Submissions from 2023
cyjShiny: A cytoscape.js R Shiny Widget for network visualization and analysis., Augustin Luna, Omar Shah, Chris Sander, and Paul Shannon
Disease-specific loss of microbial cross-feeding interactions in the human gut, Vanessa R. Marcelino, Caitlin Welsh, Christian Diener, Emily L. Gulliver, Emily L. Rutten, Remy B. Young, Edward M. Giles, Sean M Gibbons, Chris Greening, and Samuel C. Forster
Rare predicted loss-of-function variants of type I IFN immunity genes are associated with life-threatening COVID-19., Daniela Matuozzo, Estelle Talouarn, Astrid Marchal, Peng Zhang, Jeremy Manry, Yoann Seeleuthner, Yu Zhang, Alexandre Bolze, Matthieu Chaldebas, Baptiste Milisavljevic, Adrian Gervais, Paul Bastard, Takaki Asano, Lucy Bizien, Federica Barzaghi, Hassan Abolhassani, Ahmad Abou Tayoun, Alessandro Aiuti, Ilad Alavi Darazam, Luis M Allende, Rebeca Alonso-Arias, Andrés Augusto Arias, Gokhan Aytekin, Peter Bergman, Simone Bondesan, Yenan T Bryceson, Ingrid G Bustos, Oscar Cabrera-Marante, Sheila Carcel, Paola Carrera, Giorgio Casari, Khalil Chaïbi, Roger Colobran, Antonio Condino-Neto, Laura E Covill, Ottavia M Delmonte, Loubna El Zein, Carlos Flores, Peter K Gregersen, Marta Gut, Filomeen Haerynck, Rabih Halwani, Selda Hancerli, Lennart Hammarström, Nevin Hatipoğlu, Adem Karbuz, Sevgi Keles, Christèle Kyheng, Rafael Leon-Lopez, Jose Luis Franco, Davood Mansouri, Javier Martinez-Picado, Ozge Metin Akcan, Isabelle Migeotte, Pierre-Emmanuel Morange, Guillaume Morelle, Andrea Martin-Nalda, Giuseppe Novelli, Antonio Novelli, Tayfun Ozcelik, Figen Palabiyik, Qiang Pan-Hammarström, Rebeca Pérez de Diego, Laura Planas-Serra, Daniel E Pleguezuelo, Carolina Prando, Aurora Pujol, Luis Felipe Reyes, Jacques G Rivière, Carlos Rodriguez-Gallego, Julian Rojas, Patrizia Rovere-Querini, Agatha Schlüter, Mohammad Shahrooei, Ali Sobh, Pere Soler-Palacin, Yacine Tandjaoui-Lambiotte, Imran Tipu, Cristina Tresoldi, Jesus Troya, Diederik van de Beek, Mayana Zatz, Pawel Zawadzki, Saleh Zaid Al-Muhsen, Mohammed Faraj Alosaimi, Fahad M Alsohime, Hagit Baris-Feldman, Manish J Butte, Stefan N Constantinescu, Megan A Cooper, Clifton L Dalgard, Jacques Fellay, James R Heath, Yu-Lung Lau, Richard P Lifton, Tom Maniatis, Trine H Mogensen, Horst von Bernuth, Alban Lermine, Michel Vidaud, Anne Boland, Jean-François Deleuze, Robert Nussbaum, Amanda Kahn-Kirby, France Mentre, Sarah Tubiana, Guy Gorochov, Florence Tubach, Pierre Hausfater, COVID Human Genetic Effort, COVIDeF Study Group, French COVID Cohort Study Group, CoV-Contact Cohort, COVID-STORM Clinicians, COVID Clinicians, Orchestra Working Group, Amsterdam UMC Covid-19 Biobank, NIAID-USUHS COVID Study Group, Isabelle Meyts, Shen-Ying Zhang, Anne Puel, Luigi D Notarangelo, Stephanie Boisson-Dupuis, Helen C Su, Bertrand Boisson, Emmanuelle Jouanguy, Jean-Laurent Casanova, Qian Zhang, Laurent Abel, and Aurélie Cobat
Vacuum Insulated Probe Heated Electrospray Ionization Source Enhances Microflow Rate Chromatography Signals in the Bruker timsTOF Mass Spectrometer., Mukul K Midha, Charu Kapil, Michal Maes, David H Baxter, Seamus R Morrone, Timothy J Prokop, and Robert L Moritz
Novel TCF4:TCF12 heterodimer inhibits glioblastoma growth., Svetlana A Mikheeva, Cory C Funk, Philip J Horner, Robert C Rostomily, and Andrei M Mikheev
Optimizing preclinical models of ageing for translation to clinical trials., Sarah J Mitchell, Michael R MacArthur, and Alice E Kane
The scalable precision medicine open knowledge engine (SPOKE): a massive knowledge graph of biomedical information., John H Morris, Karthik Soman, Rabia E Akbas, Xiaoyuan Zhou, Brett Smith, Elaine C Meng, Conrad C Huang, Gabriel Cerono, Gundolf Schenk, Angela Rizk-Jackson, Adil Harroud, Lauren Sanders, Sylvain V Costes, Krish Bharat, Arjun Chakraborty, Alexander R Pico, Taline Mardirossian, Michael Keiser, Alice Tang, Josef Hardi, Yongmei Shi, Mark Musen, Sharat Israni, Sui Huang, Peter W Rose, Charlotte A Nelson, and Sergio E Baranzini
Optimization of Instrument Parameters for Efficient Phosphopeptide Identification and Localization by Data-dependent Analysis Using Orbitrap Tribrid Mass Spectrometers, Seamus R. Morrone, Michael R Hoopmann, David Shteynberg, Ulrike Kusebauch, and Robert L Moritz
Integrated analysis of proteomics, epigenomics and metabolomics data revealed divergent pathway activation patterns in the recent versus chronic post-traumatic stress disorder., Seid Muhie, Aarti Gautam, Burook Misganaw, Ruoting Yang, Synthia H Mellon, Allison Hoke, Janine Flory, Bernie Daigle, Kevin Swift, PTSD Systems Biology Consortium, Leroy Hood, Francis J Doyle, Owen M Wolkowitz, Charles R Marmar, Kerry Ressler, Rachel Yehuda, Rasha Hammamieh, and Marti Jett
Molecular signatures of post-traumatic stress disorder in war-zone-exposed veteran and active-duty soldiers., Seid Muhie, Aarti Gautam, Ruoting Yang, Burook Misganaw, Bernie J Daigle, Synthia H Mellon, Janine D Flory, Duna Abu-Amara, Inyoul Lee, Kai Wang, Ryan Rampersaud, PTSD Systems Biology Consortium, Leroy Hood, Rachel Yehuda, Charles R Marmar, Owen M Wolkowitz, Kerry J Ressler, Francis J Doyle, Rasha Hammamieh, and Marti Jett
Signaling landscape of mitochondrial non-coding RNAs., Gnanavel Mutharasu, Akshaya Murugesan, Saravnan Kondamani, Ramesh Thiyagarajan, Olli Yli-Harja, and Meenakshisundaram Kandhavelu
