Submissions from 2022
Single-cell analysis of human glioma and immune cells identifies S100A4 as an immunotherapy target., Nourhan Abdelfattah, Parveen Kumar, Caiyi Wang, Jia-Shiun Leu, William F Flynn, Ruli Gao, David S Baskin, Kumar Pichumani, Omkar B Ijare, Stephanie L Wood, Suzanne Z Powell, David L Haviland, Brittany C Parker Kerrigan, Frederick F Lang, Sujit S Prabhu, Kristin M Huntoon, Wen Jiang, Betty Y S Kim, Joshy George, and Kyuson Yun
Open Problems in Extracellular RNA Data Analysis: Insights From an ERCC Online Workshop., Roger P Alexander, Robert R Kitchen, Juan Pablo Tosar, Matthew Roth, Pieter Mestdagh, Klaas E A Max, Joel Rozowsky, Karolina Elżbieta Kaczor-Urbanowicz, Justin Chang, Leonora Balaj, Bojan Losic, Eric L Van Nostrand, Emily LaPlante, Bogdan Mateescu, Brian S White, Rongshan Yu, Aleksander Milosavljevic, Gustavo Stolovitzky, and Ryan M Spengler
The Mutant Mouse Resource and Research Center (MMRRC): the NIH-supported National Public Repository and Distribution Archive of Mutant Mouse Models in the USA., James Amos-Landgraf, Craig Franklin, Virginia Godfrey, Franziska Grieder, Kristin Grimsrud, Ian Korf, Cathleen Lutz, Terry Magnuson, Oleg Mirochnitchenko, Samit Patel, Laura G Reinholdt, and K C Kent Lloyd
Interchromosomal interaction of homologous Stat92E alleles regulates transcriptional switch during stem-cell differentiation., Matthew Antel, Romir Raj, Madona Y G Masoud, Ziwei Pan, Sheng Li, Barbara G Mellone, and Mayu Inaba
Measuring cardiomyocyte cell-cycle activity and proliferation in the age of heart regeneration., John Auchampach, Lu Han, Guo N Huang, Bernhard Kühn, John W Lough, Caitlin C O'Meara, Alexander Y Payumo, Nadia Rosenthal, Henry M Sucov, Katherine E Yutzey, and Michaela Patterson
Glucose metabolic profiles evaluated by PET associated with molecular characteristic landscape of gastric cancer., Seong-Woo Bae, Felix Berlth, Kyoung-Yun Jeong, Ji-Hyeon Park, Jong-Ho Choi, Shin-Hoo Park, Yun-Suhk Suh, Seong-Ho Kong, Do-Joong Park, Hyuk-Joon Lee, Charles Lee, Jong-Il Kim, Hyewon Youn, Hongyoon Choi, Gi Jeong Cheon, Keon Wook Kang, and Han-Kwang Yang
Inhibition of mitochondrial complex I reverses NOTCH1-driven metabolic reprogramming in T-cell acute lymphoblastic leukemia., Natalia Baran, Alessia Lodi, Yogesh Dhungana, Shelley Herbrich, Meghan Collins, Shannon Sweeney, Renu Pandey, Anna Skwarska, Shraddha Patel, Mathieu Tremblay, Vinitha Mary Kuruvilla, Antonio Cavazos, Mecit Kaplan, Marc O Warmoes, Diogo Troggian Veiga, Ken Furudate, Shanti Rojas-Sutterin, Andre Haman, Yves Gareau, Anne Marinier, Helen Ma, Karine Harutyunyan, May Daher, Luciana Melo Garcia, Gheath Al-Atrash, Sujan Piya, Vivian Ruvolo, Wentao Yang, Sriram Saravanan Shanmugavelandy, Ningping Feng, Jason Gay, Di Du, Jun J Yang, Fieke W Hoff, Marcin Kaminski, Katarzyna Tomczak, R Eric Davis, Daniel Herranz, Adolfo Ferrando, Elias J Jabbour, M Emilia Di Francesco, David T Teachey, Terzah M Horton, Steven Kornblau, Katayoun Rezvani, Guy Sauvageau, Mihai Gagea, Michael Andreeff, Koichi Takahashi, Joseph R Marszalek, Philip L Lorenzi, Jiyang Yu, Stefano Tiziani, Trang Hoang, and Marina Konopleva
Single-cell transcriptome analysis defines mesenchymal stromal cells in the mouse incisor dental pulp., Dashzeveg Bayarsaihan, Badam Enkhmandakh, Anushree Vijaykumar, Paul Robson, and Mina Mina
RNA-Seq for the detection of gene fusions in solid tumors: development and validation of the JAX FusionSeq™ 2.0 assay., Daniel Bergeron, Harshpreet Chandok, Qian Nie, Matthew Prego, Melissa Soucy, Kevin Kelly, Guruprasad Ananda, Andrew N Hesse, and Honey V Reddi
Derivation of extra-embryonic and intra-embryonic macrophage lineages from human pluripotent stem cells., Andrea L Bredemeyer, Junedh M Amrute, Andrew L Koenig, Rachel A Idol, Li He, Stephanie A Luff, Carissa Dege, Jamison M Leid, Joel D Schilling, J Travis Hinson, Mary C Dinauer, Christopher M Sturgeon, and Kory J Lavine
The impact of genetic background on mouse models of kidney disease., Rei Bufi and Ron Korstanje
Brain Research Special Issue on CMT, Editorial., Robert W. Burgess and Mario A Saporta
Genetic control of the pluripotency epigenome determines differentiation bias in mouse embryonic stem cells., Candice Byers, Catrina Spruce, Haley J Fortin, Ellen I Hartig, Anne M Czechanski, Steven C. Munger, Laura G Reinholdt, Daniel A Skelly, and Christopher L. Baker
