Submissions from 2021
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
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
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
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
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
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
Limitations of Explainability for Established Prognostic Biomarkers of Prostate Cancer., Kalifa Manjang, Olli Yli-Harja, Matthias Dehmer, and Frank Emmert-Streib
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
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
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
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
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
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
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
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
Curation Guidelines for de novo Generated Transposable Element Families., Jessica Storer, Robert Hubley, Jeb Rosen, and Arian F A Smit
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
A novel microRNA-based prognostic model outperforms standard prognostic models in patients with acetaminophen-induced acute liver failure., Oliver D Tavabie, Constantine J Karvellas, Siamak Salehi, Jaime L Speiser, Christopher F Rose, Krishna Menon, Andreas Prachalias, Michael A Heneghan, Kosh Agarwal, William M Lee, Mark J W McPhail, Varuna R Aluvihare, United States Acute Liver Failure Study Group, and Oren K Fix (United States Acute Liver Failure Study Group)
A Caenorhabditis elegans behavioral assay distinguishes early stage prostate cancer patient urine from controls, Morgan Thompson, Noemi Sarabia Feria, Ally Yoshioka, Eugene Tu, Fehmi Civitci, Suzanne Estes, and Josiah T Wagner
Assessment of Cell-Free microRNA by NGS Whole-Transcriptome Analysis in Cutaneous Melanoma Patients' Blood., Kevin Tran, Rebecca Gross, Negin Rahimzadeh, Shanthy Chenathukattil, Dave Hoon, and Matias A Bustos
The Arabidopsis PeptideAtlas: Harnessing worldwide proteomics data to create a comprehensive community proteomics resource., Klaas J van Wijk, Tami Leppert, Qi Sun, Sascha S Boguraev, Zhi Sun, Luis Mendoza, and Eric W Deutsch
Genetic program activity delineates risk, relapse, and therapy responsiveness in multiple myeloma., Matthew A Wall, Serdar Turkarslan, Wei-Ju Wu, Samuel A Danziger, David J Reiss, Mike J Mason, Andrew P Dervan, Matthew W B Trotter, Douglas Bassett, Robert M Hershberg, Adrián López García de Lomana, Alexander V Ratushny, and Nitin S Baliga
CIDer: A Statistical Framework for Interpreting Differences in CID and HCD Fragmentation., Damien B Wilburn, Alicia L Richards, Danielle L Swaney, and Brian C Searle
A DNA methylation clock associated with age-related illnesses and mortality is accelerated in men with combat PTSD., Ruoting Yang, Gwyneth W Y Wu, Josine E Verhoeven, Aarti Gautam, Victor I Reus, Jee In Kang, Janine D Flory, Duna Abu-Amara, PTSD Systems Biology Consortium, Leroy Hood, Francis J Doyle, Rachel Yehuda, Charles R Marmar, Marti Jett, Rasha Hammamieh, Synthia H Mellon, and Owen M Wolkowitz
The geometry of clinical labs and wellness states from deeply phenotyped humans., Anat Zimmer, Yael Korem, Noa Rappaport, Tomasz Wilmanski, Priyanka Baloni, Kathleen Jade, Max Robinson, Andrew T Magis, Jennifer Lovejoy, Sean M Gibbons, Leroy Hood, and Nathan D Price
Phenotyping Cardiogenic Shock., Elric Zweck, Katherine L Thayer, Ole K L Helgestad, Manreet Kanwar, Mohyee Ayouty, A Reshad Garan, Jaime Hernandez-Montfort, Claudius Mahr, Detlef Wencker, Shashank S Sinha, Esther Vorovich, Jacob Abraham, William O'Neill, Song Li, Gavin W Hickey, Jakob Josiassen, Christian Hassager, Lisette O Jensen, Lene Holmvang, Henrik Schmidt, Hanne B Ravn, Jacob E Møller, Daniel Burkhoff, and Navin K Kapur
