Submissions from 2022
Evaluation of phenotype-driven gene prioritization methods for Mendelian diseases., Julius O B Jacobsen, Catherine Kelly, Valentina Cipriani, Peter N Robinson, and Damian Smedley
Direct cell-to-cell transfer in stressed tumor microenvironment aggravates tumorigenic or metastatic potential in pancreatic cancer., Giyong Jang, Jaeik Oh, Eunsung Jun, Jieun Lee, Jee Young Kwon, Jaesang Kim, Sang-Hyuk Lee, Song Cheol Kim, Sung-Yup Cho, and Charles Lee
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
Phenotype-aware prioritisation of rare Mendelian disease variants., Catherine Kelly, Anita Szabo, Nikolas Pontikos, Gavin Arno, Peter N Robinson, Jules O B Jacobsen, Damian Smedley, and Valentina Cipriani
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
Bifidobacterial carbohydrate/nucleoside metabolism enhances oxidative phosphorylation in white adipose tissue to protect against diet-induced obesity., Gihyeon Kim, Youngmin Yoon, Jin Ho Park, Jae Won Park, Myung-Guin Noh, Hyun Kim, Changho Park, Hyuktae Kwon, Jeong-Hyeon Park, Yena Kim, Jinyoung Sohn, Shinyoung Park, Hyeonhui Kim, Sun-Kyoung Im, Yeongmin Kim, Ha Yung Chung, Myung Hee Nam, Jee Young Kwon, Il Yong Kim, Yong Jae Kim, Ji Hyeon Baek, Hak Su Kim, George M Weinstock, Belong Cho, Charles Lee, Sungsoon Fang, Hansoo Park, and Je Kyung Seong
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
Associations of the skin, oral and gut microbiome with aging, frailty and infection risk reservoirs in older adults., Peter J Larson, Wei Zhou, Alba Santiago, Sarah Driscoll, Elizabeth Fleming, Anita Y Voigt, Ock K Chun, James J Grady, George A Kuchel, Julie T Robison, and Julia Oh
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
Taxonomic assessment of two wild house mouse subspecies using whole-genome sequencing., Raman Akinyanju Lawal, Verity L Mathis, Mary Barter, Jeremy R. Charette, Alexis Garretson, and Beth L Dumont
'Poisoning' of the transcriptome by ultraconserved elements., Nathan Leclair and Olga Anczuków
Early experience with targeted therapy as a first-line adjuvant treatment for pediatric low-grade glioma., Nathan K Leclair, William Lambert, Kimberley Roche, Eileen Gillan, Joanna J Gell, Ching C Lau, Gregory Wrubel, Joshua Knopf, Shirali Amin, Megan Anderson, Jonathan E Martin, Markus J Bookland, and David S Hersh
Landscape of genetic variants in sporadic meningiomas captured with clinical genomics., Nathan K Leclair, Erica Shen, Qian Wu, Leo Wolansky, Kevin Becker, Lei Li, and Ketan R Bulsara
High-Throughput Production of Diverse Xenobiotic Metabolites with Cytochrome P450-Transduced Huh7 Hepatoma Cell Lines., Choon-Myung Lee, Ken H Liu, Grant Singer, Gary W Miller, Shuzhao Li, Dean P Jones, and Edward T Morgan
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
SVision: a deep learning approach to resolve complex structural variants., Jiadong Lin, Songbo Wang, Peter A Audano, Deyu Meng, Jacob I Flores, Walter Kosters, Xiaofei Yang, Peng Jia, Tobias Marschall, Christine R Beck, and Kai Ye
Mako: A Graph-based Pattern Growth Approach to Detect Complex Structural Variants., Jiadong Lin, Xiaofei Yang, Walter Kosters, Tun Xu, Yanyan Jia, Songbo Wang, Qihui Zhu, Mallory Ryan, Li Guo, Chengsheng Zhang, The Human Genome Structural Variation Consortium, Charles Lee, Scott E Devine, Evan E Eichler, and Kai Ye
Deciphering the role of RNA structure in translation efficiency., Jianan Lin, Yang Chen, Yuping Zhang, Haifan Lin, and Zhengqing Ouyang
