Submissions from 2021
Circadian rhythms and the gut microbiome synchronize the host's metabolic response to diet., Diana E Gutierrez Lopez, Laura M Lashinger, George M. Weinstock, and Molly S Bray
The National COVID Cohort Collaborative (N3C): Rationale, design, infrastructure, and deployment., Melissa A Haendel, Christopher G Chute, Tellen D Bennett, David A Eichmann, Justin Guinney, Warren A Kibbe, Philip R O Payne, Emily R Pfaff, Peter N Robinson, Joel H Saltz, Heidi Spratt, Christine Suver, John Wilbanks, Adam B Wilcox, Andrew E Williams, Chunlei Wu, Clair Blacketer, Robert L Bradford, James J Cimino, Marshall Clark, Evan W Colmenares, Patricia A Francis, Davera Gabriel, Alexis Graves, Raju Hemadri, Stephanie S Hong, George Hripscak, Dazhi Jiao, Jeffrey G Klann, Kristin Kostka, Adam M Lee, Harold P Lehmann, Lora Lingrey, Robert T Miller, Michele Morris, Shawn N Murphy, Karthik Natarajan, Matvey B Palchuk, Usman Sheikh, Harold Solbrig, Shyam Visweswaran, Anita Walden, Kellie M Walters, Griffin M Weber, Xiaohan Tanner Zhang, Richard L Zhu, Benjamin Amor, Andrew T Girvin, Amin Manna, Nabeel Qureshi, Michael G Kurilla, Sam G Michael, Lili M Portilla, Joni L Rutter, Christopher P Austin, and Ken R Gersing
Patterns and mechanisms of sex ratio distortion in the Collaborative Cross mouse mapping population., Brett A Haines, Francesca Barradale, and Beth L Dumont
Letter to the Editor: Response to Biesecker et al., Ada Hamosh, Joanna S Amberger, Carol A Bocchini, Joann Bodurtha, Carol J Bult, Christopher G Chute, Garry R Cutting, Harry C Dietz, Helen V Firth, Richard A Gibbs, Wayne W Grody, Melissa A Haendel, James R Lupski, Jennifer E Posey, Peter N Robinson, Lynn M Schriml, Alan F Scott, Nara L Sobreira, David Valle, Nan Wu, and Sonja A Rasmussen
JAK2 regulates paclitaxel resistance in triple negative breast cancers., Jongmin Han, Jihui Yun, Mingji Quan, Wonyoung Kang, Ji-Gwang Jung, Woohang Heo, Songbin Li, Kyu Jin Lee, Hye-Youn Son, Ju Hee Kim, Jaeyong Choi, Dong-Young Noh, Deukchae Na, Han Suk Ryu, Charles Lee, Jong-Il Kim, and Hyeong-Gon Moon
An in vivo screen of noncoding loci reveals that Daedalus is a gatekeeper of an Ikaros-dependent checkpoint during haematopoiesis., Christian C D Harman, Will Bailis, Jun Zhao, Louisa Hill, Rihao Qu, Ruaidhrí P Jackson, Justin A Shyer, Holly R Steach, Yuval Kluger, Loyal A Goff, John L Rinn, Adam Williams, Jorge Henao-Mejia, and Richard A Flavell
17-a-estradiol late in life extends lifespan in aging UM-HET3 male mice; nicotinamide riboside and three other drugs do not affect lifespan in either sex., David E Harrison, Randy Strong, Peter C. Reifsnyder, Navasuja Kumar, Elizabeth Fernandez, Kevin Flurkey, Martin A Javors, Marisa Lopez-Cruzan, Francesca Macchiarini, James F Nelson, Alessandro Bitto, Amy L Sindler, Gino Cortopassi, Kylie Kavanagh, Lin Leng, Richard Bucala, Nadia Rosenthal, Adam Salmon, Timothy M Stearns, Molly A. Bogue, and Richard A Miller
Combined inhibition of XIAP and BCL2 drives maximal therapeutic efficacy in genetically diverse aggressive acute myeloid leukemia, M Hashimoto, Y Saito, R Nakagawa, I Ogahara, S Takagi, S Takata, H Amitani, M Endo, H Yuki, J A. Ramilowski, Leonard D. Shultz, and Et Al
A case for revisiting Nodal signaling in human pluripotent stem cells., Kevin Hayes, Yun-Kyo Kim, and Martin F Pera
The X chromosome from telomere to telomere: key achievements and future opportunities., Edith Heard, Alexander D Johnson, Jan O Korbel, Charles Lee, Michael P Snyder, and David Sturgill
An Asp to Strike Out Cancer? Therapeutic Possibilities Arising from Aspartate's Emerging Roles in Cell Proliferation and Survival., Iiro Taneli Helenius, Hanumantha Rao Madala, and Jing-Ruey Joanna Yeh
A cross-species interaction with a symbiotic commensal enables cell-density-dependent growth and in vivo virulence of an oral pathogen., Anilei Hoare, Hui Wang, Archana Meethil, Loreto Abusleme, Bo-Young Hong, Niki M Moutsopoulos, Philip D Marsh, George Hajishengallis, and Patricia I Diaz
