Submissions from 2021
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
A systems-biology clinical trial of a personalized multimodal lifestyle intervention for early Alzheimer's disease., Sarah C McEwen, David A Merrill, Jennifer Bramen, Verna Porter, Stella Panos, Scott Kaiser, John Hodes, Aarthi Ganapathi, Lesley Bell, Tess Bookheimer, Ryan Glatt, Molly Rapozo, Mary Kay Ross, Nathan D Price, Daniel Kelly, Cory C Funk, Leroy Hood, and Jared C Roach
Microglia show differential transcriptomic response to Aβ peptide aggregates ex vivo and in vivo., Karen N McFarland, Carolina Ceballos, Awilda Rosario, Thomas Ladd, Brenda Moore, Griffin Golde, Xue Wang, Mariet Allen, Nilüfer Ertekin-Taner, Cory C Funk, Max Robinson, Priyanka Baloni, Noa Rappaport, Paramita Chakrabarty, and Todd E Golde
The type VI secretion system of Xanthomonas phaseoli pv. manihotis is involved in virulence and in vitro motility., Nathaly Andrea Montenegro Benavides, Alejandro Alvarez B, Mario L Arrieta-Ortiz, Luis Miguel Rodriguez-R, David Botero, Javier Felipe Tabima, Luisa Castiblanco, Cesar Trujillo, Silvia Restrepo, and Adriana Bernal
Molecular modeling and dynamics studies of the synthetic small molecule agonists with GPR17 and P2Y1 receptor., Akshaya Murugesan, Phung Nguyen, Thiyagarajan Ramesh, Olli Yli-Harja, Meenakshisundaram Kandhavelu, and Konda Mani Saravanan
A systems-level gene regulatory network model for Plasmodium falciparum., Maxwell L Neal, Ling Wei, Eliza Jr Peterson, Mario L Arrieta-Ortiz, Samuel A Danziger, Nitin Baliga, Alexis Kaushansky, and John D Aitchison
HLA-A, Pavlo A Nesterenko, Jami McLaughlin, Brandon L Tsai, Giselle Burton Sojo, Donghui Cheng, Daniel Zhao, Zhiyuan Mao, Nathanael J Bangayan, Matthew B Obusan, Yapeng Su, Rachel H Ng, William Chour, Jingyi Xie, Yan-Ruide Li, Derek Lee, Miyako Noguchi, Camille Carmona, John W Phillips, Jocelyn T Kim, Lili Yang, James R Heath, Paul C Boutros, and Owen N Witte
Synthesis and Preclinical Validation of Novel Indole Derivatives as a GPR17 Agonist for Glioblastoma Treatment., Phung Nguyen, Phuong Doan, Tatu Rimpilainen, Saravanan Konda Mani, Akshaya Murugesan, Olli Yli-Harja, Nuno R Candeias, and Meenakshisundaram Kandhavelu
Autophagy as a Mechanism for Adaptive Prediction-Mediated Emergence of Drug Resistance., Nivedita Nivedita, John D Aitchison, and Nitin Baliga
PRoBE the cloud toolkit: finding the best biomarkers of drug response within a breast cancer clinical trial., Nicholas O'Grady, David L Gibbs, Kawther Abdilleh, Adam Asare, Smita Asare, Sara Venters, Lamorna Brown-Swigart, Gillian L Hirst, Denise Wolf, Christina Yau, Laura J van 't Veer, Laura Esserman, and Amrita Basu
Towards early risk biomarkers: serum metabolic signature in childhood predicts cardio-metabolic risk in adulthood., Xiaowei Ojanen, Runtan Cheng, Timo Törmäkangas, Noa Rappaport, Tomasz Wilmanski, Na Wu, Erik Fung, Rozenn Nedelec, Sylvain Sebert, Dimitris Vlachopoulos, Wei Yan, Nathan D Price, Sulin Cheng, and Petri Wiklund
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
Marine Polymer-Gels' Relevance in the Atmosphere as Aerosols and CCN., Monica V Orellana, Dennis A Hansell, Patricia A Matrai, and Caroline Leck