Stereochemical engineering yields a multifunctional peptide macrocycle inhibitor of Akt2 by fine-tuning macrocycle-cell membrane interactions., Arundhati Nag, Amirhossein Mafi, Samir Das, Mary Beth Yu, Belen Alvarez-Villalonga, Soo-Kyung Kim, Yapeng Su, William A Goddard, and James R Heath
Toward an Integrated Machine Learning Model of a Proteomics Experiment., Benjamin A Neely, Viktoria Dorfer, Lennart Martens, Isabell Bludau, Robbin Bouwmeester, Sven Degroeve, Eric W Deutsch, Siegfried Gessulat, Lukas Käll, Pawel Palczynski, Samuel H Payne, Tobias Greisager Rehfeldt, Tobias Schmidt, Veit Schwämmle, Julian Uszkoreit, Juan Antonio Vizcaíno, Mathias Wilhelm, and Magnus Palmblad
Computational capabilities of a multicellular reservoir computing system., Vladimir Nikolić, Moriah Echlin, Boris Aguilar, and Ilya Shmulevich
Insights into mammalian TE diversity through the curation of 248 genome assemblies., Austin B Osmanski, Nicole S Paulat, Jenny Korstian, Jenna R Grimshaw, Michaela Halsey, Kevin A M Sullivan, Diana D Moreno-Santillán, Claudia Crookshanks, Jacquelyn Roberts, Carlos Garcia, Matthew G Johnson, Llewellyn D Densmore, Richard D Stevens, Jeb Rosen, Jessica Storer, Robert Hubley, Arian F A Smit, Liliana M Dávalos, Elinor K Karlsson, Kerstin Lindblad-Toh, and David A Ray
Chiropterans Are a Hotspot for Horizontal Transfer of DNA Transposons in Mammalia., Nicole S Paulat, Jessica Storer, Diana D Moreno-Santillán, Austin B Osmanski, Kevin A M Sullivan, Jenna R Grimshaw, Jennifer Korstian, Michaela Halsey, Carlos J Garcia, Claudia Crookshanks, Jaquelyn Roberts, Arian F A Smit, Robert Hubley, Jeb Rosen, Emma C Teeling, Sonja C Vernes, Eugene Myers, Martin Pippel, Thomas Brown, Michael Hiller, Danny Rojas, Liliana M Dávalos, Kerstin Lindblad-Toh, Elinor K Karlsson, and David A Ray
MtrA modulates Mycobacterium tuberculosis cell division in host microenvironments to mediate intrinsic resistance and drug tolerance., Eliza J R Peterson, Aaron N Brooks, David J Reiss, Amardeep Kaur, Julie Do, Min Pan, Wei-Ju Wu, Robert Morrison, Vivek Srinivas, Warren Carter, Mario L Arrieta-Ortiz, Rene A Ruiz, Apoorva Bhatt, and Nitin S Baliga
What Can Ribo-Seq, Immunopeptidomics, and Proteomics Tell Us About the Noncanonical Proteome?, John R Prensner, Jennifer G Abelin, Leron W Kok, Karl R Clauser, Jonathan M Mudge, Jorge Ruiz-Orera, Michal Bassani-Sternberg, Robert L Moritz, Eric W Deutsch, and Sebastiaan van Heesch
Neoantigen-targeted CD8+ T cell responses with PD-1 blockade therapy, Cristina Puig-Saus, Barbara Sennino, Songming Peng, Clifford L Wang, Zheng Pan, Benjamin Yuen, Bhamini Purandare, Duo An, Boi B Quach, Diana Nguyen, Huiming Xia, Sameeha Jilani, Kevin Shao, Claire McHugh, John Greer, Phillip Peabody, Saparya Nayak, Jonathan Hoover, Sara Said, Kyle Jacoby, Olivier Dalmas, Susan P Foy, Andrew Conroy, Michael C Yi, Christine Shieh, William Lu, Katharine Heeringa, Yan Ma, Shahab Chizari, Melissa J Pilling, Marc Ting, Ramya Tunuguntla, Salemiz Sandoval, Robert Moot, Theresa Hunter, Sidi Zhao, Justin D Saco, Ivan Perez-Garcilazo, Egmidio Medina, Agustin Vega-Crespo, Ignacio Baselga-Carretero, Gabriel Abril-Rodriguez, Grace Cherry, Deborah J Wong, Jasreet Hundal, Bartosz Chmielowski, Daniel E Speiser, Michael T Bethune, Xiaoyan R Bao, Alena Gros, Obi L Griffith, Malachi Griffith, James R Heath, Alex Franzusoff, Stefanie J Mandl, and Antoni Ribas
A meta-analysis of rice phosphoproteomics data to understand variation in cell signalling across the rice pan-genome., Kerry A Ramsbottom, Ananth Prakash, Yasset Perez Riverol, Oscar Martin Camacho, Zhi Sun, Deepti J Kundu, Emily Bowler-Barnett, Maria Martin, Jun Fan, Dmytro Chebotarov, Kenneth L McNally, Eric W Deutsch, Juan Antonio Vizcaíno, and Andrew R Jones
Biological BMI uncovers hidden health risks and is more responsive to lifestyle shifts, Noa Rappaport and Kengo Watanabe
ProteomicsML: An Online Platform for Community-Curated Data sets and Tutorials for Machine Learning in Proteomics., Tobias G Rehfeldt, Ralf Gabriels, Robbin Bouwmeester, Siegfried Gessulat, Benjamin A Neely, Magnus Palmblad, Yasset Perez-Riverol, Tobias Schmidt, Juan Antonio Vizcaíno, and Eric W Deutsch
The complete sequence of a human Y chromosome., Arang Rhie, Sergey Nurk, Monika Cechova, Savannah J Hoyt, Dylan J Taylor, Nicolas Altemose, Paul W Hook, Sergey Koren, Mikko Rautiainen, Ivan A Alexandrov, Jamie Allen, Mobin Asri, Andrey V Bzikadze, Nae-Chyun Chen, Chen-Shan Chin, Mark Diekhans, Paul Flicek, Giulio Formenti, Arkarachai Fungtammasan, Carlos Garcia Giron, Erik Garrison, Ariel Gershman, Jennifer L Gerton, Patrick G S Grady, Andrea Guarracino, Leanne Haggerty, Reza Halabian, Nancy F Hansen, Robert Harris, Gabrielle A Hartley, William T Harvey, Marina Haukness, Jakob Heinz, Thibaut Hourlier, Robert M Hubley, Sarah E Hunt, Stephen Hwang, Miten Jain, Rupesh K Kesharwani, Alexandra P Lewis, Heng Li, Glennis A Logsdon, Julian K Lucas, Wojciech Makalowski, Christopher Markovic, Fergal J Martin, Ann M Mc Cartney, Rajiv C McCoy, Jennifer McDaniel, Brandy M McNulty, Paul Medvedev, Alla Mikheenko, Katherine M Munson, Terence D Murphy, Hugh E Olsen, Nathan D Olson, Luis F Paulin, David Porubsky, Tamara Potapova, Fedor Ryabov, Steven L Salzberg, Michael E G Sauria, Fritz J Sedlazeck, Kishwar Shafin, Valery A Shepelev, Alaina Shumate, Jessica M Storer, Likhitha Surapaneni, Angela M Taravella Oill, Françoise Thibaud-Nissen, Winston Timp, Marta Tomaszkiewicz, Mitchell R Vollger, Brian P Walenz, Allison C Watwood, Matthias H Weissensteiner, Aaron M Wenger, Melissa A Wilson, Samantha Zarate, Yiming Zhu, Justin M Zook, Evan E Eichler, Rachel J O'Neill, Michael C Schatz, Karen H Miga, Kateryna D Makova, and Adam M Phillippy
