matthew Buerger, Domnita V Rusnac, Ulysses Foote-McNabb, William Chour, James R Heath, Jean S Campbell, Robert H Pierce, and Roland K Strong
Inhibition of Microsomal Prostaglandin E2 Synthase Reduces Collagen Deposition in Melanoma Tumors and May Improve Immunotherapy Efficacy by Reducing T-cell Exhaustion., Yasunari Fukuda, Sun-Hee Kim, Matias A Bustos, Sung-Nam Cho, Jason Roszik, Jared K Burks, Hong Kim, Dave S B Hoon, Elizabeth A Grimm, and Suhendan Ekmekcioglu
Spatial profiling of cancer-associated fibroblasts of sporadic early onset colon cancer microenvironment., Satoru Furuhashi, Matias A Bustos, Shodai Mizuno, Suyeon Ryu, Yalda Naeini, Anton J Bilchik, and Dave SB Hoon
Evidence-based procedures to improve the reliability of circulating miRNA biomarker assays., Sarah R Greytak, Kelly B Engel, Dave S B Hoon, Kevin M Elias, Christina M Lockwood, Ping Guan, and Helen M Moore
Publisher Correction: The DNA sequence and analysis of human chromosome 14., Roland Heilig, Ralph Eckenberg, Jean-Louis Petit, Núria Fonknechten, Corinne Da Silva, Laurence Cattolico, Michaël Levy, Valérie Barbe, Véronique de Berardinis, Abel Ureta-Vidal, Eric Pelletier, Virginie Vico, Véronique Anthouard, Lee Rowen, Anup Madan, Shizhen Qin, Hui Sun, Hui Du, Kymberlie Pepin, François Artiguenave, Catherine Robert, Corinne Cruaud, Thomas Brüls, Olivier Jaillon, Lucie Friedlander, Gaelle Samson, Philippe Brottier, Susan Cure, Béatrice Ségurens, Franck Anière, Sylvie Samain, Hervé Crespeau, Nissa Abbasi, Nathalie Aiach, Didier Boscus, Rachel Dickhoff, Monica Dors, Ivan Dubois, Cynthia Friedman, Michel Gouyvenoux, Rose James, Anuradha Madan, Barbara Mairey-Estrada, Sophie Mangenot, Nathalie Martins, Manuela Ménard, Sophie Oztas, Amber Ratcliffe, Tristan Shaffer, Barbara Trask, Benoit Vacherie, Chadia Bellemere, Caroline Belser, Marielle Besnard-Gonnet, Delphine Bartol-Mavel, Magali Boutard, Stéphanie Briez-Silla, Stephane Combette, Virginie Dufossé-Laurent, Carolyne Ferron, Christophe Lechaplais, Claudine Louesse, Delphine Muselet, Ghislaine Magdelenat, Emilie Pateau, Emmanuelle Petit, Peggy Sirvain-Trukniewicz, Arnaud Trybou, Nathalie Vega-Czarny, Elodie Bataille, Elodie Bluet, Isabelle Bordelais, Maria Dubois, Corinne Dumont, Thomas Guérin, Sébastien Haffray, Rachid Hammadi, Jacqueline Muanga, Virginie Pellouin, Dominique Robert, Edith Wunderle, Gilbert Gauguet, Alice Roy, Laurent Sainte-Marthe, Jean Verdier, Claude Verdier-Discala, LaDeana Hillier, Lucinda Fulton, John McPherson, Fumihiko Matsuda, Richard Wilson, Claude Scarpelli, Gábor Gyapay, Patrick Wincker, William Saurin, Francis Quétier, Robert Waterston, Leroy Hood, and Jean Weissenbach
Improved Analysis of Cross-Linking Mass Spectrometry Data with Kojak 2.0, Advanced by Integration into the Trans-Proteomic Pipeline., Michael R Hoopmann, David D Shteynberg, Alex Zelter, Michael Riffle, Andrew S Lyon, David A Agard, Qing Luan, Brad J Nolen, Michael J MacCoss, Trisha N Davis, and Robert L Moritz
The Vicious Cycle of Melanoma-Microglia Crosstalk: Inter-Melanoma Variations in the Brain-Metastasis-Promoting IL-6/JAK/STAT3 Signaling Pathway., Sivan Izraely, Shlomit Ben-Menachem, Sapir Malka, Orit Sagi-Assif, Matias A Bustos, Orit Adir, Tsipi Meshel, Maharrish Chelladurai, Suyeon Ryu, Romela Irene Ramos, Metsada Pasmanik-Chor, Dave S B Hoon, and Isaac P Witz
