Impact of essential genes on the success of genome editing experiments generating 3313 new genetically engineered mouse lines

Authors: Hillary Elrick, Kevin A. Peterson, Brandon J. Willis, Denise G. Lanza, Elif F. Acar, Edward J. Ryder, Lydia Teboul, Petr Kasparek, Marie-Christine Birling, David J. Adams, Allan Bradley, Robert E. Braun, Steve D. Brown, Adam Caulder, Gemma F. Codner, Francesco J. DeMayo, Mary E. Dickinson, Brendan Doe, Graham Duddy, Marina Gertsenstein, Leslie O. Goodwin, Yann Hérault, Lauri G. Lintott, K. C. Kent Lloyd, Isabel Lorenzo, Matthew Mackenzie, Ann-Marie Mallon, Colin McKerlie, Helen Parkinson, Ramiro Ramirez-Solis, John R. Seavitt, Radislav Sedlacek, William C. Skarnes, Damien Smedley, Sara Wells, Jacqueline K. White, Joshua A. Wood, International Mouse Phenotyping Consortium, Stephen A. Murray, Jason D. Heaney, Lauryl M. J. Nutter

Source: Scientific Reports, Vol 14, Iss 1, Pp 1-15 (2024)

Subject Terms: Cas9, Genome editing, Mouse, Knockout, Medicine, Science

File Description: electronic resource

Relation: https://doaj.org/toc/2045-2322

Access URL: https://doaj.org/article/0788cc9d0e59472c90243baecc221f96

Protocol for the functional evaluation of genetic variants using saturation genome editing

Authors: Sofia Obolenski, Rebeca Olvera-León, Dijue Sun, David J. Adams, Andrew J. Waters

Source: STAR Protocols, Vol 6, Iss 2, Pp 103710- (2025)

Subject Terms: CRISPR, Genetics, Genomics, High-Throughput Screening, Science (General), Q1-390

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2666166725001169; https://doaj.org/toc/2666-1667

Access URL: https://doaj.org/article/f3f60236635544cf9c790e356b1c7320

Variant ranking pipeline for complex familial disorders

Authors: Sneha Ralli, Tariq Vira, Carla Daniela Robles-Espinoza, David J. Adams, Angela R. Brooks-Wilson

Source: Scientific Reports, Vol 14, Iss 1, Pp 1-14 (2024)

Subject Terms: Medicine, Science

File Description: electronic resource

Relation: https://doaj.org/toc/2045-2322

Access URL: https://doaj.org/article/af953d68929d48dc8c6cf1de580b5a4b

Interrater reliability of interictal EEG waveforms in Lennox–Gastaut Syndrome

Authors: Derek K. Hu, Mandeep Rana, David J. Adams, Linda Do, Daniel W. Shrey, Shaun A. Hussain, Beth A. Lopour

Source: Epilepsia Open, Vol 9, Iss 1, Pp 176-186 (2024)

Subject Terms: epilepsy, epileptic encephalopathy, generalized paroxysmal fast activity, interictal epileptiform discharge, sleep spindle, spike and slow wave, Neurology. Diseases of the nervous system, RC346-429

File Description: electronic resource

Relation: https://doaj.org/toc/2470-9239

Access URL: https://doaj.org/article/5fd47000ea5042abb53ac29aa85b4297

Modeling methyl-sensitive transcription factor motifs with an expanded epigenetic alphabet

Authors: Coby Viner, Charles A. Ishak, James Johnson, Nicolas J. Walker, Hui Shi, Marcela K. Sjöberg-Herrera, Shu Yi Shen, Santana M. Lardo, David J. Adams, Anne C. Ferguson-Smith, Daniel D. De Carvalho, Sarah J. Hainer, Timothy L. Bailey, Michael M. Hoffman

Source: Genome Biology, Vol 25, Iss 1, Pp 1-46 (2024)

Subject Terms: Biology (General), QH301-705.5, Genetics, QH426-470

File Description: electronic resource

Relation: https://doaj.org/toc/1474-760X

Access URL: https://doaj.org/article/e7bb424ddc9949f19963f6d42c94377b

Saturation genome editing of DDX3X clarifies pathogenicity of germline and somatic variation

Authors: Elizabeth J. Radford, Hong-Kee Tan, Malin H. L. Andersson, James D. Stephenson, Eugene J. Gardner, Holly Ironfield, Andrew J. Waters, Daniel Gitterman, Sarah Lindsay, Federico Abascal, Iñigo Martincorena, Anna Kolesnik-Taylor, Elise Ng-Cordell, Helen V. Firth, Kate Baker, John R. B. Perry, David J. Adams, Sebastian S. Gerety, Matthew E. Hurles