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
Editorial: Stromal and immune microenvironment in breast cancer metastasis., Xin Lu, Xia Liu, Toni Celià-Terrassa, and Guangwen Ren
Novel skewed usage of B-cell receptors in COVID-19 patients with various clinical presentations., Junpeng Ma, Han Bai, Tian Gong, Weikang Mao, Yijun Nie, Xuan Zhang, Yanyan Da, Xiaorui Wang, Hongyu Qin, Qiqi Zeng, Fang Hu, Xin Qi, Bingyin Shi, and Chengsheng Zhang
Genomic Medicine Year in Review: 2022., Teri A Manolio, Jahnavi Narula, Carol J Bult, Rex L Chisholm, Patricia A Deverka, Geoffrey S Ginsburg, Madison Goldrich, Eric D Green, Gail P Jarvik, George A Mensah, Erin M Ramos, Mary V Relling, Dan M Roden, Robb Rowley, and Marc S Williams
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
Autosomal recessive LRP1-related syndrome featuring cardiopulmonary dysfunction, bone dysmorphology, and corneal clouding., Paul R Mark, Stephen A. Murray, Tao Yang, Alexandra Eby, Angela Lai, Di Lu, Jacob Zieba, Surender Rajasekaran, Elizabeth A VanSickle, Linda Z Rossetti, Lucia Guidugli, Kelly Watkins, Meredith S Wright, Caleb P Bupp, and Jeremy W Prokop
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
Multiplex immunofluorescence-guided laser capture microdissection for spatial transcriptomics of metastatic melanoma tissues., Jan Martinek, Te-Chia Wu, Lili Sun, Jianan Lin, Kyung In Kim, Florentina Marches, Paul Robson, Joshy George, 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
Loss of Pex1 in Inner Ear Hair Cells Contributes to Cochlear Synaptopathy and Hearing Loss., Stephanie A Mauriac, Thibault Peineau, Aamir Zuberi, Cathleen Lutz, and Gwénaëlle S G Géléoc
PTS is activated by ATF4 and promotes lung adenocarcinoma development via the Wnt pathway, Wei Ma, Chao Wang, Ruzhen Li, Zhaohui Han, Yuanzhu Jiang, Xiangwei Zhang, Duilio Divisi, Enrico Capobianco, Lin Zhang, and Wei Dong
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
Functional genomics of complex cancer genomes., Francesca Menghi and Edison 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
Blackcurrants Reduce the Risk of Postmenopausal Osteoporosis: A Pilot Double-Blind, Randomized, Placebo-Controlled Clinical Trial., Briana M Nosal, Junichi R Sakaki, Zachary Macdonald, Kyle Mahoney, Kijoon Kim, Matthew Madore, Staci Thornton, Thi Dong Binh Tran, George M. Weinstock, Elaine Choung-Hee Lee, and Ock K Chun
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
Lesion environments direct transplanted neural progenitors towards a wound repair astroglial phenotype in mice., T M O'Shea, Y Ao, S Wang, A L Wollenberg, J H Kim, R A Ramos Espinoza, Anne M. Czechanski, Laura G. Reinholdt, T J Deming, and M V Sofroniew
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
Single-Cell RNA Sequencing Reveals Molecular Features of Heterogeneity in the Murine Retinal Pigment Epithelium., Ravi S Pandey, Mark P. Krebs, Mohan Bolisetty, Jeremy R. Charette, Juergen K. Naggert, Paul Robson, Patsy M. Nishina, and Gregory W. Carter
