The Institute for Systems Biology is a not-for-profit biomedical research organization that is part of the Providence St. Joseph Health family. The scientists and engineers at ISB are working to unlock the mystery of the genome to learn how we can keep people healthy well into their 90s.

This is a proactive approach to medicine that will help us shift from a disease focus to a wellness focus. With ISB, we are pursuing research in the areas of breast cancer survivorship, Alzheimer’s, glioblastoma and markers to help us identify and reverse disease at the earliest possible stages. Our partnership gives us the opportunity to bring these advances to people in the communities we serve.

Follow

Submissions from 2022

Link

Protein Catalyzed Capture (PCC) Agents for Antigen Targeting., Matthew N Idso, Bert T Lai, Heather D Agnew, and James R Heath

Submissions from 2021

Link

The quantitative metabolome is shaped by abiotic constraints., Amir Akbari, James T Yurkovich, Daniel C Zielinski, and Bernhard O Palsson

Link

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

Link

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

Link

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

Link

Systems modeling of metabolic dysregulation in neurodegenerative diseases., Priyanka Baloni, Cory C Funk, Ben Readhead, and Nathan D Price

Link

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

Link

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

Link

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

Link

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

Link

Proteomic/transcriptomic analysis of erythropoiesis., Marjorie Brand and Jeffrey A Ranish

Link

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

Link

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

Link

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

Link

Editorial: Personal Genomes: Accessing, Sharing, and Interpretation., Manuel Corpas, Stephan Beck, Gustavo Glusman, and Mahsa Shabani

PDF

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

PDF

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

Link

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

Link

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

Link

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

Link

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

Link

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

Link

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

Link

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

Link

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

Link

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

Link

Molluscan mitochondrial genomes break the rules., Fabrizio Ghiselli, André Gomes-Dos-Santos, Coen M Adema, Manuel Lopes-Lima, Joel Sharbrough, and Jeffrey L Boore

Link

Patient-Specific Cell Communication Networks Associate With Disease Progression in Cancer., David L Gibbs, Boris Aguilar, Vésteinn Thorsson, Alexander V Ratushny, and Ilya Shmulevich

Link

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

Link

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

Link

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

PDF

Identifying the miRNA Signature Association with Aging-Related Senescence in Glioblastoma., Mutharasu Gnanavel, Akshaya Murugesan, Saravanan Konda Mani, Olli Yli-Harja, and Meenakshisundaram Kandhavelu

Link

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

Link

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

Link

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

Link

Debris-stimulated tumor growth: a Pandora's box?, Victoria M Haak, Sui Huang, and Dipak Panigrahy

Link

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

Link

Dissolved Organic Matter in the Global Ocean: A Primer., Dennis A Hansell and Monica V Orellana

Link

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

Link

Op-Ed: How science education can stave off demagogues, Leroy Hood and Matthew D. LaPlante

Link

Reconciling Non-Genetic Plasticity with Somatic Evolution in Cancer., Sui Huang

Link

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

PDF

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

Link

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

Link

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

Link

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

Link

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

Link

THP1 proteomics in response to mycobacterium tuberculosis infection, Ajay Kumar, Mukul K Midha, and Kanury Vs Rao

Link

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

Link

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

Link

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

Link

Constraint Closure Drove Major Transitions in the Origins of Life., Niles E Lehman and Stuart A Kauffman

Link

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

Link

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

Link

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

Link

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

Link

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

Link

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

PDF

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

Link

Limitations of Explainability for Established Prognostic Biomarkers of Prostate Cancer., Kalifa Manjang, Olli Yli-Harja, Matthias Dehmer, and Frank Emmert-Streib

Link

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

Link

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

Link

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

Link

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

PDF

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

Link

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

Link

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

Link

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

Link

Autophagy as a Mechanism for Adaptive Prediction-Mediated Emergence of Drug Resistance., Nivedita Nivedita, John D Aitchison, and Nitin Baliga

Link

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

Link

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

Link

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

Link

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

Link

Molecular interaction study of novel indoline derivatives with EGFR-kinase domain using multiple computational analysis., Suresh Palanivel, Olli Yli-Harja, and Meenakshisundaram Kandhavelu

Link

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

Link

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

Link

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

Link

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

Link

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

Link

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

Link

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

Link

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

Link

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

PDF

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

Link

Curation Guidelines for de novo Generated Transposable Element Families., Jessica Storer, Robert Hubley, Jeb Rosen, and Arian F A Smit

PDF

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

PDF

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

Link

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

Link

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

Link

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

Link

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

Link

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

Link

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

Link

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

Link

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

Link

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

Link

2021 Special Issue on Software Tools and Resources: Finding the Right Tools for the Job., Susan T Weintraub, Michael R Hoopmann, and Magnus Palmblad

Link

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

Link

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

Link

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