Source: Nature Communications, Vol 14, Iss 1, Pp 1-17 (2023)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/787606f0736b45d2b045e1283e0cd595

IFI207, a young and fast‐evolving protein, controls retroviral replication via the STING pathway

Authors: Eileen A. Moran, Karen Salas-Briceno, Wenming Zhao, Takuji Enya, Alexya N. Aguilera, Ivan Acosta, Francis Alonzo, Dara Kiani, Judith Behnsen, Catalina Alvarez, Thomas M. Keane, David J. Adams, Jingtao Lilue, Susan R. Ross

Source: mBio, Vol 15, Iss 7 (2024)

Subject Terms: AIM-2-like receptor, viral immunity, evolution of gene function, nucleic acid sensor, Microbiology, QR1-502

File Description: electronic resource

Relation: https://doaj.org/toc/2150-7511

Access URL: https://doaj.org/article/dc580ccc007e4157abcf0818a77211f2

Knockout or inhibition of USP30 protects dopaminergic neurons in a Parkinson’s disease mouse model

Authors: Tracy-Shi Zhang Fang, Yu Sun, Andrew C. Pearce, Simona Eleuteri, Mark Kemp, Christopher A. Luckhurst, Rachel Williams, Ross Mills, Sarah Almond, Laura Burzynski, Nóra M. Márkus, Christopher J. Lelliott, Natasha A. Karp, David J. Adams, Stephen P. Jackson, Jin-Feng Zhao, Ian G. Ganley, Paul W. Thompson, Gabriel Balmus, David K. Simon

Source: Nature Communications, Vol 14, Iss 1, Pp 1-16 (2023)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/231adfbea4cd447195e9caff8d44823d

Cross-species oncogenomics offers insight into human muscle-invasive bladder cancer

Authors: Kim Wong, Federico Abascal, Latasha Ludwig, Heike Aupperle-Lellbach, Julia Grassinger, Colin W. Wright, Simon J. Allison, Emma Pinder, Roger M. Phillips, Laura P. Romero, Arnon Gal, Patrick J. Roady, Isabel Pires, Franco Guscetti, John S. Munday, Maria C. Peleteiro, Carlos A. Pinto, Tânia Carvalho, João Cota, Elizabeth C. Du Plessis, Fernando Constantino-Casas, Stephanie Plog, Lars Moe, Simone de Brot, Ingrid Bemelmans, Renée Laufer Amorim, Smitha R. Georgy, Justina Prada, Jorge del Pozo, Marianne Heimann, Louisiane de Carvalho Nunes, Outi Simola, Paolo Pazzi, Johan Steyl, Rodrigo Ubukata, Peter Vajdovich, Simon L. Priestnall, Alejandro Suárez-Bonnet, Franco Roperto, Francesca Millanta, Chiara Palmieri, Ana L. Ortiz, Claudio S. L. Barros, Aldo Gava, Minna E. Söderström, Marie O’Donnell, Robert Klopfleisch, Andrea Manrique-Rincón, Inigo Martincorena, Ingrid Ferreira, Mark J. Arends, Geoffrey A. Wood, David J. Adams, Louise van der Weyden

Source: Genome Biology, Vol 24, Iss 1, Pp 1-29 (2023)

Subject Terms: Canine, Feline, Bovine, Urinary bladder, Cancer, Mutational signature, Biology (General), QH301-705.5, Genetics, QH426-470

File Description: electronic resource

Relation: https://doaj.org/toc/1474-760X

Access URL: https://doaj.org/article/7c66e401481649aaa960de808d382f15

An Atlas of Variant Effects to understand the genome at nucleotide resolution

Authors: Douglas M. Fowler, David J. Adams, Anna L. Gloyn, William C. Hahn, Debora S. Marks, Lara A. Muffley, James T. Neal, Frederick P. Roth, Alan F. Rubin, Lea M. Starita, Matthew E. Hurles

Source: Genome Biology, Vol 24, Iss 1, Pp 1-12 (2023)

Subject Terms: Multiplexed assay of variant effect, Genome interpretation, Variant effect, Saturation mutagenesis, Functional genomics, Global alliance, Biology (General), QH301-705.5, Genetics, QH426-470

