James Knight, PhD
Research Scientist in Genetics
Research & Publications
Biography
News
Coauthors
Selected Publications
- Determining the serotype composition of mixed samples of pneumococcus using whole-genome sequencingKnight JR, Dunne EM, Mulholland EK, Saha S, Satzke C, Tothpal A, Weinberger DM. Determining the serotype composition of mixed samples of pneumococcus using whole-genome sequencing. Microbial Genomics 2020, 7: mgen000494. PMID: 33355528, PMCID: PMC8115901, DOI: 10.1099/mgen.0.000494.
- Integrative molecular and clinical profiling of acral melanoma links focal amplification of 22q11.21 to metastasisFarshidfar F, Rhrissorrakrai K, Levovitz C, Peng C, Knight J, Bacchiocchi A, Su J, Yin M, Sznol M, Ariyan S, Clune J, Olino K, Parida L, Nikolaus J, Zhang M, Zhao S, Wang Y, Huang G, Wan M, Li X, Cao J, Yan Q, Chen X, Newman AM, Halaban R. Integrative molecular and clinical profiling of acral melanoma links focal amplification of 22q11.21 to metastasis. Nature Communications 2022, 13: 898. PMID: 35197475, PMCID: PMC8866401, DOI: 10.1038/s41467-022-28566-4.
- HERV1-env Induces Unfolded Protein Response Activation in Autoimmune Liver Disease: A Potential Mechanism for Regulatory T Cell Dysfunction.Subramanian K, Paul S, Libby A, Patterson J, Arterbery A, Knight J, Castaldi C, Wang G, Avitzur Y, Martinez M, Lobritto S, Deng Y, Geliang G, Kroemer A, Fishbein T, Mason A, Dominguez-Villar M, Mariappan M, Ekong U. HERV1-env Induces Unfolded Protein Response Activation in Autoimmune Liver Disease: A Potential Mechanism for Regulatory T Cell Dysfunction. The Journal Of Immunology 2023, 210: 732-744. PMID: 36722941, PMCID: PMC10691554, DOI: 10.4049/jimmunol.2100186.
- Application of multiplex amplicon deep-sequencing (MAD-seq) to screen for putative drug resistance markers in the Necator americanus isotype-1 β-tubulin geneGeorge S, Suwondo P, Akorli J, Otchere J, Harrison LM, Bilguvar K, Knight JR, Humphries D, Wilson MD, Caccone A, Cappello M. Application of multiplex amplicon deep-sequencing (MAD-seq) to screen for putative drug resistance markers in the Necator americanus isotype-1 β-tubulin gene. Scientific Reports 2022, 12: 11459. PMID: 35794459, PMCID: PMC9259660, DOI: 10.1038/s41598-022-15718-1.
- 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 DiseaseDrelichman G, Escobar N, Soberon B, Basack N, Frabasil J, Schenone A, Aguilar G, Larroudé M, Knight J, Zhao D, Ruan J, Mistry PK, Disease A. 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. Molecular Genetics And Metabolism Reports 2021, 29: 100820. PMID: 34820281, PMCID: PMC8600149, DOI: 10.1016/j.ymgmr.2021.100820.
- DIAPH1 Variants in Non–East Asian Patients With Sporadic Moyamoya DiseaseKundishora AJ, Peters ST, Pinard A, Duran D, Panchagnula S, Barak T, Miyagishima DF, Dong W, Smith H, Ocken J, Dunbar A, Nelson-Williams C, Haider S, Walker RL, Li B, Zhao H, Thumkeo D, Marlier A, Duy PQ, Diab NS, Reeves BC, Robert SM, Sujijantarat N, Stratman AN, Chen YH, Zhao S, Roszko I, Lu Q, Zhang B, Mane S, Castaldi C, López-Giráldez F, Knight JR, Bamshad MJ, Nickerson DA, Geschwind DH, Chen SL, Storm PB, Diluna ML, Matouk CC, Orbach DB, Alper SL, Smith ER, Lifton RP, Gunel M, Milewicz DM, Jin SC, Kahle KT. DIAPH1 Variants in Non–East Asian Patients With Sporadic Moyamoya Disease. JAMA Neurology 2021, 78: 993-1003. PMID: 34125151, PMCID: PMC8204259, DOI: 10.1001/jamaneurol.2021.1681.