Editorial: Insights in human and medical genomics: 2022., Jared C. Roach and Maxim B. Freidin
Evolutionary origins and interactomes of human, young microproteins and small peptides translated from short open reading frames., Clara-L Sandmann, Jana F Schulz, Jorge Ruiz-Orera, Marieluise Kirchner, Matthias Ziehm, Eleonora Adami, Maike Marczenke, Annabel Christ, Nina Liebe, Johannes Greiner, Aaron Schoenenberger, Michael B Muecke, Ning Liang, Robert L Moritz, Zhi Sun, Eric W Deutsch, Michael Gotthardt, Jonathan M Mudge, John R Prensner, Thomas E Willnow, Philipp Mertins, Sebastiaan van Heesch, and Norbert Hubner
The NCI Imaging Data Commons as a platform for reproducible research in computational pathology., Daniela P Schacherer, Markus D Herrmann, David A Clunie, Henning Höfener, William Clifford, William J R Longabaugh, Steve Pieper, Ron Kikinis, Andrey Fedorov, and André Homeyer
Single-molecule Sequencing of an Animal Mitochondrial Genome Reveals Chloroplast-like Architecture and Repeat-mediated Recombination., Joel Sharbrough, Laura Bankers, Emily Cook, Peter D Fields, Joseph Jalinsky, Kyle E McElroy, Maurine Neiman, John M Logsdon, and Jeffrey L Boore
Prediction of HLA genotypes from single-cell transcriptome data., Benjamin D Solomon, Hong Zheng, Laura W Dillon, Jason D Goldman, Christopher S Hourigan, James R Heath, and Purvesh Khatri
Genome-wide coancestry reveals details of ancient and recent male-driven reticulation in baboons., Erik F Sørensen, R Alan Harris, Liye Zhang, Muthuswamy Raveendran, Lukas F K Kuderna, Jerilyn A Walker, Jessica Storer, Martin Kuhlwilm, Claudia Fontsere, Lakshmi Seshadri, Christina M Bergey, Andrew S Burrell, Juraj Bergman, Jane E Phillips-Conroy, Fekadu Shiferaw, Kenneth L Chiou, Idrissa S Chuma, Julius D Keyyu, Julia Fischer, Marie-Claude Gingras, Sejal Salvi, Harshavardhan Doddapaneni, Mikkel H Schierup, Mark A Batzer, Clifford J Jolly, Sascha Knauf, Dietmar Zinner, Kyle K-H Farh, Tomas Marques-Bonet, Kasper Munch, Christian Roos, and Jeffrey Rogers
Framework of the, Jessica Storer, Jerilyn A Walker, Jasmine N Baker, Shifat Hossain, Christian Roos, Travis J Wheeler, and Mark A Batzer
Extensive Independent Amplification of Platy-1 Retroposons in Tamarins, Genus, Jessica Storer, Jerilyn A Walker, Thomas O Beckstrom, and Mark A Batzer
Development of a Definition of Postacute Sequelae of SARS-CoV-2 Infection., Tanayott Thaweethai, Sarah E Jolley, Elizabeth W Karlson, Emily B Levitan, Bruce Levy, Grace A McComsey, Lisa McCorkell, Girish N Nadkarni, Sairam Parthasarathy, Upinder Singh, Tiffany A Walker, Caitlin A Selvaggi, Daniel J Shinnick, Carolin C M Schulte, Rachel Atchley-Challenner, George A Alba, Radica Alicic, Natasha Altman, Khamal Anglin, Urania Argueta, Hassan Ashktorab, Gaston Baslet, Ingrid V Bassett, Lucinda Bateman, Brahmchetna Bedi, Shamik Bhattacharyya, Marie-Abele Bind, Andra L Blomkalns, Hector Bonilla, Patricia A Bush, Mario Castro, James Chan, Alexander W Charney, Peter Chen, Lori B Chibnik, Helen Y Chu, Rebecca G Clifton, Maged M Costantine, Sushma K Cribbs, Sylvia I Davila Nieves, Steven G Deeks, Alexandria Duven, Ivette F Emery, Nathan Erdmann, Kristine M Erlandson, Kacey C Ernst, Rachael Farah-Abraham, Cheryl E Farner, Elen M Feuerriegel, Judes Fleurimont, Vivian Fonseca, Nicholas Franko, Vivian Gainer, Jennifer C Gander, Edward M Gardner, Linda N Geng, Kelly S Gibson, Minjoung Go, Jason D Goldman, Halle Grebe, Frank L Greenway, Mounira Habli, John Hafner, Jenny E Han, Keith A Hanson, James Heath, Carla Hernandez, Rachel Hess, Sally L Hodder, Matthew K Hoffman, Susan E Hoover, Beatrice Huang, Brenna L Hughes, Prasanna Jagannathan, Janice John, Michael R Jordan, Stuart D Katz, Elizabeth S Kaufman, John D Kelly, Sara W Kelly, Megan M Kemp, John P Kirwan, Jonathan D Klein, Kenneth S Knox, Jerry A Krishnan, Andre Kumar, Adeyinka O Laiyemo, Allison A Lambert, Margaret Lanca, Joyce K Lee-Iannotti, Brian P Logarbo, Michele T Longo, Carlos A Luciano, Karen Lutrick, Jason H Maley, Jai G Marathe, Vincent Marconi, Gailen D Marshall, Christopher F Martin, Yuri Matusov, Alem Mehari, Hector Mendez-Figueroa, Robin Mermelstein, Torri D Metz, Richard Morse, Jarrod Mosier, Christian Mouchati, Janet Mullington, Shawn N Murphy, Robert B Neuman, Janko Z Nikolich, Ighovwerha Ofotokun, Elizabeth Ojemakinde, Anna Palatnik, Kristy Palomares, Tanyalak Parimon, Samuel Parry, Jan E Patterson, Thomas F Patterson, Rachel E Patzer, Michael J Peluso, Priscilla Pemu, Christian M Pettker, Beth A Plunkett, Kristen Pogreba-Brown, Athena Poppas, John G Quigley, Uma Reddy, Rebecca Reece, Harrison Reeder, W B Reeves, Eric M Reiman, Franz Rischard, Jonathan Rosand, Dwight J Rouse, Adam Ruff, George Saade, Grecio J Sandoval, Shannon M Schlater, Fitzgerald Shepherd, Zaki A Sherif, Hyagriv Simhan, Nora G Singer, Daniel W Skupski, Amber Sowles, Jeffrey A Sparks, Fatima I Sukhera, Barbara S Taylor, Larissa Teunis, Robert J Thomas, John M Thorp, Paul Thuluvath, Amberly Ticotsky, Alan T Tita, Katherine R Tuttle, Alfredo E Urdaneta, Daisy Valdivieso, Timothy M VanWagoner, Andrew Vasey, Monica Verduzco-Gutierrez, Zachary S Wallace, Honorine D Ward, David E Warren, Steven J Weiner, Shelley Welch, Sidney W Whiteheart, Zanthia Wiley, Juan P Wisnivesky, Lynn M Yee, Sokratis Zisis, Leora I Horwitz, Andrea S Foulkes, and RECOVER Consortium