3D genomics across the tree of life reveals condensin II as a determinant of architecture type., Claire Hoencamp, Olga Dudchenko, Ahmed M O Elbatsh, Sumitabha Brahmachari, Jonne A Raaijmakers, Tom van Schaik, Ángela Sedeño Cacciatore, Vinícius G Contessoto, Roy G H P van Heesbeen, Bram van den Broek, Aditya N Mhaskar, Hans Teunissen, Brian Glenn St Hilaire, David Weisz, Arina D Omer, Melanie Pham, Zane Colaric, Zhenzhen Yang, Suhas S P Rao, Namita Mitra, Christopher Lui, Weijie Yao, Ruqayya Khan, Leonid L Moroz, Andrea Kohn, Judy St Leger, Alexandria Mena, Karen Holcroft, Maria Cristina Gambetta, Fabian Lim, Emma Farley, Nils Stein, Alexander Haddad, Daniel Chauss, Ayse Sena Mutlu, Meng C Wang, Neil D Young, Evin Hildebrandt, Hans H Cheng, Christopher J Knight, Theresa L U Burnham, Kevin A Hovel, Andrew J Beel, Pierre-Jean Mattei, Roger D Kornberg, Wesley C Warren, Gregory Cary, José Luis Gómez-Skarmeta, Veronica Hinman, Kerstin Lindblad-Toh, Federica Di Palma, Kazuhiro Maeshima, Asha S Multani, Sen Pathak, Liesl Nel-Themaat, Richard R Behringer, Parwinder Kaur, René H Medema, Bas van Steensel, Elzo de Wit, José N Onuchic, Michele Di Pierro, Erez Lieberman Aiden, and Benjamin D Rowland
Cisplatin increases immune activity of monocytes and cytotoxic T-cells in a murine model of epithelial ovarian cancer., Daniel Hopkins, Hector Sanchez, Brent Berwin, and Ivy Wilkinson-Ryan
Do gene expression findings from mouse models of cocaine use recapitulate human cocaine use disorder in reward circuitry?, Spencer B Huggett, Jason A. Bubier, Elissa J Chesler, and Rohan H C Palmer
Genes identified in rodent studies of alcohol intake are enriched for heritability of human substance use., Spencer B Huggett, Emma C Johnson, Alexander S Hatoum, Dongbing Lai, Jenani Srijeyanthan, Jason A. Bubier, Elissa J Chesler, Arpana Agrawal, Abraham A Palmer, Howard J Edenberg, and Rohan H C Palmer
Multiple PDZ domain protein maintains patterning of the apical cytoskeleton in sensory hair cells., Amandine Jarysta and Basile Tarchini
Therapeutic implications of activating noncanonical PIK3CA mutations in head and neck squamous cell carcinoma., Nan Jin, Bhumsuk Keam, Janice Cho, Michelle J Lee, Hye Ryun Kim, Hayarpi Torosyan, Natalia Jura, Patrick Ks Ng, Gordon B Mills, Hua Li, Yan Zeng, Zohar Barbash, Gabi Tarcic, Hyunseok Kang, Julie E Bauman, Mi-Ok Kim, Nathan K VanLandingham, Danielle L Swaney, Nevan J Krogan, Daniel E Johnson, and Jennifer R Grandis
The microbiome: From description to function in endocrine and metabolic research, Jethro S Johnson and George M. Weinstock
Single-cell multimodal glioma analyses identify epigenetic regulators of cellular plasticity and environmental stress response., Kevin C Johnson, Kevin J Anderson, Elise T Courtois, Amit D Gujar, Floris P Barthel, Frederick S Varn, Diane Luo, Martine Seignon, Eunhee Yi, Hoon Kim, Marcos R H Estecio, Dacheng Zhao, Ming Tang, Nicholas E Navin, Rahul Maurya, Chew Yee Ngan, Niels Verburg, Philip C de Witt Hamer, Ketan Bulsara, Michael Samuels, Sunit Das, Paul Robson, and Roel G W Verhaak
Serum cell-free DNA epigenetic biomarkers aid glioma diagnostics and monitoring., Kevin C Johnson and Roel G W Verhaak
CRISPR screens identify a novel combination treatment targeting BCL-X L and WNT signaling for KRAS/BRAF-mutated colorectal cancers, Hae Rim Jung, Yumi Oh, Deukchae Na, Seoyeon Min, Jinjoo Kang, Dongjun Jang, Seungjae Shin, Jiwon Kim, Sang Eun Lee, Eui Man Jeong, Joon Yong An, Chang Ohk Sung, Won-Suk Lee, Charles Lee, and Sung-Yup Cho
muCNV: Genotyping Structural Variants for Population-level Sequencing., Goo Jun, Fritz Sedlazeck, Qihui Zhu, Adam English, Ginger Metcalf, Hyun Min Kang, Human Genome Structural Variation Consortium, Charles Lee, Richard Gibbs, and Eric Boerwinkle