- Genetics of agenesis/hypoplasia of the uterus and vagina: narrowing down the number of candidate genes for Mayer–Rokitansky–Küster–Hauser SyndromeMikhael S, Dugar S, Morton M, Chorich LP, Tam KB, Lossie AC, Kim HG, Knight J, Taylor HS, Mukherjee S, Capra JA, Phillips JA, Friez M, Layman LC. Genetics of agenesis/hypoplasia of the uterus and vagina: narrowing down the number of candidate genes for Mayer–Rokitansky–Küster–Hauser Syndrome. Human Genetics 2021, 140: 667-680. PMID: 33469725, PMCID: PMC9211441, DOI: 10.1007/s00439-020-02239-y.
- Mutations disrupting neuritogenesis genes confer risk for cerebral palsyJin SC, Lewis SA, Bakhtiari S, Zeng X, Sierant MC, Shetty S, Nordlie SM, Elie A, Corbett MA, Norton BY, van Eyk CL, Haider S, Guida BS, Magee H, Liu J, Pastore S, Vincent JB, Brunstrom-Hernandez J, Papavasileiou A, Fahey MC, Berry JG, Harper K, Zhou C, Zhang J, Li B, Zhao H, Heim J, Webber DL, Frank MSB, Xia L, Xu Y, Zhu D, Zhang B, Sheth AH, Knight JR, Castaldi C, Tikhonova IR, López-Giráldez F, Keren B, Whalen S, Buratti J, Doummar D, Cho M, Retterer K, Millan F, Wang Y, Waugh JL, Rodan L, Cohen JS, Fatemi A, Lin AE, Phillips JP, Feyma T, MacLennan SC, Vaughan S, Crompton KE, Reid SM, Reddihough DS, Shang Q, Gao C, Novak I, Badawi N, Wilson YA, McIntyre SJ, Mane SM, Wang X, Amor DJ, Zarnescu DC, Lu Q, Xing Q, Zhu C, Bilguvar K, Padilla-Lopez S, Lifton RP, Gecz J, MacLennan AH, Kruer MC. Mutations disrupting neuritogenesis genes confer risk for cerebral palsy. Nature Genetics 2020, 52: 1046-1056. PMID: 32989326, PMCID: PMC9148538, DOI: 10.1038/s41588-020-0695-1.
- HERV1-env dependent unfolded protein response activation is a potential initiator of autoreactivity in autoimmune liver diseaseEkong U, Yao J, Knight J, Mehta S, Avitzur Y, Martinez M, Lobritto S, Mason A. HERV1-env dependent unfolded protein response activation is a potential initiator of autoreactivity in autoimmune liver disease. The Journal Of Immunology 2020, 204: 224.7-224.7. DOI: 10.4049/jimmunol.204.supp.224.7.
- The omentum of obese girls harbors small adipocytes and browning transcriptsTarabra E, Nouws J, Vash-Margita A, Nadzam GS, Goldberg-Gell R, Van Name M, Pierpont B, Knight J, Shulman GI, Caprio S. The omentum of obese girls harbors small adipocytes and browning transcripts. JCI Insight 2020, 5 PMID: 32125283, PMCID: PMC7213797, DOI: 10.1172/jci.insight.135448.
- The Use of Whole Exome Sequencing in a Cohort of Transgender Individuals to Identify Rare Genetic Variants.Theisen JG, Sundaram V, Filchak MS, Chorich LP, Sullivan ME, Knight J, Kim HG, Layman LC. The Use of Whole Exome Sequencing in a Cohort of Transgender Individuals to Identify Rare Genetic Variants. Scientific Reports 2019, 9: 20099. PMID: 31882810, PMCID: PMC6934803, DOI: 10.1038/s41598-019-53500-y.