Detection and editing of the updated Arabidopsis plastid- and mitochondrial-encoded proteomes through PeptideAtlas., Klaas J van Wijk, Stephane Bentolila, Tami Leppert, Qi Sun, Zhi Sun, Luis Mendoza, Margaret Li, and Eric W Deutsch
Does the Ubiquitination Degradation Pathway Really Reach inside of the Chloroplast? A Re-Evaluation of Mass Spectrometry-Based Assignments of Ubiquitination., Klaas J van Wijk, Tami Leppert, Zhi Sun, and Eric W Deutsch
Genetic manipulation of Patescibacteria provides mechanistic insights into microbial dark matter and the epibiotic lifestyle., Yaxi Wang, Larry A Gallagher, Pia A Andrade, Andi Liu, Ian R Humphreys, Serdar Turkarslan, Kevin J Cutler, Mario L Arrieta-Ortiz, Yaqiao Li, Matthew C Radey, Jeffrey S McLean, Qian Cong, David Baker, Nitin Baliga, S Brook Peterson, and Joseph D Mougous
Discovery of a glutathione utilization pathway in Francisella that shows functional divergence between environmental and pathogenic species., Yaxi Wang, Hannah E Ledvina, Catherine A Tower, Stanimir Kambarev, Elizabeth Liu, James C Charity, Lieselotte S M Kreuk, Qing Tang, Qiwen Chen, Larry A Gallagher, Matthew C Radey, Guilhem F Rerolle, Yaqiao Li, Kelsi M Penewit, Serdar Turkarslan, Shawn J Skerrett, Stephen J Salipante, Nitin S Baliga, Joshua J Woodward, Simon L Dove, S Brook Peterson, Jean Celli, and Joseph D Mougous
Cell population growth kinetics in the presence of stochastic heterogeneity of cell phenotype., Yue Wang, Joseph X Zhou, Edoardo Pedrini, Irit R Rubin, May Khalil, Roberto Taramelli, Hong Qian, and Sui Huang
Lifespan-extending interventions induce consistent patterns of fatty acid oxidation in mouse livers., Kengo Watanabe, Tomasz Wilmanski, Priyanka Baloni, Max Robinson, Gonzalo G Garcia, Michael R Hoopmann, Mukul K Midha, David H Baxter, Michal Maes, Seamus R Morrone, Kelly M Crebs, Charu Kapil, Ulrike Kusebauch, Jack Wiedrick, Jodi Lapidus, Lance Pflieger, Christopher Lausted, Jared C Roach, Gwênlyn Glusman, Steven R Cummings, Nicholas J Schork, Nathan D Price, Leroy Hood, Richard A Miller, Robert L Moritz, and Noa Rappaport
Multiomic signatures of body mass index identify heterogeneous health phenotypes and responses to a lifestyle intervention., Kengo Watanabe, Tomasz Wilmanski, Christian Diener, John C Earls, Anat Zimmer, Briana Lincoln, Jennifer J Hadlock, Jennifer C Lovejoy, Sean M Gibbons, Andrew T Magis, Leroy Hood, Nathan D Price, and Noa Rappaport
Engineering a tunable micropattern-array assay to sort single extracellular vesicles and particles to detect RNA and protein in situ., Jingjing Zhang, Xilal Y Rima, Xinyu Wang, Luong T H Nguyen, Kristin Huntoon, Yifan Ma, Paola Loreto Palacio, Kim Truc Nguyen, Karunya Albert, Minh-Dao Duong-Thi, Nicole Walters, Kwang Joo Kwak, Min Jin Yoon, Hong Li, Jacob Doon-Ralls, Colin L Hisey, Daeyong Lee, Yifan Wang, Jonghoon Ha, Kelsey Scherler, Shannon Fallen, Inyoul Lee, Andre F Palmer, Wen Jiang, Setty M Magaña, Kai Wang, Betty Y S Kim, L James Lee, and Eduardo Reátegui
Integrating Genetics, Transcriptomics, and Proteomics in Lung Tissue to Investigate COPD., Yu-Hang Zhang, Michael H Cho, Jarrett D Morrow, Peter J Castaldi, Craig P Hersh, Mukul K Midha, Michael R Hoopmann, Sharon M Lutz, Robert L Moritz, and Edwin K Silverman
Submissions from 2022
Abrogation of Rb Tumor Suppression Initiates GBM in Differentiated Astrocytes by Driving a Progenitor Cell Program., Amit S Adhikari, Teresa Sullivan, Rhishikesh Bargaje, Lucy Lu, T Norene O'Sullivan, Yurong Song, and Terry Van Dyke
Cytoplasmic Sensing in Innate Immunity, Ajay Suresh Akhade and Naeha Subramanian
A model for the intrinsic limit of cancer therapy: Duality of treatment-induced cell death and treatment-induced stemness., Erin Angelini, Yue Wang, Joseph X Zhou, Hong Qian, and Sui Huang
Disrupting the ArcA Regulatory Network Amplifies the Fitness Cost of Tetracycline Resistance in Escherichia coli., Mario L Arrieta-Ortiz, Min Pan, Amardeep Kaur, Evan Pepper-Tunick, Vivek Srinivas, Ananya Dash, Selva Rupa Christinal Immanuel, Aaron N Brooks, Tyson R Shepherd, and Nitin S Baliga
Multi-Omic analyses characterize the ceramide/sphingomyelin pathway as a therapeutic target in Alzheimer's disease., Priyanka Baloni, Matthias Arnold, Luna Buitrago, Kwangsik Nho, Herman Moreno, Kevin Huynh, Barbara Brauner, Gregory Louie, Alexandra Kueider-Paisley, Karsten Suhre, Andrew J Saykin, Kim Ekroos, Peter J Meikle, Leroy Hood, Nathan D Price, Alzheimer’s Disease Metabolomics Consortium, P Murali Doraiswamy, Cory C Funk, A Iván Hernández, Gabi Kastenmüller, Rebecca Baillie, Xianlin Han, and Rima Kaddurah-Daouk
Can precision medicine be personal; Can personalized medicine be precise?, Y. Michael Barilan (Ed), Margherita Brusa (Ed), Aaron Ciechanover (Ed), Leroy Hood (Contributing Author), and Nathan D Price (Contributing Author)
