Submissions from 2021
iNetModels 2.0: an interactive visualization and database of multi-omics data., Muhammad Arif, Cheng Zhang, Xiangyu Li, Cem Güngör, Buğra Çakmak, Metin Arslantürk, Abdellah Tebani, Berkay Özcan, Oğuzhan Subaş, Wenyu Zhou, Brian Piening, Hasan Turkez, Linn Fagerberg, Nathan Price, Leroy Hood, Michael Snyder, Jens Nielsen, Mathias Uhlen, and Adil Mardinoglu
Predictive regulatory and metabolic network models for systems analysis of Clostridioides difficile., Mario L Arrieta-Ortiz, Selva Rupa Christinal Immanuel, Serdar Turkarslan, Wei-Ju Wu, Brintha P Girinathan, Jay N Worley, Nicholas DiBenedetto, Olga Soutourina, Johann Peltier, Bruno Dupuy, Lynn Bry, and Nitin S Baliga
History and Future Perspectives on the Discipline of Quantitative Systems Pharmacology Modeling and Its Applications., Karim Azer, Chanchala D Kaddi, Jeffrey S Barrett, Jane P F Bai, Sean T McQuade, Nathaniel J Merrill, Benedetto Piccoli, Susana Neves-Zaph, Luca Marchetti, Rosario Lombardo, Silvia Parolo, Selva Rupa Christinal Immanuel, and Nitin S Baliga
Systems modeling of metabolic dysregulation in neurodegenerative diseases., Priyanka Baloni, Cory C Funk, Ben Readhead, and Nathan D Price
Data management of sensitive human proteomics data: current practices, recommendations and perspectives for the future., Nuno Bandeira, Eric W Deutsch, Oliver Kohlbacher, Lennart Martens, and Juan Antonio Vizcaíno
Autoantibodies neutralizing type I IFNs are present in, Paul Bastard, Adrian Gervais, Tom Le Voyer, Jérémie Rosain, Quentin Philippot, Jérémy Manry, Eleftherios Michailidis, Hans-Heinrich Hoffmann, Shohei Eto, Marina Garcia-Prat, Lucy Bizien, Alba Parra-Martínez, Rui Yang, Liis Haljasmägi, Mélanie Migaud, Karita Särekannu, Julia Maslovskaja, Nicolas de Prost, Yacine Tandjaoui-Lambiotte, Charles-Edouard Luyt, Blanca Amador-Borrero, Alexandre Gaudet, Julien Poissy, Pascal Morel, Pascale Richard, Fabrice Cognasse, Jesus Troya, Sophie Trouillet-Assant, Alexandre Belot, Kahina Saker, Pierre Garçon, Jacques G Rivière, Jean-Christophe Lagier, Stéphanie Gentile, Lindsey B Rosen, Elana Shaw, Tomohiro Morio, Junko Tanaka, David Dalmau, Pierre-Louis Tharaux, Damien Sene, Alain Stepanian, Bruno Megarbane, Vasiliki Triantafyllia, Arnaud Fekkar, James R Heath, José Luis Franco, Juan-Manuel Anaya, Jordi Solé-Violán, Luisa Imberti, Andrea Biondi, Paolo Bonfanti, Riccardo Castagnoli, Ottavia M Delmonte, Yu Zhang, Andrew L Snow, Steven M Holland, Catherine Biggs, Marcela Moncada-Vélez, Andrés Augusto Arias, Lazaro Lorenzo, Soraya Boucherit, Boubacar Coulibaly, Dany Anglicheau, Anna M Planas, Filomeen Haerynck, Sotirija Duvlis, Robert L Nussbaum, Tayfun Ozcelik, Sevgi Keles, Ahmed A Bousfiha, Jalila El Bakkouri, Carolina Ramirez-Santana, Stéphane Paul, Qiang Pan-Hammarström, Lennart Hammarström, Annabelle Dupont, Alina Kurolap, Christine N Metz, Alessandro Aiuti, Giorgio Casari, Vito Lampasona, Fabio Ciceri, Lucila A Barreiros, Elena Dominguez-Garrido, Mateus Vidigal, Mayana Zatz, Diederik van de Beek, Sabina Sahanic, Ivan Tancevski, Yurii Stepanovskyy, Oksana Boyarchuk, Yoko Nukui, Miyuki Tsumura, Loreto