Submissions from 2020
Selective carbon sources influence the end products of microbial nitrate respiration., Hans K Carlson, Lauren M Lui, Morgan N Price, Alexey E Kazakov, Alex V Carr, Jennifer V Kuehl, Trenton K Owens, Torben Nielsen, Adam P Arkin, and Adam M Deutschbauer
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
Systematic comparison of sea urchin and sea star developmental gene regulatory networks explains how novelty is incorporated in early development., Gregory A Cary, Brenna S McCauley, Olga Zueva, Joseph Pattinato, William J R Longabaugh, and Veronica F Hinman
Society for Immunotherapy of Cancer clinical and biomarkers data sharing resource document: Volume II-practical challenges., Alessandra Cesano, Michael A Cannarile, Sacha Gnjatic, Bruno Gomes, Justin Guinney, Vaios Karanikas, Mohan Karkada, John M Kirkwood, Beatrix Kotlan, Giuseppe V Masucci, Els Meeusen, Anne Monette, Aung Naing, Vésteinn Thorsson, Nicholas Tschernia, Ena Wang, Daniel K Wells, Timothy L Wyant, and Sergio Rutella
Cancer Systems Biology in the Era of Single-Cell Multi-Omics., Hanjun Cheng, Rong Fan, and Wei Wei
A novel landscape of nuclear human CDK2 substrates revealed by in situ phosphorylation., Yong Chi, John H Carter, Jherek Swanger, Alexander V Mazin, Robert L Moritz, and Bruce E Clurman
Unique challenges for glioblastoma immunotherapy - Discussions across neuro-oncology and non-neuro-oncology experts in cancer immunology., Pavlina Chuntova, Frances Chow, Payal Watchmaker, Mildred Galvez, Amy B Heimberger, Evan W Newell, Aaron Diaz, Ronald A DePinho, Ming O Li, E John Wherry, Duane Mitchell, Masaki Terabe, Derek A Wainwright, Jay A Berzofsky, Christel Herold-Mende, James R Heath, Michael Lim, Kim A Margolin, E Antonio Chiocca, Noriyuki Kasahara, Benjamin M Ellingson, Christine Brown, Yvonne Chen, Peter Fecci, David A Reardon, Gavin P Dunn, Linda M Liau, Joseph F Costello, Wolfgang Wick, Timothy Cloughesy, William C Timmer, Patrick Y Wen, Robert M Prins, Michael Platten, and Hideho Okada
Inferring evolutionary pathways and directed genotype networks of foodborne pathogens., Oliver M Cliff, Natalia McLean, Vitali Sintchenko, Kristopher M Fair, Tania C Sorrell, Stuart Kauffman, and Mikhail Prokopenko
Synthesizing Systems Biology Knowledge from Omics Using Genome-Scale Models., Sanjeev Dahal, James T Yurkovich, Hao Xu, Bernhard O Palsson, and Laurence Yang
Characterizing diversity in the tumor-immune microenvironment of distinct subclasses of gastroesophageal adenocarcinomas., S Derks, L K de Klerk, X Xu, T Fleitas, K X Liu, Y Liu, F Dietlein, C Margolis, A M Chiaravalli, A C Da Silva, S Ogino, F G Akarca, G J Freeman, S J Rodig, J L Hornick, E van Allen, B Li, S X Liu, V Thorsson, and A J Bass
The ProteomeXchange consortium in 2020: enabling 'big data' approaches in proteomics., Eric W Deutsch, Nuno Bandeira, Vagisha Sharma, Yasset Perez-Riverol, Jeremy J Carver, Deepti J Kundu, David García-Seisdedos, Andrew F Jarnuczak, Suresh Hewapathirana, Benjamin S Pullman, Julie Wertz, Zhi Sun, Shin Kawano, Shujiro Okuda, Yu Watanabe, Henning Hermjakob, Brendan MacLean, Michael J MacCoss, Yunping Zhu, Yasushi Ishihama, and Juan A Vizcaíno
MICOM: Metagenome-Scale Modeling To Infer Metabolic Interactions in the Gut Microbiota., Christian Diener, Sean M Gibbons, and Osbaldo Resendis-Antonio
Progressive Shifts in the Gut Microbiome Reflect Prediabetes and Diabetes Development in a Treatment-Naive Mexican Cohort., Christian Diener, María de Lourdes Reyes-Escogido, Lilia M Jimenez-Ceja, Mariana Matus, Claudia M Gomez-Navarro, Nathaniel D Chu, Vivian Zhong, M Elizabeth Tejero, Eric Alm, Osbaldo Resendis-Antonio, and Rodolfo Guardado-Mendoza
Glioblastoma Multiforme Stem Cell Cycle Arrest by Alkylaminophenol Through the Modulation of EGFR and CSC Signaling Pathways., Phuong Doan, Aliyu Musa, Akshaya Murugesan, Vili Sipilä, Nuno R Candeias, Frank Emmert-Streib, Pekka Ruusuvuori, Kirsi Granberg, Olli Yli-Harja, and Meenakshisundaram Kandhavelu
