2024
- DITTO: An Explainable Machine-Learning Model for Transcript-Specific Variant Pathogenicity Prediction
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Tarun Karthik Kumar Mamidi, Brandon M. Wilk, Manavalan Gajapathy, Elizabeth A. WortheyPreprints, 2024. https://doi.org/10.20944/preprints202404.0837.v1
- Critical assessment of variant prioritization methods for rare disease diagnosis within the rare genomes project
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Sarah L. Stenton, Melanie C. O’Leary, Gabrielle Lemire, Grace E. VanNoy, Stephanie DiTroia, Vijay S. Ganesh, Emily Groopman, Emily O’Heir, Brian Mangilog, Ikeoluwa Osei-Owusu, Lynn S. Pais, Jillian Serrano, Moriel Singer-Berk, Ben Weisburd, Michael W. Wilson, Christina Austin-Tse, Marwa Abdelhakim, Azza Althagafi, Giulia Babbi, Riccardo Bellazzi, Samuele Bovo, Maria Giulia Carta, Rita Casadio, Pieter-Jan Coenen, Federica De Paoli, Matteo Floris, Manavalan Gajapathy, Robert Hoehndorf, Julius O. B. Jacobsen, Thomas Joseph, Akash Kamandula, Panagiotis Katsonis, Cyrielle Kint, Olivier Lichtarge, Ivan Limongelli, Yulan Lu, Paolo Magni, Tarun Karthik Kumar Mamidi, Pier Luigi Martelli, Marta Mulargia, Giovanna Nicora, Keith Nykamp, Vikas Pejaver, Yisu Peng, Thi Hong Cam Pham, Maurizio S. Podda, Aditya Rao, Ettore Rizzo, Vangala G. Saipradeep, Castrense Savojardo, Peter Schols, Yang Shen, Naveen Sivadasan, Damian Smedley, Dorian Soru, Rajgopal Srinivasan, Yuanfei Sun, Uma Sunderam, Wuwei Tan, Naina Tiwari, Xiao Wang, Yaqiong Wang, Amanda Williams, Elizabeth A. Worthey, Rujie Yin, Yuning You, Daniel Zeiberg, Susanna Zucca, Constantina Bakolitsa, Steven E. Brenner, Stephanie M. Fullerton, Predrag Radivojac, Heidi L. Rehm, Anne O’Donnell-LuriaHuman Genomics, 2024. https://doi.org/10.1186/s40246-024-00604-w
- Genotype–Phenotype Correlation in Neurofibromatosis Type 1: Evidence for a Mild Phenotype Associated with Splicing Variants Leading to In-Frame Skipping of NF1 Exon 24 [19a]
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Yunjia Chen, Yulong Fu, Magdalena Koczkowska, Tom Callens, Alicia Gomes, Jian Liu, William Bradley, Bryce Brown, Brandon Shaw, Daniela D’Agostino, Chuanhua Fu, Deeann WallisCancers, 2024. https://doi.org/10.3390/cancers16132406
- The landscape of SETBP1 gene expression and transcription factor activity across human tissues
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Jordan H. Whitlock, Elizabeth J. Wilk, Timothy C. Howton, Amanda D. Clark, Brittany N. LasseignePLOS ONE, 2024. https://doi.org/10.1371/journal.pone.0296328
- Sex-biased gene expression and gene-regulatory networks of sex-biased adverse event drug targets and drug metabolism genes
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Jennifer L. Fisher, Amanda D. Clark, Emma F. Jones, Brittany N. LasseigneBMC Pharmacology and Toxicology, 2024. https://doi.org/10.1186/s40360-023-00727-1
- Lack of Nuclear Localization of the Creb3l1 Transcription Factor Causes Defects in Caudal Fin Bifurcation in Zebrafish Danio rerio
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Peyton E VanWinkle, Bridge Wynn, Eunjoo Lee, Tomasz J Nawara, Holly Thomas, John M Parant, Cecilia Alvarez, Rosa Serra, Elizabeth SztulCells Tissues Organs, 2024. https://doi.org/10.1159/000540103
- Disruption of the creb3l1 gene causes defects in caudal fin regeneration and patterning in zebrafish Danio rerio
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Peyton E. VanWinkle, Eunjoo Lee, Bridge Wynn, Tomasz J. Nawara, Holly Thomas, John Parant, Cecilia Alvarez, Rosa Serra, Elizabeth SztulDevelopmental Dynamics, 2024. https://doi.org/10.1002/dvdy.726
- Standardization of zebrafish drug testing parameters for muscle diseases
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Muthukumar Karuppasamy, Katherine G. English, Clarissa A. Henry, M. Chiara Manzini, John M. Parant, Melissa A. Wright, Avnika A. Ruparelia, Peter D. Currie, Vandana A. Gupta, James J. Dowling, Lisa Maves, Matthew S. AlexanderDisease Models & Mechanisms, 2024. https://doi.org/10.1242/dmm.050339
