Submissions from 2023
Publisher Correction: The DNA sequence and analysis of human chromosome 14., Roland Heilig, Ralph Eckenberg, Jean-Louis Petit, Núria Fonknechten, Corinne Da Silva, Laurence Cattolico, Michaël Levy, Valérie Barbe, Véronique de Berardinis, Abel Ureta-Vidal, Eric Pelletier, Virginie Vico, Véronique Anthouard, Lee Rowen, Anup Madan, Shizhen Qin, Hui Sun, Hui Du, Kymberlie Pepin, François Artiguenave, Catherine Robert, Corinne Cruaud, Thomas Brüls, Olivier Jaillon, Lucie Friedlander, Gaelle Samson, Philippe Brottier, Susan Cure, Béatrice Ségurens, Franck Anière, Sylvie Samain, Hervé Crespeau, Nissa Abbasi, Nathalie Aiach, Didier Boscus, Rachel Dickhoff, Monica Dors, Ivan Dubois, Cynthia Friedman, Michel Gouyvenoux, Rose James, Anuradha Madan, Barbara Mairey-Estrada, Sophie Mangenot, Nathalie Martins, Manuela Ménard, Sophie Oztas, Amber Ratcliffe, Tristan Shaffer, Barbara Trask, Benoit Vacherie, Chadia Bellemere, Caroline Belser, Marielle Besnard-Gonnet, Delphine Bartol-Mavel, Magali Boutard, Stéphanie Briez-Silla, Stephane Combette, Virginie Dufossé-Laurent, Carolyne Ferron, Christophe Lechaplais, Claudine Louesse, Delphine Muselet, Ghislaine Magdelenat, Emilie Pateau, Emmanuelle Petit, Peggy Sirvain-Trukniewicz, Arnaud Trybou, Nathalie Vega-Czarny, Elodie Bataille, Elodie Bluet, Isabelle Bordelais, Maria Dubois, Corinne Dumont, Thomas Guérin, Sébastien Haffray, Rachid Hammadi, Jacqueline Muanga, Virginie Pellouin, Dominique Robert, Edith Wunderle, Gilbert Gauguet, Alice Roy, Laurent Sainte-Marthe, Jean Verdier, Claude Verdier-Discala, LaDeana Hillier, Lucinda Fulton, John McPherson, Fumihiko Matsuda, Richard Wilson, Claude Scarpelli, Gábor Gyapay, Patrick Wincker, William Saurin, Francis Quétier, Robert Waterston, Leroy Hood, and Jean Weissenbach
Serum miRNA profiles are altered in patients with primary sclerosing cholangitis receiving high-dose ursodeoxycholic acid., Jessica T Hochberg, Aalam Sohal, Priya Handa, Bryan D Maliken, Take-Kyun Kim, Kai Wang, Eric Gochanour, Yu Li, J Bart Rose, James E Nelson, Keith D Lindor, Nicholas F LaRusso, and Kris V Kowdley
Improved Analysis of Cross-Linking Mass Spectrometry Data with Kojak 2.0, Advanced by Integration into the Trans-Proteomic Pipeline., Michael R Hoopmann, David D Shteynberg, Alex Zelter, Michael Riffle, Andrew S Lyon, David A Agard, Qing Luan, Brad J Nolen, Michael J MacCoss, Trisha N Davis, and Robert L Moritz
Researching COVID to Enhance Recovery (RECOVER) adult study protocol: Rationale, objectives, and design., Leora I Horwitz, Tanayott Thaweethai, Shari B Brosnahan, Mine S Cicek, Megan L Fitzgerald, Jason D Goldman, Rachel Hess, S L Hodder, Vanessa L Jacoby, Michael R Jordan, Jerry A Krishnan, Adeyinka O Laiyemo, Torri D Metz, Lauren Nichols, Rachel E Patzer, Anisha Sekar, Nora G Singer, Lauren E Stiles, Barbara S Taylor, Shifa Ahmed, Heather A Algren, Khamal Anglin, Lisa Aponte-Soto, Hassan Ashktorab, Ingrid V Bassett, Brahmchetna Bedi, Nahid Bhadelia, Christian Bime, Marie-Abele C Bind, Lora J Black, Andra L Blomkalns, Hassan Brim, Mario Castro, James Chan, Alexander W Charney, Benjamin K Chen, Li Qing Chen, Peter Chen, David Chestek, Lori B Chibnik, Dominic C Chow, Helen Y Chu, Rebecca G Clifton, Shelby Collins, Maged M Costantine, Sushma K Cribbs, Steven G Deeks, John D Dickinson, Sarah E Donohue, Matthew S Durstenfeld, Ivette F Emery, Kristine M Erlandson, Julio C Facelli, Rachael Farah-Abraham, Aloke V Finn, Melinda S Fischer, Valerie J Flaherman, Judes Fleurimont, Vivian Fonseca, Emily J Gallagher, Jennifer C Gander, Maria Laura Gennaro, Kelly