Raman-guided subcellular pharmaco-metabolomics for metastatic melanoma cells., Jiajun Du, Yapeng Su, Chenxi Qian, Dan Yuan, Kun Miao, Dongkwan Lee, Alphonsus H C Ng, Reto S Wijker, Antoni Ribas, Raphael D Levine, James R Heath, and Lu Wei
CRI iAtlas: an interactive portal for immuno-oncology research., James A Eddy, Vésteinn Thorsson, Andrew E Lamb, David L Gibbs, Carolina Heimann, Jia Xin Yu, Verena Chung, Yooree Chae, Kristen Dang, Benjamin G Vincent, Ilya Shmulevich, and Justin Guinney
Artificial Intelligence: A Clarification of Misconceptions, Myths and Desired Status., Frank Emmert-Streib, Olli Yli-Harja, and Matthias Dehmer
Extending Comet for Global Amino Acid Variant and Post-Translational Modification Analysis using the PSI Extended FASTA Format (PEFF)., Jimmy K Eng and Eric W Deutsch
Resolution of eicosanoid/cytokine storm prevents carcinogen and inflammation-initiated hepatocellular cancer progression., Anna Fishbein, Weicang Wang, Haixia Yang, Jun Yang, Victoria M Hallisey, Jianjun Deng, Sanne M L Verheul, Sung Hee Hwang, Allison Gartung, Yuxin Wang, Diane R Bielenberg, Sui Huang, Mark W Kieran, Bruce D Hammock, and Dipak Panigrahy
Transcriptional portrait of M. bovis BCG during biofilm production shows genes differentially expressed during intercellular aggregation and substrate attachment., Mario Alberto Flores-Valdez, Michel de Jesús Aceves-Sánchez, Eliza Jr Peterson, Nitin Baliga, Jorge Bravo-Madrigal, Miguel Ángel De la Cruz-Villegas, Miguel A Ares, Sarah Born, Martin Voskuil, Nayeli Areli Pérez-Padilla, Mirna Burciaga-Flores, Tanya Amanda Camacho-Villegas, and María Guadalupe Espinoza-Jorge
RepeatModeler2 for automated genomic discovery of transposable element families., Jullien M Flynn, Robert Hubley, Clément Goubert, Jeb Rosen, Andrew G Clark, Cédric Feschotte, and Arian F Smit
Atlas of Transcription Factor Binding Sites from ENCODE DNase Hypersensitivity Data across 27 Tissue Types., Cory C Funk, Alex M Casella, Segun Jung, Matthew A Richards, Alex Rodriguez, Paul Shannon, Rory Donovan-Maiye, Ben Heavner, Kyle Chard, Yukai Xiao, Gustavo Glusman, Nilufer Ertekin-Taner, Todd E Golde, Arthur Toga, Leroy Hood, John D Van Horn, Carl Kesselman, Ian Foster, Ravi Madduri, Nathan D Price, and Seth A Ament
Alterations in plasma microRNA and protein levels in war veterans with chronic mild traumatic brain injury., Vikas Ghai, Shannon Fallen, David Baxter, Kelsey Scherler, Taek-Kyun Kim, Yong Zhou, James Meabon, Aric Logsdon, William Allen Banks, Abigail Schindler, David Cook, Elaine Peskind, Inyoul Lee, and Kai Wang
Keystone taxa indispensable for microbiome recovery., Sean M Gibbons
Publisher Correction: Keystone taxa indispensable for microbiome recovery., Sean M Gibbons
Absolute quantification of transcription factors in human erythropoiesis using selected reaction monitoring mass spectrometry., Mark A Gillespie, Carmen G Palii, Daniel Sanchez-Taltavull, Theodore J Perkins, Marjorie Brand, and Jeffrey A Ranish
Absolute Quantification of Transcription Factors Reveals Principles of Gene Regulation in Erythropoiesis., Mark A Gillespie, Carmen G Palii, Daniel Sanchez-Taltavull, Paul Shannon, William J R Longabaugh, Damien J Downes, Karthi Sivaraman, Herbert M Espinoza, Jim R Hughes, Nathan D Price, Theodore J Perkins, Jeffrey A Ranish, and Marjorie Brand
Interdisciplinary Profile: An Established Chemist Journeys into Different Disciplines., James R Heath
Integration of time-series meta-omics data reveals how microbial ecosystems respond to disturbance., Malte Herold, Susana Martínez Arbas, Shaman Narayanasamy, Abdul R Sheik, Luise A K Kleine-Borgmann, Laura A Lebrun, Benoît J Kunath, Hugo Roume, Irina Bessarab, Rohan B H Williams, John D Gillece, James M Schupp, Paul S Keim, Christian Jäger, Michael R Hoopmann, Robert L Moritz, Yuzhen Ye, Sujun Li, Haixu Tang, Anna Heintz-Buschart, Patrick May, Emilie E L Muller, Cedric C Laczny, and Paul Wilmes