- Genomic sites hypersensitive to ultraviolet radiationPremi S, Han L, Mehta S, Knight J, Zhao D, Palmatier MA, Kornacker K, Brash DE. Genomic sites hypersensitive to ultraviolet radiation. Proceedings Of The National Academy Of Sciences Of The United States Of America 2019, 116: 24196-24205. PMID: 31723047, PMCID: PMC6883822, DOI: 10.1073/pnas.1907860116.
- Correlations between genomic subgroup and clinical features in a cohort of more than 3000 meningiomas.Youngblood MW, Duran D, Montejo JD, Li C, Omay SB, Özduman K, Sheth AH, Zhao AY, Tyrtova E, Miyagishima DF, Fomchenko EI, Hong CS, Clark VE, Riche M, Peyre M, Boetto J, Sohrabi S, Koljaka S, Baranoski JF, Knight J, Zhu H, Pamir MN, Avşar T, Kilic T, Schramm J, Timmer M, Goldbrunner R, Gong Y, Bayri Y, Amankulor N, Hamilton RL, Bilguvar K, Tikhonova I, Tomak PR, Huttner A, Simon M, Krischek B, Kalamarides M, Erson-Omay EZ, Moliterno J, Günel M. Correlations between genomic subgroup and clinical features in a cohort of more than 3000 meningiomas. Journal Of Neurosurgery 2019, 133: 1-10. PMID: 31653806, DOI: 10.3171/2019.8.jns191266.
- Mutations in Chromatin Modifier and Ephrin Signaling Genes in Vein of Galen MalformationDuran D, Zeng X, Jin SC, Choi J, Nelson-Williams C, Yatsula B, Gaillard J, Furey CG, Lu Q, Timberlake AT, Dong W, Sorscher MA, Loring E, Klein J, Allocco A, Hunt A, Conine S, Karimy JK, Youngblood MW, Zhang J, DiLuna ML, Matouk CC, Mane S, Tikhonova IR, Castaldi C, López-Giráldez F, Knight J, Haider S, Soban M, Alper SL, Komiyama M, Ducruet AF, Zabramski JM, Dardik A, Walcott BP, Stapleton CJ, Aagaard-Kienitz B, Rodesch G, Jackson E, Smith ER, Orbach DB, Berenstein A, Bilguvar K, Vikkula M, Gunel M, Lifton RP, Kahle KT. Mutations in Chromatin Modifier and Ephrin Signaling Genes in Vein of Galen Malformation. Neuron 2018, 101: 429-443.e4. PMID: 30578106, PMCID: PMC10292091, DOI: 10.1016/j.neuron.2018.11.041.
- Insights into the evolution and drug susceptibility of Babesia duncani from the sequence of its mitochondrial and apicoplast genomesVirji AZ, Thekkiniath J, Ma W, Lawres L, Knight J, Swei A, Roch KL, Mamoun C. Insights into the evolution and drug susceptibility of Babesia duncani from the sequence of its mitochondrial and apicoplast genomes. International Journal For Parasitology 2018, 49: 105-113. PMID: 30176236, PMCID: PMC6395566, DOI: 10.1016/j.ijpara.2018.05.008.
- Inflammasome Priming Mediated via Toll-Like Receptors 2 and 4, Induces Th1-Like Regulatory T Cells in De Novo Autoimmune HepatitisArterbery AS, Yao J, Ling A, Avitzur Y, Martinez M, Lobritto S, Deng Y, Geliang G, Mehta S, Wang G, Knight J, Ekong UD. Inflammasome Priming Mediated via Toll-Like Receptors 2 and 4, Induces Th1-Like Regulatory T Cells in De Novo Autoimmune Hepatitis. Frontiers In Immunology 2018, 9: 1612. PMID: 30072988, PMCID: PMC6060440, DOI: 10.3389/fimmu.2018.01612.