Systematic mutagenesis of TFIIH subunit p52/Tfb2 identifies residues required for XPB/Ssl2 subunit function and genetic interactions with TFB6., Jacob Bassett, Jenna K Rimel, Shrabani Basu, Pratik Basnet, Jie Luo, Krysta L Engel, Michael Nagel, Alexander Woyciehowsky, Christopher C Ebmeier, Craig D Kaplan, Dylan J Taatjes, and Jeffrey A Ranish
Imputing Missing Observations with Time Sliced Synthetic Minority Oversampling Technique, Andrew M Baumgartner, Sevda Molani, Qi Wei, and Jennifer J Hadlock
On the Criticality of Adaptive Boolean Network Robots., Michele Braccini, Andrea Roli, Edoardo Barbieri, and Stuart A Kauffman
MadR mediates acyl CoA-dependent regulation of mycolic acid desaturation in mycobacteria., Charlotte Cooper, Eliza Jr Peterson, Rebeca Bailo, Min Pan, Albel Singh, Patrick Moynihan, Makoto Nakaya, Nagatoshi Fujiwara, Nitin Baliga, and Apoorva Bhatt
PARK7/DJ-1 promotes pyruvate dehydrogenase activity and maintains T, Egle Danileviciute, Ni Zeng, Christophe M Capelle, Nicole Paczia, Mark A Gillespie, Henry Kurniawan, Mohaned Benzarti, Myriam P Merz, Djalil Coowar, Sabrina Fritah, Daniela Maria Vogt Weisenhorn, Gemma Gomez Giro, Melanie Grusdat, Alexandre Baron, Coralie Guerin, Davide G Franchina, Cathy Léonard, Olivia Domingues, Sylvie Delhalle, Wolfgang Wurst, Jonathan D Turner, Jens Christian Schwamborn, Johannes Meiser, Rejko Krüger, Jeff Ranish, Dirk Brenner, Carole L Linster, Rudi Balling, Markus Ollert, and Feng Q Hefeng
The ProteomeXchange consortium at 10 years: 2023 update., Eric W Deutsch, Nuno Bandeira, Yasset Perez-Riverol, Vagisha Sharma, Jeremy J Carver, Luis Mendoza, Deepti J Kundu, Shengbo Wang, Chakradhar Bandla, Selvakumar Kamatchinathan, Suresh Hewapathirana, Benjamin S Pullman, Julie Wertz, Zhi Sun, Shin Kawano, Shujiro Okuda, Yu Watanabe, Brendan MacLean, Michael J MacCoss, Yunping Zhu, Yasushi Ishihama, and Juan Antonio Vizcaíno
Genome-microbiome interplay provides insight into the determinants of the human blood metabolome., Christian Diener, Chengzhen L Dai, Tomasz Wilmanski, Priyanka Baloni, Brett Smith, Noa Rappaport, Leroy Hood, Andrew T Magis, and Sean M Gibbons
Angiotensin-Converting Enzyme (ACE) Inhibitors May Moderate COVID-19 Hyperinflammatory Response: An Observational Study with Deep Immunophenotyping., Venkata R Duvvuri, Andrew Baumgartner, Sevda Molani, Patricia V Hernandez, Dan Yuan, Ryan T Roper, Wanessa F Matos, Max Robinson, Yapeng Su, Naeha Subramanian, Jason D Goldman, James R Heath, and Jennifer J Hadlock
What Is a Digital Twin? Experimental Design for a Data-Centric Machine Learning Perspective in Health., Frank Emmert-Streib and Olli Yli-Harja
ASO Visual Abstract: Epigenetic Signatures Predict Pathologic Nodal Stage in Breast Cancer Patients with Estrogen-Receptor-Positive, Clinically Node-Positive Disease., Miquel Ensenyat-Mendez, Dennis Rünger, Javier I Orozco, Julie Le, Jennifer L Baker, Joanne Weidhaas, Diego M Marzese, and Maggie L DiNome
Progress toward a universal biomedical data translator., Karamarie Fecho, Anne E Thessen, Sergio E Baranzini, Chris Bizon, Jennifer J Hadlock, Sui Huang, Ryan Roper, Noel Southall, Casey Ta, Paul B Watkins, Mark D Williams, Hao Xu, William Byrd, Vlado Dančík, Marc P Duby, Michel Dumontier, Gustavo Glusman, Nomi L Harris, Eugene W Hinderer, Greg Hyde, Adam Johs, Andrew I Su, Guangrong Qin, and Qian Zhu
Roadmap on plasticity and epigenetics in cancer., Jasmine Foo, David Basanta, Russell C Rockne, Carly Strelez, Curran Shah, Kimya Ghaffarian, Shannon M Mumenthaler, Kelly Mitchell, Justin D Lathia, David Frankhouser, Sergio Branciamore, Ya-Huei Kuo, Guido Marcucci, Robert Vander Velde, Andriy Marusyk, Sui Huang, Kishore Hari, Mohit Kumar Jolly, Haralampos Hatzikirou, Kamrine Poels, Mary Spilker, Blerta Shtylla, Mark Robertson-Tessi, and Alexander R A Anderson
Non-viral precision T cell receptor replacement for personalized cell therapy., Susan P Foy, Kyle Jacoby, Daniela A Bota, Theresa Hunter, Zheng Pan, Eric Stawiski, Yan Ma, William Lu, Songming Peng, Clifford L Wang, Benjamin Yuen, Olivier Dalmas, Katharine Heeringa, Barbara Sennino, Andy Conroy, Michael T Bethune, Ines Mende, William White, Monica Kukreja, Swetha Gunturu, Emily Humphrey, Adeel Hussaini, Duo An, Adam J Litterman, Boi Bryant Quach, Alphonsus H C Ng, Yue Lu, Chad Smith, Katie M Campbell, Daniel Anaya, Lindsey Skrdlant, Eva Yi-Hsuan Huang, Ventura Mendoza, Jyoti Mathur, Luke Dengler, Bhamini Purandare, Robert Moot, Michael C Yi, Roel Funke, Alison Sibley, Todd Stallings-Schmitt, David Y Oh, Bartosz Chmielowski, Mehrdad Abedi, Yuan Yuan, Jeffrey A Sosman, Sylvia M Lee, Adam J Schoenfeld, David Baltimore, James R Heath, Alex Franzusoff, Antoni Ribas, Arati V Rao, and Stefanie J Mandl
Label-free plasma proteomics for the identification of the putative biomarkers of oral squamous cell carcinoma., Shashyendra Singh Gautam, Raghwendra Pratap Singh, Kajal Karsauliya, Ashish Kumar Sonker, Panga Jaipal Reddy, Divya Mehrotra, Sameer Gupta, Sudhir Singh, Rashmi Kumar, and Sheelendra Pratap Singh
Perspective: Leveraging the Gut Microbiota to Predict Personalized Responses to Dietary, Prebiotic, and Probiotic Interventions., Sean M Gibbons, Thomas Gurry, Johanna W Lampe, Anirikh Chakrabarti, Veerle Dam, Amandine Everard, Almudena Goas, Gross Gabriele, Michiel Kleerebez, Jonathan Lane, Johanna Maukonen, Ana Lucia Barretto Penna, Bruno Pot, Ana M Valdes, Gemma Walton, Adrienne Weiss, Yoghatama Cindya Zanzer, Naomi V Venlet, and Michela Miani