Lumenal calcification and microvasculopathy in fetuin-A-deficient mice lead to multiple organ morbidity., Marietta Herrmann, Anne Babler, Irina Moshkova, Felix Gremse, Fabian Kiessling, Ulrike Kusebauch, Valentin Nelea, Rafael Kramann, Robert L Moritz, Marc D McKee, and Willi Jahnen-Dechent
Facebook Live: Dr. Rod Hochman, Providence CEO and Prof. Jim Health Ph.D. discuss the science around Coronavirus., Rod Hochman and Jim Heath
Insights from the First Phosphopeptide Challenge of the MS Resource Pillar of the HUPO Human Proteome Project., Michael R Hoopmann, Ulrike Kusebauch, Magnus Palmblad, Nuno Bandeira, David Shteynberg, Lingjie He, Bin Xia, Stoyan H Stoychev, Gilbert S Omenn, Susan T Weintraub, and Robert L Moritz
Average Fitness Differences on NK Landscapes., Wim Hordijk, Stuart A Kauffman, and Peter F Stadler
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
Modulation of Immune Checkpoints by Chemotherapy in Human Colorectal Liver Metastases., Neda Jabbari, Heidi L Kenerson, Christopher Lausted, Xiaowei Yan, Changting Meng, Kevin M Sullivan, Priyanka Baloni, Dani E Bergey, Venu G Pillarisetty, Leroy Hood, Raymond S Yeung, and Qiang Tian
Comparative lipidomics of 5-Fluorouracil-sensitive and -resistant colorectal cancer cells reveals altered sphingomyelin and ceramide controlled by acid sphingomyelinase (SMPD1)., Jae Hun Jung, Kohei Taniguchi, Hyeong Min Lee, Min Young Lee, Raju Bandu, Kazumasa Komura, Kil Yeon Lee, Yukihiro Akao, and Kwang Pyo Kim
National Cancer Institute Think-Tank Meeting Report on Proteomic Cartography and Biomarkers at the Single-Cell Level: Interrogation of Premalignant Lesions., Jacob Kagan, Robert L Moritz, Richard Mazurchuk, Je Hyuk Lee, Peter Vasili Kharchenko, Orit Rozenblatt-Rosen, Eytan Ruppin, Fredrik Edfors, Fiona Ginty, Yury Goltsev, James A Wells, John LaCava, Jessica L Riesterer, Ronald N Germain, Tujin Shi, Mark S Chee, Bogdan A Budnik, John R Yates, Brian T Chait, Jeffery R Moffitt, Richard D Smith, and Sudhir Srivastava
Answering Schrödinger's "What Is Life?", Stuart Kauffman
Theory of chemical evolution of molecule compositions in the universe, in the Miller-Urey experiment and the mass distribution of interstellar and intergalactic molecules., Stuart A Kauffman, Dávid Péter Jelenfi, and Gábor Vattay
Theory of chemical evolution of molecule compositions in the universe, in the Miller-Urey experiment and the mass distribution of interstellar and intergalactic molecules., Stuart A Kauffman, Dávid Péter Jelenfi, and Gábor Vattay
An Exploratory Pilot Study with Plasma Protein Signatures Associated with Response of Patients with Depression to Antidepressant Treatment for 10 Weeks., Eun Young Kim, Hee-Sung Ahn, Min Young Lee, Jiyoung Yu, Jeonghun Yeom, Hwangkyo Jeong, Hophil Min, Hyun Jeong Lee, Kyunggon Kim, and Yong Min Ahn
Assembly of SNAPc, Bdp1, and TBP on the U6 snRNA gene promoter in Drosophila melanogaster., Mun Kyoung Kim, An Tranvo, Ann Marie Hurlburt, Neha Verma, Phuc Phan, Jie Luo, Jeff Ranish, and William E Stumph
Core transcriptional regulatory circuits in prion diseases., Taek-Kyun Kim, Inyoul Lee, Ji-Hoon Cho, Brenda Canine, Andrew Keller, Nathan D Price, Daehee Hwang, George Carlson, and Leroy Hood
Plasma levels of soluble ACE2are associated with sex, Metabolic Syndrome, and its biomarkers in a large cohort, pointing to a possible mechanism for increased severity in COVID-19., Sergey A Kornilov, Isabelle Lucas, Kathleen Jade, Chengzhen L Dai, Jennifer C Lovejoy, and Andrew T Magis
Epigenome signatures landscaped by histone H3K9me3 are associated with the synaptic dysfunction in Alzheimer's disease., Min Young Lee, Junghee Lee, Seung Jae Hyeon, Hyesun Cho, Yu Jin Hwang, Jong-Yeon Shin, Ann C McKee, Neil W Kowall, Jong-Il Kim, Thor D Stein, Daehee Hwang, and Hoon Ryu