Long noncoding RNA ZFP36L2-AS functions as a metabolic modulator to regulate muscle development., Bolin Cai, Manting Ma, Jing Zhang, Shaofen Kong, Zhen Zhou, Zhenhui Li, Bahareldin Ali Abdalla, Haiping Xu, Xiquan Zhang, Raman Akinyanju Lawal, and Qinghua Nie
Selective elimination of pluripotent stem cells by PIKfyve specific inhibitors., Arup R Chakraborty, Alex Vassilev, Sushil K Jaiswal, Constandina E O'Connell, John F Ahrens, Barbara S Mallon, Martin Pera, and Melvin L DePamphilis
Alterations in subgingival microbiota during full-fixed appliance orthodontic treatment-A prospective study., Isaac Chen, Jennifer Chung, Raven Vella, George M. Weinstock, Yanjiao Zhou, and Andrew H Jheon
Corneal Changes and Strategies to Improve Survival of Hypomorphic Collagen VII-Deficient Mice for the Study of Ocular Dystrophic Epidermolysis Bullosa., Vicki M Chen, Karrie Southwell, Erin Huynh, Stefanie Gavett, Lauren Richey, and Michael Esmail
Editorial: Fibrosis and Inflammation in Tissue Pathophysiology., Isotta Chimenti, Susanne Sattler, Gonzalo Del Monte-Nieto, and Elvira Forte
The Clinical Variant Analysis Tool: Analyzing the evidence supporting reported genomic variation in clinical practice., Hui-Lin Chin, Nour Gazzaz, Stephanie Huynh, Iulia Handra, Lynn Warnock, Ashley Moller-Hansen, Pierre Boerkoel, Julius O B Jacobsen, Christèle du Souich, Nan Zhang, Kent Shefchek, Leah M Prentice, Nicole Washington, Melissa Haendel, Linlea Armstrong, Lorne Clarke, Wenhui Laura Li, Damian Smedley, Peter N Robinson, and Cornelius F Boerkoel
An expansion of the non-coding genome and its regulatory potential underlies vertebrate neuronal diversity., Michael Closser, Yuchun Guo, Ping Wang, Tulsi Patel, Sumin Jang, Jennifer Hammelman, Joriene C De Nooij, Rachel Kopunova, Esteban O Mazzoni, Yijun Ruan, David K Gifford, and Hynek Wichterle
CRISPR-mediated multiplexed live cell imaging of nonrepetitive genomic loci with one guide RNA per locus., Patricia A Clow, Menghan Du, Nathaniel L. Jillette, Aziz Taghbalout, Jacqueline J Zhu, and Albert Cheng
Risk of new-onset psychiatric sequelae of COVID-19 in the early and late post-acute phase., Ben D Coleman, Elena Casiraghi, Hannah Blau, Lauren Chan, Melissa A Haendel, Bryan Laraway, Tiffany J Callahan, Rachel R Deer, Kenneth J Wilkins, Justin Reese, and Peter N Robinson
A Splicing Mutation in Slc4a5 Results in Retinal Detachment and Retinal Pigment Epithelium Dysfunction, Gayle B. Collin, Lanying Shi, Minzhong Yu, Nurten Akturk, Jeremy R. Charette, Lillian F Hyde, Sonia M Weatherly, Martin Pera, Juergen K. Naggert, Neal S Peachey, Patsy M. Nishina, and Mark P. Krebs
A Bayesian model selection approach to mediation analysis., Wesley L Crouse, Gregory R Keele, Madeleine S Gastonguay, Gary Churchill, and William Valdar
Metagenomics and chemotherapy-induced nausea: A roadmap for future research., Sylvia L Crowder, Aasha I Hoogland, Taylor L Welniak, Elizabeth A LaFranchise, Kristen M Carpenter, Daneng Li, Daniel M Rotroff, Arshiya Mariam, Christine M Pierce, Stacy M Fischer, Anita Y Kinney, Thi Dong Binh Tran, Farzaneh Rastegari, Donna L Berry, Martine Extermann, Richard D Kim, Danielle B Tometich, Jane C Figueiredo, Jameel Muzaffar, Shahla Bari, Kea Turner, George M. Weinstock, and Heather S L Jim
Antibody Responses to SARS-CoV-2 After Infection or Vaccination in Children and Young Adults With Inflammatory Bowel Disease., Joelynn Dailey, Lina Kozhaya, Mikail Dogan, Dena Hopkins, Blaine Lapin, Katherine Herbst, Michael Brimacombe, Kristen Grandonico, Fatih Karabacak, John Schreiber, Bruce Tsan-Liang Liang, Juan C Salazar, Derya Unutmaz, and Jeffrey S Hyams
SvAnna: efficient and accurate pathogenicity prediction of coding and regulatory structural variants in long-read genome sequencing., Daniel Danis, Julius O B Jacobsen, Parithi Balachandran, Qihui Zhu, Feyza Yilmaz, Justin Reese, Matthias Haimel, Gholson J Lyon, Ingo Helbig, Christopher J Mungall, Christine R Beck, Charles Lee, Damian Smedley, and Peter N Robinson
Tissue origin of cytotoxic natural killer cells dictates their differential roles in mouse digit tip regeneration and progenitor cell survival., Nadjib Dastagir, Zachery Beal, and James W Godwin
Genome-wide variant calling in reanalysis of exome sequencing data uncovered a pathogenic TUBB3 variant., Elke de Boer, Burcu Yaldiz, Anne-Sophie Denommé-Pichon, Leslie Matalonga, Steve Laurie, Solve-RD SNV-indel working group, Daniel Danis, Peter N Robinson, and Solve-RD-DITF ITHACA