- Precision preclinical modeling to advance cancer treatment
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David H Gutmann, Jesse S Boehm, Elinor K Karlsson, Eric Padron, Mukund Seshadri, Deeann Wallis, Joshua C SnyderJNCI: Journal of the National Cancer Institute, 2024. https://doi.org/10.1093/jnci/djae249
- Rab35 Is Required for Embryonic Development and Kidney and Ureter Homeostasis through Regulation of Epithelial Cell Junctions
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Kelsey R. Clearman, Napassawon Timpratoom, Dharti Patel, Addison B. Rains, Courtney J. Haycraft, Mandy J. Croyle, Jeremy F. Reiter, Bradley K. YoderJournal of the American Society of Nephrology, 2024. https://doi.org/10.1681/asn.0000000000000335
- NF1 mutation-driven neuronal hyperexcitability sets a threshold for tumorigenesis and therapeutic targeting of murine optic glioma
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Corina Anastasaki, Jit Chatterjee, Joshua P Koleske, Yunqing Gao, Stephanie L Bozeman, Chloe M Kernan, Lara I Marco Y Marquez, Ji-Kang Chen, Caitlin E Kelly, Connor J Blair, Dennis J Dietzen, Robert A Kesterson, David H GutmannNeuro-Oncology, 2024. https://doi.org/10.1093/neuonc/noae054
- Riding the gene therapy wave: challenges and opportunities for rare disease patients and clinicians
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Matthew S. Alexander, Nathaniel H. RobinCurrent Opinion in Pediatrics, 2024. https://doi.org/10.1097/mop.0000000000001402
- Streamlining Drug Repurposing: Optimizing Candidate Prioritization to Facilitate Clinical Adoption and Minimize Attrition Rates
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Emma Jones, Sasha Taluri, Elizabeth Wilk, Brittany LasseignePreprints, 2024. https://doi.org/10.20944/preprints202411.1592.v1
2023
- Ten simple rules for using public biological data for your research
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Vishal H. Oza, Jordan H. Whitlock, Elizabeth J. Wilk, Angelina Uno-Antonison, Brandon Wilk, Manavalan Gajapathy, Timothy C. Howton, Austyn Trull, Lara Ianov, Elizabeth A. Worthey, Brittany N. LasseignePLOS Computational Biology, 2023. https://doi.org/10.1371/journal.pcbi.1010749
- QuaC: A Pipeline Implementing Quality Control Best Practices for Genome Sequencing and Exome Sequencing Data
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Manavalan Gajapathy, Brandon M Wilk, Elizabeth A WortheyJournal of Open Source Software, 2023. https://doi.org/10.21105/joss.05313
- Rosalution: Supporting data accessibility, integration, curation, interoperability, and reuse for precision animal modeling
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Angelina E Uno-Antonison, Rabab Fatima, James Scherer, Alexander Moss, Donna Brown, Aleksandra Foksinska, Manavalan Gajapathy, Elizabeth J Wilk, Brittany N Lasseigne, Elizabeth WortheyJournal of Open Source Software, 2023. https://doi.org/10.21105/joss.05443
- CoSIA: an R Bioconductor package for CrOss Species Investigation and Analysis
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Anisha Haldar, Vishal H Oza, Nathaniel S DeVoss, Amanda D Clark, Brittany N LasseigneBioinformatics, 2023. https://doi.org/10.1093/bioinformatics/btad759
- Cell‐type‐specific gene expression and regulation in the cerebral cortex and kidney of atypical Setbp1S858R Schinzel Giedion Syndrome mice
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Jordan H. Whitlock, Tabea M. Soelter, Timothy C. Howton, Elizabeth J. Wilk, Vishal H. Oza, Brittany N. LasseigneJournal of Cellular and Molecular Medicine, 2023. https://doi.org/10.1111/jcmm.18001
- Prioritized polycystic kidney disease drug targets and repurposing candidates from pre-cystic and cystic mouse Pkd2 model gene expression reversion
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Elizabeth J. Wilk, Timothy C. Howton, Jennifer L. Fisher, Vishal H. Oza, Ryan T. Brownlee, Kasi C. McPherson, Hannah L. Cleary, Bradley K. Yoder, James F. George, Michal Mrug, Brittany N. LasseigneMolecular Medicine, 2023. https://doi.org/10.1186/s10020-023-00664-z