Characterizing the cancer-associated microbiome with small RNA sequencing data., Wei-Hao Lee, Kai-Pu Chen, Kai Wang, Hsuan-Cheng Huang, and Hsueh-Fen Juan
Toward Increased Reliability, Transparency, and Accessibility in Cross-linking Mass Spectrometry., Alexander Leitner, Alexandre M J J Bonvin, Christoph H Borchers, Robert J Chalkley, Julia Chamot-Rooke, Colin W Combe, Jürgen Cox, Meng-Qiu Dong, Lutz Fischer, Michael Götze, Fabio C Gozzo, Albert J R Heck, Michael R Hoopmann, Lan Huang, Yasushi Ishihama, Andrew R Jones, Nir Kalisman, Oliver Kohlbacher, Karl Mechtler, Robert L Moritz, Eugen Netz, Petr Novak, Evgeniy Petrotchenko, Andrej Sali, Richard A Scheltema, Carla Schmidt, David Schriemer, Andrea Sinz, Frank Sobott, Florian Stengel, Konstantinos Thalassinos, Henning Urlaub, Rosa Viner, Juan A Vizcaíno, Marc R Wilkins, and Juri Rappsilber
Longitudinal analysis reveals transition barriers between dominant ecological states in the gut microbiome., Roie Levy, Andrew T Magis, John C Earls, Ohad Manor, Tomasz Wilmanski, Jennifer Lovejoy, Sean M Gibbons, Gilbert S Omenn, Leroy Hood, and Nathan D Price
MEMOTE for standardized genome-scale metabolic model testing., Christian Lieven, Moritz E Beber, Brett G Olivier, Frank T Bergmann, Meric Ataman, Parizad Babaei, Jennifer A Bartell, Lars M Blank, Siddharth Chauhan, Kevin Correia, Christian Diener, Andreas Dräger, Birgitta E Ebert, Janaka N Edirisinghe, José P Faria, Adam M Feist, Georgios Fengos, Ronan M T Fleming, Beatriz García-Jiménez, Vassily Hatzimanikatis, Wout van Helvoirt, Christopher S Henry, Henning Hermjakob, Markus J Herrgård, Ali Kaafarani, Hyun Uk Kim, Zachary King, Steffen Klamt, Edda Klipp, Jasper J Koehorst, Matthias König, Meiyappan Lakshmanan, Dong-Yup Lee, Sang Yup Lee, Sunjae Lee, Nathan E Lewis, Filipe Liu, Hongwu Ma, Daniel Machado, Radhakrishnan Mahadevan, Paulo Maia, Adil Mardinoglu, Gregory L Medlock, Jonathan M Monk, Jens Nielsen, Lars Keld Nielsen, Juan Nogales, Intawat Nookaew, Bernhard O Palsson, Jason A Papin, Kiran R Patil, Mark Poolman, Nathan D Price, Osbaldo Resendis-Antonio, Anne Richelle, Isabel Rocha, Benjamín J Sánchez, Peter J Schaap, Rahuman S Malik Sheriff, Saeed Shoaie, Nikolaus Sonnenschein, Bas Teusink, Paulo Vilaça, Jon Olav Vik, Judith A H Wodke, Joana C Xavier, Qianqian Yuan, Maksim Zakhartsev, and Cheng Zhang
Publisher Correction: MEMOTE for standardized genome-scale metabolic model testing., Christian Lieven, Moritz E Beber, Brett G Olivier, Frank T Bergmann, Meric Ataman, Parizad Babaei, Jennifer A Bartell, Lars M Blank, Siddharth Chauhan, Kevin Correia, Christian Diener, Andreas Dräger, Birgitta E Ebert, Janaka N Edirisinghe, José P Faria, Adam M Feist, Georgios Fengos, Ronan M T Fleming, Beatriz García-Jiménez, Vassily Hatzimanikatis, Wout van Helvoirt, Christopher S Henry, Henning Hermjakob, Markus J Herrgård, Ali Kaafarani, Hyun Uk Kim, Zachary King, Steffen Klamt, Edda Klipp, Jasper J Koehorst, Matthias König, Meiyappan Lakshmanan, Dong-Yup Lee, Sang Yup Lee, Sunjae Lee, Nathan E Lewis, Filipe Liu, Hongwu Ma, Daniel Machado, Radhakrishnan Mahadevan, Paulo Maia, Adil Mardinoglu, Gregory L Medlock, Jonathan M Monk, Jens Nielsen, Lars Keld Nielsen, Juan Nogales, Intawat Nookaew, Bernhard O Palsson, Jason A Papin, Kiran R Patil, Mark Poolman, Nathan D Price, Osbaldo Resendis-Antonio, Anne Richelle, Isabel Rocha, Benjamín J Sánchez, Peter J Schaap, Rahuman S Malik Sheriff, Saeed Shoaie, Nikolaus Sonnenschein, Bas Teusink, Paulo Vilaça, Jon Olav Vik, Judith A H Wodke, Joana C Xavier, Qianqian Yuan, Maksim Zakhartsev, and Cheng Zhang
iREAD: a tool for intron retention detection from RNA-seq data., Hong-Dong Li, Cory C Funk, and Nathan D Price