Single Cell Scale Neuronal and Glial Gene Expression and Putative Cell Phenotypes and Networks in the Nucleus Tractus Solitarius in an Alcohol Withdrawal Time Series., Sean J O'Sullivan, Damani McIntosh-Clarke, James H Park, Rajanikanth Vadigepalli, and James S Schwaber
Sulfur Metabolites Play Key System-Level Roles in Modulating Denitrification., Anne E Otwell, Alex V Carr, Erica L W Majumder, Maryann K Ruiz, Regina L Wilpiszeski, Linh T Hoang, Bill Webb, Serdar Turkarslan, Sean M Gibbons, Dwayne A Elias, David A Stahl, Gary Siuzdak, and Nitin S Baliga
Molecular interaction study of novel indoline derivatives with EGFR-kinase domain using multiple computational analysis., Suresh Palanivel, Olli Yli-Harja, and Meenakshisundaram Kandhavelu
The transposable element-rich genome of the cereal pest Sitophilus oryzae., Nicolas Parisot, Carlos Vargas-Chávez, Clément Goubert, Patrice Baa-Puyoulet, Séverine Balmand, Louis Beranger, Caroline Blanc, Aymeric Bonnamour, Matthieu Boulesteix, Nelly Burlet, Federica Calevro, Patrick Callaerts, Théo Chancy, Hubert Charles, Stefano Colella, André Da Silva Barbosa, Elisa Dell'Aglio, Alex Di Genova, Gérard Febvay, Toni Gabaldón, Mariana Galvão Ferrarini, Alexandra Gerber, Benjamin Gillet, Robert Hubley, Sandrine Hughes, Emmanuelle Jacquin-Joly, Justin Maire, Marina Marcet-Houben, Florent Masson, Camille Meslin, Nicolas Montagné, Andrés Moya, Ana Tereza Ribeiro de Vasconcelos, Gautier Richard, Jeb Rosen, Marie-France Sagot, Arian F A Smit, Jessica Storer, Carole Vincent-Monegat, Agnès Vallier, Aurélien Vigneron, Anna Zaidman-Rémy, Waël Zamoum, Cristina Vieira, Rita Rebollo, Amparo Latorre, and Abdelaziz Heddi
Discovery of Small Molecule Bak Activator for Lung Cancer Therapy., Dongkyoo Park, Abu Syed Md Anisuzzaman, Andrew T Magis, Guo Chen, Maohua Xie, Guojing Zhang, Madhusmita Behera, Gabriel L Sica, Suresh S Ramalingam, Taofeek K Owonikoko, and Xingming Deng
A Systems Approach to Brain Tumor Treatment., James H Park, Adrian Lopez Garcia de Lomana, Diego M Marzese, Tiffany Juarez, Abdullah Feroze, Parvinder Hothi, Charles Cobbs, Anoop P Patel, Santosh Kesari, Sui Huang, and Nitin S Baliga
A wide-ranging Pseudomonas aeruginosa PeptideAtlas build: A useful proteomic resource for a versatile pathogen., J A Reales-Calderón, Z Sun, V Mascaraque, E Pérez-Navarro, V Vialás, E W Deutsch, R L Moritz, C Gil, J L Martínez, and G Molero
Integrative modeling identifies genetic ancestry-associated molecular correlates in human cancer., A Gordon Robertson, Christina Yau, Jian Carrot-Zhang, Jeffrey S Damrauer, Theo A Knijnenburg, Nyasha Chambwe, Katherine A Hoadley, Anab Kemal, Jean C Zenklusen, Andrew D Cherniack, Rameen Beroukhim, and Wanding Zhou
Lentivirus-mediated Conditional Gene Expression., Leah Rommereim, Ajay Suresh Akhade, Ronald N Germain, Iain D C Fraser, and Naeha Subramanian