Vidaur, Stuart G Tangye, Sonia Burrel, Darragh Duffy, Lluis Quintana-Murci, Adam Klocperk, Nelli Y Kann, Anna Shcherbina, Yu-Lung Lau, Daniel Leung, Matthieu Coulongeat, Julien Marlet, Rutger Koning, Luis Felipe Reyes, Angélique Chauvineau-Grenier, Fabienne Venet, Guillaume Monneret, Michel C Nussenzweig, Romain Arrestier, Idris Boudhabhay, Hagit Baris-Feldman, David Hagin, Joost Wauters, Isabelle Meyts, Adam H Dyer, Sean P Kennelly, Nollaig M Bourke, Rabih Halwani, Narjes Saheb Sharif-Askari, Karim Dorgham, Jérome Sallette, Souad Mehlal Sedkaoui, Suzan AlKhater, Raúl Rigo-Bonnin, Francisco Morandeira, Lucie Roussel, Donald C Vinh, Sisse Rye Ostrowski, Antonio Condino-Neto, Carolina Prando, Anastasiia Bonradenko, András N Spaan, Laurent Gilardin, Jacques Fellay, Stanislas Lyonnet, Kaya Bilguvar, Richard P Lifton, Shrikant Mane, HGID Lab, COVID Clinicians, COVID-STORM Clinicians, NIAID Immune Response to COVID Group, NH-COVAIR Study Group, Danish CHGE, Danish Blood Donor Study, St. James's Hospital, SARS CoV2 Interest group, French COVID Cohort Study Group, Imagine COVID-Group, Milieu Intérieur Consortium, CoV-Contact Cohort, Amsterdam UMC Covid-19, Biobank Investigators, COVID Human Genetic Effort, CONSTANCES cohort, 3C-Dijon Study, Cerba Health-Care, Etablissement du Sang study group, Mark S Anderson, Bertrand Boisson, Vivien Béziat, Shen-Ying Zhang, Evangelos Vandreakos, Olivier Hermine, Aurora Pujol, Pärt Peterson, Trine H Mogensen, Lee Rowen, James Mond, Stéphanie Debette, Xavier de Lamballerie, Xavier Duval, France Mentré, Marie Zins, Pere Soler-Palacin, Roger Colobran, Guy Gorochov, Xavier Solanich, Sophie Susen, Javier Martinez-Picado, Didier Raoult, Marc Vasse, Peter K Gregersen, Lorenzo Piemonti, Carlos Rodríguez-Gallego, Luigi D Notarangelo, Helen C Su, Kai Kisand, Satoshi Okada, Anne Puel, Emmanuelle Jouanguy, Charles M Rice, Pierre Tiberghien, Qian Zhang, Aurélie Cobat, Laurent Abel, and Jean-Laurent Casanova
mzMLb: A Future-Proof Raw Mass Spectrometry Data Format Based on Standards-Compliant mzML and Optimized for Speed and Storage Requirements., Ranjeet S Bhamber, Andris Jankevics, Eric W Deutsch, Andrew R Jones, and Andrew W Dowsey
Recent Progress in Lyme Disease and Remaining Challenges., Jason R Bobe, Brandon L Jutras, Elizabeth J Horn, Monica E Embers, Allison Bailey, Robert L Moritz, Ying Zhang, Mark J Soloski, Richard S Ostfeld, Richard T Marconi, John Aucott, Avi Ma'ayan, Felicia Keesing, Kim Lewis, Choukri Ben Mamoun, Alison W Rebman, Mecaila E McClune, Edward B Breitschwerdt, Panga Jaipal Reddy, Ricardo Maggi, Frank Yang, Bennett Nemser, Aydogan Ozcan, Omai Garner, Dino Di Carlo, Zachary Ballard, Hyou-Arm Joung, Albert Garcia-Romeu, Roland R Griffiths, Nicole Baumgarth, and Brian A Fallon
Proteomic/transcriptomic analysis of erythropoiesis., Marjorie Brand and Jeffrey A Ranish
Implications of Selection Bias Due to Delayed Study Entry in Clinical Genomic Studies., Samantha Brown, Jessica A Lavery, Ronglai Shen, Axel S Martin, Kenneth L Kehl, Shawn M Sweeney, Eva M Lepisto, Hira Rizvi, Caroline G McCarthy, Nikolaus Schultz, Jeremy L Warner, Ben Ho Park, Philippe L Bedard, Gregory J Riely, Deborah Schrag, Katherine S Panageas, AACR Project GENIE Consortium, Walter Urba, Brady Bernard, Brian D. Piening, and Carlo Bifulco
