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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
p53-mediated neurodegeneration in the absence of the nuclear protein Akirin2., Stacey L Peek, Peter J Bosch, Ethan Bahl, Brianna J Iverson, Mrutyunjaya Parida, Preeti Bais, J Robert Manak, Jacob J Michaelson, Robert W. Burgess, and Joshua A Weiner
Annotated expression and activity data for murine recombinase alleles and transgenes: the CrePortal resource., Michelle N Perry, Constance M. Smith, Hiroaki Onda, Martin Ringwald, Stephen A. Murray, and Cynthia L Smith
Systematic reconstruction of cellular trajectories across mouse embryogenesis., Chengxiang Qiu, Junyue Cao, Beth K Martin, Tony Li, Ian C Welsh, Sanjay Srivatsan, Xingfan Huang, Diego Calderon, William Stafford Noble, Christine M Disteche, Stephen A. Murray, Malte Spielmann, Cecilia B Moens, Cole Trapnell, and Jay Shendure
Improving mouse models for the study of Alzheimer's disease., Alaina M Reagan, Kristen D. Onos, Sarah E Heuer, Michael Sasner, and Gareth R Howell
Multiple genome viewer (MGV): a new tool for visualization and comparison of multiple annotated genomes., Joel E Richardson, Richard M. Baldarelli, and Carol J Bult
Reading Frame Repair of TTN Truncation Variants Restores Titin Quantity and Functions, Robert Romano, Shahnaz Ghahremani, Talia Zimmerman, Nicholas Legere, Ketan Thakar, Feria A Ladha, Anthony M Pettinato, and J Travis Hinson
The Human Disease Ontology 2022 update., Lynn M Schriml, James B Munro, Mike Schor, Dustin Olley, Carrie McCracken, Victor Felix, J Allen Baron, Rebecca Jackson, Susan M. Bello, Cynthia Bearer, Richard Lichenstein, Katharine Bisordi, Nicole Campion Dialo, Michelle Giglio, and Carol Greene
A Need for More Molecular Profiling in Brain Metastases., Erica Shen, Amanda E D Van Swearingen, Meghan J Price, Ketan Bulsara, Roel G W Verhaak, César Baëta, Brice D Painter, Zachary J Reitman, April K S Salama, Jeffrey M Clarke, Carey K Anders, Peter E Fecci, C Rory Goodwin, and Kyle M Walsh
Stride-level analysis of mouse open field behavior using deep-learning-based pose estimation., Keith Sheppard, Justin Gardin, Gautam S Sabnis, Asaf Peer, Megan Darrell, Sean P Deats, Brian Q Geuther, Cathleen Lutz, and Vivek Kumar
Common Genetic Variants Contribute to Risk of Transposition of the Great Arteries., Doris Škorić-Milosavljević, Rafik Tadros, Fernanda M Bosada, Federico Tessadori, Jan Hendrik van Weerd, Odilia I Woudstra, Fleur V Y Tjong, Najim Lahrouchi, Fanny Bajolle, Heather J Cordell, A J Agopian, Gillian M Blue, Daniela Q C M Barge-Schaapveld, Marc Gewillig, Christoph Preuss, Elisabeth M Lodder, Phil Barnett, Aho Ilgun, Leander Beekman, Karel van Duijvenboden, Regina Bokenkamp, Martina Müller-Nurasyid, Hubert W Vliegen, Thelma C Konings, Joost P van Melle, Arie P J van Dijk, Roland R J van Kimmenade, Jolien W Roos-Hesselink, Gertjan T Sieswerda, Folkert Meijboom, Hashim Abdul-Khaliq, Felix Berger, Sven Dittrich, Marc-Phillip Hitz, Julia Moosmann, Frank-Thomas Riede, Stephan Schubert, Pilar Galan, Mark Lathrop, Hans M Munter, Ammar Al-Chalabi, Christopher E Shaw, Pamela J Shaw, Karen E Morrison, Jan H Veldink, Leonard H van den Berg, Sylvia Evans, Marcelo A Nobrega, Ivy Aneas, Milena Radivojkov-Blagojević, Thomas Meitinger, Erwin Oechslin, Tapas Mondal, Lynn Bergin, John F Smythe, Luis Altamirano-Diaz, Jane Lougheed, Berto J Bouma, Marie-A Chaix, Jennie Kline, Anne S Bassett, Gregor Andelfinger, Roel L F van der Palen, Patrice Bouvagnet, Sally-Ann B Clur, Jeroen Breckpot, Wilhelmina S Kerstjens-Frederikse, David S Winlaw, Ulrike M M Bauer, Seema Mital, Elizabeth Goldmuntz, Bernard Keavney, Damien Bonnet, Barbara J Mulder, Michael W T Tanck, Jeroen Bakkers, Vincent M Christoffels, Cornelis J Boogerd, Alex V Postma, and Connie R Bezzina