Germline genetic contribution to the immune landscape of cancer., Rosalyn W Sayaman, Mohamad Saad, Vésteinn Thorsson, Donglei Hu, Wouter Hendrickx, Jessica Roelands, Eduard Porta-Pardo, Younes Mokrab, Farshad Farshidfar, Tomas Kirchhoff, Randy F Sweis, Oliver F Bathe, Carolina Heimann, Michael J Campbell, Cynthia Stretch, Scott Huntsman, Rebecca E Graff, Najeeb Syed, Laszlo Radvanyi, Simon Shelley, Denise Wolf, Francesco M Marincola, Michele Ceccarelli, Jérôme Galon, Elad Ziv, and Davide Bedognetti
TAF8 regions important for TFIID lobe B assembly or for TAF2 interactions are required for embryonic stem cell survival., Elisabeth Scheer, Jie Luo, Andrea Bernardini, Frank Ruffenach, Jean-Marie Garnier, Isabelle Kolb-Cheynel, Kapil Gupta, Imre Berger, Jeff Ranish, and László Tora
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
Utilization of machine learning for identifying symptom severity military-related PTSD subtypes and their biological correlates., Carole E Siegel, Eugene M Laska, Ziqiang Lin, Mu Xu, Duna Abu-Amara, Michelle K Jeffers, Meng Qian, Nicholas Milton, Janine D Flory, Rasha Hammamieh, Bernie J Daigle, Aarti Gautam, Kelsey R Dean, Victor I Reus, Owen M Wolkowitz, Synthia H Mellon, Kerry J Ressler, Rachel Yehuda, Kai Wang, Leroy Hood, Francis J Doyle, Marti Jett, and Charles R Marmar
Transcriptome signature of cell viability predicts drug response and drug interaction in, Vivek Srinivas, Rene A Ruiz, Min Pan, Selva Rupa Christinal Immanuel, Eliza Jr Peterson, and Nitin S Baliga
Platelet derived growth factor receptor β (PDGFRβ) is a host receptor for the human malaria parasite adhesin TRAP., Ryan W J Steel, Vladimir Vigdorovich, Nicholas Dambrauskas, Brandon K Wilder, Silvia A Arredondo, Debashree Goswami, Sudhir Kumar, Sara Carbonetti, Kristian E Swearingen, Thao Nguyen, Will Betz, Nelly Camargo, Bridget S Fisher, Jo Soden, Helen Thomas, Jim Freeth, Robert L Moritz, D Noah Sather, and Stefan H I Kappe
Partial inhibition of mitochondrial complex I ameliorates Alzheimer's disease pathology and cognition in APP/PS1 female mice., Andrea Stojakovic, Sergey Trushin, Anthony Sheu, Layla Khalili, Su-Youne Chang, Xing Li, Trace Christensen, Jeffrey L Salisbury, Rachel E Geroux, Benjamin Gateno, Padraig J Flannery, Mrunal Dehankar, Cory C Funk, Jordan Wilkins, Anna Stepanova, Tara O'Hagan, Alexander Galkin, Jarred Nesbitt, Xiujuan Zhu, Utkarsh Tripathi, Slobodan Macura, Tamar Tchkonia, Tamar Pirtskhalava, James L Kirkland, Rachel A Kudgus, Renee A Schoon, Joel M Reid, Yu Yamazaki, Takahisa Kanekiyo, Song Zhang, Emirhan Nemutlu, Petras Dzeja, Adam Jaspersen, Ye In Christopher Kwon, Michael K Lee, and Eugenia Trushina
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
Mouse Organ-Specific Proteins and Functions., Bingyun Sun, Cynthia Lorang, Shizhen Qin, Yijuan Zhang, Ken Liu, Gray Li, Zhi Sun, Ashley Francke, Angelita G Utleg, Zhiyuan Hu, Kai Wang, Robert L Moritz, and Leroy Hood
Race differences in predictors of weight gain among a community sample of smokers enrolled in a randomized controlled trial of a multiple behavior change intervention., Marcia M Tan, Terry Bush, Jennifer C Lovejoy, Harold Javitz, Alula Jimenez Torres, Ken Wassum, and Bonnie Spring