A reference human induced pluripotent stem cell line for large-scale collaborative studies., Caroline B Pantazis, Andrian Yang, Erika Lara, Justin A McDonough, Cornelis Blauwendraat, Lirong Peng, Hideyuki Oguro, Jitendra Kanaujiya, Jizhong Zou, David Sebesta, Gretchen Pratt, Erin Cross, Jeffrey Blockwick, Philip Buxton, Lauren Kinner-Bibeau, Constance Medura, Christopher Tompkins, Stephen Hughes, Marianita Santiana, Faraz Faghri, Mike A Nalls, Daniel Vitale, Shannon Ballard, Yue A Qi, Daniel M Ramos, Kailyn M Anderson, Julia Stadler, Priyanka Narayan, Jason Papademetriou, Luke Reilly, Matthew P Nelson, Sanya Aggarwal, Leah U Rosen, Peter Kirwan, Venkat Pisupati, Steven L Coon, Sonja W Scholz, Theresa Priebe, Miriam Öttl, Jian Dong, Marieke Meijer, Lara J M Janssen, Vanessa S Lourenco, Rik van der Kant, Dennis Crusius, Dominik Paquet, Ana-Caroline Raulin, Guojun Bu, Aaron Held, Brian J Wainger, Rebecca M C Gabriele, Jackie M Casey, Selina Wray, Dad Abu-Bonsrah, Clare L Parish, Melinda S Beccari, Don W Cleveland, Emmy Li, Indigo V L Rose, Martin Kampmann, Carles Calatayud Aristoy, Patrik Verstreken, Laurin Heinrich, Max Y Chen, Birgitt Schüle, Dan Dou, Erika L F Holzbaur, Maria Clara Zanellati, Richa Basundra, Mohanish Deshmukh, Sarah Cohen, Richa Khanna, Malavika Raman, Zachary S Nevin, Madeline Matia, Jonas Van Lent, Vincent Timmerman, Bruce R Conklin, Katherine Johnson Chase, Ke Zhang, Salome Funes, Daryl A Bosco, Lena Erlebach, Marc Welzer, Deborah Kronenberg-Versteeg, Guochang Lyu, Ernest Arenas, Elena Coccia, Lily Sarrafha, Tim Ahfeldt, John C Marioni, William C Skarnes, Mark R Cookson, Michael E Ward, and Florian T Merkle
Genome-wide association mapping of ethanol sensitivity in the Diversity Outbred mouse population., Clarissa C Parker, Vivek M. Philip, Daniel M. Gatti, Steven Kasparek, Andrew M Kreuzman, Lauren Kuffler, Benjamin Mansky, Sophie Masneuf, Kayvon Sharif, Erica Sluys, Dominik Taterra, Walter M Taylor, Mary Thomas, Oksana Polesskaya, Abraham A Palmer, Andrew Holmes, and Elissa J Chesler
Super-resolution visualization of chromatin loop folding in human lymphoblastoid cells using interferometric photoactivated localization microscopy., Zofia Parteka-Tojek, Jacqueline Jufen Zhu, Byoungkoo Lee, Karolina Jodkowska, Ping Wang, Jesse Aaron, Teng-Leong Chew, Krzysztof Banecki, Dariusz Plewczynski, and Yijun Ruan
Extrachromosomal DNA (ecDNA): an origin of tumor heterogeneity, genomic remodeling, and drug resistance., Lauren T Pecorino, Roel G W Verhaak, Anton Henssen, and Paul S Mischel
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
Pluripotent cell states and unexpected fates., Martin Pera
Adding gene transcripts into genomic prediction improves accuracy and reveals sampling time dependence., Bruno C Perez, Marco C A M Bink, Karen L. Svenson, Gary Churchill, and Mario P L Calus
Prediction performance of linear models and gradient boosting machine on complex phenotypes in outbred mice., Bruno C Perez, Marco C A M Bink, Karen L. Svenson, Gary Churchill, and Mario P L Calus
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
Progress towards completing the mutant mouse null resource., Kevin A Peterson and Stephen A. Murray
Combining genomic and epidemiological data to compare the transmissibility of SARS-CoV-2 variants Alpha and Iota., Mary E Petrone, Jessica E Rothman, Mallery I Breban, Isabel M Ott, Alexis Russell, Erica Lasek-Nesselquist, Hamada Badr, Kevin Kelly, Gregory Omerza, Nicholas Renzette, Anne E Watkins, Chaney C Kalinich, Tara Alpert, Anderson F Brito, Rebecca Earnest, Irina R Tikhonova, Christopher Castaldi, John P Kelly, Matthew Shudt, Jonathan Plitnick, Erasmus Schneider, Steven Murphy, Caleb Neal, Eva Laszlo, Ahmad Altajar, Claire Pearson, Anthony Muyombwe, Randy Downing, Jafar Razeq, Linda Niccolai, Madeline S Wilson, Margaret L Anderson, Jianhui Wang, Chen Liu, Pei Hui, Shrikant Mane, Bradford P Taylor, William P Hanage, Marie L Landry, David R Peaper, Kaya Bilguvar, Joseph R Fauver, Chantal B F Vogels, Lauren M Gardner, Virginia E Pitzer, Kirsten St George, Mark D Adams, and Nathan D Grubaugh