- Evaluating cancer cell line and patient‐derived xenograft recapitulation of tumor and non‐diseased tissue gene expression profiles in silico
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Avery S. Williams, Elizabeth J. Wilk, Jennifer L. Fisher, Brittany N. LasseigneCancer Reports, 2023. https://doi.org/10.1002/cnr2.1874
- The landscape of SETBP1 gene expression and transcription factor activity across human tissues
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Jordan H. Whitlock, Elizabeth J. Wilk, Timothy C. Howton, Amanda D. Clark, Brittany N. LasseignebioRxiv, 2023. https://doi.org/10.1101/2023.08.08.551337
- DOCK3 regulates normal skeletal muscle regeneration and glucose metabolism
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Adrienne Samani, Muthukumar Karuppasamy, Katherine G. English, Colin A. Siler, Yimin Wang, Jeffrey J. Widrick, Matthew S. AlexanderThe FASEB Journal, 2023. https://doi.org/10.1096/fj.202300386rr
- CINmetrics: an R package for analyzing copy number aberrations as a measure of chromosomal instability
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Vishal H. Oza, Jennifer L. Fisher, Roshan Darji, Brittany N. LasseignePeerJ, 2023. https://doi.org/10.7717/peerj.15244
- Restoration of brain dystrophin using tricyclo-DNA ASOs restores neurobehavioral deficits in DMD mice
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Muthukumar Karuppasamy, Matthew S. AlexanderMolecular Therapy – Nucleic Acids, 2023. https://doi.org/10.1016/j.omtn.2023.04.007
- Sex-biased gene expression and gene-regulatory networks of sex-biased adverse event drug targets and drug metabolism genes
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Jennifer L. Fisher, Amanda D. Clark, Emma F. Jones, Brittany N. LasseignebioRxiv, 2023. https://doi.org/10.1101/2023.05.23.541950
- Accuracy and processing time of kidney volume measurement methods in rodents polycystic kidney disease models: superiority of semiautomated kidney segmentation
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Mary Claire Doss, Sean Mullen, Ronald Roye, Juling Zhou, Phillip Chumley, Elias Mrug, Darren P. Wallace, Feng Qian, Peter C. Harris, Bradley K. Yoder, Harrison Kim, Michal MrugAmerican Journal of Physiology-Renal Physiology, 2023. https://doi.org/10.1152/ajprenal.00295.2022
2022
- DOCKopathies: A systematic review of the clinical pathologies associated with human DOCK pathogenic variants
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Adrienne Samani, Katherine G. English, Michael A. Lopez, Camille L. Birch, Donna M. Brown, Gurpreet Kaur, Elizabeth A. Worthey, Matthew S. AlexanderHuman Mutation, 2022. https://doi.org/10.1002/humu.24398
- Variable phenotypes and penetrance between and within different zebrafish ciliary transition zone mutants
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Jun Wang, Holly R. Thomas, Robert G. Thompson, Stephanie C. Waldrep, Joseph Fogerty, Ping Song, Zhang Li, Yongjie Ma, Peu Santra, Jonathan D. Hoover, Nan Cher Yeo, Iain A. Drummond, Bradley K. Yoder, Jeffrey D. Amack, Brian Perkins, John M. ParantDisease Models & Mechanisms, 2022. https://doi.org/10.1242/dmm.049568
- Reduced sister chromatid cohesion acts as a tumor penetrance modifier
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Jun Wang, Holly R. Thomas, Yu Chen, Stefanie M. Percival, Stephanie C. Waldrep, Ryne C. Ramaker, Robert G. Thompson, Sara J. Cooper, Zechen Chong, John M. ParantPLoS Genetics, 2022. https://doi.org/10.1371/journal.pgen.1010341
- Analysis of patient‐specific NF1 variants leads to functional insights for Ras signaling that can impact personalized medicine
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Ashlee Long, Hui Liu, Jian Liu, Michael Daniel, David M. Bedwell, Bruce Korf, Robert A. Kesterson, Deeann WallisHuman Mutation, 2022. https://doi.org/10.1002/humu.24290
- Functional characterization and potential therapeutic avenues for variants in the NTRK2 gene causing developmental and epileptic encephalopathies