Distant metastasis-free survival results from the randomized, phase 2 mRNA-4157-P201/KEYNOTE-942 trial., Adnan Khattak, Matthew H Taylor, and See full list of authors in comments
Selective enrichment of plasma cell-free messenger RNA in cancer-associated extracellular vesicles., Hyun Ji Kim, Matthew J Rames, Florian Goncalves, C Ward Kirschbaum, Breeshey Roskams-Hieter, Elias Spiliotopoulos, Josephine Briand, Aaron Doe, Joseph Estabrook, Josiah T. Wagner, Emek Demir, Gordon Mills, and Thuy T M Ngo
2019 Association of Biomolecular Resource Facilities Multi-Laboratory Data-Independent Acquisition Proteomics Study., Joanna Kirkpatrick, Paul M Stemmer, Brian C Searle, Laura E Herring, LeRoy Martin, Mukul K Midha, Brett S Phinney, Baozhen Shan, Magnus Palmblad, Yan Wang, Pratik D Jagtap, and Benjamin A Neely
Feasibility of circulating tumor DNA (ctDNA) to guide organ preservation in patients with node-negative rectal cancer undergoing neoadjuvant chemotherapy, excision, and observation in the phase II CCTG CO.28 trial, Jonathan M. Loree, Hagen F Kennecke, and See full list of authors in comments
Hyper-Dependence on NHEJ Enables Synergy Between DNA-PK Inhibitors and Low-Dose Doxorubicin in Leiomyosarcoma., Adrián Mariño-Enríquez, Jan Philipp Novotny, Doga C Gulhan, Isabella Klooster, Antuan V Tran, Macy Kasbo, Meijun Z Lundberg, Wen-Bin Ou, Derrick L Tao, Daniel F Pilco-Janeta, Victor Y Mao, Frank T Zenke, Brittaney A Leeper, Prafulla C Gokhale, Glenn S Cowley, Laurence H Baker, Karla V Ballman, David E Root, Joachim Albers, Peter J Park, Suzanne George, and Jonathan A Fletcher
Gene expression profiling and multiplex immunofluorescence analysis of bullous pemphigoid immune-related adverse event reveal upregulation of toll-like receptor 4/complement-induced innate immune response and increased density of T, Mario L Marques-Piubelli, Riyad N H Seervai, Kumaran M Mudaliar, Wencai Ma, Denái R Milton, Jing Wang, Aaron Muhlbauer, Edwin R Parra, Luisa M Solis, Priyadharsini Nagarajan, Jodi Speiser, Courtney Hudgens, Woo Cheal Cho, Phyu P Aung, Anisha Patel, Omar Pacha, Kelly C Nelson, Michael T Tetzlaff, Rodabe N Amaria, Carlos A Torres-Cabala, Victor G Prieto, Ignacio I Wistuba, and Jonathan L Curry
Rare predicted loss-of-function variants of type I IFN immunity genes are associated with life-threatening COVID-19., Daniela Matuozzo, Estelle Talouarn, Astrid Marchal, Peng Zhang, Jeremy Manry, Yoann Seeleuthner, Yu Zhang, Alexandre Bolze, Matthieu Chaldebas, Baptiste Milisavljevic, Adrian Gervais, Paul Bastard, Takaki Asano, Lucy Bizien, Federica Barzaghi, Hassan Abolhassani, Ahmad Abou Tayoun, Alessandro Aiuti, Ilad Alavi Darazam, Luis M Allende, Rebeca Alonso-Arias, Andrés Augusto Arias, Gokhan Aytekin, Peter Bergman, Simone Bondesan, Yenan T Bryceson, Ingrid G Bustos, Oscar Cabrera-Marante, Sheila Carcel, Paola Carrera, Giorgio Casari, Khalil Chaïbi, Roger Colobran, Antonio Condino-Neto, Laura E Covill, Ottavia M Delmonte, Loubna El Zein, Carlos Flores, Peter K Gregersen, Marta Gut, Filomeen Haerynck, Rabih Halwani, Selda