3D Bioprinting for fabrication of tissue models of COVID-19 infection., Anisha Kabir, Pallab Datta, Julia Oh, Adam Williams, Veli Ozbolat, Derya Unutmaz, and Ibrahim T Ozbolat
Development of a Novel Orthotopic Gastric Cancer Mouse Model., Wonyoung Kang, Leigh Maher, Michael Michaud, Seong-Woo Bae, Seongyeong Kim, Hye Seung Lee, Seock-Ah Im, Han-Kwang Yang, and Charles Lee
Classification of Molecular Subtypes of High-Grade Serous Ovarian Cancer by MALDI-Imaging., Wanja Kassuhn, Oliver Klein, Silvia Darb-Esfahani, Hedwig Lammert, Sylwia Handzik, Eliane T Taube, Wolfgang D Schmitt, Carlotta Keunecke, David Horst, Felix Dreher, Joshy George, David D Bowtell, Oliver Dorigo, Michael Hummel, Jalid Sehouli, Nils Blüthgen, Hagen Kulbe, and Elena I Braicu
Transcriptomic profiling of Paulownia elongata in response to heat stress., Neerja Katiyar, Niveditha Ramadoss, Dinesh Gupta, Suman B Pakala, Kerry Cooper, and Chhandak Basu
Sept8/SEPTIN8 involvement in cellular structure and kidney damage is identified by genetic mapping and a novel human tubule hypoxic model., Gregory R Keele, Jeremy W Prokop, Hong He, Katie Holl, John Littrell, Aaron W Deal, Yunjung Kim, Patrick B Kyle, Esinam Attipoe, Ashley C Johnson, Katie L Uhl, Olivia L Sirpilla, Seyedehameneh Jahanbakhsh, Melanie Robinson, Shawn Levy, William Valdar, Michael R Garrett, and Leah C Solberg Woods
Regulation of protein abundance in genetically diverse mouse populations., Gregory R Keele, Tian Zhang, Duy T. Pham, Matthew J Vincent, Timothy A Bell, Pablo Hock, Ginger D Shaw, Joao A Paulo, Steven C. Munger, Fernando Pardo-Manuel de Villena, Martin T Ferris, Steven P Gygi, and Gary Churchill
The dihydropyrimidine dehydrogenase gene contributes to heritable differences in sleep in mice., Brendan T Keenan, Raymond J Galante, Jie Lian, Lin Zhang, Xiaofeng Guo, Olivia J Veatch, Elissa J Chesler, W Timothy O'Brien, Karen L. Svenson, Gary Churchill, and Allan I Pack
Heritability of fat distributions in male mice from the founder strains of the Diversity Outbred mouse population., Brendan T Keenan, Jeanette C Webster, Andrew S Wiemken, Nir Lavi-Romer, Teresa Nguyen, Karen L. Svenson, Raymond J Galante, Gary A Churchill, Stephen Pickup, Allan I Pack, and Richard J Schwab
Long non-coding RNAs and their targets as potential biomarkers in breast cancer., Maryam Khalid, Rehan Zafar Paracha, Maryum Nisar, Sumaira Malik, Salma Tariq, Iqra Arshad, Amnah Siddiqa, Zamir Hussain, Jamil Ahmad, and Amjad Ali
Functional characterization of T2D-associated SNP effects on baseline and ER stress-responsive β cell transcriptional activation., Shubham Khetan, Susan Kales, Romy Kursawe, Alexandria Jillette, Jacob C Ulirsch, Steven K Reilly, Duygu Ucar, Ryan Tewhey, and Michael L. Stitzel
Spermidine-induced recovery of human dermal structure and barrier function by skin microbiome., Gihyeon Kim, Misun Kim, Minji Kim, Changho Park, Youngmin Yoon, Doo-Hyeon Lim, Hyeonju Yeo, Seunghyun Kang, Yeong-Geun Lee, Nam-In Beak, Jongsung Lee, Sujeong Kim, Jee Young Kwon, Won Woo Choi, Charles Lee, Kyoung Wan Yoon, Hansoo Park, and Dong-Geol Lee
High-throughput measurement of fibroblast rhythms reveals genetic heritability of circadian phenotypes in diversity outbred mice and their founder strains., Sam-Moon Kim, Chelsea A Vadnie, Vivek M. Philip, Leona H. Gagnon, Kodavali V Chowdari, Elissa J Chesler, Colleen A McClung, and Ryan W Logan
Genomic profile of metastatic breast cancer patient-derived xenografts established using percutaneous biopsy., Seongyeong Kim, Dongjin Shin, Ahrum Min, Minjung Kim, Deukchae Na, Han-Byeol Lee, Han Suk Ryu, Yaewon Yang, Go-Un Woo, Kyung-Hun Lee, Dae-Won Lee, Tae-Yong Kim, Charles Lee, Seock-Ah Im, and Jong-Il Kim
Perspective of mesenchymal transformation in glioblastoma., Yona Kim, Frederick S Varn, Sung-Hye Park, Byung Woo Yoon, Hye Ran Park, Charles Lee, Roel G W Verhaak, and Sun Ha Paek
EMX2-GPR156-Gαi reverses hair cell orientation in mechanosensory epithelia., Katie S Kindt, Anil Akturk, Amandine Jarysta, Matthew Day, Alisha Beirl, Michaela Flonard, and Basile Tarchini