IsoResolve: Predicting Splice Isoform Functions by Integrating Gene and Isoform-level Features with Domain Adaptation., Hong-Dong Li, Changhuo Yang, Zhimin Zhang, Mengyun Yang, Fang-Xiang Wu, Gilbert S Omenn, and Jianxin Wang
Selective Translation of Low Abundance and Upregulated Transcripts in Halobacterium salinarum., Adrián López García de Lomana, Ulrike Kusebauch, Arjun V Raman, Min Pan, Serdar Turkarslan, Alan P R Lorenzetti, Robert L Moritz, and Nitin Baliga
A synthesis of bacterial and archaeal phenotypic trait data., Joshua S Madin, Daniel A Nielsen, Maria Brbic, Ross Corkrey, David Danko, Kyle Edwards, Martin K M Engqvist, Noah Fierer, Jemma L Geoghegan, Michael Gillings, Nikos C Kyrpides, Elena Litchman, Christopher E Mason, Lisa Moore, Søren L Nielsen, Ian T Paulsen, Nathan D Price, T B K Reddy, Matthew A Richards, Eduardo P C Rocha, Thomas M Schmidt, Heba Shaaban, Maulik Shukla, Fran Supek, Sasha G Tetu, Sara Vieira-Silva, Alice R Wattam, David A Westfall, and Mark Westoby
Untargeted longitudinal analysis of a wellness cohort identifies markers of metastatic cancer years prior to diagnosis., Andrew T Magis, Noa Rappaport, Matthew P Conomos, Gilbert S Omenn, Jennifer C Lovejoy, Leroy Hood, and Nathan D Price
Graph-based exploitation of gene ontology using GOxploreR for scrutinizing biological significance., Kalifa Manjang, Shailesh Tripathi, Olli Yli-Harja, Matthias Dehmer, and Frank Emmert-Streib
Health and disease markers correlate with gut microbiome composition across thousands of people., Ohad Manor, Chengzhen L Dai, Sergey A Kornilov, Brett Smith, Nathan D Price, Jennifer C Lovejoy, Sean M Gibbons, and Andrew T Magis
Roles of bacteriophages, plasmids and CRISPR immunity in microbial community dynamics revealed using time-series integrated meta-omics., Susana Martínez Arbas, Shaman Narayanasamy, Malte Herold, Laura A Lebrun, Michael R Hoopmann, Sujun Li, Tony J Lam, Benoît J Kunath, Nathan D Hicks, Cindy M Liu, Lance B Price, Cedric C Laczny, John D Gillece, James M Schupp, Paul S Keim, Robert L Moritz, Karoline Faust, Haixu Tang, Yuzhen Ye, Alexander Skupin, Patrick May, Emilie E L Muller, and Paul Wilmes
A Structural Model of the Endogenous Human BAF Complex Informs Disease Mechanisms., Nazar Mashtalir, Hiroshi Suzuki, Daniel P Farrell, Akshay Sankar, Jie Luo, Martin Filipovski, Andrew R D'Avino, Roodolph St Pierre, Alfredo M Valencia, Takashi Onikubo, Robert G Roeder, Yan Han, Yuan He, Jeffrey A Ranish, Frank DiMaio, Thomas Walz, and Cigall Kadoch
Crippling life support for SARS-CoV-2 and other viruses through synthetic lethality., Fred D Mast, Arti T Navare, Almer M van der Sloot, Jasmin Coulombe-Huntington, Michael P Rout, Nitin Baliga, Alexis Kaushansky, Brian T Chait, Alan Aderem, Charles M Rice, Andrej Sali, Mike Tyers, and John D Aitchison
Author Correction: New paradigms for understanding and step changes in treating active and chronic, persistent apicomplexan infections., Martin McPhillie, Ying Zhou, Kamal El Bissati, Jitender Dubey, Hernan Lorenzi, Michael Capper, Amanda K Lukens, Mark Hickman, Stephen Muench, Shiv Kumar Verma, Christopher R Weber, Kelsey Wheeler, James Gordon, Justin Sanders, Hong Moulton, Kai Wang, Taek-Kyun Kim, Yuqing He, Tatiana Santos, Stuart Woods, Patty Lee, David Donkin, Eric Kim, Laura Fraczek, Joseph Lykins, Farida Esaa, Fatima Alibana-Clouser, Sarah Dovgin, Louis Weiss, Gael Brasseur, Dyann Wirth, Michael Kent, Leroy Hood, Brigitte Meunieur, Craig W Roberts, S Samar Hasnain, Svetlana V Antonyuk, Colin Fishwick, and Rima McLeod
Chronic elevation of plasma vascular endothelial growth factor-A (VEGF-A) is associated with a history of blast exposure., James S Meabon, David G Cook, Mayumi Yagi, Garth E Terry, Donna J Cross, Mark Muzi, Kathleen F Pagulayan, Aric F Logsdon, Abigail G Schindler, Vikas Ghai, Kai Wang, Shannon Fallen, Yong Zhou, Taek-Kyun Kim, Inyoul Lee, William A Banks, Erik S Carlson, Cynthia Mayer, Rebecca C Hendrickson, Murray A Raskind, Desiree A Marshall, Daniel P Perl, C Dirk Keene, and Elaine R Peskind