Hancerli, Lennart Hammarström, Nevin Hatipoğlu, Adem Karbuz, Sevgi Keles, Christèle Kyheng, Rafael Leon-Lopez, Jose Luis Franco, Davood Mansouri, Javier Martinez-Picado, Ozge Metin Akcan, Isabelle Migeotte, Pierre-Emmanuel Morange, Guillaume Morelle, Andrea Martin-Nalda, Giuseppe Novelli, Antonio Novelli, Tayfun Ozcelik, Figen Palabiyik, Qiang Pan-Hammarström, Rebeca Pérez de Diego, Laura Planas-Serra, Daniel E Pleguezuelo, Carolina Prando, Aurora Pujol, Luis Felipe Reyes, Jacques G Rivière, Carlos Rodriguez-Gallego, Julian Rojas, Patrizia Rovere-Querini, Agatha Schlüter, Mohammad Shahrooei, Ali Sobh, Pere Soler-Palacin, Yacine Tandjaoui-Lambiotte, Imran Tipu, Cristina Tresoldi, Jesus Troya, Diederik van de Beek, Mayana Zatz, Pawel Zawadzki, Saleh Zaid Al-Muhsen, Mohammed Faraj Alosaimi, Fahad M Alsohime, Hagit Baris-Feldman, Manish J Butte, Stefan N Constantinescu, Megan A Cooper, Clifton L Dalgard, Jacques Fellay, James R Heath, Yu-Lung Lau, Richard P Lifton, Tom Maniatis, Trine H Mogensen, Horst von Bernuth, Alban Lermine, Michel Vidaud, Anne Boland, Jean-François Deleuze, Robert Nussbaum, Amanda Kahn-Kirby, France Mentre, Sarah Tubiana, Guy Gorochov, Florence Tubach, Pierre Hausfater, COVID Human Genetic Effort, COVIDeF Study Group, French COVID Cohort Study Group, CoV-Contact Cohort, COVID-STORM Clinicians, COVID Clinicians, Orchestra Working Group, Amsterdam UMC Covid-19 Biobank, NIAID-USUHS COVID Study Group, Isabelle Meyts, Shen-Ying Zhang, Anne Puel, Luigi D Notarangelo, Stephanie Boisson-Dupuis, Helen C Su, Bertrand Boisson, Emmanuelle Jouanguy, Jean-Laurent Casanova, Qian Zhang, Laurent Abel, and Aurélie Cobat
Integrated analysis of proteomics, epigenomics and metabolomics data revealed divergent pathway activation patterns in the recent versus chronic post-traumatic stress disorder., Seid Muhie, Aarti Gautam, Burook Misganaw, Ruoting Yang, Synthia H Mellon, Allison Hoke, Janine Flory, Bernie Daigle, Kevin Swift, PTSD Systems Biology Consortium, Leroy Hood, Francis J Doyle, Owen M Wolkowitz, Charles R Marmar, Kerry Ressler, Rachel Yehuda, Rasha Hammamieh, and Marti Jett
Molecular signatures of post-traumatic stress disorder in war-zone-exposed veteran and active-duty soldiers., Seid Muhie, Aarti Gautam, Ruoting Yang, Burook Misganaw, Bernie J Daigle, Synthia H Mellon, Janine D Flory, Duna Abu-Amara, Inyoul Lee, Kai Wang, Ryan Rampersaud, PTSD Systems Biology Consortium, Leroy Hood, Rachel Yehuda, Charles R Marmar, Owen M Wolkowitz, Kerry J Ressler, Francis J Doyle, Rasha Hammamieh, and Marti Jett
Computational capabilities of a multicellular reservoir computing system., Vladimir Nikolić, Moriah Echlin, Boris Aguilar, and Ilya Shmulevich
Insights into mammalian TE diversity through the curation of 248 genome assemblies., Austin B Osmanski, Nicole S Paulat, Jenny Korstian, Jenna R Grimshaw, Michaela Halsey, Kevin A M Sullivan, Diana D Moreno-Santillán, Claudia Crookshanks, Jacquelyn Roberts, Carlos Garcia, Matthew G Johnson, Llewellyn D Densmore, Richard D Stevens, Jeb Rosen, Jessica Storer, Robert Hubley, Arian F A Smit, Liliana M Dávalos, Elinor K Karlsson, Kerstin Lindblad-Toh, and David A Ray