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Ashlee Long, Andrew Crouse, Robert A. Kesterson, Matthew Might, Deeann WallisAmerican Journal of Medical Genetics Part B: Neuropsychiatric Genetics, 2022. https://doi.org/10.1002/ajmg.b.32882
- Targeted exon skipping of NF1 exon 17 as a therapeutic for neurofibromatosis type I
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André Leier, Marc Moore, Hui Liu, Michael Daniel, Alexis M. Hyde, Ludwine Messiaen, Bruce R. Korf, Jamuna Selvakumaran, Lukasz Ciszewski, Laura Lambert, Jeremy Foote, Margaret R. Wallace, Robert A. Kesterson, George Dickson, Linda Popplewell, Deeann WallisMolecular Therapy – Nucleic Acids, 2022. https://doi.org/10.1016/j.omtn.2022.03.011
- Next-Generation SINE Compound KPT−8602 Ameliorates Dystrophic Pathology in Zebrafish and Mouse Models of DMD
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Katherine G. English, Andrea L. Reid, Adrienne Samani, Gerald J. F. Coulis, S. Armando Villalta, Christopher J. Walker, Sharon Tamir, Matthew S. AlexanderBiomedicines, 2022. https://doi.org/10.3390/biomedicines10102400
- The precision medicine process for treating rare disease using the artificial intelligence tool mediKanren
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Aleksandra Foksinska, Camerron M. Crowder, Andrew B. Crouse, Jeff Henrikson, William E. Byrd, Gregory Rosenblatt, Michael J. Patton, Kaiwen He, Thi K. Tran-Nguyen, Marissa Zheng, Stephen A. Ramsey, Nada Amin, John Osborne, UAB Precision Medicine Institute, Matthew Might, Stephen Barnes, William E. Byrd, Mei-Jan Chen, Andrew B. Crouse, Camerron M. Crowder, Mary E. Crumbley, Madeline Eckenrode, Crayton A. Fargason, Nathaniel Fehrmann, Aleksandra Foksinska, Kaiwen He, Forest Huls, Matthew Jarrell, Lindsay Jenkins, Meg McCalley, Matthew Might, Tamsyn Osborn, Michael J. Patton, Elizabeth Pollard, Gregory Rosenblatt, Sienna Rucka, Nicholas T. Southern, Thi K. Tran-Nguyen, Jillian Tinglin, Jordan H. WhitlockFrontiers in Artificial Intelligence, 2022. https://doi.org/10.3389/frai.2022.910216
2021
- Evolutionarily conserved genetic interactions between nphp-4 and bbs-5 mutations exacerbate ciliopathy phenotypes
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Melissa R Bentley-Ford, Melissa LaBonty, Holly R Thomas, Courtney J Haycraft, Mikyla Scott, Cameron LaFayette, Mandy J Croyle, Reagan S Andersen, John M Parant, Bradley K YoderGenetics, 2021. https://doi.org/10.1093/genetics/iyab209
- Cystin genetic variants cause autosomal recessive polycystic kidney disease associated with altered Myc expression
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Chaozhe Yang, Naoe Harafuji, Amber K. O’Connor, Robert A. Kesterson, Jacob A. Watts, Amar J. Majmundar, Daniela A. Braun, Monkol Lek, Kristen M. Laricchia, Hanan M. Fathy, Shrikant Mane, Shirlee Shril, Friedhelm Hildebrandt, Lisa M. Guay-WoodfordScientific Reports, 2021. https://doi.org/10.1038/s41598-021-97046-4
- Puma, noxa, p53, and p63 differentially mediate stress pathway induced apoptosis
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Jun Wang, Holly R. Thomas, Zhang Li, Nan Cher (Florence) Yeo, Hannah E. Scott, Nghi Dang, Mohammed Iqbal Hossain, Shaida A. Andrabi, John M. ParantCell Death & Disease, 2021. https://doi.org/10.1038/s41419-021-03902-6
- Aberrant regulation of a poison exon caused by a non-coding variant in a mouse model of Scn1a-associated epileptic encephalopathy
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Yuliya Voskobiynyk, Gopal Battu, Stephanie A. Felker, J. Nicholas Cochran, Megan P. Newton, Laura J. Lambert, Robert A. Kesterson, Richard M. Myers, Gregory M. Cooper, Erik D. Roberson, Gregory S. BarshPLoS Genetics, 2021. https://doi.org/10.1371/journal.pgen.1009195
- Genotype–phenotype correlations and novel molecular insights into the DHX30-associated neurodevelopmental disorders