Altered expression of genes controlling metabolism characterizes the tissue response to immune injury in lupus., Kathryn M Kingsmore, Prathyusha Bachali, Michelle D Catalina, Andrea R Daamen, Sarah E Heuer, Robert D Robl, Amrie C Grammer, and Peter E Lipsky
Radiotherapy is associated with a deletion signature that contributes to poor outcomes in patients with cancer., Emre Kocakavuk, Kevin J Anderson, Frederick S Varn, Kevin C Johnson, Samirkumar B Amin, Erik P Sulman, Martijn P Lolkema, Floris P Barthel, and Roel G W Verhaak
Gene Circuit Explorer (GeneEx): an interactive web-app for visualizing, simulating and analyzing gene regulatory circuits., Vivek Kohar, Danya Gordin, Ataur Katebi, Herbert Levine, José N Onuchic, and Mingyang Lu
The Human Phenotype Ontology in 2021., Sebastian Köhler, Michael Gargano, Nicolas Matentzoglu, Leigh Carmody, David Lewis-Smith, Nicole A Vasilevsky, Daniel Danis, Ganna Balagura, Gareth Baynam, Amy M Brower, Tiffany J Callahan, Christopher G Chute, Johanna L Est, Peter D Galer, Shiva Ganesan, Matthias Griese, Matthias Haimel, Julia Pazmandi, Marc Hanauer, Nomi L Harris, Michael J Hartnett, Maximilian Hastreiter, Fabian Hauck, Yongqun He, Tim Jeske, Hugh Kearney, Gerhard Kindle, Christoph Klein, Katrin Knoflach, Roland Krause, David Lagorce, Julie A McMurry, Jillian A Miller, Monica C Munoz-Torres, Rebecca L Peters, Christina K Rapp, Ana M Rath, Shahmir A Rind, Avi Z Rosenberg, Michael M Segal, Markus G Seidel, Damian Smedley, Tomer Talmy, Yarlalu Thomas, Samuel A Wiafe, Julie Xian, Zafer Yüksel, Ingo Helbig, Christopher J Mungall, Melissa A Haendel, and Peter N Robinson
LUMOS - Low and Intermediate Grade Glioma Umbrella Study of Molecular Guided TherapieS at relapse: Protocol for a pilot study, Benjamin Y Kong, Hao-Wen Sim, Anna K Nowak, Sonia Yip, Elizabeth H Barnes, Bryan W Day, Michael E Buckland, Roel G W Verhaak, Terrance Johns, Cleo Robinson, and et al
Impaired prenatal motor axon development necessitates early therapeutic intervention in severe SMA., Lingling Kong, David O Valdivia, Christian M Simon, Cera W Hassinan, Nicolas Delestrée, Daniel M Ramos, Jae Hong Park, Celeste M Pilato, Xixi Xu, Melissa Crowder, Chloe C Grzyb, Zachary A King, Marco Petrillo, Kathryn J Swoboda, Crystal Davis, Cathleen Lutz, Alexander H Stephan, Xin Zhao, Marla Weetall, Nikolai A Naryshkin, Thomas O Crawford, George Z Mentis, and Charlotte J Sumner
The Jackson Laboratory Nathan Shock Center: impact of genetic diversity on aging., Ron Korstanje, Luanne L. Peters, Laura Robinson, Stephen D Krasinski, and Gary Churchill
Uncovering Disease Mechanisms in a Novel Mouse Model Expressing Humanized APOEε4 and Trem2*R47H., Kevin P Kotredes, Adrian Oblak, Ravi S Pandey, Peter Bor-Chian Lin, Dylan Garceau, Harriet M. Jackson, Asli Uyar, Rita O'Rourke, Sarah O'Rourke, Cynthia Ingraham, Daria Bednarycek, Melisa Belanger, Zackary Cope, Kate E Foley, Benjamin A Logsdon, Lara M Mangravite, Stacey J Sukoff Rizzo, Paul R Territo, Gregory W. Carter, Michael Sasner, Bruce T Lamb, and Gareth R Howell
CXCL1: A new diagnostic biomarker for human tuberculosis discovered using Diversity Outbred mice., Deniz Koyuncu, Muhammad Khalid Khan Niazi, Thomas Tavolara, Claudia Abeijon, Melanie L Ginese, Yanghui Liao, Carolyn Mark, Aubrey Specht, Adam C Gower, Blanca I Restrepo, Daniel M Gatti, Igor Kramnik, Metin Gurcan, Bülent Yener, and Gillian Beamer
User testing of a diagnostic decision support system with machine-assisted chart review to facilitate clinical genomic diagnosis., Alanna Kulchak Rahm, Nephi A Walton, Lynn K Feldman, Conner Jenkins, Troy Jenkins, Thomas N Person, Joeseph Peterson, Jonathon C Reynolds, Peter N Robinson, Makenzie A Woltz, Marc S Williams, and Michael M Segal