DIALib-QC an assessment tool for spectral libraries in data-independent acquisition proteomics., Mukul K Midha, David S Campbell, Charu Kapil, Ulrike Kusebauch, Michael R Hoopmann, Samuel L Bader, and Robert L Moritz
A comprehensive spectral assay library to quantify the Escherichia coli proteome by DIA/SWATH-MS., Mukul K Midha, Ulrike Kusebauch, David Shteynberg, Charu Kapil, Samuel L Bader, Panga Jaipal Reddy, David S Campbell, Nitin Baliga, and Robert L Moritz
A Review of the Scientific Rigor, Reproducibility, and Transparency Studies Conducted by the ABRF Research Groups., Sheenah M Mische, Nancy C Fisher, Susan M Meyn, Katia Sol Church, Rebecca L Hegstad-Davies, Frances Weis-Garcia, Marie Adams, John M Ashton, Kym M Delventhal, Julie A Dragon, Laura Holmes, Pratik Jagtap, Christopher E Mason, Magnus Palmblad, Brian C Searle, Christoph W Turck, and Kevin L Knudtson
Design and synthesis of novel quinic acid derivatives:, Akshaya Murugesan, Suvi Holmstedt, Kenna C Brown, Alisa Koivuporras, Ana S Macedo, Nga Nguyen, Pedro Fonte, Patrícia Rijo, Olli Yli-Harja, Nuno R Candeias, and Meenakshisundaram Kandhavelu
Transcriptomic analysis of glioblastoma multiforme providing new insights into GPR17 signaling communication., Gnanavel Mutharasu, Akshaya Murugesan, Saravanan Konda Mani, Olli Yli-Harja, and Meenakshisundaram Kandhavelu
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
Antiproliferative and apoptotic effects of indole derivative, N-(2-hydroxy-5-nitrophenyl (4'-methylphenyl) methyl) indoline in breast cancer cells., Suresh Palanivel, Akshaya Murugesan, Kumar Subramanian, Olli Yli-Harja, and Meenakshisundaram Kandhavelu
Inflammation resolution: a dual-pronged approach to averting cytokine storms in COVID-19?, Dipak Panigrahy, Molly M Gilligan, Sui Huang, Allison Gartung, Irene Cortés-Puch, Patricia J Sime, Richard P Phipps, Charles N Serhan, and Bruce D Hammock
Deep phenotyping during pregnancy for predictive and preventive medicine., Alison G Paquette, Leroy Hood, Nathan D Price, and Yoel Sadovsky
Pre-existing immunity to influenza virus hemagglutinin stalk might drive selection for antibody-escape mutant viruses in a human challenge model., Jae-Keun Park, Yongli Xiao, Mitchell D Ramuta, Luz Angela Rosas, Sharon Fong, Alexis M Matthews, Ashley D Freeman, Monica A Gouzoulis, Natalia A Batchenkova, Xingdong Yang, Kelsey Scherler, Li Qi, Susan Reed, Rani Athota, Lindsay Czajkowski, Alison Han, David M Morens, Kathie-Anne Walters, Matthew J Memoli, John C Kash, and Jeffery K Taubenberger
Investigating the Effects of Brainstem Neuronal Adaptation on Cardiovascular Homeostasis., James H Park, Jonathan Gorky, Babatunde Ogunnaike, Rajanikanth Vadigepalli, and James S Schwaber
Intricate Genetic Programs Controlling Dormancy in Mycobacterium tuberculosis., Eliza Jr Peterson, Abrar A Abidi, Mario L Arrieta-Ortiz, Boris Aguilar, James T Yurkovich, Amardeep Kaur, Min Pan, Vivek Srinivas, Ilya Shmulevich, and Nitin Baliga
Causal mutations from adaptive laboratory evolution are outlined by multiple scales of genome annotations and condition-specificity., Patrick V Phaneuf, James T Yurkovich, David Heckmann, Muyao Wu, Troy E Sandberg, Zachary A King, Justin Tan, Bernhard O Palsson, and Adam M Feist
Ageotypes: Distinct Biomolecular Trajectories in Human Aging., Brian D. Piening, Jennifer Lovejoy, and John C Earls
Acquiring and Analyzing Data Independent Acquisition Proteomics Experiments without Spectrum Libraries., Lindsay K Pino, Seth C Just, Michael J MacCoss, and Brian C Searle