S Gibson, Minjoung Go, Steven N Goodman, Joey P Granger, Frank L Greenway, John W Hafner, Jenny E Han, Michelle S Harkins, Kristine S P Hauser, James R Heath, Carla R Hernandez, On Ho, Matthew K Hoffman, Susan E Hoover, Carol R Horowitz, Harvey Hsu, Priscilla Y Hsue, Brenna L Hughes, Prasanna Jagannathan, Judith A James, Janice John, Sarah Jolley, S E Judd, Joy J Juskowich, Diane G Kanjilal, Elizabeth W Karlson, Stuart D Katz, J Daniel Kelly, Sara W Kelly, Arthur Y Kim, John P Kirwan, Kenneth S Knox, Andre Kumar, Michelle F Lamendola-Essel, Margaret Lanca, Joyce K Lee-Lannotti, R Craig Lefebvre, Bruce D Levy, Janet Y Lin, Brian P Logarbo, Jennifer K Logue, Michele T Longo, Carlos A Luciano, Karen Lutrick, Shahdi K Malakooti, Gail Mallett, Gabrielle Maranga, Jai G Marathe, Vincent C Marconi, Gailen D Marshall, Christopher F Martin, Jeffrey N Martin, Heidi T May, Grace A McComsey, Dylan McDonald, Hector Mendez-Figueroa, Lucio Miele, Murray A Mittleman, Sindhu Mohandas, Christian Mouchati, Janet M Mullington, Girish N Nadkarni, Erica R Nahin, Robert B Neuman, Lisa T Newman, Amber Nguyen, Janko Z Nikolich, Igho Ofotokun, Princess U Ogbogu, Anna Palatnik, Kristy T S Palomares, Tanyalak Parimon, Samuel Parry, Sairam Parthasarathy, Thomas F Patterson, Ann Pearman, Michael J Peluso, Priscilla Pemu, Christian M Pettker, Beth A Plunkett, Kristen Pogreba-Brown, Athena Poppas, J Zachary Porterfield, John G Quigley, Davin K Quinn, Hengameh Raissy, Candida J Rebello, Uma M Reddy, Rebecca Reece, Harrison T Reeder, Franz P Rischard, Johana M Rosas, Clifford J Rosen, Nadine G Rouphael, Dwight J Rouse, Adam M Ruff, Christina Saint Jean, Grecio J Sandoval, Jorge L Santana, Shannon M Schlater, Frank C Sciurba, Caitlin Selvaggi, Sudha Seshadri, Howard D Sesso, Dimpy P Shah, Eyal Shemesh, Zaki A Sherif, Daniel J Shinnick, Hyagriv N Simhan, Upinder Singh, Amber Sowles, Vignesh Subbian, Jun Sun, Mehul S Suthar, Larissa J Teunis, John M Thorp, Amberly Ticotsky, Alan T N Tita, Robin Tragus, Katherine R Tuttle, Alfredo E Urdaneta, P J Utz, Timothy M VanWagoner, Andrew Vasey, Suzanne D Vernon, Crystal Vidal, Tiffany Walker, Honorine D Ward, David E Warren, Ryan M Weeks, Steven J Weiner, Jordan C Weyer, Jennifer L Wheeler, Sidney W Whiteheart, Zanthia Wiley, Natasha J Williams, Juan P Wisnivesky, John C Wood, Lynn M Yee, Natalie M Young, Sokratis N Zisis, and Andrea S Foulkes
Timing of selective serotonin reuptake inhibitor use and risk for preterm birth and related adverse events, Yeon Mi Huang, Ryan Roper, Samantha N. Piekos, Daniel A. Enquobahrie, Mary F. Herbert, Alison G. Paquette, Priyanka Baloni, Nathan D Price, Leroy Hood, and Jennifer J Hadlock
Organotypic Models for Functional Drug Testing of Human Cancers, Yu Ling Huang, Lindsay K. Dickerson, Heidi Kenerson, Xiuyun Jiang, Venu Pillarisetty, Qiang Tian, Leroy Hood, Taranjit S. Gujral, and Raymond S. Yeung
Addressing barriers in FAIR data practices for biomedical data., Laura D Hughes, Ginger Tsueng, Jack DiGiovanna, Thomas D Horvath, Luke V Rasmussen, Tor C Savidge, Thomas Stoeger, Serdar Turkarslan, Qinglong Wu, Chunlei Wu, Andrew I Su, Lars Pache, and NIAID Systems Biology Data Dissemination Working Group
Adoption of a National Prophylactic Anticoagulation Guideline for Hospitalized Pregnant Women with COVID-19: Retrospective Cohort Study., Yeon-Mi Hwang, Samantha Piekos, Tanya Sorensen, Leroy Hood, and Jennifer Hadlock
The Association of Biomolecular Resource Facilities Proteome Informatics Research Group Study on Metaproteomics (iPRG-2020)., Pratik D Jagtap, Michael R Hoopmann, Benjamin A Neely, Antony Harvey, Lukas Käll, Yasset Perez-Riverol, Milky K Abajorga, Julie A Thomas, Susan T Weintraub, and Magnus Palmblad