In Vivo Lentiviral Gene Delivery of HLA-DR and Vaccination of Humanized Mice for Improving the Human T and B Cell Immune Reconstitution., Suresh Kumar, Johannes Koenig, Andreas Schneider, Fredrik Wermeling, Sanjaykumar Boddul, Sebastian J Theobald, Miriam Vollmer, Doreen Kloos, Nico Lachmann, Frank Klawonn, Stefan Lienenklaus, Steven R Talbot, André Bleich, Nadine Wenzel, Constantin von Kaisenberg, James G. Keck, and Renata Stripecke
Actinin BioID reveals sarcomere crosstalk with oxidative metabolism through interactions with IGF2BP2., Feria A Ladha, Ketan Thakar, Anthony M Pettinato, Nicholas Legere, Shahnaz Ghahremani, Rachel Cohn, Robert Romano, Emily Meredith, Yu-Sheng Chen, and J Travis Hinson
Network Topology of Biological Aging and Geroscience-Guided Approaches to COVID-19., Alan Landay, Jenna Bartley, Dishary Banerjee, Geneva Hargis, Laura Haynes, Ali Keshavarzian, Chia-Ling Kuo, Oh Sung Kwon, Sheng Li, Shuzhao Li, Julia Oh, Ibrahim Tarik Ozbolat, Duygu Ucar, Ming Xu, Xudong Yao, Derya Unutmaz, and George A Kuchel
Challenges in Developing a Human Model System for Skin Microbiome Research., Peter J Larson, Derrick Chong, Elizabeth Fleming, and Julia Oh
Selection shapes the landscape of functional variation in wild house mice., Raman Akinyanju Lawal, Uma P Arora, and Beth L Dumont
Single Cell Analysis of Blood Mononuclear Cells Stimulated Through Either LPS or Anti-CD3 and Anti-CD28., Nathan Lawlor, Djamel Nehar-Belaid, Jessica D S Grassmann, Marlon Stoeckius, Peter Smibert, Michael L. Stitzel, Virginia Pascual, Jacques Banchereau, Adam Williams, and Duygu Ucar
Three decades of the Human Genome Organization., Charles Lee, Stylianos E Antonarakis, Ada Hamosh, and John Burn
Genome-scale CRISPR screening identifies cell cycle and protein ubiquitination processes as druggable targets for erlotinib-resistant lung cancer., Jieun Lee, Ahyoung Choi, Sung-Yup Cho, Yukyung Jun, Deukchae Na, Ahra Lee, Giyong Jang, Jee Young Kwon, Jaesang Kim, Sanghyuk Lee, and Charles Lee
Misexpression of genes lacking CpG islands drives degenerative changes during aging., Jun-Yeong Lee, Ian Davis, Elliot H H Youth, Jonghwan Kim, Gary Churchill, James R Fahey, Ron Korstanje, and Samuel Beck
Bifidobacterium bifidum strains synergize with immune checkpoint inhibitors to reduce tumour burden in mice., Se-Hoon Lee, Sung-Yup Cho, Youngmin Yoon, Changho Park, Jinyoung Sohn, Jin-Ju Jeong, Bu-Nam Jeon, Mongjoo Jang, Choa An, Suro Lee, Yun Yeon Kim, Gihyeon Kim, Sujeong Kim, Yunjae Kim, Gwang Bin Lee, Eun Ju Lee, Sang Gyun Kim, Hong Sook Kim, Yeongmin Kim, Hyun Kim, Hyun-Suk Yang, Sarang Kim, Seonggon Kim, Hayung Chung, Myeong Hee Moon, Myung Hee Nam, Jee Young Kwon, Sungho Won, Joon-Suk Park, George M. Weinstock, Charles Lee, Kyoung Wan Yoon, and Hansoo Park
Targeting the myostatin signaling pathway to treat muscle loss and metabolic dysfunction., Se-Jin Lee
Modeling seizures in the Human Phenotype Ontology according to contemporary ILAE concepts makes big phenotypic data tractable., David Lewis-Smith, Peter D Galer, Ganna Balagura, Hugh Kearney, Shiva Ganesan, Mahgenn Cosico, Margaret O'Brien, Priya Vaidiswaran, Roland Krause, Colin A Ellis, Rhys H Thomas, Peter N Robinson, and Ingo Helbig
Induction of Stress-Induced Renal Cellular Senescence In Vitro: Impact of Mouse Strain Genetic Diversity., Chieh Ming Liao, Vera Christine Wulfmeyer, Maxine Swallow, Christine Susanne Falk, Hermann Haller, Ron Korstanje, Anette Melk, and Roland Schmitt
Interactions between ALS-linked FUS and nucleoporins are associated with defects in the nucleocytoplasmic transport pathway., Yen-Chen Lin, Meenakshi Sundaram Kumar, Nandini Ramesh, Eric N Anderson, Aivi T Nguyen, Boram Kim, Simon Cheung, Justin A McDonough, William C Skarnes, Rodrigo Lopez-Gonzalez, John E Landers, Nicolas L Fawzi, Ian R A Mackenzie, Edward B Lee, Jeffrey A Nickerson, David Grunwald, Udai B Pandey, and Daryl A Bosco