Chiropterans Are a Hotspot for Horizontal Transfer of DNA Transposons in Mammalia., Nicole S Paulat, Jessica Storer, Diana D Moreno-Santillán, Austin B Osmanski, Kevin A M Sullivan, Jenna R Grimshaw, Jennifer Korstian, Michaela Halsey, Carlos J Garcia, Claudia Crookshanks, Jaquelyn Roberts, Arian F A Smit, Robert Hubley, Jeb Rosen, Emma C Teeling, Sonja C Vernes, Eugene Myers, Martin Pippel, Thomas Brown, Michael Hiller, Danny Rojas, Liliana M Dávalos, Kerstin Lindblad-Toh, Elinor K Karlsson, and David A Ray
Toward structuring real-world data: Deep learning for extracting oncology information from clinical text with patient-level supervision., Sam Preston, Mu Wei, Rajesh Rao, Robert Tinn, Naoto Usuyama, Michael Lucas, Yu Gu, Roshanthi Weerasinghe, Soohee Lee, Brian D. Piening, Paul Tittel, Naveen Valluri, Tristan Naumann, Carlo Bifulco, and Hoifung Poon
A Network Landscape of HPVOPC Reveals Methylation Alterations as Significant Drivers of Gene Expression via an Immune-Mediated GPCR Signal., Jesse R Qualliotine, Takuya Nakagawa, Sara Brin Rosenthal, Sayed Sadat, Carmen Ballesteros-Merino, Guorong Xu, Adam Mark, Art Nasamran, J Silvio Gutkind, Kathleen M Fisch, Theresa Guo, Bernard A Fox, Zubair Khan, Alfredo A Molinolo, and Joseph A Califano
ProteomicsML: An Online Platform for Community-Curated Data sets and Tutorials for Machine Learning in Proteomics., Tobias G Rehfeldt, Ralf Gabriels, Robbin Bouwmeester, Siegfried Gessulat, Benjamin A Neely, Magnus Palmblad, Yasset Perez-Riverol, Tobias Schmidt, Juan Antonio Vizcaíno, and Eric W Deutsch
Unsupervised mRNA-seq classification of heart transplant endomyocardial biopsies., Erick Romero, Esteban Tabak, Gregory Fishbein, Silvio Litovsky, Jose Tallaj, David Liem, Maral Bakir, Yeraz Khachatoorian, Brian Piening, Brendan Keating, Mario Deng, and Martin Cadeiras
2166 / 8 - Analysis of ctDNA next generation sequencing (NGS) for predicting response to amivantamab and lazertinib among patients with EGFR-mutant NSCLC after progression on osimertinib and platinum-based chemotherapy (CHRYSALIS-2 Cohort A), Rachel E Sanborn and See full list of authors in comments
Single-molecule Sequencing of an Animal Mitochondrial Genome Reveals Chloroplast-like Architecture and Repeat-mediated Recombination., Joel Sharbrough, Laura Bankers, Emily Cook, Peter D Fields, Joseph Jalinsky, Kyle E McElroy, Maurine Neiman, John M Logsdon, and Jeffrey L Boore
Prediction of HLA genotypes from single-cell transcriptome data., Benjamin D Solomon, Hong Zheng, Laura W Dillon, Jason D Goldman, Christopher S Hourigan, James R Heath, and Purvesh Khatri
Genome-wide coancestry reveals details of ancient and recent male-driven reticulation in baboons., Erik F Sørensen, R Alan Harris, Liye Zhang, Muthuswamy Raveendran, Lukas F K Kuderna, Jerilyn A Walker, Jessica Storer, Martin Kuhlwilm, Claudia Fontsere, Lakshmi Seshadri, Christina M Bergey, Andrew S Burrell, Juraj Bergman, Jane E Phillips-Conroy, Fekadu Shiferaw, Kenneth L Chiou, Idrissa S Chuma, Julius D Keyyu, Julia Fischer, Marie-Claude Gingras, Sejal Salvi, Harshavardhan Doddapaneni, Mikkel H Schierup, Mark A Batzer, Clifford J Jolly, Sascha Knauf, Dietmar Zinner, Kyle K-H Farh, Tomas Marques-Bonet, Kasper Munch, Christian Roos, and Jeffrey Rogers