The GBA1 D409V mutation exacerbates synuclein pathology to differing extents in two alpha-synuclein models., Nicole K Polinski, Terina N Martinez, Sylvie Ramboz, Michael Sasner, Mark Herberth, Robert Switzer, Syed O Ahmad, Lee J Pelligrino, Sean W Clark, Jacob N Marcus, Sean M Smith, Kuldip D Dave, and Mark A Frasier
Recurrent inversion polymorphisms in humans associate with genetic instability and genomic disorders., David Porubsky, Wolfram Höps, Hufsah Ashraf, PingHsun Hsieh, Bernardo Rodriguez-Martin, Feyza Yilmaz, Jana Ebler, Pille Hallast, Flavia Angela Maria Maggiolini, William T Harvey, Barbara Henning, Peter A Audano, David S Gordon, Peter Ebert, Patrick Hasenfeld, Eva Benito, Qihui Zhu, Charles Lee, Francesca Antonacci, Matthias Steinrücken, Christine R Beck, Ashley D Sanders, Tobias Marschall, Evan E Eichler, and Jan O Korbel
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
Conference report: Biocuration 2021 Virtual Conference., Federica Quaglia, Rama Balakrishnan, Susan M. Bello, and Nicole Vasilevsky
Editorial: Genetic basis of tolerance induction defects underlying the development of autoimmune pathologies., Jeremy Racine, Laurence Morel, Yi-Guang Chen, and David V. Serreze
The 677C > T variant in methylenetetrahydrofolate reductase causes morphological and functional cerebrovascular deficits in mice, Alaina M Reagan, Karen E Christensen, Leah C. Graham, Amanda A Bedwell, Kierra Eldridge, Rachael Speedy, Lucas L Figueiredo, Scott C Persohn, Teodoro Bottiglieri, Kwangsik Nho, Michael Sasner, Paul R Territo, Rima Rozen, and Gareth R Howell
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
NSAID use and clinical outcomes in COVID-19 patients: a 38-center retrospective cohort study., Justin T Reese, Ben D Coleman, Lauren Chan, Hannah Blau, Tiffany J Callahan, Luca Cappelletti, Tommaso Fontana, Katie R Bradwell, Nomi L Harris, Elena Casiraghi, Giorgio Valentini, Guy Karlebach, Rachel Deer, Julie A McMurry, Melissa A Haendel, Christopher G Chute, Emily Pfaff, Richard Moffitt, Heidi Spratt, Jasvinder A Singh, Christopher J Mungall, Andrew E Williams, and Peter N Robinson
Predictable Fluctuations in Excitatory Synaptic Strength Due to Natural Variation in Presynaptic Firing Rate., Naixin Ren, Ganchao Wei, Abed Ghanbari, and Ian H Stevenson
Harmonizing model organism data in the Alliance of Genome Resources., Alliance of Genome Resources Consortium, Anna V. Anagnostopoulos, Susan M. Bello, Judith A. Blake, Olin Blodgett, Carol J. Bult, Karen R. Christie, Mary E. Dolan, Paul Hale, James A. Kadin, Monica S. McAndrews, Howie Motenko, David R. Shaw, Constance M. Smith, Cynthia L. Smith, Monika Tomczuk, and Laurens G. Wilming
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
Clinical validity assessment of genes frequently tested on intellectual disability/autism sequencing panels., Erin Rooney Riggs, Taylor I Bingaman, Carrie-Ann Barry, Andrea Behlmann, Krista Bluske, Bret Bostwick, Alison Bright, Chun-An Chen, Amanda R Clause, Avinash V Dharmadhikari, Mythily Ganapathi, Claudia Gonzaga-Jauregui, Andrew R Grant, Madeline Y Hughes, Se Rin Kim, Amanda Krause, Jun Liao, Aimé Lumaka, Michelle Mah, Caitlin M Maloney, Shruthi Mohan, Ikeoluwa A Osei-Owusu, Emma Reble, Olivia Rennie, Juliann M Savatt, Hermela Shimelis, Rebecca K Siegert, Tam P Sneddon, Courtney Thaxton, Kelly A Toner, Kien Trung Tran, Ryan Webb, Emma H Wilcox, Jiani Yin, Xinming Zhuo, Masa Znidarsic, Christa Lese Martin, Catalina Betancur, Jacob A S Vorstman, David T Miller, and Christian P Schaaf