Utilizing image and caption information for biomedical document classification., Pengyuan Li, Xiangying Jiang, Gongbo Zhang, Juan Trelles Trabucco, Daniela Raciti, Cynthia Smith, Martin Ringwald, G Elisabeta Marai, Cecilia Arighi, and Hagit Shatkay
SRPK1/2 and PP1α exert opposite functions by modulating SRSF1-guided MKNK2 alternative splicing in colon adenocarcinoma., Hongda Liu, Zheng Gong, Kangshuai Li, Qun Zhang, Zekuan Xu, and Yunfei Xu
Large scale enzyme based xenobiotic identification for exposomics., Ken H Liu, Choon M Lee, Grant Singer, Preeti Bais, Francisco Castellanos, Michael H Woodworth, Thomas R Ziegler, Colleen S Kraft, Gary W Miller, Shuzhao Li, Young-Mi Go, Edward T Morgan, and Dean P Jones
DNA methylation-calling tools for Oxford Nanopore sequencing: a survey and human epigenome-wide evaluation., Yang Liu, Wojciech Rosikiewicz, Ziwei Pan, Nathaniel L. Jillette, Ping Wang, Aziz Taghbalout, Jonathan Foox, Christopher Mason, Martin Carroll, Albert Cheng, and Sheng Li
Local versus systemic control of bone and skeletal muscle mass by components of the transforming growth factor-β signaling pathway., Yewei Liu, Adam Lehar, Renata Rydzik, Harshpreet Chandok, Yun-Sil Lee, Daniel W Youngstrom, Joshy George, Martin M Matzuk, Emily L Germain-Lee, and Se-Jin Lee
Transfer learning-trained convolutional neural networks identify novel MRI biomarkers of Alzheimer's disease progression., Yi Li, Annat Haber, Christoph Preuss, Cai John, Asli Uyar, Hongtian Stanley Yang, Benjamin A Logsdon, Vivek M. Philip, Radha Krishna Murthy Karuturi, Gregory W. Carter, and Alzheimer's Disease Neuroimaging Initative
Shared and distinctive features of the gut microbiome of C57BL/6 mice from different vendors and production sites, and in response to a new vivarium., Lauren L Long, Karen L. Svenson, Anthony J Mourino, Michael Michaud, James R Fahey, Linda L Waterman, Kathy L Vandegrift, and Mark D Adams
PhenoTagger: A Hybrid Method for Phenotype Concept Recognition using Human Phenotype Ontology., Ling Luo, Shankai Yan, Po-Ting Lai, Daniel Veltri, Andrew Oler, Sandhya Xirasagar, Rajarshi Ghosh, Morgan Similuk, Peter N Robinson, and Zhiyong Lu
Profiling variable-number tandem repeat variation across populations using repeat-pangenome graphs., Tsung-Yu Lu, Human Genome Structural Variation Consortium, Mark J P Chaisson, Charles Lee, and Qihui Zhu
PIP2 depletion and altered endocytosis caused by expression of Alzheimer's disease-protective variant PLCγ2 R522., Emily Maguire, Georgina E Menzies, Thomas Phillips, Michael Sasner, Harriet M Williams, Magdalena A Czubala, Neil Evans, Emma L Cope, Rebecca Sims, Gareth R Howell, Emyr Lloyd-Evans, Julie Williams, Nicholas D Allen, and Philip R Taylor
Seroprevalence of SARS-CoV-2-Specific IgG Antibodies Among Adults Living in Connecticut: Post-Infection Prevalence (PIP) Study., Shiwani Mahajan, Rajesh Srinivasan, Carrie A Redlich, Sara K Huston, Kelly M Anastasio, Lisa Cashman, Dorothy S Massey, Andrew Dugan, Dan Witters, Jenny Marlar, Shu-Xia Li, Zhenqiu Lin, Domonique Hodge, Manas Chattopadhyay, Mark D Adams, Charles Lee, Lokinendi V Rao, Chris Stewart, Karthik Kuppusamy, Albert I Ko, and Harlan M Krumholz
Spatial regulation by multiple Gremlin1 enhancers provides digit development with cis-regulatory robustness and evolutionary plasticity., Jonas Malkmus, Laurène Ramos Martins, Shalu Jhanwar, Bonnie Kircher, Victorio Palacio, Rushikesh Sheth, Francisca Leal, Amandine Duchesne, Javier Lopez-Rios, Kevin A Peterson, Robert Reinhardt, Koh Onimaru, Martin J Cohn, Aimée Zuniga, and Rolf Zeller
Genomic medicine year in review: 2021., Teri A Manolio, Carol J Bult, Rex L Chisholm, Patricia A Deverka, Geoffrey S Ginsburg, Madison Goldrich, Gail P Jarvik, George A Mensah, Erin M Ramos, Mary V Relling, Dan M Roden, Robb Rowley, Marc S Williams, and Eric D Green
Human macrophage polarization in the response to, Alberto Marin, Kristopher Van Huss, John Corbett, Sangjin Kim, Jonathon Mohl, Bo-Young Hong, and Jorge Cervantes