Submissions from 2020
Characterization of a Novel Compound That Stimulates STING-Mediated Innate Immune Activity in an Allele-Specific Manner., Jinu Abraham, Sara Botto, Nobuyo Mizuno, Kara Pryke, Bryan Gall, Dylan Boehm, Tina M Sali, Haihong Jin, Aaron Nilsen, Michael J. Gough, Jason R Baird, Marita Chakhtoura, Caroline Subra, Lydie Trautmann, Elias K Haddad, and Victor R DeFilippis
A high-stringency blueprint of the human proteome., Subash Adhikari, Edouard C Nice, Eric W Deutsch, Lydie Lane, Gilbert S Omenn, Stephen R Pennington, Young-Ki Paik, Christopher M Overall, Fernando J Corrales, Ileana M Cristea, Jennifer E Van Eyk, Mathias Uhlén, Cecilia Lindskog, Daniel W Chan, Amos Bairoch, James C Waddington, Joshua L Justice, Joshua LaBaer, Henry Rodriguez, Fuchu He, Markus Kostrzewa, Peipei Ping, Rebekah L Gundry, Peter Stewart, Sanjeeva Srivastava, Sudhir Srivastava, Fabio C S Nogueira, Gilberto B Domont, Yves Vandenbrouck, Maggie P Y Lam, Sara Wennersten, Juan Antonio Vizcaino, Marc Wilkins, Jochen M Schwenk, Emma Lundberg, Nuno Bandeira, Gyorgy Marko-Varga, Susan T Weintraub, Charles Pineau, Ulrike Kusebauch, Robert L Moritz, Seong Beom Ahn, Magnus Palmblad, Michael P Snyder, Ruedi Aebersold, and Mark S Baker
Intratumoral delivery of tavokinogene telseplasmid yields systemic immune responses in metastatic melanoma patients., A Algazi, S Bhatia, S Agarwala, M Molina, K Lewis, M Faries, L Fong, L P Levine, M Franco, A Oglesby, C Ballesteros-Merino, C B Bifulco, B A Fox, D Bannavong, R Talia, E Browning, M H Le, R H Pierce, S Gargosky, K K Tsai, C Twitty, and A I Daud
Phase II Trial of IL-12 Plasmid Transfection and PD-1 Blockade in Immunologically Quiescent Melanoma., Alain P Algazi, Christopher G Twitty, Katy K Tsai, Mai Le, Robert Pierce, Erica Browning, Reneta Hermiz, David A Canton, Donna Bannavong, Arielle Oglesby, Murray Francisco, Lawrence Fong, Mikael J Pittet, Sean P Arlauckas, Christopher Garris, Lauren P Levine, Carlo Bifulco, Carmen Ballesteros-Merino, Shailender Bhatia, Sharron Gargosky, Robert H I Andtbacka, Bernard A Fox, Michael D Rosenblum, and Adil I Daud
Metabolic Network Analysis Reveals Altered Bile Acid Synthesis and Metabolism in Alzheimer's Disease., Priyanka Baloni, Cory C Funk, Jingwen Yan, James T Yurkovich, Alexandra Kueider-Paisley, Kwangsik Nho, Almut Heinken, Wei Jia, Siamak Mahmoudiandehkordi, Gregory Louie, Andrew J Saykin, Matthias Arnold, Gabi Kastenmüller, William J Griffiths, Ines Thiele, Alzheimer’s Disease Metabolomics Consortium, Rima Kaddurah-Daouk, and Nathan D Price
The Landscape of Glycogen synthase kinase-3 beta (GSK-3b) Genomic Alterations in Cancer., Brittany A Borden, Yasmine Baca, Joanne Xiu, Fabio Tavora, Ira Winer, Benjamin A Weinberg, Ari M VanderWalde, Sourat Darabi, W Michael Korn, Andrew P Mazar, Francis J Giles, Lorin Crawford, Howard Safran, Wafik S El-Deiry, and Benedito A Carneiro
A Pilot Study Comparing the Efficacy of Lactate Dehydrogenase Levels Versus Circulating Cell-Free microRNAs in Monitoring Responses to Checkpoint Inhibitor Immunotherapy in Metastatic Melanoma Patients., Matias A Bustos, Rebecca Gross, Negin Rahimzadeh, Hunter Cole, Linh T Tran, Kevin Tran, Ling Takeshima, Stacey L Stern, Steven O'Day, and Dave Hoon
Comprehensive Analysis of Genetic Ancestry and Its Molecular Correlates in Cancer., Jian Carrot-Zhang, Nyasha Chambwe, Jeffrey S Damrauer, Theo A Knijnenburg, A Gordon Robertson, Christina Yau, Wanding Zhou, Ashton C Berger, Kuan-Lin Huang, Justin Y Newberg, R Jay Mashl, Alessandro Romanel, Rosalyn W Sayaman, Francesca Demichelis, Ina Felau, Garrett M Frampton, Seunghun Han, Katherine A Hoadley, Anab Kemal, Peter W Laird, Alexander J Lazar, Xiuning Le, Ninad Oak, Hui Shen, Christopher K Wong, Jean C Zenklusen, Elad Ziv, Cancer Genome Atlas Analysis Network, Andrew D Cherniack, and Rameen Beroukhim