File Description: electronic resource

Relation: https://doaj.org/toc/1474-760X

Access URL: https://doaj.org/article/b9552b874a4a49a68deb254e2408b950

Association of germline variants in telomere maintenance genes (POT1, TERF2IP, ACD, and TERT) with spitzoid morphology in familial melanoma: A multi-center case seriesCapsule Summary

Authors: Alisa M. Goldstein, PhD, Richard Qin, BS, Emily Y. Chu, MD, PhD, David E. Elder, MBChB, Daniela Massi, MD, PhD, David J. Adams, PhD, Paul W. Harms, MD, PhD, Carla Daniela Robles-Espinoza, PhD, Julia A. Newton-Bishop, MD, PhD, D. Timothy Bishop, PhD, Mark Harland, PhD, Elizabeth A. Holland, BSc, Anne E. Cust, PhD, Helen Schmid, MPH, Graham J. Mann, MBBS, PhD, Susana Puig, MD, PhD, Miriam Potrony, PhD, Llucia Alos, MD, PhD, Eduardo Nagore, MD, PhD, David Millán-Esteban, PhD, Nicholas K. Hayward, PhD, Natasa Broit, PhD, Jane M. Palmer, RN, Vaishnavi Nathan, PhD, Elizabeth G. Berry, MD, Esteban Astiazaran-Symonds, MD, Xiaohong R. Yang, PhD, Margaret A. Tucker, MD, Maria Teresa Landi, MD, PhD, Ruth M. Pfeiffer, PhD, Michael R. Sargen, MD

Source: JAAD International, Vol 11, Iss , Pp 43-51 (2023)

Subject Terms: ACD, familial melanoma, melanoma, POT1, spitzoid melanoma, spitz melanoma, Dermatology, RL1-803

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2666328723000147; https://doaj.org/toc/2666-3287

Access URL: https://doaj.org/article/b6d3451b882d49dc952ed23a5da93142

NFIL3 contributes to cytotoxic T lymphocyte-mediated killing

Authors: Tiphaine Douanne, Katharina Strege, Martin Del Castillo Velasco-Herrera, Adam M. Rochussen, David J. Adams, Gillian M. Griffiths

Source: Open Biology, Vol 14, Iss 2 (2024)

Subject Terms: NFIL3, cytotoxic T cell, T-cell-mediated killing, perforin, granzyme, autoimmunity, Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://doaj.org/toc/2046-2441

Access URL: https://doaj.org/article/78f578d56464498ba49c4f17d93fc1c2

Genome-wide screening reveals the genetic basis of mammalian embryonic eye development

Authors: Justine M. Chee, Louise Lanoue, Dave Clary, Kendall Higgins, Lynette Bower, Ann Flenniken, Ruolin Guo, David J. Adams, Fatima Bosch, Robert E. Braun, Steve D. M. Brown, H.-J. Genie Chin, Mary E. Dickinson, Chih-Wei Hsu, Michael Dobbie, Xiang Gao, Sanjeev Galande, Anne Grobler, Jason D. Heaney, Yann Herault, Martin Hrabe de Angelis, Fabio Mammano, Lauryl M. J. Nutter, Helen Parkinson, Chuan Qin, Toshi Shiroishi, Radislav Sedlacek, J-K Seong, Ying Xu, The International Mouse Phenotyping Consortium, Brian Brooks, Colin McKerlie, K. C. Kent Lloyd, Henrik Westerberg, Ala Moshiri

Source: BMC Biology, Vol 21, Iss 1, Pp 1-15 (2023)

Subject Terms: MAC spectrum, Eye development, Mouse, IMPC, Serine-glycine biosynthesis, CPLANE, Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://doaj.org/toc/1741-7007

Access URL: https://doaj.org/article/f36d8250a6ce4896a0f38551711ec1ef

Towards a clinically-based common coordinate framework for the human gut cell atlas: the gut models

Authors: Albert Burger, Richard A. Baldock, David J. Adams, Shahida Din, Irene Papatheodorou, Michael Glinka, Bill Hill, Derek Houghton, Mehran Sharghi, Michael Wicks, Mark J. Arends

Source: BMC Medical Informatics and Decision Making, Vol 23, Iss 1, Pp 1-17 (2023)

Subject Terms: Human cell atlas, Human gut cell atlas, Common coordinate framework, Computer applications to medicine. Medical informatics, R858-859.7

File Description: electronic resource

Relation: https://doaj.org/toc/1472-6947

Access URL: https://doaj.org/article/5036c98cb2794b52894100234eea3c03

Analysis of genome-wide knockout mouse database identifies candidate ciliopathy genes