Single-cell profiling of D-2-hydroxyglutarate using surface-immobilized resazurin analogs., Hanjun Cheng, Zhonghan Li, Zhili Guo, Shiqun Shao, Li Mo, Wei Wei, and Min Xue
A redox-active crosslinker reveals an essential and inhibitable oxidative folding network in the endoplasmic reticulum of malaria parasites., David W Cobb, Heather M Kudyba, Alejandra Villegas, Michael R Hoopmann, Rodrigo P Baptista, Baylee Bruton, Michelle Krakowiak, Robert L Moritz, and Vasant Muralidharan
TE Hub: A community-oriented space for sharing and connecting tools, data, resources, and methods for transposable element annotation., TE Hub Consortium, Tyler A Elliott, Tony Heitkam, Robert Hubley, Hadi Quesneville, Alexander Suh, and Travis J Wheeler
Editorial: Personal Genomes: Accessing, Sharing, and Interpretation., Manuel Corpas, Stephan Beck, Gustavo Glusman, and Mahsa Shabani
Circulating exosomal microRNA expression patterns distinguish cardiac sarcoidosis from myocardial ischemia., Elliott D Crouser, Mark W Julian, Sabahattin Bicer, Vikas Ghai, Taek-Kyun Kim, Lisa A Maier, May Gillespie, Nabeel Y Hamzeh, and Kai Wang
A proteomics sample metadata representation for multiomics integration and big data analysis., Chengxin Dai, Anja Füllgrabe, Julianus Pfeuffer, Elizaveta M Solovyeva, Jingwen Deng, Pablo Moreno, Selvakumar Kamatchinathan, Deepti Jaiswal Kundu, Nancy George, Silvie Fexova, Björn Grüning, Melanie Christine Föll, Johannes Griss, Marc Vaudel, Enrique Audain, Marie Locard-Paulet, Michael Turewicz, Martin Eisenacher, Julian Uszkoreit, Tim Van Den Bossche, Veit Schwämmle, Henry Webel, Stefan Schulze, David Bouyssié, Savita Jayaram, Vinay Kumar Duggineni, Patroklos Samaras, Mathias Wilhelm, Meena Choi, Mingxun Wang, Oliver Kohlbacher, Alvis Brazma, Irene Papatheodorou, Nuno Bandeira, Eric W Deutsch, Juan Antonio Vizcaíno, Mingze Bai, Timo Sachsenberg, Lev I Levitsky, and Yasset Perez-Riverol
Lettuce (Lactuca sativa) productivity influenced by microbial inocula under nitrogen-limited conditions in aquaponics., Jessica A Day, Christian Diener, Anne E Otwell, Kourtney E Tams, Brad Bebout, Angela M Detweiler, Michael D Lee, Madeline T Scott, Wilson Ta, Monica Ha, Shienna A Carreon, Kenny Tong, Abdirizak A Ali, Sean M Gibbons, and Nitin S Baliga
Advances and Utility of the Human Plasma Proteome., Eric W Deutsch, Gilbert S Omenn, Zhi Sun, Michal Maes, Maria Pernemalm, Krishnan K Palaniappan, Natasha Letunica, Yves Vandenbrouck, Virginie Brun, Sheng-Ce Tao, Xiaobo Yu, Philipp E Geyer, Vera Ignjatovic, Robert L Moritz, and Jochen M Schwenk
Universal Spectrum Identifier for mass spectra., Eric W Deutsch, Yasset Perez-Riverol, Jeremy Carver, Shin Kawano, Luis Mendoza, Tim Van Den Bossche, Ralf Gabriels, Pierre-Alain Binz, Benjamin Pullman, Zhi Sun, Jim Shofstahl, Wout Bittremieux, Tytus D Mak, Joshua Klein, Yunping Zhu, Henry Lam, Juan Antonio Vizcaíno, and Nuno Bandeira