Synthesizing Systems Biology Knowledge from Omics Using Genome-Scale Models., Sanjeev Dahal, James T Yurkovich, Hao Xu, Bernhard O Palsson, and Laurence Yang
Genome-wide association study of INDELs identified four novel susceptibility loci associated with lung cancer risk., Juncheng Dai, Mingtao Huang, Christopher I Amos, Rayjean J Hung, Adonina Tardon, Angeline Andrew, Chu Chen, David C Christiani, Demetrius Albanes, Gadi Rennert, Jingyi Fan, Gary E Goodman, Geoffrey Liu, John K Field, Kjell Grankvist, Lambertus A Kiemeney, Loic Le Marchand, Matthew B Schabath, Mattias Johansson, Melinda C Aldrich, Mikael Johansson, Neil Caporaso, Philip Lazarus, Stephan Lam, Stig E Bojesen, Susanne Arnold, Maria Teresa Landi, Angela Risch, H-Erich Wichmann, Heike Bickeboller, Paul Brennan, Sanjay Shete, Olle Melander, Hans Brunnstrom, Shan Zienolddiny, Penella Woll, Victoria Stevens, Zhibin Hu, and Hongbing Shen
Genomic, proteomic, and immunologic associations with a durable complete remission of measurable metastatic melanoma induced by a patient-specific dendritic cell vaccine., Robert O Dillman, Gabriel I Nistor, and Aleksandra J Poole
Genomic heterogeneity and clinical characterization of SARS-CoV-2 in Oregon, Alexa K Dowdell, Kevin Matlock, Fred L. Robinson, Roshanthi Weerasinghe, Rogan Rattray, Marina Pukay, Melvin Lathara, Anastacia Harlan, Thomas R. Ward, Mary Campbell, Walter Urba, Ganapati Srinivasa, Carlo Bifulco, and Brian D. Piening
Brainstem ischemic syndrome in juvenile NF2., John W Henson, Tara Benkers, and Connor McCormick
Building a circular RNA centered gene regulation network associated with cervical squamous cell carcinoma., Wei Hu, Qingqing Li, Xiaoyi He, Ming Gao, Zhanfu Zheng, Yuanlin Ding, Kai Wang, and Yuqing He
Targeting the ERG oncogene with splice-switching oligonucleotides as a novel therapeutic strategy in prostate cancer., Ling Li, Lisa Hobson, Laura Perry, Bethany Clark, Susan Heavey, Aiman Haider, Ashwin Sridhar, Greg Shaw, John Kelly, Alex Freeman, Ian Wilson, Hayley Whitaker, Elmar Nurmemmedov, Sebastian Oltean, Sean Porazinski, and Michael Ladomery
Genetic counseling following direct-to consumer genetic testing: Consumer perspectives., Tessa Marzulla, J Scott Roberts, Raymond DeVries, Diane R Koeller, Robert C Green, and Wendy R Uhlmann
Inter-Tumor Heterogeneity-Melanomas Respond Differently to GM-CSF-Mediated Activation., Adi Moshe, Sivan Izraely, Orit Sagi-Assif, Sapir Malka, Shlomit Ben-Menachem, Tsipi Meshel, Metsada Pasmanik-Chor, Dave Hoon, and Isaac P Witz
Research on the Human Proteome Reaches a Major Milestone: >90% of Predicted Human Proteins Now Credibly Detected, According to the HUPO Human Proteome Project., Gilbert S Omenn, Lydie Lane, Christopher M Overall, Ileana M Cristea, Fernando J Corrales, Cecilia Lindskog, Young-Ki Paik, Jennifer E Van Eyk, Siqi Liu, Stephen R Pennington, Michael P Snyder, Mark S Baker, Nuno Bandeira, Ruedi Aebersold, Robert L Moritz, and Eric W Deutsch
Prevalence of class I-III BRAF mutations among 114,662 cancer patients in a large genomic database., Jeff Owsley, Matthew K Stein, Jason Porter, Gino K In, Mohamed Salem, Steven O'Day, Andrew Elliott, Kelsey Poorman, Geoffrey Gibney, and Ari VanderWalde
Obesity Drives Delayed Infarct Expansion, Inflammation, and Distinct Gene Networks in a Mouse Stroke Model., Todd C Peterson, Kendra J Lechtenberg, Brian D. Piening, Tawaun A Lucas, Eric Wei, Hassan Chaib, Alexa K Dowdell, Michael Snyder, and Marion S Buckwalter
Enabling Scalable Comprehensive Genomic Profiling from FFPE Samples, Brian D. Piening