Distinct toll-like receptor signaling in the salamander response to tissue damage., Ryan J Debuque, Sergej Nowoshilow, Katya E Chan, Nadia Rosenthal, and James W Godwin
MusMorph, a database of standardized mouse morphology data for morphometric meta-analyses., Jay Devine, Marta Vidal-García, Wei Liu, Amanda Neves, Lucas D Lo Vercio, Rebecca M Green, Heather A Richbourg, Marta Marchini, Colton M Unger, Audrey C Nickle, Bethany Radford, Nathan M Young, Paula N Gonzalez, Robert E Schuler, Alejandro Bugacov, Campbell Rolian, Christopher J Percival, Trevor Williams, Lee Niswander, Anne L Calof, Arthur D Lander, Axel Visel, Frank R Jirik, James M Cheverud, Ophir D Klein, Ramon Y Birnbaum, Amy E Merrill, Rebecca R Ackermann, Daniel Graf, Myriam Hemberger, Wendy Dean, Nils D Forkert, Stephen A. Murray, Henrik Westerberg, Ralph S Marcucio, and Benedikt Hallgrímsson
The EurOPDX Data Portal: an open platform for patient-derived cancer xenograft data sharing and visualization., Zdenka Dudová, Nathalie Conte, Jeremy Mason, Dalibor Stuchlík, Radim Peša, Csaba Halmagyi, Zinaida Perova, Abayomi Mosaku, Ross Thorne, Alex Follette, Ľuboslav Pivarč, Radim Šašinka, Muhammad Usman, Steven Neuhauser, Dale A. Begley, Debra M Krupke, Massimiliano Frassà, Alessandro Fiori, Riccardo Corsi, Luca Vezzadini, Claudio Isella, Andrea Bertotti, Carol J Bult, Helen Parkinson, Enzo Medico, Terrence Meehan, and Aleš Křenek
Nfkbid Overexpression in Nonobese Diabetic Mice Elicits Complete Type 1 Diabetes Resistance in Part Associated with Enhanced Thymic Deletion of Pathogenic CD8 T Cells and Increased Numbers and Activity of Regulatory T Cells., Jennifer R Dwyer, Jeremy Racine, Harold D Chapman, Anna Quinlan, Maximiliano Presa, Grace Stafford, Ingo Schmitz, and David V. Serreze
Comparative transmissibility of SARS-CoV-2 variants Delta and Alpha in New England, USA., Rebecca Earnest, Rockib Uddin, Nicholas Matluk, Nicholas Renzette, Sarah E Turbett, Katherine J Siddle, Christine Loreth, Gordon Adams, Christopher H Tomkins-Tinch, Mary E Petrone, Jessica E Rothman, Mallery I Breban, Robert Tobias Koch, Kendall Billig, Joseph R Fauver, Chantal B F Vogels, Kaya Bilguvar, Bony De Kumar, Marie L Landry, David R Peaper, Kevin Kelly, Greg Omerza, Heather Grieser, Sim Meak, John Martha, Hannah B Dewey, Susan Kales, Daniel Berenzy, Kristin Carpenter-Azevedo, Ewa King, Richard C Huard, Vlad Novitsky, Mark Howison, Josephine Darpolor, Akarsh Manne, Rami Kantor, Sandra C Smole, Catherine M Brown, Timelia Fink, Andrew S Lang, Glen R Gallagher, Virginia E Pitzer, Pardis C Sabeti, Stacey Gabriel, Bronwyn L MacInnis, New England Variant Investigation Team, Ryan Tewhey, Mark D Adams, Daniel J Park, Jacob E Lemieux, and Nathan D Grubaugh
Sex differences in the genetic architecture of cognitive resilience to Alzheimer's disease., Jaclyn M Eissman, Logan Dumitrescu, Emily R Mahoney, Alexandra N Smith, Shubhabrata Mukherjee, Michael L Lee, Phoebe Scollard, Seo Eun Choi, William S Bush, Corinne D Engelman, Qiongshi Lu, David W Fardo, Emily H Trittschuh, Jesse Mez, Catherine C Kaczorowski, Hector Hernandez Saucedo, Keith F Widaman, Rachel F Buckley, Michael J Properzi, Elizabeth C Mormino, Hyun Sik Yang, Theresa M Harrison, Trey Hedden, Kwangsik Nho, Shea J Andrews, Douglas Tommet, Niran Hadad, R Elizabeth Sanders, Douglas M Ruderfer, Katherine A Gifford, Xiaoyuan Zhong, Neha S Raghavan, Badri N Vardarajan, Margaret A Pericak-Vance, Lindsay A Farrer, Li San Wang, Carlos Cruchaga, Gerard D Schellenberg, Nancy J Cox, Jonathan L Haines, C Dirk Keene, Andrew J Saykin, Eric B Larson, Reisa A Sperling, Richard Mayeux, Michael L Cuccaro, David A Bennett, Julie A Schneider, Paul K Crane, Angela L Jefferson, and Timothy J Hohman
Deep learning trained on hematoxylin and eosin tumor region of Interest predicts HER2 status and trastuzumab treatment response in HER2+ breast cancer., Saman Farahmand, Aileen I Fernandez, Fahad Shabbir Ahmed, David L Rimm, Jeffrey H Chuang, Emily Reisenbichler, and Kourosh Zarringhalam
APOE ε4 and exercise interact in a sex-specific manner to modulate dementia risk factors, Kate E Foley, Cory A Diemler, Amanda A Hewes, Dylan Garceau, Michael Sasner, and Gareth R Howell
The APOEε3/ε4 Genotype Drives Distinct Gene Signatures in the Cortex of Young Mice, Kate E Foley, Amanda A Hewes, Dylan Garceau, Kevin P Kotredes, Gregory W. Carter, Michael Sasner, and Gareth R Howell