Non-responder phenotype reveals apparent microbiome-wide antibiotic tolerance in the murine gut., Christian Diener, Anna C H Hoge, Sean M Kearney, Ulrike Kusebauch, Sushmita Patwardhan, Robert L Moritz, Susan E Erdman, and Sean M Gibbons
Alkylaminophenol and GPR17 Agonist for Glioblastoma Therapy: A Combinational Approach for Enhanced Cell Death Activity., Phuong Doan, Phung Nguyen, Akshaya Murugesan, Nuno R Candeias, Olli Yli-Harja, and Meenakshisundaram Kandhavelu
Targeting Orphan G Protein-Coupled Receptor 17 with T0 Ligand Impairs Glioblastoma Growth., Phuong Doan, Phung Nguyen, Akshaya Murugesan, Kumar Subramanian, Saravanan Konda Mani, Vignesh Kalimuthu, Bobin George Abraham, Brett W Stringer, Kadalmani Balamuthu, Olli Yli-Harja, and Meenakshisundaram Kandhavelu
Mycobacterium abscessus biofilms produce an extracellular matrix and have a distinct mycolic acid profile, Anja Dokic, Eliza Peterson, Mario L Arrieta-Ortiz, Min Pan, Alessandro Di Maio, Nitin Baliga, and Apoorva Bhatt
Single-cell analysis of erythropoiesis in Rpl11 haploinsufficient mice reveals insight into the pathogenesis of Diamond Blackfan anemia., Raymond T Doty, Xiaowei Yan, Changting Meng, Christopher Lausted, Qiang Tian, and Janis L Abkowitz
Are There Limits in Explainability of Prognostic Biomarkers? Scrutinizing Biological Utility of Established Signatures., Frank Emmert-Streib, Kalifa Manjang, Matthias Dehmer, Olli Yli-Harja, and Anssi Auvinen
Application of MCAT Questions as a Testing Tool and Evaluation Metric for Knowledge Graph-based Reasoning Systems., Karamarie Fecho, James Balhoff, Chris Bizon, William E Byrd, Sui Huang, David Koslicki, Stefano E Rensi, Patrick L Schmitt, Mathias J Wawer, Mark Williams, and Stanley C Ahalt
NCI Imaging Data Commons., Andrey Fedorov, William J R Longabaugh, David Pot, David A Clunie, Steve Pieper, Hugo J W L Aerts, André Homeyer, Rob Lewis, Afshin Akbarzadeh, Dennis Bontempi, William Clifford, Markus D Herrmann, Henning Höfener, Igor Octaviano, Chad Osborne, Suzanne Paquette, James Petts, Davide Punzo, Madelyn Reyes, Daniela P Schacherer, Mi Tian, George White, Erik Ziegler, Ilya Shmulevich, Todd Pihl, Ulrike Wagner, Keyvan Farahani, and Ron Kikinis
Molluscan mitochondrial genomes break the rules., Fabrizio Ghiselli, André Gomes-Dos-Santos, Coen M Adema, Manuel Lopes-Lima, Joel Sharbrough, and Jeffrey L Boore
Patient-Specific Cell Communication Networks Associate With Disease Progression in Cancer., David L Gibbs, Boris Aguilar, Vésteinn Thorsson, Alexander V Ratushny, and Ilya Shmulevich
In vivo commensal control of Clostridioides difficile virulence., Brintha P Girinathan, Nicholas DiBenedetto, Jay N Worley, Johann Peltier, Mario L Arrieta-Ortiz, Selva Rupa Christinal Immanuel, Richard Lavin, Mary L Delaney, Christopher K Cummins, Maria Hoffman, Yan Luo, Narjol Gonzalez-Escalona, Marc Allard, Andrew B Onderdonk, Georg K Gerber, Abraham L Sonenshein, Nitin S Baliga, Bruno Dupuy, and Lynn Bry
Sex Differences in Influenza: The Challenge Study Experience., Luca T Giurgea, Adriana Cervantes-Medina, Kathie-Anne Walters, Kelsey Scherler, Alison Han, Lindsay M Czajkowski, Holly Ann Baus, Sally Hunsberger, Sabra L Klein, John C Kash, Jeffery K Taubenberger, and Matthew J Memoli