Comprehensive Genomic Profiling in Patients with Advanced Cancer in a Large US Healthcare System, Brian D. Piening, Alexa K Dowdell, Roshanthi Weerasinghe, B Bapat, R Roe, Nancy Biery, Shwetha Pindikuri, Sheila Reynolds, David Ball, Mary Campbell, Thomas R. Ward, A Stein, B Schroeder, H Poon, D Eberhard, and Carlo Bifulco
Ageotypes: Distinct Biomolecular Trajectories in Human Aging., Brian D. Piening, Jennifer Lovejoy, and John C Earls
Genetic Variants in Immune Related Genes as Predictors of Responsiveness to BCG Immunotherapy in Metastatic Melanoma Patients., Romela Irene Ramos, Misa A Shaw, Leland J Foshag, Stacey L Stern, Negin Rahimzadeh, David Elashoff, and Dave Hoon
Birds of a Feather? Genetic Counseling, Genetic Testing, and Humanism., Robert Resta
Advancing human health in the decade ahead: pregnancy as a key window for discovery: A Burroughs Wellcome Fund Pregnancy Think Tank., Yoel Sadovsky, Sam Mesiano, Graham J Burton, Michelle Lampl, Jeffrey C Murray, Rachel M Freathy, Anita Mahadevan-Jansen, Ashley Moffett, Nathan D Price, Paul H Wise, Derek E Wildman, Ralph Snyderman, Nigel Paneth, John Anthony Capra, Marcelo A Nobrega, Yaacov Barak, and Louis J Muglia
Human-engineered Treg-like cells suppress FOXP3-deficient T cells but preserve adaptive immune responses, Yohei Sato, Laura Passerini, Brian D. Piening, Molly Javier Uyeda, Marianne Goodwin, Silvia Gregori, Michael P Snyder, Alice Bertaina, Maria-Grazia Roncarolo, and Rosa Bacchetta
ECHS1 disease in two unrelated families of Samoan descent: Common variant - rare disorder., Mariella T Simon; Shaya S Eftekharian; Sacha Ferdinandusse; Sha Tang; Take Naseri; Muagututi'a Sefuiva Reupena; Stephen T McGarvey; Ryan L Minster; Daniel E Weeks; Lifestyle, and Genetic Adaptations (OLaGA) Study Group; Daniel D Nguyen; Sansan Lee; Katarzyna A Ellsworth; Frédéric M Vaz; David Dimmock; James Pitt; and Jose E Abdenur
Behavior-related gene regulatory networks: A new level of organization in the brain., Saurabh Sinha, Beryl M Jones, Ian M Traniello, Syed A Bukhari, Marc S Halfon, Hans A Hofmann, Sui Huang, Paul S Katz, Jason Keagy, Vincent J Lynch, Marla B Sokolowski, Lisa J Stubbs, Shayan Tabe-Bordbar, Mariana F Wolfner, and Gene E Robinson
Multi-omic single-cell snapshots reveal multiple independent trajectories to drug tolerance in a melanoma cell line., Yapeng Su, Melissa E Ko, Hanjun Cheng, Ronghui Zhu, Min Xue, Jessica Wang, Jihoon W Lee, Luke Frankiw, Alexander Xu, Stephanie Wong, Lidia Robert, Kaitlyn Takata, Dan Yuan, Yue Lu, Sui Huang, Antoni Ribas, Raphael Levine, Garry P Nolan, Wei Wei, Sylvia K Plevritis, Guideng Li, David Baltimore, and James R Heath
Congenital myasthenic syndrome caused by a frameshift insertion mutation in, Szabolcs Szelinger, Jonida Krate, Keri Ramsey, Samuel P Strom, Perry B Shieh, Hane Lee, Newell Belnap, Chris Balak, Ashley L Siniard, Megan Russell, Ryan Richholt, Matt De Both, Ana M Claasen, Isabelle Schrauwen, Stanley F Nelson, Matthew J Huentelman, David W Craig, Samuel Yang, Steven A Moore, Kumaraswamy Sivakumar, Vinodh Narayanan, Sampathkumar Rangasamy, and UCLA Clinical Genomics Center
The Society for Immunotherapy of Cancer statement on best practices for multiplex immunohistochemistry (IHC) and immunofluorescence (IF) staining and validation., Janis M Taube, Guray Akturk, Michael Angelo, Elizabeth L Engle, Sacha Gnjatic, Shirley Greenbaum, Noah F Greenwald, Cyrus V Hedvat, Travis J Hollmann, Jonathan Juco, Edwin R Parra, Marlon C Rebelatto, David L Rimm, Jaime Rodriguez-Canales, Kurt A Schalper, Edward C Stack, Cláudia S Ferreira, Konstanty Korski, Ana Lako, Scott J Rodig, Emanuel Schenck, Keith E Steele, Michael J Surace, Michael T Tetzlaff, Katharina von Loga, Ignacio I Wistuba, Carlo Bifulco, and Society for Immunotherapy of Cancer (SITC) Pathology Task Force.