LIFEHOUSE's Functional Nutrition Examination (Physical Exam, Anthropometrics, and Selected Biomarkers) Informs Personalized Wellness Interventions., Michael Stone, Dan Lukaczer, Christopher R D'Adamo, Nicole Dotson, Andrey Volkov, Deanna Minich, Dina Metti, Michelle Leary, Monique Class, Malisa Carullo, Erik Lundquist, Brent Eck, Jose Ordovas, Joseph Lamb, and Jeffrey Bland
Does the Ubiquitination Degradation Pathway Really Reach inside of the Chloroplast? A Re-Evaluation of Mass Spectrometry-Based Assignments of Ubiquitination., Klaas J van Wijk, Tami Leppert, Zhi Sun, and Eric W Deutsch
Lifespan-extending interventions induce consistent patterns of fatty acid oxidation in mouse livers., Kengo Watanabe, Tomasz Wilmanski, Priyanka Baloni, Max Robinson, Gonzalo G Garcia, Michael R Hoopmann, Mukul K Midha, David H Baxter, Michal Maes, Seamus R Morrone, Kelly M Crebs, Charu Kapil, Ulrike Kusebauch, Jack Wiedrick, Jodi Lapidus, Lance Pflieger, Christopher Lausted, Jared C Roach, Gwênlyn Glusman, Steven R Cummings, Nicholas J Schork, Nathan D Price, Leroy Hood, Richard A Miller, Robert L Moritz, and Noa Rappaport
Entropic analysis of antigen-specific CDR3 domains identifies essential binding motifs shared by CDR3s with different antigen specificities., Alexander M Xu, William Chour, Diana C DeLucia, Yapeng Su, Ana Jimena Pavlovitch-Bedzyk, Rachel Ng, Yusuf Rasheed, Mark M Davis, John K Lee, and James R Heath
Integrating Genetics, Transcriptomics, and Proteomics in Lung Tissue to Investigate COPD., Yu-Hang Zhang, Michael H Cho, Jarrett D Morrow, Peter J Castaldi, Craig P Hersh, Mukul K Midha, Michael R Hoopmann, Sharon M Lutz, Robert L Moritz, and Edwin K Silverman
Submissions from 2022
940 siRNA screen of upregulated genes identifies targets for a multiantigen polyepitope vaccine to prevent HNSCC, Fnu Alka, James Annis, Brady Bernard, and Sasha Stanton
Multi-modal molecular programs regulate melanoma cell state., Miles C Andrews, Junna Oba, Chang-Jiun Wu, Haifeng Zhu, Tatiana Karpinets, Caitlin A Creasy, Marie-Andrée Forget, Xiaoxing Yu, Xingzhi Song, Xizeng Mao, A Gordon Robertson, Gabriele Romano, Peng Li, Elizabeth M Burton, Yiling Lu, Robert Szczepaniak Sloane, Khalida M Wani, Kunal Rai, Alexander J Lazar, Lauren E Haydu, Matias A Bustos, Jianjun Shen, Yueping Chen, Margaret B Morgan, Jennifer A Wargo, Lawrence N Kwong, Cara L Haymaker, Elizabeth A Grimm, Patrick Hwu, Dave S B Hoon, Jianhua Zhang, Jeffrey E Gershenwald, Michael A Davies, P Andrew Futreal, Chantale Bernatchez, and Scott E Woodman
Perspectives in Immunotherapy: meeting report from the Immunotherapy Bridge, December 1st-2nd, 2021., Paolo A Ascierto, Antonio Avallone, Nina Bhardwaj, Carlo Bifulco, Sergio Bracarda, Joshua D Brody, Luigi Buonaguro, Sandra Demaria, Leisha A Emens, Robert L Ferris, Jérôme Galon, Samir N Khleif, Christopher A Klebanoff, Tamara Laskowski, Ignacio Melero, Chrystal M Paulos, Sandro Pignata, Marco Ruella, Inge Marie Svane, Janis M Taube, Bernard A Fox, Patrick Hwu, and Igor Puzanov