Plasmodium GPI-anchored micronemal antigen is essential for parasite transmission through the mosquito host., Charlie Jennison, Janna M Armstrong, Dorender A Dankwa, Nina Hertoghs, Sudhir Kumar, Biley A Abatiyow, Myo Naung, Nana K Minkah, Kristian E Swearingen, Robert Moritz, Alyssa E Barry, Stefan H I Kappe, and Ashley M Vaughan
Comprehensive Overview of Bottom-Up Proteomics using Mass Spectrometry., Yuming Jiang, Devasahayam Arokia Balaya Rex, Dina Schuster, Benjamin A Neely, Germán L Rosano, Norbert Volkmar, Amanda Momenzadeh, Trenton M Peters-Clarke, Susan B Egbert, Simion Kreimer, Emma H Doud, Oliver M Crook, Amit Kumar Yadav, Muralidharan Vanuopadath, Martín L Mayta, Anna G Duboff, Nicholas M Riley, Robert L Moritz, and Jesse G Meyer
Generally-healthy individuals with aberrant bowel movement frequencies show enrichment for microbially-derived blood metabolites associated with impaired kidney function., James P Johnson, Christian Diener, Anne E Levine, Tomasz Wilmanski, David L Suskind, Alexandra Ralevski, Jennifer J Hadlock, Andrew T Magis, Leroy Hood, Noa Rappaport, and Sean M Gibbons
Mixed anhydrides at the intersection between peptide and RNA autocatalytic sets: evolution of biological coding., S A Kauffman and N Lehman
A third transition in science?, Stuart A Kauffman and Andrea Roli
The Crux Toolkit for Analysis of Bottom-Up Tandem Mass Spectrometry Proteomics Data., Attila Kertesz-Farkas, Frank Lawrence Nii Adoquaye Acquaye, Kishankumar Bhimani, Jimmy K Eng, William E Fondrie, Charles Grant, Michael R Hoopmann, Andy Lin, Yang Y Lu, Robert L Moritz, Michael J MacCoss, and William Stafford Noble
2019 Association of Biomolecular Resource Facilities Multi-Laboratory Data-Independent Acquisition Proteomics Study., Joanna Kirkpatrick, Paul M Stemmer, Brian C Searle, Laura E Herring, LeRoy Martin, Mukul K Midha, Brett S Phinney, Baozhen Shan, Magnus Palmblad, Yan Wang, Pratik D Jagtap, and Benjamin A Neely
Structural analysis of human G-protein-coupled receptor 17 ligand binding sites., Saravanan Konda Mani, Ramesh Thiyagarajan, Olli Yli-Harja, Meenakshisundaram Kandhavelu, and Akshaya Murugesan
A comprehensive spectral assay library to quantify the Halobacterium salinarum NRC-1 proteome by DIA/SWATH-MS., Ulrike Kusebauch, Alan P R Lorenzetti, David S Campbell, Min Pan, David Shteynberg, Charu Kapil, Mukul K Midha, Adrián López García de Lomana, Nitin Baliga, and Robert L Moritz
Apposition of Fibroblasts With Metaplastic Gastric Cells Promotes Dysplastic Transition., Su-Hyung Lee, Ela W Contreras Panta, David Gibbs, Yoonkyung Won, Jimin Min, Changqing Zhang, Joseph T Roland, Se-Hoon Hong, Yoojin Sohn, Evan Krystofiak, Bogun Jang, Lorenzo Ferri, Veena Sangwan, Jiannis Ragoussis, Sophie Camilleri-Broët, Joseph Caruso, Chira Chen-Tanyolac, Michael Strasser, Philippe Gascard, Thea D Tlsty, Sui Huang, Eunyoung Choi, and James R Goldenring
Growth phase estimation for abundant bacterial populations sampled longitudinally from human stool metagenomes., Joe J Lim, Christian Diener, James Wilson, Jacob J Valenzuela, Nitin S Baliga, and Sean M Gibbons
A Genome-Scale Atlas Reveals Complex Interplay of Transcription and Translation in an Archaeon., Alan P R Lorenzetti, Ulrike Kusebauch, Lívia S Zaramela, Wei-Ju Wu, João P P de Almeida, Serdar Turkarslan, Adrián L G de Lomana, José V Gomes-Filho, Ricardo Z N Vêncio, Robert L Moritz, Tie Koide, and Nitin S Baliga
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
