JK
James R. Knight
genomicsMutationEvolution, MolecularGenetic Predisposition to Diseasecongenital heart diseaseexome sequencingGenetic VariationGenomeGenome, MitochondrialGenomics
On Valency
published · living versionsW_26xzgw86·v1 · currentpublished
Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species
with Keith R. Bradnam, Joseph N. Fass, Anton Alexandrov, Paul Baranay +86
1 version
Preprints & journals
65 papers in the corpus · 2000–2026Optimizing next-generation sequencing for genetic diagnosis in autosomal dominant polycystic kidney disease.41653026 · Ma, Deqiong, Cho, Soyoung, Meng, Xinmiao et al.2026 · 1 citationGenetics in medicine : official journal of the American College of Medical Genetics. 2026;28(4):102529
LZTR1 is a melanoma oncogene that promotes invasion and suppresses apoptosis.40885854 · Bacchiocchi, Antonella, Mak, Michael, Khan, Zerin Mahzabin et al.2025 · 2 citationsOncogene. 2025;44(41):3974-3984
Activation of Pvt1b isoform contributes to local Pvt1 abundance to repress Myc during stress.40743223 · Li, Qiao, Olivero, Christiane E, Floyd, Erin et al.2025 · 1 citationPLoS genetics. 2025;21(7):e1011790
Copy Number Variants of Uncertain Significance by Chromosome Microarray Analysis from Consecutive Pediatric Patients: Reevaluation Following Current Guidelines and Reanalysis by Genome Sequencing.40869922 · Li, Wenjiao, Xie, Xiaolei, Chai, Hongyan et al.2025 · 3 citationsGenes. 2025;16(8)
Mutations in 329 probands with suspected renal electrolyte disorders10.1101/2025.04.28.25326317v1 · Aparicio, R. E., Jin, S. C., Dong, W. et al.2025 · 0 citationsmedRxiv
Auto-sumoylation of the yeast Ubc9 E2 SUMO-conjugating enzyme extends cellular lifespan.40254622 · Jeong, Dong-Won, Lee, Do Yoon, Kim, Seung Yeon et al.2025 · 6 citationsNature communications. 2025;16(1):3735
Genomic analysis of 11,555 probands identifies 60 dominant congenital heart disease genes.40127276 · Sierant, Michael C, Jin, Sheng Chih, Bilguvar, Kaya et al.2025 · 28 citationsProceedings of the National Academy of Sciences of the United States of America. 2025;122(13):e2420343122
Recessive genetic contribution to congenital heart disease in 5,424 probands.40030011 · Dong, Weilai, Jin, Sheng Chih, Sierant, Michael C et al.2025 · 17 citationsProceedings of the National Academy of Sciences of the United States of America. 2025;122(10):e2419992122
Transcriptomic landscape of cumulus cells from patients <38 years old with a history of poor ovarian response (POR) treated with platelet-rich plasma (PRP).39976580 · Roberts, Leah M, Herlihy, Nola, Reig, Andres et al.2025 · 0 citationsAging. 2025;17(2):431-447
Hypoxia is linked to acquired resistance to immune checkpoint inhibitors in lung cancer.39585348 · Robles-Oteíza, Camila, Hastings, Katherine, Choi, Jungmin et al.2024 · 36 citationsThe Journal of experimental medicine. 2025;222(1)
Improved Survival With Adjuvant Cyclooxygenase 2 Inhibition in PIK3CA-Activated Stage III Colon Cancer: CALGB/SWOG 80702 (Alliance).38889377 · Nowak, Jonathan A, Twombly, Tyler, Ma, Chao et al.2024 · 30 citationsJournal of clinical oncology : official journal of the American Society of Clinical Oncology. 2024;42(24):2853-2859
Heterozygous ZNHIT3 variants within the 17q12 recurrent deletion region are associated with Mayer-Rokitansky-Kuster Hauser (MRKH) syndrome.38599276 · Brakta, Soumia, Du, Quansheng, Chorich, Lynn P et al.2024 · 5 citationsMolecular and cellular endocrinology. 2024;589:112237
Auto-sumoylation of the Ubc9 E2 SUMO-conjugating Enzyme Extends Cellular Lifespan.38562857 · Ryu, Hong-Yeoul, Jeong, Dong-Won, Kim, Seung Yeon et al.2025 · 1 citationResearch square. 2024
Low-frequency inherited complement receptor variants are associated with purpura fulminans.38096369 · Bendapudi, Pavan K, Nazeen, Sumaiya, Ryu, Justine et al.2024 · 9 citationsBlood. 2024;143(11):1032-1044
Activated sputum eosinophils associated with exacerbations in children on mepolizumab.38485057 · Wilson, Gabriella E, Knight, James, Liu, Qing et al.2024 · 40 citationsThe Journal of allergy and clinical immunology. 2024;154(2):297-307.e13