Multi-Omic analyses characterize the ceramide/sphingomyelin pathway as a therapeutic target in Alzheimer's disease., Priyanka Baloni, Matthias Arnold, Luna Buitrago, Kwangsik Nho, Herman Moreno, Kevin Huynh, Barbara Brauner, Gregory Louie, Alexandra Kueider-Paisley, Karsten Suhre, Andrew J Saykin, Kim Ekroos, Peter J Meikle, Leroy Hood, Nathan D Price, Alzheimer’s Disease Metabolomics Consortium, P Murali Doraiswamy, Cory C Funk, A Iván Hernández, Gabi Kastenmüller, Rebecca Baillie, Xianlin Han, and Rima Kaddurah-Daouk
Clinical actionability and therapy selection for advanced NSCLC patients tested using comprehensive genomic profiling, B Bapat, R Weerasignhe, R Meng, A Dowdell, SC Chang, B Schroeder, C Bifulco, and B Piening
Blocking UBE2N abrogates oncogenic immune signaling in acute myeloid leukemia., Laura Barreyro, Avery M Sampson, Chiharu Ishikawa, Kathleen M Hueneman, Kwangmin Choi, Mario A Pujato, Somchai Chutipongtanate, Michael Wyder, Wendy D Haffey, Eric O'Brien, Mark Wunderlich, Vighnesh Ramesh, Ellen M Kolb, Cem Meydan, Yaseswini Neelamraju, Lyndsey C Bolanos, Susanne Christie, Molly A Smith, Madeline Niederkorn, Tomoya Muto, Santosh Kesari, Francine E Garrett-Bakelman, Boris Bartholdy, Britta Will, Matthew T Weirauch, James C Mulloy, Zartash Gul, Stephen Medlin, Rhett A Kovall, Ari M Melnick, John P Perentesis, Kenneth D Greis, Elmar Nurmemmedov, William L Seibel, and Daniel T Starczynowski
Genomic Models of Practice That Support the Quadruple Aim, Carlo Bifulco
Enhancing Clinical Genomics Datasets with Multimodal EHR Data and Imaging, Carlo Bifulco and Brian Piening
A Random Forest Genomic Classifier for Tumor Agnostic Prediction of Response to Anti-PD1 Immunotherapy., Emma Bigelow, Suchi Saria, Brian D. Piening, Brendan Curti, Alexa K Dowdell, Roshanthi Weerasinghe, Carlo Bifulco, Walter Urba, Noam Finkelstein, Elana J Fertig, Alex Baras, Neeha Zaidi, Elizabeth Jaffee, and Mark Yarchoan
Cross-ancestry genome-wide meta-analysis of 61,047 cases and 947,237 controls identifies new susceptibility loci contributing to lung cancer., Jinyoung Byun, Younghun Han, Yafang Li, Jun Xia, Erping Long, Jiyeon Choi, Xiangjun Xiao, Meng Zhu, Wen Zhou, Ryan Sun, Yohan Bossé, Zhuoyi Song, Ann Schwartz, Christine Lusk, Thorunn Rafnar, Kari Stefansson, Tongwu Zhang, Wei Zhao, Rowland W Pettit, Yanhong Liu, Xihao Li, Hufeng Zhou, Kyle M Walsh, Ivan Gorlov, Olga Gorlova, Dakai Zhu, Susan M Rosenberg, Susan Pinney, Joan E Bailey-Wilson, Diptasri Mandal, Mariza de Andrade, Colette Gaba, James C Willey, Ming You, Marshall Anderson, John K Wiencke, Demetrius Albanes, Stephan Lam, Adonina Tardon, Chu Chen, Gary E Goodman, Stig Bojeson, Hermann Brenner, Maria Teresa Landi, Stephen J Chanock, Mattias Johansson, Thomas Muley, Angela Risch, H-Erich Wichmann, Heike Bickeböller, David C Christiani, Gad Rennert, Susanne Arnold, John K Field, Sanjay Shete, Loic Le Marchand, Olle Melander, Hans Brunnstrom, Geoffrey Liu, Angeline S Andrew, Lambertus A Kiemeney, Hongbing Shen, Shanbeh Zienolddiny, Kjell Grankvist, Mikael Johansson, Neil Caporaso, Angela Cox, Yun-Chul Hong, Jian-Min Yuan, Philip Lazarus, Matthew B Schabath, Melinda C Aldrich, Alpa Patel, Qing Lan, Nathaniel Rothman, Fiona Taylor, Linda Kachuri, John S Witte, Lori C Sakoda, Margaret Spitz, Paul Brennan, Xihong Lin, James McKay, Rayjean J Hung, and Christopher I Amos