- De Novo Mutation in Genes Regulating Neural Stem Cell Fate in Human Congenital HydrocephalusFurey CG, Choi J, Jin SC, Zeng X, Timberlake AT, Nelson-Williams C, Mansuri MS, Lu Q, Duran D, Panchagnula S, Allocco A, Karimy JK, Khanna A, Gaillard JR, DeSpenza T, Antwi P, Loring E, Butler WE, Smith ER, Warf BC, Strahle JM, Limbrick DD, Storm PB, Heuer G, Jackson EM, Iskandar BJ, Johnston JM, Tikhonova I, Castaldi C, López-Giráldez F, Bjornson RD, Knight JR, Bilguvar K, Mane S, Alper SL, Haider S, Guclu B, Bayri Y, Sahin Y, Apuzzo MLJ, Duncan CC, DiLuna ML, Günel M, Lifton RP, Kahle KT. De Novo Mutation in Genes Regulating Neural Stem Cell Fate in Human Congenital Hydrocephalus. Neuron 2018, 99: 302-314.e4. PMID: 29983323, PMCID: PMC7839075, DOI: 10.1016/j.neuron.2018.06.019.
- Contribution of rare inherited and de novo variants in 2,871 congenital heart disease probandsJin SC, Homsy J, Zaidi S, Lu Q, Morton S, DePalma SR, Zeng X, Qi H, Chang W, Sierant MC, Hung WC, Haider S, Zhang J, Knight J, Bjornson RD, Castaldi C, Tikhonoa IR, Bilguvar K, Mane SM, Sanders SJ, Mital S, Russell MW, Gaynor JW, Deanfield J, Giardini A, Porter GA, Srivastava D, Lo CW, Shen Y, Watkins WS, Yandell M, Yost HJ, Tristani-Firouzi M, Newburger JW, Roberts AE, Kim R, Zhao H, Kaltman JR, Goldmuntz E, Chung WK, Seidman JG, Gelb BD, Seidman CE, Lifton RP, Brueckner M. Contribution of rare inherited and de novo variants in 2,871 congenital heart disease probands. Nature Genetics 2017, 49: 1593-1601. PMID: 28991257, PMCID: PMC5675000, DOI: 10.1038/ng.3970.
- Integrated genomic characterization of IDH1-mutant glioma malignant progressionBai H, Harmancı AS, Erson-Omay EZ, Li J, Coşkun S, Simon M, Krischek B, Özduman K, Omay SB, Sorensen EA, Turcan Ş, Bakırcığlu M, Carrión-Grant G, Murray PB, Clark VE, Ercan-Sencicek AG, Knight J, Sencar L, Altınok S, Kaulen LD, Gülez B, Timmer M, Schramm J, Mishra-Gorur K, Henegariu O, Moliterno J, Louvi A, Chan TA, Tannheimer SL, Pamir MN, Vortmeyer AO, Bilguvar K, Yasuno K, Günel M. Integrated genomic characterization of IDH1-mutant glioma malignant progression. Nature Genetics 2015, 48: 59-66. PMID: 26618343, PMCID: PMC4829945, DOI: 10.1038/ng.3457.
- Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate speciesBradnam KR, Fass JN, Alexandrov A, Baranay P, Bechner M, Birol I, Boisvert S, Chapman JA, Chapuis G, Chikhi R, Chitsaz H, Chou WC, Corbeil J, Del Fabbro C, Docking TR, Durbin R, Earl D, Emrich S, Fedotov P, Fonseca NA, Ganapathy G, Gibbs RA, Gnerre S, Godzaridis É, Goldstein S, Haimel M, Hall G, Haussler D, Hiatt JB, Ho IY, Howard J, Hunt M, Jackman SD, Jaffe DB, Jarvis ED, Jiang H, Kazakov S, Kersey PJ, Kitzman JO, Knight JR, Koren S, Lam TW, Lavenier D, Laviolette F, Li Y, Li Z, Liu B, Liu Y, Luo R, MacCallum I, MacManes MD, Maillet N, Melnikov S, Naquin D, Ning Z, Otto TD, Paten B, Paulo OS, Phillippy AM, Pina-Martins F, Place M, Przybylski D, Qin X, Qu C, Ribeiro FJ, Richards S, Rokhsar DS, Ruby JG, Scalabrin S, Schatz MC, Schwartz DC, Sergushichev A, Sharpe T, Shaw TI, Shendure J, Shi Y, Simpson JT, Song H, Tsarev F, Vezzi F, Vicedomini R, Vieira BM, Wang J, Worley KC, Yin S, Yiu SM, Yuan J, Zhang G, Zhang H, Zhou S, Korf IF. Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. GigaScience 2013, 2: 10. PMID: 23870653, PMCID: PMC3844414, DOI: 10.1186/2047-217x-2-10.
- The bonobo genome compared with the chimpanzee and human genomes.Prüfer K, Munch K, Hellmann I, Akagi K, Miller JR, Walenz B, Koren S, Sutton G, Kodira C, Winer R, Knight JR, Mullikin JC, Meader SJ, Ponting CP, Lunter G, Higashino S, Hobolth A, Dutheil J, Karakoç E, Alkan C, Sajjadian S, Catacchio CR, Ventura M, Marques-Bonet T, Eichler EE, André C, Atencia R, Mugisha L, Junhold J, Patterson N, Siebauer M, Good JM, Fischer A, Ptak SE, Lachmann M, Symer DE, Mailund T, Schierup MH, Andrés AM, Kelso J, Pääbo S. The bonobo genome compared with the chimpanzee and human genomes. Nature 2012, 486: 527-31. PMID: 22722832, PMCID: PMC3498939, DOI: 10.1038/nature11128.
- Sequencing the nuclear genome of the extinct woolly mammoth.Miller W, Drautz DI, Ratan A, Pusey B, Qi J, Lesk AM, Tomsho LP, Packard MD, Zhao F, Sher A, Tikhonov A, Raney B, Patterson N, Lindblad-Toh K, Lander ES, Knight JR, Irzyk GP, Fredrikson KM, Harkins TT, Sheridan S, Pringle T, Schuster SC. Sequencing the nuclear genome of the extinct woolly mammoth. Nature 2008, 456: 387-90. PMID: 19020620, DOI: 10.1038/nature07446.
- Assessing the feasibility of GS FLX Pyrosequencing for sequencing the Atlantic salmon genome.Quinn NL, Levenkova N, Chow W, Bouffard P, Boroevich KA, Knight JR, Jarvie TP, Lubieniecki KP, Desany BA, Koop BF, Harkins TT, Davidson WS. Assessing the feasibility of GS FLX Pyrosequencing for sequencing the Atlantic salmon genome. BMC Genomics 2008, 9: 404. PMID: 18755037, PMCID: PMC2532694, DOI: 10.1186/1471-2164-9-404.
- Genome sequencing in microfabricated high-density picolitre reactors.Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ, Chen Z, Dewell SB, Du L, Fierro JM, Gomes XV, Godwin BC, He W, Helgesen S, Ho CH, Irzyk GP, Jando SC, Alenquer ML, Jarvie TP, Jirage KB, Kim JB, Knight JR, Lanza JR, Leamon JH, Lefkowitz SM, Lei M, Li J, Lohman KL, Lu H, Makhijani VB, McDade KE, McKenna MP, Myers EW, Nickerson E, Nobile JR, Plant R, Puc BP, Ronan MT, Roth GT, Sarkis GJ, Simons JF, Simpson JW, Srinivasan M, Tartaro KR, Tomasz A, Vogt KA, Volkmer GA, Wang SH, Wang Y, Weiner MP, Yu P, Begley RF, Rothberg JM. Genome sequencing in microfabricated high-density picolitre reactors. Nature 2005, 437: 376-80. PMID: 16056220, PMCID: PMC1464427, DOI: 10.1038/nature03959.