Functional characterization of HIC, a P2Y1 agonist, as a p53 stabilizer for prostate cancer cell death induction., Hien Thi Thu Le, Akshaya Murugesan, Nuno R Candeias, Olli Yli-Harja, and Meenakshisundaram Kandhavelu
Synergistic epistasis enhances the co-operativity of mutualistic interspecies interactions., Serdar Turkarslan, Nejc Stopnisek, Anne W Thompson, Christina E Arens, Jacob J Valenzuela, James Wilson, Kristopher A Hunt, Jessica Hardwicke, Adrián López García de Lomana, Sujung Lim, Yee Mey Seah, Ying Fu, Liyou Wu, Jizhong Zhou, Kristina L Hillesland, David A Stahl, and Nitin Baliga
Correction for Vangay et al., "Microbiome Metadata Standards: Report of the National Microbiome Data Collaborative's Workshop and Follow-On Activities"., Pajau Vangay, Josephine Burgin, Anjanette Johnston, Kristen L Beck, Daniel C Berrios, Kai Blumberg, Shane Canon, Patrick Chain, John-Marc Chandonia, Danielle Christianson, Sylvain V Costes, Joan Damerow, William D Duncan, Jose Pablo Dundore-Arias, Kjiersten Fagnan, Jonathan M Galazka, Sean M Gibbons, David Hays, Judson Hervey, Bin Hu, Bonnie L Hurwitz, Pankaj Jaiswal, Marcin P Joachimiak, Linda Kinkel, Joshua Ladau, Stanton L Martin, Lee Ann McCue, Kayd Miller, Nigel Mouncey, Chris Mungall, Evangelos Pafilis, T B K Reddy, Lorna Richardson, Simon Roux, Lynn M Schriml, Justin P Shaffer, Jagadish Chandrabose Sundaramurthi, Luke R Thompson, Ruth E Timme, Jie Zheng, Elisha M Wood-Charlson, and Emiley A Eloe-Fadrosh
Microbiome Metadata Standards: Report of the National Microbiome Data Collaborative's Workshop and Follow-On Activities., Pajau Vangay, Josephine Burgin, Anjanette Johnston, Kristen L Beck, Daniel C Berrios, Kai Blumberg, Shane Canon, Patrick Chain, John-Marc Chandonia, Danielle Christianson, Sylvain V Costes, Joan Damerow, William D Duncan, Jose Pablo Dundore-Arias, Kjiersten Fagnan, Jonathan M Galazka, Sean M Gibbons, David Hays, Judson Hervey, Bin Hu, Bonnie L Hurwitz, Pankaj Jaiswal, Marcin P Joachimiak, Linda Kinkel, Joshua Ladau, Stanton L Martin, Lee Ann McCue, Kayd Miller, Nigel Mouncey, Chris Mungall, Evangelos Pafilis, T B K Reddy, Lorna Richardson, Simon Roux, Justin P Shaffer, Jagadish Chandrabose Sundaramurthi, Luke R Thompson, Ruth E Timme, Jie Zheng, Elisha M Wood-Charlson, and Emiley A Eloe-Fadrosh
Bile acid synthesis, modulation, and dementia: A metabolomic, transcriptomic, and pharmacoepidemiologic study., Vijay R Varma, Youjin Wang, Yang An, Sudhir Varma, Murat Bilgel, Jimit Doshi, Cristina Legido-Quigley, João C Delgado, Anup M Oommen, Jackson A Roberts, Dean F Wong, Christos Davatzikos, Susan M Resnick, Juan C Troncoso, Olga Pletnikova, Richard O'Brien, Eelko Hak, Brenda N Baak, Ruth Pfeiffer, Priyanka Baloni, Siamak Mohmoudiandehkordi, Kwangsik Nho, Rima Kaddurah-Daouk, David A Bennett, Shahinaz M Gadalla, and Madhav Thambisetty
Contrasting heat stress response patterns of coral holobionts across the Red Sea suggest distinct mechanisms of thermal tolerance., Christian R Voolstra, Jacob J Valenzuela, Serdar Turkarslan, Anny Cárdenas, Benjamin C C Hume, Gabriela Perna, Carol Buitrago-López, Katherine Rowe, Monica V Orellana, Nitin S Baliga, Suman Paranjape, Guilhem Banc-Prandi, Jessica Bellworthy, Maoz Fine, Sarah Frias-Torres, and Daniel J Barshis