TALE.Sense: A Versatile DNA Sensor Platform for Live Mammalian Cells., Aziz Taghbalout, Nathaniel L. Jillette, and Albert W Cheng
3D patient-derived tumor models to recapitulate pediatric brain tumors In Vitro., Min D Tang-Schomer, Harshpreet Chandok, Wei-Biao Wu, Ching C Lau, Markus J Bookland, and Joshy George
Genetic resiliency associated with dominant lethal TPM1 mutation causing atrial septal defect with high heritability, Polakit Teekakirikul, Wenjuan Zhu, Xinxiu Xu, Cullen B Young, Tuantuan Tan, Amanda M Smith, Chengdong Wang, Kevin A Peterson, George C Gabriel, Sebastian Ho, Yi Sheng, Anne Moreau de Bellaing, Daniel A Sonnenberg, Jiuann-Huey Lin, Elisavet Fotiou, Gennadiy Tenin, Michael X Wang, Yijen L Wu, Timothy Feinstein, William Devine, Honglan Gou, Abha S Bais, Benjamin J Glennon, Maliha Zahid, Timothy C Wong, Ferhaan Ahmad, Michael J Rynkiewicz, William J Lehman, Bernard Keavney, Tero-Pekka Alastalo, Mary-Louise Freckmann, Kyle Orwig, Stephen A Murray, Stephanie M Ware, Hui Zhao, Brian Feingold, and Cecilia W Lo
Targeting p21Cip1 highly expressing cells in adipose tissue alleviates insulin resistance in obesity, Lichao Wang, Binsheng Wang, Nathan S Gasek, Yueying Zhou, Rachel L Cohn, Dominique E Martin, Wulin Zuo, William F Flynn, Chun Guo, Evan R Jellison, Taewan Kim, Larissa G P Langhi Prata, Allyson K Palmer, Ming Li, Christina L Inman, Lauren S Barber, Iman M A Al-Naggar, Yanjiao Zhou, Wenqiang Du, Kshitiz, George A Kuchel, Alexander Meves, Tamar Tchkonia, James L Kirkland, Paul Robson, and Ming Xu
Spatiotemporal dynamics of clonal selection and diversification in normal endometrial epithelium., Manako Yamaguchi, Hirofumi Nakaoka, Kazuaki Suda, Kosuke Yoshihara, Tatsuya Ishiguro, Nozomi Yachida, Kyota Saito, Haruka Ueda, Kentaro Sugino, Yutaro Mori, Kaoru Yamawaki, Ryo Tamura, Sundaramoorthy Revathidevi, Teiichi Motoyama, Kazuki Tainaka, Roel G W Verhaak, Ituro Inoue, and Takayuki Enomoto
Live-Cell Imaging Shows Uneven Segregation of Extrachromosomal DNA Elements and Transcriptionally Active Extrachromosomal DNA Hubs in Cancer., Eunhee Yi, Amit D Gujar, Molly Guthrie, Hoon Kim, Dacheng Zhao, Kevin C Johnson, Samirkumar B Amin, Megan L Costa, Qianru Yu, Sunit Das, Nathaniel L. Jillette, Patricia A Clow, Albert W Cheng, and Roel G W Verhaak
Intermittent fasting and caloric restriction interact with genetics to shape physiological health in mice., Guozhu Zhang, Andrew Deighan, Anil Raj, Laura Robinson, Hannah J Donato, Gaven Garland, Mackenzie Leland, Baby Martin-McNulty, Ganesh A Kolumam, Johannes Riegler, Adam Freund, Kevin M Wright, and Gary A Churchill
SMN protein is required throughout life to prevent spinal muscular atrophy disease progression., Xin Zhao, Zhihua Feng, Nicole Risher, Anna Mollin, Josephine Sheedy, Karen K Y Ling, Jana Narasimhan, Amal Dakka, John D Baird, Hasane Ratni, Cathleen Lutz, Karen S Chen, Nikolai A Naryshkin, Chien-Ping Ko, Ellen Welch, Friedrich Metzger, and Marla Weetall