Deep learning features encode interpretable morphologies within histological images., Ali Foroughi Pour, Brian S White, Jonghanne Park, Todd B Sheridan, and Jeffrey H Chuang
Adult mouse fibroblasts retain organ-specific transcriptomic identity., Elvira Forte, Mirana Ramialison, Hieu T Nim, Madison Mara, Jacky Y Li, Rachel Cohn, Sandra Daigle, Sarah Boyd, Edouard G Stanley, Andrew G Elefanty, J Travis Hinson, Mauro W Costa, Nadia Rosenthal, and Milena B Furtado
Genome-wide transcript and protein analysis highlights the role of protein homeostasis in the aging mouse heart., Isabela Gerdes Gyuricza, Joel M Chick, Gregory R Keele, Andrew Deighan, Steven C. Munger, Ron Korstanje, Steven P Gygi, and Gary Churchill
Oral anaphylaxis to peanut in a mouse model is associated with gut permeability but not with Tlr4 or Dock8 mutations., Jake A Gertie, Biyan Zhang, Elise G Liu, Laura R Hoyt, Xiangyun Yin, Lan Xu, Lauren L Long, Arielle Soldatenko, Uthaman Gowthaman, Adam Williams, and Stephanie C Eisenbarth
High-throughput visual assessment of sleep stages in mice using machine learning., Brian Q Geuther, Mandy Chen, Raymond J Galante, Owen Han, Jie Lian, Joshy George, Allan I Pack, and Vivek Kumar
Genetic Interaction between Mfrp and Adipor1 Mutations Affect Retinal Disease Phenotypes, Navdeep Gogna, Sonia Weatherly, Fuxin Zhao, Gayle B. Collin, Jai Pinkney, Lisa Stone, Juergen K. Naggert, Gregory W. Carter, and Patsy M. Nishina
An Artifact in Intracellular Cytokine Staining for Studying T Cell Responses and Its Alleviation., Zheng Gong, Qing Li, Jiayuan Shi, and Guangwen Ren
Mouse mutagenesis and phenotyping to generate models of development and disease., Thomas Gridley and Stephen A. Murray
A human breast cancer-derived xenograft and organoid platform for drug discovery and precision oncology., Katrin P Guillen, Maihi Fujita, Andrew J Butterfield, Sandra D Scherer, Matthew H Bailey, Zhengtao Chu, Yoko S DeRose, Ling Zhao, Emilio Cortes-Sanchez, Chieh-Hsiang Yang, Jennifer Toner, Guoying Wang, Yi Qiao, Xiaomeng Huang, Jeffery A Greenland, Jeffery M Vahrenkamp, David H Lum, Rachel E Factor, Edward W Nelson, Cindy B Matsen, Jane M Poretta, Regina Rosenthal, Anna C Beck, Saundra S Buys, Christos Vaklavas, John H Ward, Randy L Jensen, Kevin B Jones, Zheqi Li, Steffi Oesterreich, Lacey E Dobrolecki, Satya S Pathi, Xing Yi Woo, Kristofer C Berrett, Mark E Wadsworth, Jeffrey H Chuang, Michael T Lewis, Gabor T Marth, Jason Gertz, Katherine E Varley, Bryan E Welm, and Alana L Welm
Curation and expansion of Human Phenotype Ontology for defined groups of inborn errors of immunity., Matthias Haimel, Julia Pazmandi, Raúl Jiménez Heredia, Jasmin Dmytrus, Sevgi Köstel Bal, Samaneh Zoghi, Paul van Daele, Tracy A Briggs, Carine Wouters, Brigitte Bader-Meunier, Florence A Aeschlimann, Roberta Caorsi, Despina Eleftheriou, Esther Hoppenreijs, Elisabeth Salzer, Shahrzad Bakhtiar, Beata Derfalvi, Francesco Saettini, Maaike A A Kusters, Reem Elfeky, Johannes Trück, Jacques G Rivière, Mirjam van der Burg, Marco Gattorno, Markus G Seidel, Siobhan Burns, Klaus Warnatz, Fabian Hauck, Paul Brogan, Kimberly C Gilmour, Catharina Schuetz, Anna Simon, Christoph Bock, Sophie Hambleton, Esther de Vries, Peter N Robinson, Marielle van Gijn, and Kaan Boztug
Epistemic Beliefs: Relationship to Future Expectancies and Quality of Life in Cancer Patients., Paul K J Han, Elizabeth Scharnetzki, Eric Anderson, John DiPalazzo, Tania D Strout, Caitlin Gutheil, F Lee Lucas, Emily A Edelman, and Jens Rueter
An Integrated Approach to Studying Rare Neuromuscular Diseases Using Animal and Human Cell-Based Models., Timothy J Hines, Cathleen Lutz, Stephen A. Murray, and Robert W. Burgess
Molecular genetic mechanisms of dilated cardiomyopathy., John Travis Hinson
Sex Differences in the Brain Transcriptome Related to Alcohol Effects and Alcohol Use Disorder., Robert Hitzemann, Susan E Bergeson, Ari E Berman, Jason A. Bubier, Elissa J Chesler, Deborah A Finn, Matthew Hein, Paula Hoffman, Andrew Holmes, Brent R Kisby, Denesa Lockwood, Kerrie H Lodowski, Michelle McManus, Julie A Owen, Angela R Ozburn, Praneetha Panthagani, Igor Ponomarev, Laura Saba, Boris Tabakoff, Aashlesha Walchale, Robert W Williams, and Tamara J Phillips