Absence of full-length dystrophin impairs normal maturation and contraction of cardiomyocytes derived from human-induced pluripotent stem cells., J Manuel Pioner, Xuan Guan, Jordan M Klaiman, Alice W Racca, Lil Pabon, Veronica Muskheli, Jesse Macadangdang, Cecilia Ferrantini, Michael R Hoopmann, Robert L Moritz, Deok-Ho Kim, Chiara Tesi, Corrado Poggesi, Charles E Murry, Martin K Childers, David L Mack, and Michael Regnier
Emergence of Organisms., Andrea Roli and Stuart A Kauffman
A small sustained increase in NOD1 abundance promotes ligand-independent inflammatory and oncogene transcriptional responses., Leah M Rommereim, Ajay Suresh Akhade, Bhaskar Dutta, Carolyn Hutcheon, Nicolas W Lounsbury, Clifford C Rostomily, Ram Savan, Iain D C Fraser, Ronald N Germain, and Naeha Subramanian
Composition of Caenorhabditis elegans extracellular vesicles suggests roles in metabolism, immunity, and aging., Joshua C Russell, Taek-Kyun Kim, Ayush Noori, Gennifer E Merrihew, Julia E Robbins, Alexandra Golubeva, Kai Wang, Michael J MacCoss, and Matt Kaeberlein
Society for Immunotherapy of Cancer clinical and biomarkers data sharing resource document: Volume I-conceptual challenges., Sergio Rutella, Michael A Cannarile, Sacha Gnjatic, Bruno Gomes, Justin Guinney, Vaios Karanikas, Mohan Karkada, John M Kirkwood, Beatrix Kotlan, Giuseppe V Masucci, Els Meeusen, Anne Monette, Aung Naing, Vésteinn Thorsson, Nicholas Tschernia, Ena Wang, Daniel K Wells, Timothy L Wyant, and Alessandra Cesano
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
Defining the proteolytic landscape during enterovirus infection., Mohsan Saeed, Sebastian Kapell, Nicholas T Hertz, Xianfang Wu, Kierstin Bell, Alison W Ashbrook, Milica Tesic Mark, Henry A Zebroski, Maxwell L Neal, Malin Flodström-Tullberg, Margaret R MacDonald, John D Aitchison, Henrik Molina, and Charles M Rice
Generating high quality libraries for DIA MS with empirically corrected peptide predictions., Brian C Searle, Kristian E Swearingen, Christopher A Barnes, Tobias Schmidt, Siegfried Gessulat, Bernhard Küster, and Mathias Wilhelm
Serum-borne lipids amplify TLR-activated inflammatory responses., Naveen Sharma, Ajay Suresh Akhade, Sana Ismaeel, and Ayub Qadri
Circulating MicroRNAs and Extracellular Vesicle-Containing MicroRNAs as Response Biomarkers of Anti-programmed Cell Death Protein 1 or Programmed Death-Ligand 1 Therapy in NSCLC., Takehito Shukuya, Vikas Ghai, Joseph M Amann, Tamio Okimoto, Konstantin Shilo, Taek-Kyun Kim, Kai Wang, and David P Carbone
Current Status and Future Prospects of Genome-Scale Metabolic Modeling to Optimize the Use of Mesenchymal Stem Cells in Regenerative Medicine., Þóra Sigmarsdóttir, Sarah McGarrity, Óttar Rolfsson, James T Yurkovich, and Ólafur E Sigurjónsson
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
PerSort Facilitates Characterization and Elimination of Persister Subpopulation in Mycobacteria., Vivek Srinivas, Mario L Arrieta-Ortiz, Amardeep Kaur, Eliza Jr Peterson, and Nitin Baliga
Dynamics of a birth-death process based on combinatorial innovation., Mike Steel, Wim Hordijk, and Stuart A Kauffman
Multiomic Immunophenotyping of COVID-19 Patients Reveals Early Infection Trajectories., Yapeng Su, Daniel Chen, Christopher Lausted, Dan Yuan, Jongchan Choi, Cheng Dai, Valentin Voillet, Kelsey Scherler, Pamela Troisch, Venkata R Duvvuri, Priyanka Baloni, Guangrong Qin, Brett Smith, Sergey Kornilov, Clifford Rostomily, Alex Xu, Jing Li, Shen Dong, Alissa Rothchild, Jing Zhou, Kim Murray, Rick Edmark, Sunga Hong, Lesley Jones, Yong Zhou, Ryan Roper, Sean Mackay, D Shane O'Mahony, Christopher Dale, Julie A Wallick, Heather A Algren, Zager A Michael, Andrew T Magis, Wei Wei, Nathan D Price, Sui Huang, Naeha Subramanian, Kai Wang, Jennifer Hadlock, Leroy Hood, Alan Aderem, Jeffrey A Bluestone, Lewis L Lanier, Phil Greenberg, Raphael Gottardo, Mark M Davis, Jason D Goldman, James R Heath, and ISB-Swedish COVID19 Biobanking Unit