Meta-Analysis of the Alzheimer's Disease Human Brain Transcriptome and Functional Dissection in Mouse Models., Ying-Wooi Wan, Rami Al-Ouran, Carl G Mangleburg, Thanneer M Perumal, Tom V Lee, Katherine Allison, Vivek Swarup, Cory C Funk, Chris Gaiteri, Mariet Allen, Minghui Wang, Sarah M Neuner, Catherine C Kaczorowski, Vivek M Philip, Gareth R Howell, Heidi Martini-Stoica, Hui Zheng, Hongkang Mei, Xiaoyan Zhong, Jungwoo Wren Kim, Valina L Dawson, Ted M Dawson, Ping-Chieh Pao, Li-Huei Tsai, Jean-Vianney Haure-Mirande, Michelle E Ehrlich, Paramita Chakrabarty, Yona Levites, Xue Wang, Eric B Dammer, Gyan Srivastava, Sumit Mukherjee, Solveig K Sieberts, Larsson Omberg, Kristen D Dang, James A Eddy, Phil Snyder, Yooree Chae, Sandeep Amberkar, Wenbin Wei, Winston Hide, Christoph Preuss, Ayla Ergun, Phillip J Ebert, David C Airey, Sara Mostafavi, Lei Yu, Hans-Ulrich Klein, Accelerating Medicines Partnership, Alzheimer’s Disease Consortium, Gregory W Carter, David A Collier, Todd E Golde, Allan I Levey, David A Bennett, Karol Estrada, T Matthew Townsend, Bin Zhang, Eric Schadt, Philip L De Jager, Nathan D Price, Nilüfer Ertekin-Taner, Zhandong Liu, Joshua M Shulman, Lara M Mangravite, and Benjamin A Logsdon
A primary human T-cell spectral library to facilitate large scale quantitative T-cell proteomics., Harshi Weerakoon, Jeremy Potriquet, Alok K Shah, Sarah Reed, Buddhika Jayakody, Charu Kapil, Mukul K Midha, Robert L Moritz, Ailin Lepletier, Jason Mulvenna, John J Miles, and Michelle M Hill
Epigenetic biotypes of post-traumatic stress disorder in war-zone exposed veteran and active duty males., Ruoting Yang, Aarti Gautam, Derese Getnet, Bernie J Daigle, Stacy Miller, Burook Misganaw, Kelsey R Dean, Raina Kumar, Seid Muhie, Kai Wang, Inyoul Lee, Duna Abu-Amara, Janine D Flory, PTSD Systems Biology Consortium, Leroy Hood, Owen M Wolkowitz, Synthia H Mellon, Francis J Doyle, Rachel Yehuda, Charles R Marmar, Kerry J Ressler, Rasha Hammamieh, and Marti Jett
Correction: A DNA methylation clock associated with age-related illnesses and mortality is accelerated in men with combat PTSD., Ruoting Yang, Gwyneth W Y Wu, Josine E Verhoeven, Aarti Gautam, Victor I Reus, Jee In Kang, Janine D Flory, Duna Abu-Amara, PTSD Systems Biology Consortium, Leroy Hood, Francis J Doyle, Rachel Yehuda, Charles R Marmar, Marti Jett, Rasha Hammamieh, Synthia H Mellon, and Owen M Wolkowitz
Submissions from 2019
Perspectives in immunotherapy: meeting report from the "Immunotherapy Bridge 2018" (28-29 November, 2018, Naples, Italy)., Paolo A Ascierto, Carlo Bifulco, Luigi Buonaguro, Leisha A Emens, Robert L Ferris, Bernard A Fox, Greg M Delgoffe, Jérôme Galon, Cesare Gridelli, Marco Merlano, Paul Nathan, Kunle Odunsi, Hideho Okada, Chrystal M Paulos, Sandro Pignata, Kurt A Schalper, Stefani Spranger, Giampaolo Tortora, Hassane Zarour, Lisa H Butterfield, and Igor Puzanov
Pre-Analytic Variables and Tissue Stewardship for Reliable Next-Generation Sequencing (NGS) Clinical Analysis., Paolo A Ascierto, Carlo Bifulco, Giuseppe Palmieri, Solange Peters, and Nikoletta Sidiropoulos
The Society for Immunotherapy of Cancer consensus statement on immunotherapy for the treatment of squamous cell carcinoma of the head and neck (HNSCC)., Ezra E W Cohen, Richard Bryan Bell, Carlo Bifulco, Barbara Burtness, Maura L Gillison, Kevin J Harrington, Quynh-Thu Le, Nancy Y Lee, Rom Leidner, Rebecca L Lewis, Lisa Licitra, Hisham Mehanna, Loren K Mell, Adam Raben, Andrew G Sikora, Ravindra Uppaluri, Fernanda Whitworth, Dan P Zandberg, and Robert L Ferris