Loss of cis-PTase function in the liver promotes a highly penetrant form of fatty liver disease that rapidly transitions to hepatocellular carcinoma.38014178 · Singh, Abhishek K, Chaube, Balkrishna, Citrin, Kathryn M et al.2024 · 1 citationbioRxiv : the preprint server for biology. 2023
Super-enhancer hijacking drives ectopic expression of hedgehog pathway ligands in meningiomas.37805627 · Youngblood, Mark W, Erson-Omay, Zeynep, Li, Chang et al.2023 · 19 citationsNature communications. 2023;14(1):6279
Integrated exome sequencing and microarray analyses detected genetic defects and underlying pathways of hepatocellular carcinoma.37418972 · Chong, Mei Ling, Knight, James, Peng, Gang et al.2023 · 3 citationsCancer genetics. 2023;276-277:30-35
Transcriptomic identification of genes expressed in invasive S. aureus diabetic foot ulcer infection.37434783 · Agidigbi, Taiwo Samuel, Kwon, Hyuk-Kwon, Knight, James R et al.2023 · 10 citationsFrontiers in cellular and infection microbiology. 2023;13:1198115
HERV1-env Induces Unfolded Protein Response Activation in Autoimmune Liver Disease: A Potential Mechanism for Regulatory T Cell Dysfunction.36722941 · Subramanian, Kumar, Paul, Saikat, Libby, Andrew et al.2023 · 8 citationsJournal of immunology (Baltimore, Md. : 1950). 2023;210(6):732-744
Multiomic analyses implicate a neurodevelopmental program in the pathogenesis of cerebral arachnoid cysts.36879130 · Kundishora, Adam J, Allington, Garrett, McGee, Stephen et al.2023 · 22 citationsNature medicine. 2023;29(3):667-678
Application of multiplex amplicon deep-sequencing (MAD-seq) to screen for putative drug resistance markers in the Necator americanus isotype-1 β-tubulin gene.35794459 · George, Santosh, Suwondo, Peter, Akorli, Jewelna et al.2022 · 10 citationsScientific reports. 2022;12(1):11459
Author Correction: Integrative molecular and clinical profiling of acral melanoma links focal amplification of 22q11.21 to metastasis.35538087 · Farshidfar, Farshad, Rhrissorrakrai, Kahn, Levovitz, Chaya et al.2022 · 2 citationsNature communications. 2022;13(1):2704
Integrative molecular and clinical profiling of acral melanoma links focal amplification of 22q11.21 to metastasis.35197475 · Farshidfar, Farshad, Rhrissorrakrai, Kahn, Levovitz, Chaya et al.2022 · 55 citationsNature communications. 2022;13(1):898
Long-read single molecule real-time (SMRT) sequencing of GBA1 locus in Gaucher disease national cohort from Argentina reveals high frequency of complex allele underlying severe skeletal phenotypes: Collaborative study from the Argentine Group for Diagnosis and Treatment of Gaucher Disease.34820281 · Drelichman, Guillermo I, Fernández Escobar, Nicolas, Soberon, Barbara C et al.2022 · 7 citationsMolecular genetics and metabolism reports. 2021;29:100820
D-bifunctional protein deficiency caused by splicing variants in a neonate with severe peroxisomal dysfunction and persistent hypoglycemia.34623748 · Werner, Kelly M, Cox, Allison J, Qian, Emily et al.2022 · 8 citationsAmerican journal of medical genetics. Part A. 2022;188(1):357-363
DIAPH1 Variants in Non-East Asian Patients With Sporadic Moyamoya Disease.34125151 · Kundishora, Adam J, Peters, Samuel T, Pinard, Amélie et al.2022 · 54 citationsJAMA neurology. 2021;78(8):993-1003
Integrative molecular and clinical profiling of acral melanoma identifies LZTR1 as a key tumor promoter and therapeutic target10.1101/2021.04.20.440286v1 · Farshidfar, F., Peng, C., Levovitz, C. et al.2021 · 2 citationsbioRxiv
Author Correction: Mutations disrupting neuritogenesis genes confer risk for cerebral palsy.33432185 · Jin, Sheng Chih, Lewis, Sara A, Bakhtiari, Somayeh et al.2021 · 3 citationsNature genetics. 2021;53(3):412
Genetics of agenesis/hypoplasia of the uterus and vagina: narrowing down the number of candidate genes for Mayer-Rokitansky-Küster-Hauser Syndrome.33469725 · Mikhael, Sasha, Dugar, Sonal, Morton, Madison et al.2021 · 34 citationsHuman genetics. 2021;140(4):667-680
Determining the serotype composition of mixed samples of pneumococcus using whole-genome sequencing.33355528 · Knight, James R, Dunne, Eileen M, Mulholland, E Kim et al.2021 · 27 citationsMicrobial genomics. 2021;7(1)
A two-pronged approach for rapid and high-throughput SARS-CoV-2 nucleic acid testing10.1101/2020.12.04.20234450v1 · Gandotra, N., Tikhonova, I., Cheermarla, N. R. et al.2020 · 0 citationsmedRxiv