Multi-omics resolves a sharp disease-state shift between mild and moderate COVID-19, Yapeng Su, Daniel Chen, Dan Yuan, Christopher Lausted, Jongchan Choi, Chengzhen L Dai, Valentin Voillet, Venkata R Duvvuri, Kelsey Scherler, Pamela Troisch, Priyanka Baloni, Guangrong Qin, Brett Smith, Sergey A Kornilov, Clifford Rostomily, Alex Xu, Jing Li, Shen Dong, Alissa Rothchild, Jing Zhou, Kim Murray, Rick Edmark, Sunga Hong, John Heath, John Earls, Rongyu Zhang, Jingyi Xie, Sarah Li, Ryan Roper, Lesley Jones, Yong Zhou, Lee Rowen, Rachel Liu, Sean Mackay, D Shane O'Mahony, chris dale, Julie A Wallick, Heather A Algren, Zager A. Michael, ISB-Swedish COVID19 Biobanking Unit, Wei Wei, Nathan D Price, Sui Huang, Naeha Subramanian, Kai Wang, Andrew T Magis, Jennifer Hadlock, Leroy Hood, Alan Aderem, Jeffrey A. Bluestone, Lewis L. Lanier, Philip D. Greenberg, Raphael Gottardo, Mark M. Davis, Jason D Goldman, and James R. Heath
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
Active learning narrows achievement gaps for underrepresented students in undergraduate science, technology, engineering, and math., Elli J Theobald, Mariah J Hill, Elisa Tran, Sweta Agrawal, E Nicole Arroyo, Shawn Behling, Nyasha Chambwe, Dianne Laboy Cintrón, Jacob D Cooper, Gideon Dunster, Jared A Grummer, Kelly Hennessey, Jennifer Hsiao, Nicole Iranon, Leonard Jones, Hannah Jordt, Marlowe Keller, Melissa E Lacey, Caitlin E Littlefield, Alexander Lowe, Shannon Newman, Vera Okolo, Savannah Olroyd, Brandon R Peecook, Sarah B Pickett, David L Slager, Itzue W Caviedes-Solis, Kathryn E Stanchak, Vasudha Sundaravardan, Camila Valdebenito, Claire R Williams, Kaitlin Zinsli, and Scott Freeman
Multiplatform Integrative Analysis of Immunogenomic Data for Biomarker Discovery., Vésteinn Thorsson
Sequential Wnt Agonist Then Antagonist Treatment Accelerates Tissue Repair and Minimizes Fibrosis., Xiao-Jun Tian, Dong Zhou, Haiyan Fu, Rong Zhang, Xiaojie Wang, Sui Huang, Youhua Liu, and Jianhua Xing
Biofilms of the non-tuberculous Mycobacterium chelonae form an extracellular matrix and display distinct expression patterns, Perla Vega-Dominguez, Eliza Jr Peterson, Min Pan, Alessandro Di Maio, Saumya Singh, Siva Umapathy, Deepak K Saini, Nitin Baliga, and Apoorva Bhatt
Erratum: Viswanathan, A., et al. Battling Glioblastoma: A Novel Tyrosine Kinase Inhibitor with Multi-Dimensional Anti-Tumor Effect (Running Title: Cancer Cells Death Signalling Activation)., Anisha Viswanathan, Aliyu Musa, Akshaya Murugesan, João R Vale, Carlos A M Afonso, Saravanan Konda Mani, Olli Yli-Harja, Nuno R Candeias, and Meenakshisundaram Kandhavelu
BioHackathon 2015: Semantics of data for life sciences and reproducible research., Rutger A Vos, Toshiaki Katayama, Hiroyuki Mishima, Shin Kawano, Shuichi Kawashima, Jin-Dong Kim, Yuki Moriya, Toshiaki Tokimatsu, Atsuko Yamaguchi, Yasunori Yamamoto, Hongyan Wu, Peter Amstutz, Erick Antezana, Nobuyuki P Aoki, Kazuharu Arakawa, Jerven T Bolleman, Evan Bolton, Raoul J P Bonnal, Hidemasa Bono, Kees Burger, Hirokazu Chiba, Kevin B Cohen, Eric W Deutsch, Jesualdo T Fernández-Breis, Gang Fu, Takatomo Fujisawa, Atsushi Fukushima, Alexander García, Naohisa Goto, Tudor Groza, Colin Hercus, Robert Hoehndorf, Kotone Itaya, Nick Juty, Takeshi Kawashima, Jee-Hyub Kim, Akira R Kinjo, Masaaki Kotera, Kouji Kozaki, Sadahiro Kumagai, Tatsuya Kushida, Thomas Lütteke, Masaaki Matsubara, Joe Miyamoto, Attayeb Mohsen, Hiroshi Mori, Yuki Naito, Takeru Nakazato, Jeremy Nguyen-Xuan, Kozo Nishida, Naoki Nishida, Hiroyo Nishide, Soichi Ogishima, Tazro Ohta, Shujiro Okuda, Benedict Paten, Jean-Luc Perret, Philip Prathipati, Pjotr Prins, Núria Queralt-Rosinach, Daisuke Shinmachi, Shinya Suzuki, Tsuyosi Tabata, Terue Takatsuki, Kieron Taylor, Mark Thompson, Ikuo Uchiyama, Bruno Vieira, Chih-Hsuan Wei, Mark Wilkinson, Issaku Yamada, Ryota Yamanaka, Kazutoshi Yoshitake, Akiyasu C Yoshizawa, Michel Dumontier, Kenjiro Kosaki, and Toshihisa Takagi