Significant differences in outcome between Immunoscore categories in stage I colon cancer patients., J Galon, F Hermitte, B Mlecnik, F Marliot, Carlo Bifulco, A Lugli, I Nagtegaal, A Hartmann, M Van den Eynde, M Roehrl, P Ohashi, E Zavadova, T Torigoe, P Patel, Y Wang, Y Kawakami, F Marincola, P Ascierto, Bernard A Fox, and F Pagès
Comprehensive Genomic Tumor Profiling, Brian D. Piening
Differential Effects of Influenza Virus NA, HA Head, and HA Stalk Antibodies on Peripheral Blood Leukocyte Gene Expression during Human Infection., Kathie-Anne Walters, Ruoqing Zhu, Michael Welge, Kelsey Scherler, Jae-Keun Park, Zainab Rahil, Hao Wang, Loretta Auvil, Colleen Bushell, Min Young Lee, David Baxter, Tyler Bristol, Luz Angela Rosas, Adriana Cervantes-Medina, Lindsay Czajkowski, Alison Han, Matthew J Memoli, Jeffery K Taubenberger, and John C Kash
Multispectral Fluorescence Imaging Allows for Distinctive Topographic Assessment and Subclassification of Tumor-Infiltrating and Surrounding Immune Cells., Claudia Wickenhauser, Daniel Bethmann, Zipei Feng, Shawn M. Jensen, Carmen Ballesteros-Merino, Chiara Massa, Andre Steven, Marcus Bauer, Peter Kaatzsch, Nikolaos Pazaitis, Georgiana Toma, Carlo Bifulco, Bernard A Fox, and Barbara Seliger
Longitudinal multi-omics of host-microbe dynamics in prediabetes., Wenyu Zhou, M Reza Sailani, Kévin Contrepois, Yanjiao Zhou, Sara Ahadi, Shana R Leopold, Martin J Zhang, Varsha Rao, Monika Avina, Tejaswini Mishra, Jethro Johnson, Brittany Lee-McMullen, Songjie Chen, Ahmed A Metwally, Thi Dong Binh Tran, Hoan Nguyen, Xin Zhou, Brandon Albright, Bo-Young Hong, Lauren Petersen, Eddy Bautista, Blake Hanson, Lei Chen, Daniel Spakowicz, Amir Bahmani, Denis Salins, Benjamin Leopold, Melanie Ashland, Orit Dagan-Rosenfeld, Shannon Rego, Patricia Limcaoco, Elizabeth Colbert, Candice Allister, Dalia Perelman, Colleen Craig, Eric Wei, Hassan Chaib, Daniel Hornburg, Jessilyn Dunn, Liang Liang, Sophia Miryam Schüssler-Fiorenza Rose, Kim Kukurba, Brian D. Piening, Hannes Rost, David Tse, Tracey McLaughlin, Erica Sodergren, George M Weinstock, and Michael Snyder
Submissions from 2018
Perspectives in melanoma: Meeting report from the Melanoma Bridge (30 November-2 December, 2017, Naples, Italy)., Paolo A Ascierto, Igor Puzanov, Sanjiv S Agarwala, Carlo Bifulco, Gerardo Botti, Corrado Caracò, Gennaro Ciliberto, Michael A Davies, Reinhard Dummer, Soldano Ferrone, Thomas F Gajewski, Claus Garbe, Jason J Luke, Francesco M Marincola, Giuseppe Masucci, Janice M Mehnert, Nicola Mozzillo, Giuseppe Palmieri, Michael A Postow, Stephen P Schoenberger, Ena Wang, and Magdalena Thurin
The Role of Precision Medicine in the Diagnosis and Treatment of Patients with Rare Cancers., Michael J Demeure
Applying genomics in heart transplantation., Brendan J Keating, Alexandre C Pereira, Michael Snyder, and Brian D. Piening
Novel frontiers in detecting cancer metastasis., Stanley P Leong, Carmen Ballesteros-Merino, Shawn M Jensen, Sebastian Marwitz, Carlo Bifulco, Bernard A Fox, and Mojca Skoberne
PD-L1 expression with immune-infiltrate evaluation and outcome prediction in melanoma patients treated with ipilimumab., Gabriele Madonna, Carmen Ballesteros-Merino, Zipei Feng, Carlo Bifulco, Mariaelena Capone, Diana Giannarelli, Domenico Mallardo, Ester Simeone, Antonio M Grimaldi, Corrado Caracò, Gerardo Botti, Bernard A Fox, and Paolo A Ascierto