Distribution of 54 polygenic risk scores for common diseases in long lived individuals and their offspring., Sophia Gunn, Michael Wainberg, Zeyuan Song, Stacy Andersen, Robert Boudreau, Mary F Feitosa, Qihua Tan, May E Montasser, Jeffrey R O'Connell, Nathan Stitziel, Nathan D Price, Thomas Perls, Nicholas J Schork, and Paola Sebastiani
Rare variants implicate NMDA receptor signaling and cerebellar gene networks in risk for bipolar disorder., Naushaba Hasin, Lace M Riggs, Tatyana Shekhtman, Justin Ashworth, Robert Lease, Rediet T Oshone, Elizabeth M Humphries, Judith A Badner, Pippa A Thomson, David C Glahn, David W Craig, Howard J Edenberg, Elliot S Gershon, Francis J McMahon, John I Nurnberger, Peter P Zandi, John R Kelsoe, Jared C Roach, Todd D Gould, and Seth A Ament
P4 Medicine & What 21st Century Medicine Should Be, Leroy Hood
Autocatalytic Sets Arising in a Combinatorial Model of Chemical Evolution., Wim Hordijk, Mike Steel, and Stuart Kauffman
From telomere to telomere: The transcriptional and epigenetic state of human repeat elements., Savannah J Hoyt, Jessica Storer, Gabrielle A Hartley, Patrick G S Grady, Ariel Gershman, Leonardo G de Lima, Charles Limouse, Reza Halabian, Luke Wojenski, Matias Rodriguez, Nicolas Altemose, Arang Rhie, Leighton J Core, Jennifer L Gerton, Wojciech Makalowski, Daniel Olson, Jeb Rosen, Arian F A Smit, Aaron F Straight, Mitchell R Vollger, Travis J Wheeler, Michael C Schatz, Evan E Eichler, Adam M Phillippy, Winston Timp, Karen H Miga, and Rachel J O'Neill
A Wipe-Based Stool Collection and Preservation Kit for Microbiome Community Profiling., Hui Hua, Cem Meydan, Evan E Afshin, Loukia N Lili, Christopher R D'Adamo, Nate Rickard, Joel T Dudley, Nathan D Price, Bodi Zhang, and Christopher E Mason
Towards a unification of the 2 meanings of "epigenetics"., Sui Huang
Accuracy of multiple sequence alignment methods in the reconstruction of transposable element families., Robert Hubley, Travis J Wheeler, and Arian F A Smit
Deletion of Abi3/Gngt2 influences age-progressive amyloid β and tau pathologies in distinctive ways., Kristen R Ibanez, Karen N McFarland, Jennifer Phillips, Mariet Allen, Christian B Lessard, Lillian Zobel, Elsa Gonzalez De La Cruz, Shivani Shah, Quan Vo, Xue Wang, Zachary Quicksall, Daniel Ryu, Cory C Funk, Nilüfer Ertekin-Taner, Stefan Prokop, Todd E Golde, and Paramita Chakrabarty
Protein Catalyzed Capture (PCC) Agents for Antigen Targeting., Matthew N Idso, Bert T Lai, Heather D Agnew, and James R Heath
Is DIA proteomics data FAIR? Current data sharing practices, available bioinformatics infrastructure and recommendations for the future., Andrew R Jones, Eric W Deutsch, and Juan Antonio Vizcaíno
Profiling the Human Phosphoproteome to Estimate the True Extent of Protein Phosphorylation., Anton Kalyuzhnyy, Patrick A Eyers, Claire E Eyers, Emily Bowler-Barnett, Maria J Martin, Zhi Sun, Eric W Deutsch, and Andrew R Jones
Programmed cell death detection methods: a systematic review and a categorical comparison., Sana Kari, Kumar Subramanian, Ilenia Agata Altomonte, Akshaya Murugesan, Olli Yli-Harja, and Meenakshisundaram Kandhavelu
A Testable Theory for the Emergence of the Classical World., Stuart Kauffman and Sudip Patra
Proteomics Standards Initiative's ProForma 2.0: Unifying the Encoding of Proteoforms and Peptidoforms., Richard D LeDuc, Eric W Deutsch, Pierre-Alain Binz, Ryan T Fellers, Anthony J Cesnik, Joshua A Klein, Tim Van Den Bossche, Ralf Gabriels, Arshika Yalavarthi, Yasset Perez-Riverol, Jeremy Carver, Wout Bittremieux, Shin Kawano, Benjamin Pullman, Nuno Bandeira, Neil L Kelleher, Paul M Thomas, and Juan Antonio Vizcaíno
Recent Advances in RNA Therapy and Its Carriers to Treat the Single-Gene Neurological Disorders., Ming-Jen Lee, Inyoul Lee, and Kai Wang
Decompression only versus fusion in octogenarians with spinal epidural abscesses: early complications, clinical and radiological outcome with 2-year follow-up., Pavlina Lenga, Gelo Gülec, Awais Akbar Bajwa, Mohammed Issa, Rod J Oskouian, Jens R Chapman, Karl Kiening, Andreas W Unterberg, and Basem Ishak
KIR + CD8 + T cells suppress pathogenic T cells and are active in autoimmune diseases and COVID-19, Jing Li, Maxim Zaslavsky, Yapeng Su, Jing Guo, Michael J Sikora, Vincent van Unen, Asbjørn Christophersen, Shin-Heng Chiou, Liang Chen, Jiefu Li, Xuhuai Ji, Julie Wilhelmy, Alana M McSween, Brad A Palanski, Venkata Vamsee Aditya Mallajosyula, Nathan A Bracey, Gopal Krishna R Dhondalay, Kartik Bhamidipati, Joy Pai, Lucas B Kipp, Jeffrey E Dunn, Stephen L Hauser, Jorge R Oksenberg, Ansuman T Satpathy, William H Robinson, Cornelia L Dekker, Lars M Steinmetz, Chaitan Khosla, Paul J Utz, Ludvig M Sollid, Yueh-Hsiu Chien, James R Heath, Nielsen Q Fernandez-Becker, Kari C Nadeau, Naresha Saligrama, and Mark M Davis
Addendum: Transcriptomics and proteomics reveal two waves of translational repression during the maturation of malaria parasite sporozoites., Scott E Lindner, Kristian E Swearingen, Melanie J Shears, Aswathy Sebastian, Michael P Walker, Erin N Vrana, Kevin J Hart, Allen M Minns, Istvan Albert, Photini Sinnis, Robert L Moritz, and Stefan H I Kappe