Nucleic Acid-Sensing and Interferon-Inducible Pathways Show Differential Methylation in MZ Twins Discordant for Lupus and Overexpression in Independent Lupus Samples: Implications for Pathogenic Mechanism and Drug Targeting., Miranda C Marion, Paula S Ramos, Prathyusha Bachali, Adam C Labonte, Kip D Zimmerman, Hannah C Ainsworth, Sarah E Heuer, Robert D Robl, Michelle D Catalina, Jennifer A Kelly, Timothy D Howard, Peter E Lipsky, Amrie C Grammer, and Carl D Langefeld
Solving patients with rare diseases through programmatic reanalysis of genome-phenome data., Leslie Matalonga, Carles Hernández-Ferrer, Davide Piscia, Rebecca Schüle, Matthis Synofzik, Ana Töpf, Lisenka E L M Vissers, Richarda de Voer, Raul Tonda, Steven Laurie, Marcos Fernandez-Callejo, Daniel Picó, Carles Garcia-Linares, Anastasios Papakonstantinou, Alberto Corvó, Ricky Joshi, Hector Diez, Ivo Gut, Alexander Hoischen, Holm Graessner, Sergi Beltran, Solve-RD Consortia, and Peter N Robinson
Developing and validating model systems for immuno-oncology., Claire E McCarthy, Nastaran Zahir, Mariam Eljanne, Elad Sharon, Emile E Voest, and Karolina Palucka
Cognitive Reserve in Model Systems for Mechanistic Discovery: The Importance of Longitudinal Studies., Joseph A McQuail, Amy R Dunn, Yaakov Stern, Carol A Barnes, Gerd Kempermann, Peter R Rapp, Catherine C Kaczorowski, and Thomas C Foster
Breast-Specific Molecular Clocks Comprised of ELF5 Expression and Promoter Methylation Identify Individuals Susceptible to Cancer Initiation, Masaru Miyano, Rosalyn W Sayaman, Sundus F Shalabi, Parijat Senapati, Jennifer C Lopez, Brittany Lynn Angarola, Stefan Hinz, Arrianna Zirbes, Olga Anczuków, Lisa D Yee, Mina S Sedrak, Martha R Stampfer, Victoria L Seewaldt, and Mark A LaBarge
The Clp1 R140H mutation alters tRNA metabolism and mRNA 3' processing in mouse models of pontocerebellar hypoplasia, Caitlin E Monaghan, Scott I Adamson, Mridu Kapur, Jeffrey H Chuang, and Susan L Ackerman
Endometrial receptivity and implantation require uterine BMP signaling through an ACVR2A-SMAD1/SMAD5 axis., Diana Monsivais, Takashi Nagashima, Renata Prunskaite-Hyyryläinen, Kaori Nozawa, Keisuke Shimada, Suni Tang, Clark Hamor, Julio E Agno, Fengju Chen, Ramya P Masand, Steven L Young, Chad J Creighton, Francesco J DeMayo, Masahito Ikawa, Se-Jin Lee, and Martin M Matzuk
Genetic Differences in Dorsal Hippocampus Acetylcholinesterase Activity Predict Contextual Fear Learning Across Inbred Mouse Strains., Sean M Mooney-Leber, Dana Zeid, Prescilla Garcia-Trevizo, Laurel R Seemiller, Molly A. Bogue, Stephen C. Grubb, Gary Peltz, and Thomas J Gould
Biomedical and societal impacts of in vitro embryo models of mammalian development., Naomi Moris, Cantas Alev, Martin Pera, and Alfonso Martinez Arias
Embryonic and Neonatal Mouse Cochleae Are Susceptible to Zika Virus Infection., Vidhya Munnamalai, Nabilah H Sammudin, Caryl A Young, Ankita Thawani, Richard J Kuhn, and Donna M Fekete
Construction of logic gates exploiting resonance phenomena in nonlinear systems., K Murali, S Rajasekar, Manaoj V Aravind, Vivek Kohar, W L Ditto, and Sudeshna Sinha
Harnessing tipping points for logic operations, K Murali, Sudeshna Sinha, Vivek Kohar, and William L Ditto
Enrichment of Neurodegenerative Microglia Signature in Brain-Derived Extracellular Vesicles Isolated from Alzheimer's Disease Mouse Models., Satoshi Muraoka, Mark P Jedrychowski, Naotoshi Iwahara, Mohammad Abdullah, Kristen D. Onos, Kelly J Keezer, Jianqiao Hu, Seiko Ikezu, Gareth R Howell, Steven P Gygi, and Tsuneya Ikezu
Association of Coding Variants in Hydroxysteroid 17-beta Dehydrogenase 14 (, Josyf C Mychaleckyj, Erkka Valo, Takaharu Ichimura, Tarunveer S Ahluwalia, Christian Dina, Rachel G Miller, Ivan G Shabalin, Beata Gyorgy, JingJing Cao, Suna Onengut-Gumuscu, Eiichiro Satake, Adam M Smiles, Jani K Haukka, David-Alexandre Tregouet, Tina Costacou, Kristina O'Neil, Andrew D Paterson, Carol Forsblom, Hillary A Keenan, Marcus G Pezzolesi, Marlon Pragnell, Andrzej Galecki, Stephen S Rich, Niina Sandholm, Ronald Klein, Barbara E Klein, Katalin Susztak, Trevor J Orchard, Ron Korstanje, George L King, Samy Hadjadj, Peter Rossing, Joseph V Bonventre, Per-Henrik Groop, James H Warram, and Andrzej S Krolewski