International validation of the consensus Immunoscore for the classification of colon cancer: a prognostic and accuracy study., Franck Pagès, Bernhard Mlecnik, Florence Marliot, Gabriela Bindea, Fang-Shu Ou, Carlo Bifulco, Alessandro Lugli, Inti Zlobec, Tilman T Rau, Martin D Berger, Iris D Nagtegaal, Elisa Vink-Börger, Arndt Hartmann, Carol Geppert, Julie Kolwelter, Susanne Merkel, Robert Grützmann, Marc Van den Eynde, Anne Jouret-Mourin, Alex Kartheuser, Daniel Léonard, Christophe Remue, Julia Y Wang, Prashant Bavi, Michael H A Roehrl, Pamela S Ohashi, Linh T Nguyen, SeongJun Han, Heather L MacGregor, Sara Hafezi-Bakhtiari, Bradly G Wouters, Giuseppe V Masucci, Emilia K Andersson, Eva Zavadova, Michal Vocka, Jan Spacek, Lubos Petruzelka, Bohuslav Konopasek, Pavel Dundr, Helena Skalova, Kristyna Nemejcova, Gerardo Botti, Fabiana Tatangelo, Paolo Delrio, Gennaro Ciliberto, Michele Maio, Luigi Laghi, Fabio Grizzi, Tessa Fredriksen, Bénédicte Buttard, Mihaela Angelova, Angela Vasaturo, Pauline Maby, Sarah E Church, Helen K Angell, Lucie Lafontaine, Daniela Bruni, Carine El Sissy, Nacilla Haicheur, Amos Kirilovsky, Anne Berger, Christine Lagorce, Jeffrey P Meyers, Christopher Paustian, Zipei Feng, Carmen Ballesteros-Merino, Jeroen Dijkstra, Carlijn van de Water, Shannon van Lent-van Vliet, Nikki Knijn, Ana-Maria Mușină, Dragos-Viorel Scripcariu, Boryana Popivanova, Mingli Xu, Tomonobu Fujita, Shoichi Hazama, Nobuaki Suzuki, Hiroaki Nagano, Kiyotaka Okuno, Toshihiko Torigoe, Noriyuki Sato, Tomohisa Furuhata, Ichiro Takemasa, Kyogo Itoh, Prabhu S Patel, Hemangini H Vora, Birva Shah, Jayendrakumar B Patel, Kruti N Rajvik, Shashank J Pandya, Shilin N Shukla, Yili Wang, Guanjun Zhang, Yutaka Kawakami, Francesco M Marincola, Paolo A Ascierto, Daniel J Sargent, Bernard A Fox, and Jérôme Galon
Effects of Delivering SLCO1B1 Pharmacogenetic Information in Randomized Trial and Observational Settings., Bruce Peyser, Emily P Perry, Kavisha Singh, Rosalynn D Gill, Michael R Mehan, Susanne B Haga, Michael D Musty, Nicholas A Milazzo, Dillon Savard, Yi-Ju Li, Gloria Trujilio, and Deepak Voora
New Clues to Human Longevity, Brian D. Piening
The Integrated Genomic Landscape of Thymic Epithelial Tumors., Milan Radovich, Curtis R Pickering, Ina Felau, Gavin Ha, Hailei Zhang, Heejoon Jo, Katherine A Hoadley, Pavana Anur, Jiexin Zhang, Mike McLellan, Reanne Bowlby, Thomas Matthew, Ludmila Danilova, Apurva M Hegde, Jaegil Kim, Mark D M Leiserson, Geetika Sethi, Charles Lu, Michael Ryan, Xiaoping Su, Andrew D Cherniack, Gordon Robertson, Rehan Akbani, Paul Spellman, John N Weinstein, D Neil Hayes, Ben Raphael, Tara Lichtenberg, Kristen Leraas, Jean Claude Zenklusen, Junya Fujimoto, Cristovam Scapulatempo-Neto, Andre L Moreira, David Hwang, James Huang, Mirella Marino, Robert Korst, Giuseppe Giaccone, Yesim Gokmen-Polar, Sunil Badve, Arun Rajan, Philipp Ströbel, Nicolas Girard, Ming S Tsao, Alexander Marx, Anne S Tsao, and Patrick J Loehrer
Glioblastoma radiomics: can genomic and molecular characteristics correlate with imaging response patterns?, Michael H Soike, Emory R McTyre, Nameeta Shah, Ralph B Puchalski, Jordan A Holmes, Anna K Paulsson, Lance D Miller, Christina K Cramer, Glenn J Lesser, Roy E Strowd, William H Hinson, Ryan T Mott, Annette J Johnson, Hui-Wen Lo, Adrian W Laxton, Stephen B Tatter, Waldemar Debinski, and Michael D Chan