Standards for the classification of pathogenicity of somatic variants in cancer (oncogenicity): Joint recommendations of Clinical Genome Resource (ClinGen), Cancer Genomics Consortium (CGC), and Variant Interpretation for Cancer Consortium (VICC)., Peter Horak, Malachi Griffith, Arpad M Danos, Beth A Pitel, Subha Madhavan, Xuelu Liu, Cynthia Chow, Heather Williams, Leigh Carmody, Lisa Barrow-Laing, Damian Rieke, Simon Kreutzfeldt, Albrecht Stenzinger, David Tamborero, Manuela Benary, Padma Sheila Rajagopal, Cristiane M Ida, Harry Lesmana, Laveniya Satgunaseelan, Jason D Merker, Michael Y Tolstorukov, Paulo Vidal Campregher, Jeremy L Warner, Shruti Rao, Maya Natesan, Haolin Shen, Jeffrey Venstrom, Somak Roy, Kayoko Tao, Rashmi Kanagal-Shamanna, Xinjie Xu, Deborah I Ritter, Kym Pagel, Kilannin Krysiak, Adrian Dubuc, Yassmine M Akkari, Xuan Shirley Li, Jennifer Lee, Ian King, Gordana Raca, Alex H Wagner, Marylin M Li, Sharon E Plon, Shashikant Kulkarni, Obi L Griffith, Debyani Chakravarty, and Dmitriy Sonkin
Programmable RNA-Guided Large DNA Transgenesis by CRISPR/Cas9 and Site-Specific Integrase Bxb1., Vishnu Hosur, Benjamin E. Low, and Michael V. Wiles
The GA4GH Phenopacket schema defines a computable representation of clinical data., Julius O B Jacobsen, Michael Baudis, Gareth S Baynam, Jacques S Beckmann, Sergi Beltran, Orion J Buske, Tiffany J Callahan, Christopher G Chute, Mélanie Courtot, Daniel Danis, Olivier Elemento, Andrea Essenwanger, Robert R Freimuth, Michael Gargano, Tudor Groza, Ada Hamosh, Nomi L Harris, Rajaram Kaliyaperumal, Kevin C Kent Lloyd, Aly Khalifa, Peter M Krawitz, Sebastian Köhler, Brian J Laraway, Heikki Lehväslaiho, Leslie Matalonga, Julie A McMurry, Alejandro Metke-Jimenez, Christopher J Mungall, Monica C Munoz-Torres, Soichi Ogishima, Anastasios Papakonstantinou, Davide Piscia, Nikolas Pontikos, Núria Queralt-Rosinach, Marco Roos, Julian Sass, Paul N Schofield, Dominik Seelow, Anastasios Siapos, Damian Smedley, Lindsay D Smith, Robin Steinhaus, Jagadish Chandrabose Sundaramurthi, Emilia M Swietlik, Sylvia Thun, Nicole A Vasilevsky, Alex H Wagner, Jeremy L Warner, Claus Weiland, GAGH Phenopacket Modeling Consortium, Melissa A Haendel, and Peter N Robinson
Phenotype-driven approaches to enhance variant prioritization and diagnosis of rare disease., Julius O B Jacobsen, Catherine Kelly, Valentina Cipriani, Genomics England Research Consortium, Christopher J Mungall, Justin Reese, Daniel Danis, Peter N Robinson, and Damian Smedley
Evaluation of phenotype-driven gene prioritization methods for Mendelian diseases., Julius O B Jacobsen, Catherine Kelly, Valentina Cipriani, Peter N Robinson, and Damian Smedley
A novel clinically relevant graft-versus-leukemia model in humanized mice., Bei Jia, Chenchen Zhao, Michael Bayerl, Hiroko Shike, David F Claxton, W Christopher Ehmann, Shin Mineishi, Todd D Schell, Pan Zheng, Yi Zhang, Leonard D. Shultz, K Sandeep Prabhu, Robert F Paulson, and Hong Zheng
Deficiency in Lyst function leads to accumulation of secreted proteases and reduced retinal adhesion., Xiaojie Ji, Lihong Zhao, Ankita Umapathy, Bernie Fitzmaurice, Jieping Wang, David S Williams, Bo Chang, Juergen K. Naggert, and Patsy M. Nishina
Association of gut microbiota and environment in children with AD, comparison of three cohorts of children., Kylie Jungles, Thi Dong Binh Tran, Maresa Botha, Heather E Rasmussen, Victoria Teixeira-Reis, Erica Sodergren, Claudia Gray, Nonhlanhla Lunjani, Carol Hlela, Wisdom Basera, Lelani Hobane, Alexandra Watkins, Phillip Engen, Avumile Mankahla, Ben Gaunt, Heidi Facey-Thomas, Alan Landay, George M. Weinstock, Ali Keshavarzian, Michael E Levin, and Mahboobeh Mahdavinia
Comprehensive Analysis of Alternative Splicing in Gastric Cancer Identifies Epithelial-Mesenchymal Transition Subtypes Associated with Survival., Yukyung Jun, Yun-Suhk Suh, SungHee Park, Jieun Lee, Jong-Il Kim, Sanghyuk Lee, Wan-Ping Lee, Olga Anczuków, Han-Kwang Yang, and Charles Lee
Auriculocondylar syndrome 2 results from the dominant-negative action of PLCB4 variants., Stanley M Kanai, Caleb Heffner, Timothy C Cox, Michael L Cunningham, Francisco A Perez, Aaron M Bauer, Philip Reigan, Cristan Carter, Stephen A. Murray, and David E Clouthier
Betacoronavirus-specific alternate splicing., Guy Karlebach, Bruce Aronow, Stephen B Baylin, Daniel Butler, Jonathan Foox, Shawn Levy, Cem Meydan, Christopher Mozsary, Amanda M Saravia-Butler, Deanne M Taylor, Eve Wurtele, Christopher E Mason, Afshin Beheshti, and Peter N Robinson
Loss-of-function mutation in Pcsk1 increases serum APOA1 level and LCAT activity in mice., Aleksandra Aljakna Khan, Nakyung Kim, Ron Korstanje, and Seungbum Choi