The effect of calcium and magnesium on activity, immunogenicity, and efficacy of a recombinant N1/N2 neuraminidase vaccine., Luca T Giurgea, Jae-Keun Park, Kathie-Anne Walters, Kelsey Scherler, Adriana Cervantes-Medina, Ashley Freeman, Luz Angela Rosas, John C Kash, Jeffery K Taubenberger, and Matthew J Memoli
Identifying the miRNA Signature Association with Aging-Related Senescence in Glioblastoma., Mutharasu Gnanavel, Akshaya Murugesan, Saravanan Konda Mani, Olli Yli-Harja, and Meenakshisundaram Kandhavelu
DUOX2 variants associate with preclinical disturbances in microbiota-immune homeostasis and increased inflammatory bowel disease risk., Helmut Grasberger, Andrew T Magis, Elisa Sheng, Matthew P Conomos, Min Zhang, Lea S Garzotto, Guoqing Hou, Shrinivas Bishu, Hiroko Nagao-Kitamoto, Mohamad El-Zataari, Sho Kitamoto, Nobuhiko Kamada, Ryan Stidham, Yasutada Akiba, Jonathan Kaunitz, Yael Haberman, Subra Kugathasan, Lee A Denson, Gilbert S Omenn, and John Y Kao
Elevated rates of horizontal gene transfer in the industrialized human microbiome., Mathieu Groussin, Mathilde Poyet, Ainara Sistiaga, Sean M Kearney, Katya Moniz, Mary Noel, Jeff Hooker, Sean M Gibbons, Laure Segurel, Alain Froment, Rihlat Said Mohamed, Alain Fezeu, Vanessa A Juimo, Sophie Lafosse, Francis E Tabe, Catherine Girard, Deborah Iqaluk, Le Thanh Tu Nguyen, B Jesse Shapiro, Jenni Lehtimäki, Lasse Ruokolainen, Pinja P Kettunen, Tommi Vatanen, Shani Sigwazi, Audax Mabulla, Manuel Domínguez-Rodrigo, Yvonne A Nartey, Adwoa Agyei-Nkansah, Amoako Duah, Yaw A Awuku, Kenneth A Valles, Shadrack O Asibey, Mary Y Afihene, Lewis R Roberts, Amelie Plymoth, Charles A Onyekwere, Roger E Summons, Ramnik J Xavier, and Eric J Alm
Single-Cell Profiling of Fatty Acid Uptake Using Surface-Immobilized Dendrimers., Zhili Guo, Hanjun Cheng, Zhonghan Li, Shiqun Shao, Priyanka Sarkar, Siwen Wang, Rohit Chaudhuri, Nicole G Perkins, Fei Ji, Wei Wei, and Min Xue
Debris-stimulated tumor growth: a Pandora's box?, Victoria M Haak, Sui Huang, and Dipak Panigrahy
MASSpy: Building, simulating, and visualizing dynamic biological models in Python using mass action kinetics., Zachary B Haiman, Daniel C Zielinski, Yuko Koike, James T Yurkovich, and Bernhard O Palsson
Dissolved Organic Matter in the Global Ocean: A Primer., Dennis A Hansell and Monica V Orellana
Digital twins for predictive oncology will be a paradigm shift for precision cancer care., Tina Hernandez-Boussard, Paul Macklin, Emily J Greenspan, Amy L Gryshuk, Eric Stahlberg, Tanveer Syeda-Mahmood, and Ilya Shmulevich
Measuring the Efficacy of Pathology Career Recruitment Strategies in US Medical Students., Patricia V Hernandez, Dana Razzano, Nicole D Riddle, John T Fallon, Humayun K Islam, Kamran M Mirza, Rugved Pattarkine, Tania Platero, Daniela Hermelin, Patricia V Adem, Adam L Booth, Eunice Mbela Nachinga, Kalpana S Reddy, Angelica Mares, and Patrick A Lento
Op-Ed: How science education can stave off demagogues, Leroy Hood and Matthew D. LaPlante
Reconciling Non-Genetic Plasticity with Somatic Evolution in Cancer., Sui Huang