The viral hypothesis: how herpesviruses may contribute to Alzheimer's disease., Michael Wainberg, Tain Luquez, David M Koelle, Ben Readhead, Christine Johnston, Martin Darvas, and Cory C Funk
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
Alzheimer's disease and progressive supranuclear palsy share similar transcriptomic changes in distinct brain regions., Xue Wang, Mariet Allen, Özkan İş, Joseph S Reddy, Frederick Q Tutor-New, Monica Castanedes Casey, Minerva M Carrasquillo, Stephanie R Oatman, Yuhao Min, Yan W Asmann, Cory C Funk, Thuy Nguyen, Charlotte Cg Ho, Kimberly G Malphrus, Nicholas T Seyfried, Allan I Levey, Steven G Younkin, Melissa E Murray, Dennis W Dickson, Nathan D Price, Todd E Golde, and Nilufer Ertekin-Taner
Circulating activated immune cells as a potential blood biomarkers of non-small cell lung cancer occurrence and progression., Yingyi Wang, Na Zhou, Rui Zhu, Xiaoyuan Li, Zhao Sun, Yang Gao, Wei Liu, Changting Meng, Yuping Ge, Chunmei Bai, Taisheng Li, and Hongsheng Liu
2021 Special Issue on Software Tools and Resources: Finding the Right Tools for the Job., Susan T Weintraub, Michael R Hoopmann, and Magnus Palmblad
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
Author Correction: Gut microbiome pattern reflects healthy ageing and predicts survival in humans., Tomasz Wilmanski, Christian Diener, Noa Rappaport, Sushmita Patwardhan, Jack Wiedrick, Jodi Lapidus, John C Earls, Anat Zimmer, Gustavo Glusman, Max Robinson, James T Yurkovich, Deborah M Kado, Jane A Cauley, Joseph Zmuda, Nancy E Lane, Andrew T Magis, Jennifer C Lovejoy, Leroy Hood, Sean M Gibbons, Eric S Orwoll, and Nathan D Price
Gut microbiome pattern reflects healthy ageing and predicts survival in humans., Tomasz Wilmanski, Christian Diener, Noa Rappaport, Sushmita Patwardhan, Jack Wiedrick, Jodi Lapidus, John C Earls, Anat Zimmer, Gustavo Glusman, Max Robinson, James T Yurkovich, Deborah M Kado, Jane A Cauley, Joseph Zmuda, Nancy E Lane, Andrew T Magis, Jennifer C Lovejoy, Leroy Hood, Sean M Gibbons, Eric S Orwoll, and Nathan D Price
From taxonomy to metabolic output: what factors define gut microbiome health?, Tomasz Wilmanski, Noa Rappaport, Christian Diener, Sean M Gibbons, and Nathan D Price
Serum brain-derived neurotrophic factor remains elevated after long term follow-up of combat veterans with chronic post-traumatic stress disorder., Gwyneth W Y Wu, Owen M Wolkowitz, Victor I Reus, Jee In Kang, Mathea Elnar, Reuben Sarwal, Janine D Flory, Duna Abu-Amara, Rasha Hammamieh, Aarti Gautam, Francis J Doyle, Rachel Yehuda, Charles R Marmar, Marti Jett, Synthia H Mellon, SBPBC Collaborators, Leroy Hood, Kai Wang, and Inyoul Lee
Hexokinase 2 discerns a novel circulating tumor cell population associated with poor prognosis in lung cancer patients., Liu Yang, Xiaowei Yan, Jie Chen, Qiong Zhan, Yingqi Hua, Shili Xu, Ziming Li, Zhuo Wang, Yu Dong, Dongqing Zuo, Min Xue, Yin Tang, Harvey R Herschman, Shun Lu, Qihui Shi, and Wei Wei
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