Author Correction: Comparative and demographic analysis of orang-utan genomes., Devin P Locke, LaDeana W Hillier, Wesley C Warren, Kim C Worley, Lynne V Nazareth, Donna M Muzny, Shiaw-Pyng Yang, Zhengyuan Wang, Asif T Chinwalla, Pat Minx, Makedonka Mitreva, Lisa Cook, Kim D Delehaunty, Catrina Fronick, Heather Schmidt, Lucinda A Fulton, Robert S Fulton, Joanne O Nelson, Vincent Magrini, Craig Pohl, Tina A Graves, Chris Markovic, Andy Cree, Huyen H Dinh, Jennifer Hume, Christie L Kovar, Gerald R Fowler, Gerton Lunter, Stephen Meader, Andreas Heger, Chris P Ponting, Tomas Marques-Bonet, Can Alkan, Lin Chen, Ze Cheng, Jeffrey M Kidd, Evan E Eichler, Simon White, Stephen Searle, Albert J Vilella, Yuan Chen, Paul Flicek, Jian Ma, Brian Raney, Bernard Suh, Richard Burhans, Javier Herrero, David Haussler, Rui Faria, Olga Fernando, Fleur Darré, Domènec Farré, Elodie Gazave, Meritxell Oliva, Arcadi Navarro, Roberta Roberto, Oronzo Capozzi, Nicoletta Archidiacono, Giuliano Della Valle, Stefania Purgato, Mariano Rocchi, Miriam K Konkel, Jerilyn A Walker, Brygg Ullmer, Mark A Batzer, Arian F A Smit, Robert Hubley, Claudio Casola, Daniel R Schrider, Matthew W Hahn, Victor Quesada, Xose S Puente, Gonzalo R Ordoñez, Carlos López-Otín, Tomas Vinar, Brona Brejova, Aakrosh Ratan, Robert S Harris, Webb Miller, Carolin Kosiol, Heather A Lawson, Vikas Taliwal, André L Martins, Adam Siepel, Arindam RoyChoudhury, Xin Ma, Jeremiah Degenhardt, Carlos D Bustamante, Ryan N Gutenkunst, Thomas Mailund, Julien Y Dutheil, Asger Hobolth, Mikkel H Schierup, Oliver A Ryder, Yuko Yoshinaga, Pieter J de Jong, George M Weinstock, Jeffrey Rogers, Elaine R Mardis, Richard A Gibbs, and Richard K Wilson
A Comprehensive Evaluation of Consensus Spectrum Generation Methods in Proteomics., Xiyang Luo, Wout Bittremieux, Johannes Griss, Eric W Deutsch, Timo Sachsenberg, Lev I Levitsky, Mark V Ivanov, Julia A Bubis, Ralf Gabriels, Henry Webel, Aniel Sanchez, Mingze Bai, Lukas Käll, and Yasset Perez-Riverol
The risk of COVID-19 death is much greater and age dependent with type I IFN autoantibodies., Jérémy Manry, Paul Bastard, Adrian Gervais, Tom Le Voyer, Jérémie Rosain, Quentin Philippot, 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, Jesús 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 Mégarbane, 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 M Biggs, Marcela Moncada-Vélez, Andrés Augusto Arias, Lazaro Lorenzo, Soraya Boucherit, Dany Anglicheau, Anna M Planas, Filomeen Haerynck, Sotirija Duvlis, 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, Fatemeh Saheb Sharif-Askari, Karim Dorgham, Jérôme Sallette, Souad Mehlal Sedkaoui, Suzan AlKhater, Raúl Rigo-Bonnin, Francisco Morandeira, Lucie Roussel, Donald C Vinh, Christian Erikstrup, Antonio Condino-Neto, Carolina Prando, Anastasiia Bondarenko, András N Spaan, Laurent Gilardin, Jacques Fellay, Stanislas Lyonnet, Kaya Bilguvar, Richard P Lifton, Shrikant Mane, Mark S Anderson, Bertrand Boisson, Vivien Béziat, Shen-Ying Zhang, Evangelos Andreakos, Olivier Hermine, Aurora Pujol, Pärt Peterson, Trine H Mogensen, Lee Rowen, James Mond, Stéphanie Debette, Xavier de Lamballerie, Charles Burdet, Lila Bouadma, 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, Jean-Laurent Casanova, Laurent Abel, and Aurélie Cobat
Physical and in silico immunopeptidomic profiling of a cancer antigen prostatic acid phosphatase reveals targets enabling TCR isolation., Zhiyuan Mao, Pavlo A Nesterenko, Jami McLaughlin, Weixian Deng, Giselle Burton Sojo, Donghui Cheng, Miyako Noguchi, William Chour, Diana C DeLucia, Kathryn A Finton, Yu Qin, Matthew B Obusan, Wendy Tran, Liang Wang, Nathanael J Bangayan, Lisa Ta, Chia-Chun Chen, Christopher S Seet, Gay M Crooks, John W Phillips, James R Heath, Roland K Strong, John K Lee, James A Wohlschlegel, and Owen N Witte
Engineered SH2 Domains for Targeted Phosphoproteomics., Gregory D Martyn, Gianluca Veggiani, Ulrike Kusebauch, Seamus R Morrone, Bradley P Yates, Alex U Singer, Jiefei Tong, Noah Manczyk, Gerald Gish, Zhi Sun, Igor Kurinov, Frank Sicheri, Michael F Moran, Robert L Moritz, and Sachdev S Sidhu
More Thumbs Than Rules: Is Rationality an Exaptation?, Antonio Mastrogiorgio, Teppo Felin, Stuart Kauffman, and Mariano Mastrogiorgio
Phase 2 of extracellular RNA communication consortium charts next-generation approaches for extracellular RNA research., Bogdan Mateescu, Jennifer C Jones, Roger P Alexander, Eric Alsop, Ji Yeong An, Mohammad Asghari, Alex Boomgarden, Laura Bouchareychas, Alfonso Cayota, Hsueh-Chia Chang, Al Charest, Daniel T Chiu, Robert J Coffey, Saumya Das, Peter De Hoff, Andrew deMello, Crislyn D'Souza-Schorey, David Elashoff, Kiarash R Eliato, Jeffrey L Franklin, David J Galas, Mark B Gerstein, Ionita H Ghiran, David B Go, Stephen Gould, Tristan R Grogan, James N Higginbotham, Florian Hladik, Tony Jun Huang, Xiaoye Huo, Elizabeth Hutchins, Dennis K Jeppesen, Tijana Jovanovic-Talisman, Betty Y S Kim, Sung Kim, Kyoung-Mee Kim, Yong Kim, Robert R Kitchen, Vaughan Knouse, Emily L LaPlante, Carlito B Lebrilla, L James Lee, Kathleen M Lennon, Guoping Li, Feng Li, Tieyi Li, Tao Liu, Zirui Liu, Adam L Maddox, Kyle McCarthy, Bessie Meechoovet, Nalin Maniya, Yingchao Meng, Aleksandar Milosavljevic, Byoung-Hoon Min, Amber Morey, Martin Ng, John Nolan, Getulio P De Oliveira Junior, Michael E Paulaitis, Tuan Anh Phu, Robert L Raffai, Eduardo Reátegui, Matthew E Roth, David A Routenberg, Joel Rozowsky, Joseph Rufo, Satyajyoti Senapati, Sigal Shachar, Himani Sharma, Anil K Sood, Stavros Stavrakis, Alessandra Stürchler, Muneesh Tewari, Juan P Tosar, Alexander K Tucker-Schwartz, Andrey Turchinovich, Nedyalka Valkov, Kendall Van Keuren-Jensen, Kasey C Vickers, Lucia Vojtech, Wyatt N Vreeland, Ceming Wang, Kai Wang, ZeYu Wang, Joshua A Welsh, Kenneth W Witwer, David T W Wong, Jianping Xia, Ya-Hong Xie, Kaichun Yang, Mikołaj P Zaborowski, Chenguang Zhang, Qin Zhang, Angela M Zivkovic, and Louise C Laurent