DNA methylome combined with chromosome cluster-oriented analysis provides an early signature for cutaneous melanoma aggressiveness., Arnaud Carrier, Cécile Desjobert, Loic Ponger, Laurence Lamant, Matias A Bustos, Jorge Torres-Ferreira, Rui Henrique, Carmen Jeronimo, Luisa Lanfrancone, Audrey Delmas, Gilles Favre, Antoine Daunay, Florence Busato, Dave S B Hoon, Jorg Tost, Chantal Etievant, Joëlle Riond, and Paola B Arimondo
Analysis of germline-driven ancestry-associated gene expression in cancers., Nyasha Chambwe, Rosalyn W Sayaman, Donglei Hu, Scott Huntsman, Cancer Genome Analysis Network, Anab Kemal, Samantha Caesar-Johnson, Jean C Zenklusen, Elad Ziv, Rameen Beroukhim, and Andrew D Cherniack
Genomic Correlates of Outcome in Tumor-Infiltrating Lymphocyte Therapy for Metastatic Melanoma., Caitlin A Creasy, Yuzhong Jeff Meng, Marie-Andrée Forget, Tatiana Karpinets, Katarzyna Tomczak, Chip Stewart, Carlos A Torres-Cabala, Shari Pilon-Thomas, Amod A Sarnaik, James J Mule, Levi Garraway, Matias A Bustos, Jianhua Zhang, Sapna P Patel, Adi Diab, Isabella C Glitza, Cassian Yee, Hussein Tawbi, Michael K Wong, Jennifer McQuade, Dave S B Hoon, Michael A Davies, Patrick Hwu, Rodabe N Amaria, Cara Haymaker, Rameen Beroukhim, and Chantale Bernatchez
The TP53 Database: transition from the International Agency for Research on Cancer to the US National Cancer Institute., Kelvin César de Andrade, Elaine E Lee, Elise M Tookmanian, Chimene A Kesserwan, James J Manfredi, Jessica N Hatton, Jennifer K Loukissas, Jiri Zavadil, Lei Zhou, Magali Olivier, Megan N Frone, Owais Shahzada, William J R Longabaugh, Christian P Kratz, David Malkin, Pierre Hainaut, and Sharon A Savage
Genome-microbiome interplay provides insight into the determinants of the human blood metabolome., Christian Diener, Chengzhen L Dai, Tomasz Wilmanski, Priyanka Baloni, Brett Smith, Noa Rappaport, Leroy Hood, Andrew T Magis, and Sean M Gibbons
Automatic Patient Matching for Genome-Guided Adoptive Cell Immunotherapy Trials at a Large Health System, Alexa K Dowdell, Tucker Bower, Benjamin Cosgrove, Roshanthi Weerasinghe, Ann Vita, Brian D. Piening, Carlo Bifulco, Eric Tran, and Rom Leidner
Latinx attitudes, barriers, and experiences with genetic counseling and testing: A systematic review., Heather A Dron, Daiana Bucio, Jennifer L Young, Holly K Tabor, and Mildred K Cho
What Is a Digital Twin? Experimental Design for a Data-Centric Machine Learning Perspective in Health., Frank Emmert-Streib and Olli Yli-Harja
Epigenetic Signatures Predict Pathologic Nodal Stage in Breast Cancer Patients with Estrogen Receptor-Positive, Clinically Node-Positive Disease., Miquel Ensenyat-Mendez, Dennis Rünger, Javier I Orozco, Julie Le, Jennifer L Baker, Joanne Weidhaas, Diego M Marzese, and Maggie L DiNome
Correction: Interplay between soluble CD74 and macrophage-migration inhibitory factor drives tumor growth and influences patient survival in melanoma., Yasunari Fukuda, Matias A Bustos, Sung-Nam Cho, Jason Roszik, Suyeon Ryu, Victor M Lopez, Jared K Burks, Jeffrey E Lee, Elizabeth A Grimm, Dave S B Hoon, and Suhendan Ekmekcioglu