Exome sequencing implicates genetic disruption of prenatal neuro-gliogenesis in sporadic congenital hydrocephalus.33077954 · Jin, Sheng Chih, Dong, Weilai, Kundishora, Adam J et al.2021 · 156 citationsNature medicine. 2020;26(11):1754-1765
Mutations disrupting neuritogenesis genes confer risk for cerebral palsy.32989326 · Jin, Sheng Chih, Lewis, Sara A, Bakhtiari, Somayeh et al.2020 · 180 citationsNature genetics. 2020;52(10):1046-1056
Exome Sequencing Implicates Impaired GABA Signaling and Neuronal Ion Transport in Trigeminal Neuralgia.33083721 · Dong, Weilai, Jin, Sheng Chih, Allocco, August et al.2022 · 47 citationsiScience. 2020;23(10):101552
The omentum of obese girls harbors small adipocytes and browning transcripts.32125283 · Tarabra, Elena, Nouws, Jessica, Vash-Margita, Alla et al.2021 · 9 citationsJCI insight. 2020;5(6)
The Use of Whole Exome Sequencing in a Cohort of Transgender Individuals to Identify Rare Genetic Variants.31882810 · Theisen, J Graham, Sundaram, Viji, Filchak, Mary S et al.2020 · 67 citationsScientific reports. 2019;9(1):20099
Genomic sites hypersensitive to ultraviolet radiation.31723047 · Premi, Sanjay, Han, Lynn, Mehta, Sameet et al.2020 · 95 citationsProceedings of the National Academy of Sciences of the United States of America. 2019;116(48):24196-24205
Correlations between genomic subgroup and clinical features in a cohort of more than 3000 meningiomas.31653806 · Youngblood, Mark W, Duran, Daniel, Montejo, Julio D et al.2024 · 181 citationsJournal of neurosurgery. 2020;133(5):1345-1354
Distinct adaptive mechanisms drive recovery from aneuploidy caused by loss of the Ulp2 SUMO protease.30575729 · Ryu, Hong-Yeoul, López-Giráldez, Francesc, Knight, James et al.2019 · 30 citationsNature communications. 2018;9(1):5417
Mutations in Chromatin Modifier and Ephrin Signaling Genes in Vein of Galen Malformation.30578106 · Duran, Daniel, Zeng, Xue, Jin, Sheng Chih et al.2019 · 79 citationsNeuron. 2019;101(3):429-443.e4
Hypokalemia Associated With a Claudin 10 Mutation: A Case Report.30482581 · Meyers, Nicole, Nelson-Williams, Carol, Malaga-Dieguez, Laura et al.2019 · 32 citationsAmerican journal of kidney diseases : the official journal of the National Kidney Foundation. 2019;73(3):425-428
Clonal evolution analysis of paired anaplastic and well-differentiated thyroid carcinomas reveals shared common ancestor.30136351 · Dong, Weilai, Nicolson, Norman G, Choi, Jungmin et al.2019 · 33 citationsGenes, chromosomes & cancer. 2018;57(12):645-652
Insights into the evolution and drug susceptibility of Babesia duncani from the sequence of its mitochondrial and apicoplast genomes.30176236 · Virji, Azan Z, Thekkiniath, Jose, Ma, Wenxiu et al.2019 · 27 citationsInternational journal for parasitology. 2019;49(2):105-113
Inflammasome Priming Mediated via Toll-Like Receptors 2 and 4, Induces Th1-Like Regulatory T Cells in De Novo Autoimmune Hepatitis.30072988 · Arterbery, Adam S, Yao, Jie, Ling, Andrew et al.2024 · 24 citationsFrontiers in immunology. 2018;9:1612
De Novo Mutation in Genes Regulating Neural Stem Cell Fate in Human Congenital Hydrocephalus.29983323 · Furey, Charuta Gavankar, Choi, Jungmin, Jin, Sheng Chih et al.2019 · 154 citationsNeuron. 2018;99(2):302-314.e4
Translocation of a gut pathobiont drives autoimmunity in mice and humans.29590047 · Manfredo Vieira, S, Hiltensperger, M, Kumar, V et al.2018 · 841 citationsScience (New York, N.Y.). 2018;359(6380):1156-1161
Contribution of rare inherited and de novo variants in 2,871 congenital heart disease probands.28991257 · Jin, Sheng Chih, Homsy, Jason, Zaidi, Samir et al.2017 · 875 citationsNature genetics. 2017;49(11):1593-1601
Isolated polycystic liver disease genes define effectors of polycystin-1 function.28862642 · Besse, Whitney, Dong, Ke, Choi, Jungmin et al.2019 · 50 citationsThe Journal of clinical investigation. 2017;127(9):3558
Isolated polycystic liver disease genes define effectors of polycystin-1 function.28375157 · Besse, Whitney, Dong, Ke, Choi, Jungmin et al.2017 · 203 citationsThe Journal of clinical investigation. 2017;127(5):1772-1785
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