Comparative genomic analysis of vertebrate mitochondrial reveals a differential of rearrangements rate between taxonomic class., Paula Montaña-Lozano, Manuela Moreno-Carmona, Mauricio Ochoa-Capera, Natalia S Medina, Jeffrey L Boore, and Carlos F Prada
Synthetic lethal kinases in Ras/p53 mutant squamous cell carcinoma., Russell Moser, Kay E Gurley, Olga Nikolova, Guangrong Qin, Rashmi Joshi, Eduardo Mendez, Ilya Shmulevich, Amanda Ashley, Carla Grandori, and Christopher J Kemp
Standardized annotation of translated open reading frames., Jonathan M Mudge, Jorge Ruiz-Orera, John R Prensner, Marie A Brunet, Ferriol Calvet, Irwin Jungreis, Jose Manuel Gonzalez, Michele Magrane, Thomas F Martinez, Jana Felicitas Schulz, Yucheng T Yang, M Mar Albà, Julie L Aspden, Pavel V Baranov, Ariel A Bazzini, Elspeth Bruford, Maria Jesus Martin, Lorenzo Calviello, Anne-Ruxandra Carvunis, Jin Chen, Juan Pablo Couso, Eric W Deutsch, Paul Flicek, Adam Frankish, Mark Gerstein, Norbert Hubner, Nicholas T Ingolia, Manolis Kellis, Gerben Menschaert, Robert L Moritz, Uwe Ohler, Xavier Roucou, Alan Saghatelian, Jonathan S Weissman, and Sebastiaan van Heesch
Constraint-Based Reconstruction and Analyses of Metabolic Models: Open-Source Python Tools and Applications to Cancer., Rachel H Ng, Jihoon W Lee, Priyanka Baloni, Christian Diener, James R Heath, and Yapeng Su
GPR17 Signaling Activation by CHBC Agonist Induced Cell Death via Modulation of MAPK Pathway in Glioblastoma., Phung Nguyen, Phuong Doan, Akshaya Murugesan, Thiyagarajan Ramesh, Tatu Rimpilainen, Nuno R Candeias, Olli Yli-Harja, and Meenakshisundaram Kandhavelu
Organ-Based Proteome and Post-Translational Modification Profiling of a Widely Cultivated Tropical Water Fish, Labeo rohita, Mehar Un Nissa, Nevil Pinto, Arijit Mukherjee, Panga Jaipal Reddy, Biplab Ghosh, Zhi Sun, Saicharan Ghantasala, Chetanya Chetanya, Sanjyot Vinayak Shenoy, Robert L Moritz, Mukunda Goswami, and Sanjeeva Srivastava
The PeptideAtlas of a widely cultivated fish Labeo rohita: A resource for the Aquaculture Community., Mehar Un Nissa, Panga Jaipal Reddy, Nevil Pinto, Zhi Sun, Biplab Ghosh, Robert L Moritz, Mukunda Goswami, and Sanjeeva Srivastava
The complete sequence of a human genome., Sergey Nurk, Sergey Koren, Arang Rhie, Mikko Rautiainen, Andrey V Bzikadze, Alla Mikheenko, Mitchell R Vollger, Nicolas Altemose, Lev Uralsky, Ariel Gershman, Sergey Aganezov, Savannah J Hoyt, Mark Diekhans, Glennis A Logsdon, Michael Alonge, Stylianos E Antonarakis, Matthew Borchers, Gerard G Bouffard, Shelise Y Brooks, Gina V Caldas, Nae-Chyun Chen, Haoyu Cheng, Chen-Shan Chin, William Chow, Leonardo G de Lima, Philip C Dishuck, Richard Durbin, Tatiana Dvorkina, Ian T Fiddes, Giulio Formenti, Robert S Fulton, Arkarachai Fungtammasan, Erik Garrison, Patrick G S Grady, Tina A Graves-Lindsay, Ira M Hall, Nancy F Hansen, Gabrielle A Hartley, Marina Haukness, Kerstin Howe, Michael W Hunkapiller, Chirag Jain, Miten Jain, Erich D Jarvis, Peter Kerpedjiev, Melanie Kirsche, Mikhail Kolmogorov, Jonas Korlach, Milinn Kremitzki, Heng Li, Valerie V Maduro, Tobias Marschall, Ann M McCartney, Jennifer McDaniel, Danny E Miller, James C Mullikin, Eugene W Myers, Nathan D Olson, Benedict Paten, Paul Peluso, Pavel A Pevzner, David Porubsky, Tamara Potapova, Evgeny I Rogaev, Jeffrey A Rosenfeld, Steven L Salzberg, Valerie A Schneider, Fritz J Sedlazeck, Kishwar Shafin, Colin J Shew, Alaina Shumate, Ying Sims, Arian F A Smit, Daniela C Soto, Ivan Sović, Jessica Storer, Aaron Streets, Beth A Sullivan, Françoise Thibaud-Nissen, James Torrance, Justin Wagner, Brian P Walenz, Aaron Wenger, Jonathan M D Wood, Chunlin Xiao, Stephanie M Yan, Alice C Young, Samantha Zarate, Urvashi Surti, Rajiv C McCoy, Megan Y Dennis, Ivan A Alexandrov, Jennifer L Gerton, Rachel J O'Neill, Winston Timp, Justin M Zook, Michael C Schatz, Evan E Eichler, Karen H Miga, and Adam M Phillippy
The 2022 Report on the Human Proteome from the HUPO Human Proteome Project., Gilbert S Omenn, Lydie Lane, Christopher M Overall, Charles Pineau, Nicolle H Packer, Ileana M Cristea, Cecilia Lindskog, Susan T Weintraub, Sandra Orchard, Michael H A Roehrl, Edouard Nice, Siqi Liu, Nuno Bandeira, Yu-Ju Chen, Tiannan Guo, Ruedi Aebersold, Robert L Moritz, and Eric W Deutsch
Personal Dense Dynamic Data Clouds Connect Systems Biomedicine to Scientific Wellness., Gilbert S Omenn, Andrew T Magis, Nathan D Price, and Leroy Hood
ToPP: Tumor online prognostic analysis platform for prognostic feature selection and clinical patient subgroup selection., Jian Ouyang, Guangrong Qin, Zhenhao Liu, Xingxing Jian, Tieliu Shi, and Lu Xie
A single-cell based precision medicine approach using glioblastoma patient-specific models., James H Park, Abdullah H Feroze, Samuel N Emerson, Anca B Mihalas, C Dirk Keene, Patrick J Cimino, Adrian Lopez Garcia de Lomana, Kavya Kannan, Wei-Ju Wu, Serdar Turkarslan, Nitin S Baliga, and Anoop P Patel