Interplay between soluble CD74 and macrophage-migration inhibitory factor drives tumor growth and influences patient survival in melanoma., Yasunari Fukuda, Matias A Bustos, Sung-Nam Cho, Jason Roszik, Suyeon Ryu, Victor M Renteria-Lopez, Jared K Burks, Jeffrey E Lee, Elizabeth A Grimm, Dave Hoon, and Suhendan Ekmekcioglu
Distribution of 54 polygenic risk scores for common diseases in long lived individuals and their offspring., Sophia Gunn, Michael Wainberg, Zeyuan Song, Stacy Andersen, Robert Boudreau, Mary F Feitosa, Qihua Tan, May E Montasser, Jeffrey R O'Connell, Nathan Stitziel, Nathan D Price, Thomas Perls, Nicholas J Schork, and Paola Sebastiani
Rare variants implicate NMDA receptor signaling and cerebellar gene networks in risk for bipolar disorder., Naushaba Hasin, Lace M Riggs, Tatyana Shekhtman, Justin Ashworth, Robert Lease, Rediet T Oshone, Elizabeth M Humphries, Judith A Badner, Pippa A Thomson, David C Glahn, David W Craig, Howard J Edenberg, Elliot S Gershon, Francis J McMahon, John I Nurnberger, Peter P Zandi, John R Kelsoe, Jared C Roach, Todd D Gould, and Seth A Ament
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
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
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
Towards a unification of the 2 meanings of "epigenetics"., Sui Huang
Accuracy of multiple sequence alignment methods in the reconstruction of transposable element families., Robert Hubley, Travis J Wheeler, and Arian F A Smit
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
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
Genomic Amplification of, Yuta Kobayashi, Matias A Bustos, Yoshiaki Shoji, Ron D Jachimowicz, Yosef Shiloh, and Dave S B Hoon
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
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
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
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
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
The epigenetic impact of adverse childhood experiences through the lens of personalized medicine., Sheldon Levy and John Muench
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
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
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
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
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
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
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
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
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
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
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
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
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
Personal Dense Dynamic Data Clouds Connect Systems Biomedicine to Scientific Wellness., Gilbert S Omenn, Andrew T Magis, Nathan D Price, and Leroy Hood
The Human Tumor Atlas Network's beginning steps toward the future of collaborative multi-omic discovery., David B Page
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
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
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
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