Modulation of SETDB1 activity by APQ ameliorates heterochromatin condensation, motor function, and neuropathology in a Huntington's disease mouse model., Yu Jin Hwang, Seung Jae Hyeon, Younghee Kim, Sungsu Lim, Min Young Lee, Jieun Kim, Ashwini M Londhe, Lizaveta Gotina, Yunha Kim, Ae Nim Pae, Yong Seo Cho, Jihye Seong, Hyemyung Seo, Yun Kyung Kim, Hyunah Choo, Hoon Ryu, and Sun-Joon Min
Quantitative prediction of conditional vulnerabilities in regulatory and metabolic networks using PRIME., Selva Rupa Christinal Immanuel, Mario L Arrieta-Ortiz, Rene A Ruiz, Min Pan, Adrián López García de Lomana, Eliza Jr Peterson, and Nitin S Baliga
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
Angiotensin II receptor I auto-antibodies following SARS-CoV-2 infection., Yonghou Jiang, Fergal Duffy, Jennifer J Hadlock, Andrew Raappana, Sheila Styrchak, Ingrid Beck, Fred D Mast, Leslie R Miller, William Chour, John Houck, Blair Armistead, Venkata R Duvvuri, Winnie Yeung, Micaela Haglund, Jackson Wallner, Julie A Wallick, Samantha Hardy, Alyssa Oldroyd, Daisy Ko, Ana Gervassi, Kim M Murray, Henry G Kaplan, John D Aitchison, James R Heath, D Noah Sather, Jason D Goldman, Lisa Frenkel, and Whitney E Harrington
SPACEPro: A Software Tool for Analysis of Protein Sample Cleavage for Tandem Mass Spectrometry., Vidur Kailash, Luis Mendoza, Robert L Moritz, and Michael R Hoopmann
The World Is Not a Theorem., Stuart Kauffman and Andrea Roli
Genomic and functional characterization of a mucosal symbiont involved in early-stage colorectal cancer., Melissa C Kordahi, Ian B Stanaway, Marion Avril, Denise Chac, Marie-Pierre Blanc, Benjamin Ross, Christian Diener, Sumita Jain, Paul McCleary, Ana Parker, Vincent Friedman, Jennifer Huang, Wynn Burke, Sean M Gibbons, Amy D Willis, Richard P Darveau, William M Grady, Cynthia W Ko, and R William DePaolo
Early IFN-α signatures and persistent dysfunction are distinguishing features of NK cells in severe COVID-19., Benjamin Krämer, Rainer Knoll, Lorenzo Bonaguro, Michael ToVinh, Jan Raabe, Rosario Astaburuaga-García, Jonas Schulte-Schrepping, Kim Melanie Kaiser, Gereon J Rieke, Jenny Bischoff, Malte B Monin, Christoph Hoffmeister, Stefan Schlabe, Elena De Domenico, Nico Reusch, Kristian Händler, Gary Reynolds, Nils Blüthgen, Gudrun Hack, Claudia Finnemann, Hans D Nischalke, Christian P Strassburg, Emily Stephenson, Yapeng Su, Louis Gardner, Dan Yuan, Daniel Chen, Jason D Goldman, Philipp Rosenstiel, Susanne V Schmidt, Eicke Latz, Kevin Hrusovsky, Andrew J Ball, Joe M Johnson, Paul-Albert Koenig, Florian I Schmidt, Muzlifah Haniffa, James R Heath, Beate M Kümmerer, Verena Keitel, Björn Jensen, Paula Stubbemann, Florian Kurth, Leif E Sander, Birgit Sawitzki, Deutsche COVID-19 OMICS Initiative (DeCOI), Anna C Aschenbrenner, Joachim L Schultze, and Jacob Nattermann
THP1 proteomics in response to mycobacterium tuberculosis infection, Ajay Kumar, Mukul K Midha, and Kanury Vs Rao
Plasmodium falciparum Calcium-Dependent Protein Kinase 4 is Critical for Male Gametogenesis and Transmission to the Mosquito Vector., Sudhir Kumar, Meseret T Haile, Michael R Hoopmann, Linh T Tran, Samantha A Michaels, Seamus R Morrone, Kayode K Ojo, Laura M Reynolds, Ulrike Kusebauch, Ashley M Vaughan, Robert L Moritz, Stefan H I Kappe, and Kristian E Swearingen