Lung proteomic biomarkers associated with chronic obstructive pulmonary disease., Yu-Hang Zhang, Michael R Hoopmann, Peter J Castaldi, Kirsten Simonsen, Mukul K Midha, Michael H Cho, Gerard J Criner, Raphael Bueno, Jiangyuan Liu, Robert L Moritz, and Edwin K Silverman
Multi-cohort analysis of host immune response identifies conserved protective and detrimental modules associated with severity across viruses., Hong Zheng, Aditya M Rao, Denis Dermadi, Jiaying Toh, Lara Murphy Jones, Michele Donato, Yiran Liu, Yapeng Su, Cheng L Dai, Sergey A Kornilov, Minas Karagiannis, Theodoros Marantos, Yehudit Hasin-Brumshtein, Yudong D He, Evangelos J Giamarellos-Bourboulis, James R Heath, and Purvesh Khatri
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
Submissions from 2020
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
A Near-Optimal Control Method for Stochastic Boolean Networks., Boris Aguilar, Pan Fang, Reinhard Laubenbacher, and David Murrugarra
A generalizable data-driven multicellular model of pancreatic ductal adenocarcinoma., Boris Aguilar, David L Gibbs, David J Reiss, Mark McConnell, Samuel A Danziger, Andrew Dervan, Matthew Trotter, Douglas Bassett, Robert Hershberg, Alexander V Ratushny, and Ilya Shmulevich
Type 1 interferon-dependent repression of NLRC4 and iPLA2 licenses down-regulation of, Ajay Suresh Akhade, Shaikh M Atif, Bhavana S Lakshmi, Neha Dikshit, Kelly T Hughes, Ayub Qadri, and Naeha Subramanian
The Proteasome Activators Blm10/PA200 Enhance the Proteasomal Degradation of N-Terminal Huntingtin., Azzam Aladdin, Yanhua Yao, Ciyu Yang, Günther Kahlert, Marvi Ghani, Nikolett Király, Anita Boratkó, Karen Uray, Gunnar Dittmar, and Krisztina Tar
Inference of Bacterial Small RNA Regulatory Networks and Integration with Transcription Factor-Driven Regulatory Networks., Mario L Arrieta-Ortiz, Christoph Hafemeister, Bentley Shuster, Nitin Baliga, Richard Bonneau, and Patrick Eichenberger
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
Integrative network modeling reveals mechanisms underlying T cell exhaustion., Hamid Bolouri, Mary Young, Joshua Beilke, Rebecca Johnson, Brian Fox, Lu Huang, Cristina Costa Santini, Christopher Mark Hill, Anne-Renee van der Vuurst de Vries, Paul Shannon, Andrew Dervan, Pallavur Sivakumar, Matthew Trotter, Douglas Bassett, and Alexander Ratushny
Visualizing metabolic network dynamics through time-series metabolomic data., Lea F Buchweitz, James T Yurkovich, Christoph Blessing, Veronika Kohler, Fabian Schwarzkopf, Zachary A King, Laurence Yang, Freyr Jóhannsson, Ólafur E Sigurjónsson, Óttar Rolfsson, Julian Heinrich, and Andreas Dräger
Discovery of driver non-coding splice-site-creating mutations in cancer., Song Cao, Daniel Cui Zhou, Clara Oh, Reyka G Jayasinghe, Yanyan Zhao, Christopher J Yoon, Matthew A Wyczalkowski, Matthew H Bailey, Terrence Tsou, Qingsong Gao, Andrew Malone, Sheila Reynolds, Ilya Shmulevich, Michael C Wendl, Feng Chen, and Li Ding
Community standards to facilitate development and address challenges in metabolic modeling., Maureen A Carey, Andreas Dräger, Moritz E Beber, Jason A Papin, and James T Yurkovich
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