PLD3 is a neuronal lysosomal phospholipase D associated with β-amyloid plaques and cognitive function in Alzheimer's disease., Alex G Nackenoff, Timothy J Hohman, Sarah M Neuner, Carolyn S Akers, Nicole C Weitzel, Alena Shostak, Shawn M Ferguson, Bret Mobley, David A Bennett, Julie A Schneider, Angela L Jefferson, Catherine C Kaczorowski, and Matthew S Schrag
Predictive biomarkers for 5-fluorouracil and oxaliplatin-based chemotherapy in gastric cancers via profiling of patient-derived xenografts., Deukchae Na, Jeesoo Chae, Sung-Yup Cho, Wonyoung Kang, Ahra Lee, Seoyeon Min, Jinjoo Kang, Min Jung Kim, Jaeyong Choi, Woochan Lee, Dongjin Shin, Ahrum Min, Yu-Jin Kim, Kyung-Hun Lee, Tae-Yong Kim, Yun-Suhk Suh, Seong-Ho Kong, Hyuk-Joon Lee, Woo-Ho Kim, Hansoo Park, Seock-Ah Im, Han-Kwang Yang, Charles Lee, and Jong-Il Kim
GLIS1 regulates trabecular meshwork function and intraocular pressure and is associated with glaucoma in humans., K Saidas Nair, Chitrangda Srivastava, Robert V Brown, Swanand Koli, Hélène Choquet, Hong Soon Kang, Yien-Ming Kuo, Sara A Grimm, Caleb Sutherland, Alexandra Badea, G Allan Johnson, Yin Zhao, Jie Yin, Kyoko Okamoto, Graham Clark, Terete Borrás, Gulab Zode, Krishnakumar Kizhatil, Subhabrata Chakrabarti, Simon W M John, Eric Jorgenson, and Anton M Jetten
Hotspots of Human Mutation., Alex V Nesta, Denisse Tafur, and Christine R Beck
A novel treatment strategy for lapatinib resistance in a subset of HER2-amplified gastric cancer., Gang Ning, Qihui Zhu, Wonyoung Kang, Hamin Lee, Leigh Maher, Yun-Suhk Suh, Michael Michaud, Mayerlin Silva, Jee Young Kwon, Chengsheng Zhang, and Charles Lee
Ensuring best practice in genomics education and evaluation: reporting item standards for education and its evaluation in genomics (RISE2 Genomics)., Amy Nisselle, Monika Janinski, Melissa Martyn, Belinda McClaren, Nadia Kaunein, Kristine Barlow-Stewart, Andrea Belcher, John A Bernat, Stephanie Best, Michelle Bishop, June C Carroll, Martina Cornel, Vajira H W Dissanayake, Agnes Dodds, Kate Dunlop, Gunjan Garg, Russell Gear, Debra Graves, Ken Knight, Bruce Korf, Dhavendra Kumar, Mercy Laurino, Alan Ma, Jane Maguire, Andrew Mallett, Maria McCarthy, Alison McEwen, Nicola Mulder, Chirag Patel, Catherine Quinlan, Kate Reed, Erin Rooney Riggs, Ingrid Sinnerbrink, Anne Slavotinek, Vijayaprakash Suppiah, Bronwyn Terrill, Edward S Tobias, Emma Tonkin, Steve Trumble, Tina-Marie Wessels, Sylvia Metcalfe, Helen Jordan, and Clara Gaff
HEMDAG: a family of modular and scalable hierarchical ensemble methods to improve Gene Ontology term prediction., Marco Notaro, Marco Frasca, Alessandro Petrini, Jessica Gliozzo, Elena Casiraghi, Peter N Robinson, and Giorgio Valentini
Comprehensive Evaluation of the 5XFAD Mouse Model for Preclinical Testing Applications: A MODEL-AD Study., Adrian L Oblak, Peter B Lin, Kevin P Kotredes, Ravi S Pandey, Dylan Garceau, Harriet M. Jackson, Asli Uyar, Rita O'Rourke, Sarah O'Rourke, Cynthia Ingraham, Daria Bednarczyk, Melisa Belanger, Zackary A Cope, Gabriela J Little, Sean-Paul G Williams, Carl Ash, Adam Bleckert, Tim Ragan, Benjamin A Logsdon, Lara M Mangravite, Stacey J Sukoff Rizzo, Paul R Territo, Gregory W. Carter, Gareth R Howell, Michael Sasner, and Bruce T Lamb
Targeting antioxidant enzymes enhances the therapeutic efficacy of the BCL-X, Yumi Oh, Hae Rim Jung, Seoyeon Min, Jinjoo Kang, Dongjun Jang, Seungjae Shin, Jiwon Kim, Sang Eun Lee, Chang Ohk Sung, Won-Suk Lee, Charles Lee, Eui Man Jeong, and Sung-Yup Cho
Spatial and temporal expression of PORCN is highly dynamic in the developing mouse cochlea., Brianna L Oliver, Caryl A Young, and Vidhya Munnamalai