Independent DSG4 frameshift variants in cats with hair shaft dystrophy., Sarah Kiener, Ana Rostaher, Silvia Rüfenacht, Vidhya Jagannathan, John P Sundberg, Monika Welle, and Tosso Leeb
Expanding homogeneous culture of human primordial germ cell-like cells maintaining germline features without serum or feeder layers., Mutsumi Kobayashi, Misato Kobayashi, Junko Odajima, Keiko Shioda, Young Sun Hwang, Kotaro Sasaki, Pranam Chatterjee, Christian Kramme, Richie E Kohman, George M Church, Amanda R Loehr, Robert S Weiss, Harald Jüppner, Joanna J Gell, Ching C Lau, and Toshi Shioda
PDXNet portal: patient-derived Xenograft model, data, workflow and tool discovery., Soner Koc, Michael W Lloyd, Jeffrey W Grover, Nan Xiao, Sara Seepo, Sai Lakshmi Subramanian, Manisha Ray, Christian Frech, John DiGiovanna, Phillip Webster, Steven Neuhauser, Anuj Srivastava, Xing Yi Woo, Brian J Sanderson, Brian White, Paul Lott, Lacey E Dobrolecki, Heidi Dowst, PDX Consortium, Yvonne A Evrard, Tiffany A Wallace, Jeffrey A Moscow, James H Doroshow, Nicholas Mitsiades, Salma Kaochar, Chong-Xian Pan, Moon S Chen, Luis Carvajal-Carmona, Alana L Welm, Bryan E Welm, Michael T Lewis, Ramaswamy Govindan, Li Ding, Shunqiang Li, Meenhard Herlyn, Michael A Davies, Jack Roth, Funda Meric-Bernstam, Peter N Robinson, Carol J Bult, Brandi Davis-Dusenbery, Dennis A Dean, and Jeffrey H Chuang
State of Residency: Microbial Strain Diversity in the Skin., Heidi H Kong and Julia Oh
Effects of paternal high-fat diet and maternal rearing environment on the gut microbiota and behavior., Austin C Korgan, Christine L Foxx, Heraa Hashmi, Saydie A Sago, Christopher E Stamper, Jared D Heinze, Elizabeth O'Leary, Jillian L King, Tara S Perrot, Christopher A Lowry, and Ian C G Weaver
Bronchial epithelium epithelial-mesenchymal plasticity forms aberrant basaloid-like cells in vitro., Dinesh B Uthaya Kumar, Efthymios Motakis, Marina Yurieva, Vivek Kohar, Jan Martinek, Te-Chia Wu, Johad Khoury, Jessica D S Grassmann, Mingyang Lu, Karolina Palucka, Naftali Kaminski, Jonathan L Koff, and Adam Williams
Macrophages in dermatology: pathogenic roles and targeted therapeutics., Drew Kuraitis, Nadia Rosenthal, Erin Boh, and Elizabeth McBurney
Synthetic DNA spike-ins (SDSIs) enable sample tracking and detection of inter-sample contamination in SARS-CoV-2 sequencing workflows., Kim A Lagerborg, Erica Normandin, Matthew R Bauer, Gordon Adams, Katherine Figueroa, Christine Loreth, Adrianne Gladden-Young, Bennett M Shaw, Leah R Pearlman, Daniel Berenzy, Hannah B Dewey, Susan Kales, Sabrina T Dobbins, Erica S Shenoy, David Hooper, Virginia M Pierce, Kimon C Zachary, Daniel J Park, Bronwyn L MacInnis, Ryan Tewhey, Jacob E Lemieux, Pardis C Sabeti, Steven K Reilly, and Katherine J Siddle
The RD-Connect Genome-Phenome Analysis Platform: Accelerating diagnosis, research, and gene discovery for rare diseases., Steven Laurie, Davide Piscia, Leslie Matalonga, Alberto Corvó, Marcos Fernández-Callejo, Carles Garcia-Linares, Carles Hernandez-Ferrer, Cristina Luengo, Inés Martínez, Anastasios Papakonstantinou, Daniel Picó-Amador, Joan Protasio, Rachel Thompson, Raul Tonda, Mònica Bayés, Gemma Bullich, Jordi Camps-Puchadas, Ida Paramonov, Jean-Rémi Trotta, Angel Alonso, Marcella Attimonelli, Christophe Béroud, Virginie Bros-Facer, Orion J Buske, Andrés Cañada-Pallarés, José M Fernández, Mats G Hansson, Rita Horvath, Julius O B Jacobsen, Rajaram Kaliyaperumal, Séverine Lair-Préterre, Luana Licata, Pedro Lopes, Estrella López-Martín, Deborah Mascalzoni, Lucia Monaco, Luis A Pérez-Jurado, Manuel Posada de la Paz, Jordi Rambla, Ana Rath, Olaf Riess, Peter N Robinson, David Salgado, Damian Smedley, Dylan Spalding, Peter A C 't Hoen, Ana Töpf, Irina Zaharieva, Holm Graessner, Ivo G Gut, Hanns Lochmüller, and Sergi Beltran
Functional replacement of myostatin with GDF-11 in the germline of mice., Se-Jin Lee, Adam Lehar, Renata Rydzik, Daniel W Youngstrom, Shalender Bhasin, Yewei Liu, and Emily L Germain-Lee
The hyperpolarization-activated, cyclic nucleotide-gated channel resides on myocytes in mouse bladders and contributes to adrenergic-induced detrusor relaxation., Fouad Lemtiri-Chlieh, Dylan Baker, Iman M Al-Naggar, Ramalakshmi Ramasamy, George A Kuchel, Eric S Levine, Paul Robson, and Phillip P Smith
Murine Model for Measuring Effects of Humanized-Dosing of Antibiotics on the Gut Microbiome., Shana Leopold, Kamilia Abdelraouf, David P Nicolau, Hanako Agresta, Jethro Johnson, Kathleen Teter, Wm Michael Dunne, David Broadwell, Alex van Belkum, Lisa M Schechter, Erica J Sodergren, and George M. Weinstock