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Ilaria Mannucci, Nghi D. P. Dang, Hannes Huber, Jaclyn B. Murry, Jeff Abramson, Thorsten Althoff, Siddharth Banka, Gareth Baynam, David Bearden, Ana Beleza-Meireles, Paul J. Benke, Siren Berland, Tatjana Bierhals, Frederic Bilan, Laurence A. Bindoff, Geir Julius Braathen, Øyvind L. Busk, Jirat Chenbhanich, Jonas Denecke, Luis F. Escobar, Caroline Estes, Julie Fleischer, Daniel Groepper, Charlotte A. Haaxma, Maja Hempel, Yolanda Holler-Managan, Gunnar Houge, Adam Jackson, Laura Kellogg, Boris Keren, Catherine Kiraly-Borri, Cornelia Kraus, Christian Kubisch, Gwenael Le Guyader, Ulf W. Ljungblad, Leslie Manace Brenman, Julian A. Martinez-Agosto, Matthew Might, David T. Miller, Kelly Q. Minks, Billur Moghaddam, Caroline Nava, Stanley F. Nelson, John M. Parant, Trine Prescott, Farrah Rajabi, Hanitra Randrianaivo, Simone F. Reiter, Janneke Schuurs-Hoeijmakers, Perry B. Shieh, Anne Slavotinek, Sarah Smithson, Alexander P. A. Stegmann, Kinga Tomczak, Kristian Tveten, Jun Wang, Jordan H. Whitlock, Christiane Zweier, Kirsty McWalter, Jane Juusola, Fabiola Quintero-Rivera, Utz Fischer, Nan Cher Yeo, Hans-Jürgen Kreienkamp, Davor LesselGenome Medicine, 2021. https://doi.org/10.1186/s13073-021-00900-3
- Mechanics of dystrophin deficient skeletal muscles in very young mice and effects of age
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Michael A. Lopez, Sherina Bontiff, Mary Adeyeye, Aziz I. Shaibani, Matthew S. Alexander, Shari Wynd, Aladin M. BoriekAmerican Journal of Physiology-Cell Physiology, 2021. https://doi.org/10.1152/ajpcell.00155.2019
- A ciliopathy complex builds distal appendages to initiate ciliogenesis
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Dhivya Kumar, Addison Rains, Vicente Herranz-Pérez, Quanlong Lu, Xiaoyu Shi, Danielle L. Swaney, Erica Stevenson, Nevan J. Krogan, Bo Huang, Christopher Westlake, Jose Manuel Garcia-Verdugo, Bradley K. Yoder, Jeremy F. ReiterJournal of Cell Biology, 2021. https://doi.org/10.1083/jcb.202011133
- A mouse model of BBS identifies developmental and homeostatic effects of BBS5 mutation and identifies novel pituitary abnormalities
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Melissa R Bentley-Ford, Staci E Engle, Kelsey R Clearman, Courtney J Haycraft, Reagan S Andersen, Mandy J Croyle, Addison B Rains, Nicolas F Berbari, Bradley K YoderHuman Molecular Genetics, 2021. https://doi.org/10.1093/hmg/ddab039
- ATXN10 Is Required for Embryonic Heart Development and Maintenance of Epithelial Cell Phenotypes in the Adult Kidney and Pancreas
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Melissa R. Bentley-Ford, Reagan S. Andersen, Mandy J. Croyle, Courtney J. Haycraft, Kelsey R. Clearman, Jeremy B. Foote, Jeremy F. Reiter, Bradley K. YoderFrontiers in Cell and Developmental Biology, 2021. https://doi.org/10.3389/fcell.2021.705182
- Restoration of Normal NF1 Function with Antisense Morpholino Treatment of Recurrent Pathogenic Patient-Specific Variant c.1466A>G; p.Y489C
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Elias K. Awad, Marc Moore, Hui Liu, Lukasz Ciszewski, Laura Lambert, Bruce R. Korf, Linda Popplewell, Robert A. Kesterson, Deeann WallisJournal of Personalized Medicine, 2021. https://doi.org/10.3390/jpm11121320
2020
- DOCK3 is a dosage-sensitive regulator of skeletal muscle and Duchenne muscular dystrophy-associated pathologies
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Andrea L Reid, Yimin Wang, Adrienne Samani, Rylie M Hightower, Michael A Lopez, Shawn R Gilbert, Lara Ianov, David K Crossman, Louis J Dell’Italia, Douglas P Millay, Thomas van Groen, Ganesh V Halade, Matthew S AlexanderHuman Molecular Genetics, 2020. https://doi.org/10.1093/hmg/ddaa173
- BBSome Component BBS5 Is Required for Cone Photoreceptor Protein Trafficking and Outer Segment Maintenance
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Katie L. Bales, Melissa R. Bentley, Mandy J. Croyle, Robert A. Kesterson, Bradley K. Yoder, Alecia K. GrossInvestigative Ophthalmology & Visual Science, 2020. https://doi.org/10.1167/iovs.61.10.17