Authors: Kendall Higgins, Bret A. Moore, Zorana Berberovic, Hibret A. Adissu, Mohammad Eskandarian, Ann M. Flenniken, Andy Shao, Denise M. Imai, Dave Clary, Louise Lanoue, Susan Newbigging, Lauryl M. J. Nutter, David J. Adams, Fatima Bosch, Robert E. Braun, Steve D. M. Brown, Mary E. Dickinson, Michael Dobbie, Paul Flicek, Xiang Gao, Sanjeev Galande, Anne Grobler, Jason D. Heaney, Yann Herault, Martin Hrabe de Angelis, Hsian-Jean Genie Chin, Fabio Mammano, Chuan Qin, Toshihiko Shiroishi, Radislav Sedlacek, J.-K. Seong, Ying Xu, The IMPC Consortium, K. C. Kent Lloyd, Colin McKerlie, Ala Moshiri

Source: Scientific Reports, Vol 12, Iss 1, Pp 1-17 (2022)

Subject Terms: Medicine, Science

File Description: electronic resource

Relation: https://doaj.org/toc/2045-2322

Access URL: https://doaj.org/article/c0d5d5cc412449dba2430740f3a4e375

SHLD1 is dispensable for 53BP1-dependent V(D)J recombination but critical for productive class switch recombination

Authors: Estelle Vincendeau, Wenming Wei, Xuefei Zhang, Cyril Planchais, Wei Yu, Hélène Lenden-Hasse, Thomas Cokelaer, Juliana Pipoli da Fonseca, Hugo Mouquet, David J. Adams, Frederick W. Alt, Stephen P. Jackson, Gabriel Balmus, Chloé Lescale, Ludovic Deriano

Source: Nature Communications, Vol 13, Iss 1, Pp 1-16 (2022)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/29536601a7d546f9b2f28d98202fe331

The role of ion channels in T cell function and disease

Authors: Nicholas Manolios, John Papaemmanouil, David J. Adams

Source: Frontiers in Immunology, Vol 14 (2023)

Subject Terms: ion channels, calcium signalling, T cells, antigen receptor, signal transduction, therapeutics, Immunologic diseases. Allergy, RC581-607

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fimmu.2023.1238171/full; https://doaj.org/toc/1664-3224

Access URL: https://doaj.org/article/de8722ed837c4be0b5aeacb5f13d2fec

Acetaldehyde and defective mismatch repair increase colonic tumours in a Lynch syndrome model with Aldh1b1 inactivation

Authors: Guia Cerretelli, Ying Zhou, Mike F. Müller, David J. Adams, Mark J. Arends

Source: Disease Models & Mechanisms, Vol 16, Iss 8 (2023)

Subject Terms: lynch syndrome, mismatch repair, msh2, aldh1b1, ethanol, acetaldehyde, colorectal cancer, adenoma, Medicine, Pathology, RB1-214

File Description: electronic resource

Relation: http://dmm.biologists.org/content/16/8/dmm050240; https://doaj.org/toc/1754-8403; https://doaj.org/toc/1754-8411

Access URL: https://doaj.org/article/c375c528246b4f8fbe724d90fe6dc9b4

eIF6 rebinding dynamically couples ribosome maturation and translation

Authors: Pekka Jaako, Alexandre Faille, Shengjiang Tan, Chi C. Wong, Norberto Escudero-Urquijo, Pablo Castro-Hartmann, Penny Wright, Christine Hilcenko, David J. Adams, Alan J. Warren

Source: Nature Communications, Vol 13, Iss 1, Pp 1-11 (2022)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/453b7a70084349bea9b8597caaa6ef1f

Identification and characterisation of spontaneous mutations causing deafness from a targeted knockout programme

Authors: Morag A. Lewis, Neil J. Ingham, Jing Chen, Selina Pearson, Francesca Di Domenico, Sohinder Rekhi, Rochelle Allen, Matthew Drake, Annelore Willaert, Victoria Rook, Johanna Pass, Thomas Keane, David J. Adams, Abigail S. Tucker, Jacqueline K. White, Karen P. Steel

Source: BMC Biology, Vol 20, Iss 1, Pp 1-27 (2022)

Subject Terms: Spontaneous mutations, Large-scale mutagenesis programme, Deafness, Progressive hearing loss, Non-segregating phenotypes, Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://doaj.org/toc/1741-7007

Access URL: https://doaj.org/article/65098ed95b304c7e91044004c6edaebd