Advancing Physiology with Expanded Multi-Omics., Mingyu Liang, Allen W Cowley, Andrew S Greene, Aron M Geurts, Pengyuan Liu, Yong Liu, and Sridhar Rao
Efficient targeted transgenesis of large donor DNA into multiple mouse genetic backgrounds using bacteriophage Bxb1 integrase., Benjamin E. Low, Vishnu Hosur, Simon Lesbirel, and Michael V. Wiles
Deep learning modeling m6A deposition reveals the importance of downstream cis-element sequences., Zhiyuan Luo, Jiacheng Zhang, Jingyi Fei, and Shengdong Ke
CDC20 regulates sensitivity to chemotherapy and radiation in glioblastoma stem cells., Diane D Mao, Ryan T Cleary, Amit D Gujar, Tatenda Mahlokozera, and Albert H Kim
Vascular derived endothelin receptor A controls endothelin-induced retinal ganglion cell death., Olivia J Marola, Gareth R Howell, and Richard T Libby
Transcriptional profiling of macrophages in situ in metastatic melanoma reveals localization-dependent phenotypes and function., Jan Martinek, Jianan Lin, Kyung In Kim, Victor G Wang, Te-Chia Wu, Michael Chiorazzi, Hannah Boruchov, Ananya Gulati, Shamreethaa Seeniraj, Lili Sun, Florentina Marches, Paul Robson, Anthony Rongvaux, Richard A Flavell, Joshy George, Jeffrey Chuang, Jacques Banchereau, and Karolina Palucka
A Simple Standard for Sharing Ontological Mappings (SSSOM)., Nicolas Matentzoglu, James P Balhoff, Susan M. Bello, Chris Bizon, Matthew Brush, Tiffany J Callahan, Christopher G Chute, William D Duncan, Chris T Evelo, Davera Gabriel, John Graybeal, Alasdair Gray, Benjamin M Gyori, Melissa Haendel, Henriette Harmse, Nomi L Harris, Ian Harrow, Harshad B Hegde, Amelia L Hoyt, Charles T Hoyt, Dazhi Jiao, Ernesto Jiménez-Ruiz, Simon Jupp, Hyeongsik Kim, Sebastian Koehler, Thomas Liener, Qinqin Long, James Malone, James A McLaughlin, Julie A McMurry, Sierra Moxon, Monica C Munoz-Torres, David Osumi-Sutherland, James A Overton, Bjoern Peters, Tim Putman, Núria Queralt-Rosinach, Kent Shefchek, Harold Solbrig, Anne Thessen, Tania Tudorache, Nicole Vasilevsky, Alex H Wagner, and Christopher J Mungall
Providing a Helping Hand: Metabolic Regulation of T Follicular Helper Cells and Their Association With Disease., Colleen L Mayberry, Natalie A Logan, John J Wilson, and Chih-Hao Chang
Consensus Recommendation for Mouse Models of Ocular Hypertension to Study Aqueous Humor Outflow and Its Mechanisms., Colleen M McDowell, Krishnakumar Kizhatil, Michael H Elliott, Darryl R Overby, Joseph van Batenburg-Sherwood, J Cameron Millar, Markus H Kuehn, Gulab Zode, Ted S Acott, Michael G Anderson, Sanjoy K Bhattacharya, Jacques A Bertrand, Terete Borras, Diane E Bovenkamp, Lin Cheng, John Danias, Michael Lucio De Ieso, Yiqin Du, Jennifer A Faralli, Rudolf Fuchshofer, Preethi S Ganapathy, Haiyan Gong, Samuel Herberg, Humberto Hernandez, Peter Humphries, Simon W M John, Paul L Kaufman, Kate E Keller, Mary J Kelley, Ruth A Kelly, David Krizaj, Ajay Kumar, Brian C Leonard, Raquel L Lieberman, Paloma Liton, Yutao Liu, Katy C Liu, Navita N Lopez, Weiming Mao, Timur Mavlyutov, Fiona McDonnell, Gillian J McLellan, Philip Mzyk, Andrews Nartey, Louis R Pasquale, Gaurang C Patel, Padmanabhan P Pattabiraman, Donna M Peters, Vijaykrishna Raghunathan, Ponugoti Vasantha Rao, Naga Rayana, Urmimala Raychaudhuri, Ester Reina-Torres, Ruiyi Ren, Douglas Rhee, Uttio Roy Chowdhury, John R Samples, E Griffen Samples, Najam Sharif, Joel S Schuman, Val C Sheffield, Cooper H Stevenson, Avinash Soundararajan, Preeti Subramanian, Chenna Kesavulu Sugali, Yang Sun, Carol B Toris, Karen Y Torrejon, Amir Vahabikashi, Janice A Vranka, Ting Wang, Colin E Willoughby, Chen Xin, Hongmin Yun, Hao F Zhang, Michael P Fautsch, Ernst R Tamm, Abbot F Clark, C Ross Ethier, and W Daniel Stamer
Genomic and epigenomic BRCA alterations predict adaptive resistance and response to platinum-based therapy in patients with triple-negative breast and ovarian carcinomas, Francesca Menghi, Kalyan Banda, Pooja A Kumar, Robert Straub, Lacey Dobrolecki, Isabel V Rodriguez, Susan E Yost, Harshpreet Chandok, Marc R Radke, George Somlo, Yuan Yuan, Michael T Lewis, Elizabeth M Swisher, and Edison T Liu
Characterization of single nucleotide polymorphisms for a forward genetics approach using genetic crosses in C57BL/6 and BALB/c substrains of mice., Ikuo Miura, Yoshiaki Kikkawa, Shumpei P Yasuda, Akiko Shinogi, Daiki Usuda, Vivek Kumar, Joseph S Takahashi, Masaru Tamura, Hiroshi Masuya, and Shigeharu Wakana