High-temporal resolution profiling reveals distinct immune trajectories following the first and second doses of COVID-19 mRNA vaccines., Darawan Rinchai, Sara Deola, Gabriele Zoppoli, Basirudeen Syed Ahamed Kabeer, Sara Taleb, Igor Pavlovski, Selma Maacha, Giusy Gentilcore, Mohammed Toufiq, Lisa Mathew, Li Liu, Fazulur Rehaman Vempalli, Ghada Mubarak, Stephan Lorenz, Irene Sivieri, Gabriella Cirmena, Chiara Dentone, Paola Cuccarolo, Daniele Roberto Giacobbe, Federico Baldi, Alberto Garbarino, Benedetta Cigolini, Paolo Cremonesi, Michele Bedognetti, Alberto Ballestrero, Matteo Bassetti, Boris P Hejblum, Tracy Augustine, Nicholas Van Panhuys, Rodolphe Thiebaut, Ricardo Branco, Tracey Chew, Maryam Shojaei, Kirsty Short, Carl G Feng, PREDICT-19 Consortium, Susu M Zughaier, Andrea De Maria, Benjamin Tang, Ali Ait Hssain, Davide Bedognetti, Jean-Charles Grivel, and Damien Chaussabel
Mouse Genome Informatics (MGI): latest news from MGD and GXD., Martin Ringwald, Joel E Richardson, Richard M. Baldarelli, Judith A. Blake, James A. Kadin, Cynthia Smith, and Carol J Bult
[Rare-disease data standards]., Peter N Robinson and Holm Graessner
Genomic heterogeneity underlies multidrug resistance in Pseudomonas aeruginosa: A population-level analysis beyond susceptibility testing., Laura J Rojas, Mohamad Yasmin, Jacquelynn Benjamino, Steven M Marshall, Kailynn J DeRonde, Nikhil P Krishnan, Federico Perez, Andrew A Colin, Monica Cardenas, Octavio Martinez, Armando Pérez-Cardona, Daniel D Rhoads, Michael R Jacobs, John J LiPuma, Michael W Konstan, Alejandro J Vila, Andrea Smania, Andrew R Mack, Jacob G Scott, Mark D Adams, Lilian M Abbo, and Robert A Bonomo
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
Circulating CD34+ cells of primary myelofibrosis patients contribute to myeloid-dominant hematopoiesis and bone marrow fibrosis in immunodeficient mice., Noriyuki Saito, Takuji Yamauchi, Noriaki Kawano, Rintaro Ono, Shuro Yoshida, Toshihiro Miyamoto, Tomohiko Kamimura, Leonard D. Shultz, Yoriko Saito, Katsuto Takenaka, Kazuya Shimoda, Mine Harada, Koichi Akashi, and Fumihiko Ishikawa
Performance Modeling of Scalable Resource Allocations with the Imperial PEPA Compiler, William S. Sanders, Srishti Srivastava, and Ionana Banicescu
Voluntary workplace genomic testing: wellness benefit or Pandora's box?, Kunal Sanghavi, Betty Cohn, Anya E R Prince, W Gregory Feero, Kerry A Ryan, Kayte Spector-Bagdady, Wendy R Uhlmann, Charles Lee, J Scott Roberts, and Debra J H Mathews
Cell origin-dependent cooperativity of mutant Dnmt3a and Npm1 in clonal hematopoiesis and myeloid malignancy., Jennifer M SanMiguel, Elizabeth Eudy, Matthew A Loberg, Linde A Miles, Timothy M Stearns, Jayna J Mistry, Michael J Rauh, Ross L Levine, and Jennifer J. Trowbridge
Distinct Tumor Necrosis Factor Alpha Receptors Dictate Stem Cell Fitness versus Lineage Output in Dnmt3a-Mutant Clonal Hematopoiesis., Jennifer M. SanMiguel, Elizabeth Eudy, Matthew A. Loberg, Kira Young, Jayna J. Mistry, Kristina D. Mujica, Logan S. Schwartz, Timothy M. Stearns, Grant A Challen, and Jennifer J. Trowbridge