Taking Systems Medicine to Heart., Kalliopi Trachana, Rhishikesh Bargaje, Gustavo Glusman, Nathan D Price, Sui Huang, and Leroy E Hood
Submissions from 2017
IFPA meeting 2016 workshop report I: Genomic communication, bioinformatics, trophoblast biology and transport systems., Christiane Albrecht, Julie C Baker, Cassidy Blundell, Shawn L Chavez, Lucia Carbone, Larry Chamley, Roberta L Hannibal, Nick Illsley, Peter Kurre, Louise C Laurent, Charles McKenzie, Diana Morales-Prieto, Priyadarshini Pantham, Alison Paquette, Katie Powell, Nathan Price, Balaji M Rao, Yoel Sadovsky, Carlos Salomon, Geetu Tuteja, Samantha Wilson, and P F O'Tierney-Ginn
The State of Systems Genetics in 2017., Nitin S Baliga, Johan L M Björkegren, Jef D Boeke, Michael Boutros, Nigel P S Crawford, Aimée M Dudley, Charles R Farber, Allan Jones, Allan I Levey, Aldons J Lusis, H Craig Mak, Joseph H Nadeau, Marcus B Noyes, Enrico Petretto, Nicholas T Seyfried, Lars M Steinmetz, and Sibylle C Vonesch
Multiparametric immune profiling in HPV- oral squamous cell cancer., Zipei Feng, Daniel Bethmann, Matthias Kappler, Carmen Ballesteros-Merino, Alexander Eckert, R Bryan Bell, Allen Cheng, Tuan Bui, Rom Leidner, Walter Urba, Kent Johnson, Clifford Hoyt, Carlo Bifulco, Juergen Bukur, Claudia Wickenhauser, Barbara Seliger, and Bernard A Fox
Differences between the genomes of lymphoblastoid cell lines and blood-derived samples., Lena M Joesch-Cohen and Gustavo Glusman
Discovering and linking public omics data sets using the Omics Discovery Index., Yasset Perez-Riverol, Mingze Bai, Felipe da Veiga Leprevost, Silvano Squizzato, Young Mi Park, Kenneth Haug, Adam J Carroll, Dylan Spalding, Justin Paschall, Mingxun Wang, Noemi Del-Toro, Tobias Ternent, Peng Zhang, Nicola Buso, Nuno Bandeira, Eric W Deutsch, David S Campbell, Ronald C Beavis, Reza M Salek, Ugis Sarkans, Robert Petryszak, Maria Keays, Eoin Fahy, Manish Sud, Shankar Subramaniam, Ariana Barbera, Rafael C Jiménez, Alexey I Nesvizhskii, Susanna-Assunta Sansone, Christoph Steinbeck, Rodrigo Lopez, Juan A Vizcaíno, Peipei Ping, and Henning Hermjakob
Rational confederation of genes and diseases: NGS interpretation via GeneCards, MalaCards and VarElect., Noa Rappaport, Simon Fishilevich, Ron Nudel, Michal Twik, Frida Belinky, Inbar Plaschkes, Tsippi Iny Stein, Dana Cohen, Danit Oz-Levi, Marilyn Safran, and Doron Lancet
The ISB Cancer Genomics Cloud: A Flexible Cloud-Based Platform for Cancer Genomics Research., Sheila M Reynolds, Michael Miller, Phyliss Lee, Kalle Leinonen, Suzanne M Paquette, Zack Rodebaugh, Abigail Hahn, David L Gibbs, Joseph Slagel, William J Longabaugh, Varsha Dhankani, Madelyn Reyes, Todd Pihl, Mark Backus, Matthew Bookman, Nicole Deflaux, Jonathan Bingham, David Pot, and Ilya Shmulevich
Genomic, Transcriptional, and Phenotypic Analysis of the Glucose Derepressed Clostridium beijerinckii Mutant Exhibiting Acid Crash Phenotype., Seung-Oh Seo, Holger Janssen, Andrew Magis, Yi Wang, Ting Lu, Nathan D Price, Yong-Su Jin, and Hans P Blaschek
Submissions from 2016
Image processing method and system for analyzing a multi-channel image obtained from a biological tissue sample being stained by multiple stains, Michael Barnes, Carlo Bifulco, Ting Chen, and Alisa Tubbs
Rationale and design of the SLCO1B1 genotype guided statin therapy trial., Kavisha Singh, Bruce Peyser, Gloria Trujillo, Nicholas Milazzo, Dillon Savard, Susanne B Haga, Michael Musty, and Deepak Voora