3D-cardiomics: A spatial transcriptional atlas of the mammalian heart., Monika Mohenska, Nathalia M Tan, Alex Tokolyi, Milena B Furtado, Mauro W Costa, Andrew J Perry, Jessica Hatwell-Humble, Karel van Duijvenboden, Hieu T Nim, Yuan M M Ji, Natalie Charitakis, Denis Bienroth, Francesca Bolk, Celine Vivien, Anja S Knaupp, David R Powell, David A Elliott, Enzo R Porrello, Susan K Nilsson, Gonzalo Del Monte-Nieto, Nadia A Rosenthal, Fernando J Rossello, Jose M Polo, and Mirana Ramialison
Prioritization of autoimmune disease-associated genetic variants that perturb regulatory element activity in T cells., Kousuke Mouri, Michael H Guo, Carl G de Boer, Michelle M Lissner, Ingrid A Harten, Gregory A Newby, Hannah A DeBerg, Winona F Platt, Matteo Gentili, David R Liu, Daniel J Campbell, Nir Hacohen, Ryan Tewhey, and John P Ray
Perspectives on Cognitive Phenotypes and Models of Vascular Disease., Selen C Muratoglu, Marc F Charette, Zorina S Galis, Adam S Greenstein, Alan Daugherty, Anne Joutel, Beth A Kozel, Donna M Wilcock, Emily C Collins, Farzaneh A Sorond, Gareth R Howell, Hyacinth I Hyacinth, Kent K C Lloyd, Kurt R Stenmark, Manfred Boehm, Mark L Kahn, Roderick Corriveau, Sara Wells, Timothy J Bussey, Stacey J Sukoff Rizzo, and M Luisa Iruela-Arispe
Airpart: interpretable statistical models for analyzing allelic imbalance in single-cell datasets., Wancen Mu, Hirak Sarkar, Avi Srivastava, Kwangbom Choi, Rob Patro, and Michael I Love
Central nervous system immune interactome is a function of cancer lineage, tumor microenvironment, and STAT3 expression., Hinda Najem, Martina Ott, Cynthia Kassab, Arvind Rao, Ganesh Rao, Anantha Marisetty, Adam M Sonabend, Craig Horbinski, Roel G W Verhaak, Anand Shankar, Santhoshi N Krishnan, Frederick S Varn, Víctor A Arrieta, Pravesh Gupta, Sherise D Ferguson, Jason T Huse, Gregory N Fuller, James P Long, Daniel E Winkowski, Ben A Freiberg, Charles David James, Leonidas C Platanias, Maciej S Lesniak, Jared K Burks, and Amy B Heimberger
Translational approaches to understanding resilience to Alzheimer's disease., Sarah M Neuner, Maria Telpoukhovskaia, Vilas Menon, Kristen M S O'Connell, Timothy J Hohman, and Catherine Kaczorowski
Mortality Prediction Analysis among COVID-19 Inpatients Using Clinical Variables and Deep Learning Chest Radiography Imaging Features., Xuan V Nguyen, Engin Dikici, Sema Candemir, Robyn L Ball, and Luciano M Prevedello
Prophylactic evaluation of verubecestat on disease- and symptom-modifying effects in 5XFAD mice., Adrian L Oblak, Zackary A Cope, Sara K Quinney, Ravi S Pandey, Carla Biesdorf, Andi R Masters, Kristen D. Onos, Leslie Haynes, Kelly J Keezer, Jill A Meyer, Jonathan S Peters, Scott A Persohn, Amanda A Bedwell, Kierra Eldridge, Rachael Speedy, Gabriela Little, Sean-Paul Williams, Brenda Noarbe, Andre Obenaus, Michael Sasner, Gareth R Howell, Gregory W. Carter, Harriet M. Jackson, Bruce T Lamb, Paul R Territo, and Stacey J Sukoff Rizzo
Plcg2M28L Interacts With High Fat/High Sugar Diet to Accelerate Alzheimer's Disease-Relevant Phenotypes in Mice., Adrian L Oblak, Kevin P Kotredes, Ravi S Pandey, Alaina M Reagan, Cynthia Ingraham, Bridget Perkins, Christopher Lloyd, Deborah Baker, Peter B Lin, Disha M Soni, Andy P Tsai, Scott A Persohn, Amanda A Bedwell, Kierra Eldridge, Rachael Speedy, Jill A Meyer, Johnathan S Peters, Lucas L Figueiredo, Michael Sasner, Paul R Territo, Stacey J Sukoff Rizzo, Gregory W. Carter, Bruce T Lamb, and Gareth R Howell
Differential Regulation of Mouse Hippocampal Gene Expression Sex Differences by Chromosomal Content and Gonadal Sex., Sarah R Ocañas, Victor A Ansere, Kyla B Tooley, Niran Hadad, Ana J Chucair-Elliott, David R Stanford, Shannon Rice, Benjamin Wronowski, Kevin D Pham, Jessica M Hoffman, Steven N Austad, Michael B Stout, and Willard M Freeman
Dendritic Cell Differentiation from Human Induced Pluripotent Stem Cells: Challenges and Progress., Nélio A J Oliveira and Handan Sevim
Life-long dietary restrictions have negligible or damaging effects on late-life cognitive performance: A key role for genetics in outcomes., Andrew R Ouellette, Niran Hadad, Andrew Deighan, Laura Robinson, Kristen M S O'Connell, Adam Freund, Gary Churchill, and Catherine Kaczorowski
Editorial: Pediatric Microbiome in Health and Disease: Recent Advances., Amy Y Pan, George M. Weinstock, and Jill L Maron