Ambulatory risk models for long-term prevention of sepsis: Retrospective Analysis and Predictive Model., Jewel Y Lee, Sevda Molani, Chen Fang, Kathleen Jade, Shane O'Mahony, Sergey A Kornilov, Lindsay T Mico, and Jennifer J Hadlock
Cordycepin inhibits the proliferation of malignant peripheral nerve sheath tumor cells through the p53/Sp1/tubulin pathway., Ming-Jen Lee, Jen-Chieh Lee, Jung-Hsien Hsieh, May-Yao Lin, I-An Shih, Huey-Ling You, and Kai Wang
Molecular interaction of HIC, an agonist of P2Y1 receptor, and its role in prostate cancer apoptosis., Hien Thi Thu Le, Akshaya Murugesan, Thiyagarajan Ramesh, Olli Yli-Harja, Saravanan Konda Mani, and Meenakshisundaram Kandhavelu
Constraint Closure Drove Major Transitions in the Origins of Life., Niles E Lehman and Stuart A Kauffman
Modulating innate immune activation states impacts the efficacy of specific Aβ immunotherapy., Yona Levites, Cory Funk, Xue Wang, Paramita Chakrabarty, Karen N McFarland, Baxter Bramblett, Veronica O'Neal, Xufei Liu, Thomas Ladd, Max Robinson, Mariet Allen, Minerva M Carrasquillo, Dennis Dickson, Pedro Cruz, Danny Ryu, Hong-Dong Li, Nathan D Price, NIlüfer Ertekin-Taner, and Todd E Golde
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
A CRISPR/Cas9-engineered ARID1A-deficient human gastric cancer organoid model reveals essential and non-essential modes of oncogenic transformation., Yuan-Hung Lo, Kevin S Kolahi, Yuhong Du, Chiung-Ying Chang, Andrey Krokhotin, Ajay Nair, Walter D Sobba, Kasper Karlsson, Sunny J Jones, Teri A Longacre, Amanda T Mah, Bahar Tercan, Alexandra Sockell, Hang Xu, Jose A Seoane, Jin Chen, Ilya Shmulevich, Jonathan S Weissman, Christina Curtis, Andrea Califano, Haian Fu, Gerald R Crabtree, and Calvin J Kuo
Mechanism Across Scales: A Holistic Modeling Framework Integrating Laboratory and Field Studies for Microbial Ecology., Lauren M Lui, Erica L-W Majumder, Heidi J Smith, Hans K Carlson, Frederick von Netzer, Matthew W Fields, David A Stahl, Jizhong Zhou, Terry C Hazen, Nitin S Baliga, Paul D Adams, and Adam P Arkin
Resolution of tissue signatures of therapy response in patients with recurrent GBM treated with neoadjuvant anti-PD1., Yue Lu, Alphonsus H C Ng, Frances E Chow, Richard G Everson, Beth A Helmink, Michael T Tetzlaff, Rohit Thakur, Jennifer A Wargo, Timothy F Cloughesy, Robert M Prins, and James R Heath
Hallstatt miners consumed blue cheese and beer during the Iron Age and retained a non-Westernized gut microbiome until the Baroque period., Frank Maixner, Mohamed S Sarhan, Kun D Huang, Adrian Tett, Alexander Schoenafinger, Stefania Zingale, Aitor Blanco-Míguez, Paolo Manghi, Jan Cemper-Kiesslich, Wilfried Rosendahl, Ulrike Kusebauch, Seamus R Morrone, Michael R Hoopmann, Omar Rota-Stabelli, Thomas Rattei, Robert L Moritz, Klaus Oeggl, Nicola Segata, Albert Zink, Hans Reschreiter, and Kerstin Kowarik
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
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
