Publications: Bioinformatics Lab - UT Southwestern, Dallas, Texas

Bioinformatics Lab actively collaborates with the investigators on various projects involving bioinformatics and biostatistics. Our collaboration projects were published in high impact journals. Below are our featured collaborative publications and a list of publications by years.

You are welcome to contact us for collaborations.

Featured Publications

Ramalingam H., Kashyap S., Cobo-Stark P., Flaten A., Chang C. M., Hajarnis S., Hein K. Z., Lika J., Warner G. M., Espindola-Netto J. M., Kumar A., Kanchwala M., Xing C., Chini E. N., & Patel V. (2021). A methionine-Mettl3-N(6)-methyladenosine axis promotes polycystic kidney disease. Cell Metab, 33(6): 1234-1247.e1237

Chen B., Aredo B., Ding Y., Zhong X., Zhu Y., Zhao C. X., Kumar A., Xing C., Gautron L., Lyon S., Russell J., Li X., Tang M., Anderton P., Ludwig S., Moresco E. M. Y., Beutler B., & Ufret-Vincenty R. L. (2020). Forward genetic analysis using OCT screening identifies Sfxn3 mutations leading to progressive outer retinal degeneration in mice. Proc Natl Acad Sci U S A, 117(23): 12931-12942

Nguyen N. U. N., Canseco D. C., Xiao F., Nakada Y., Li S., Lam N. T., Muralidhar S. A., Savla J. J., Hill J. A., Le V., Zidan K. A., El-Feky H. W., Wang Z., Ahmed M. S., Hubbi M. E., Menendez-Montes I., Moon J., Ali S. R., Le V., Villalobos E., Mohamed M. S., Elhelaly W. M., Thet S., Anene-Nzelu C. G., Tan W. L. W., Foo R. S., Meng X., Kanchwala M., Xing C., Roy J., Cyert M. S., Rothermel B. A., & Sadek H. A. (2020). A calcineurin-Hoxb13 axis regulates growth mode of mammalian cardiomyocytes. Nature, 582(7811): 271-276

Suresh S., Chen B., Zhu J., Golden R. J., Lu C., Evers B. M., Novaresi N., Smith B., Zhan X., Schmid V., Jun S., Karacz C. M., Peyton M., Zhong L., Wen Z., Sathe A. A., Xing C., Behrens C., Wistuba, II, Xiao G., Xie Y., Fu Y. X., Minna J. D., Mendell J. T., & O'Donnell K. A. (2020). eIF5B drives integrated stress response-dependent translation of PD-L1 in lung cancer. Nat Cancer, 1(5): 533-545

Liu Z., Mar K. B., Hanners N. W., Perelman S. S., Kanchwala M., Xing C., Schoggins J. W., & Alto N. M. (2019). A NIK-SIX signalling axis controls inflammation by targeted silencing of non-canonical NF-kappaB. Nature, 568(7751): 249-253

Wambach J. A., Wegner D. J., Patni N., Kircher M., Willing M. C., Baldridge D., Xing C., Agarwal A. K., Vergano S. A. S., Patel C., Grange D. K., Kenney A., Najaf T., Nickerson D. A., Bamshad M. J., Cole F. S., & Garg A. (2018). Bi-allelic POLR3A Loss-of-Function Variants Cause Autosomal-Recessive Wiedemann-Rautenstrauch Syndrome. Am J Hum Genet, 103(6): 968-975

Richardson R. B., Ohlson M. B., Eitson J. L., Kumar A., McDougal M. B., Boys I. N., Mar K. B., De La Cruz-Rivera P. C., Douglas C., Konopka G., Xing C., & Schoggins J. W. (2018). A CRISPR screen identifies IFI6 as an ER-resident interferon effector that blocks flavivirus replication. Nat Microbiol, 3(11): 1214-1223

De Nisco N. J., Kanchwala M., Li P., Fernandez J., Xing C., & Orth K. (2017). The cytotoxic type 3 secretion system 1 of Vibrio rewires host gene expression to subvert cell death and activate cell survival pathways. Sci Signal, 10(479)

Choi E., Zhang X., Xing C., & Yu H. (2016). Mitotic Checkpoint Regulators Control Insulin Signaling and Metabolic Homeostasis. Cell, 166(3): 567-581

Starokadomskyy P., Gemelli T., Rios J. J., Xing C., Wang R. C., Li H., Pokatayev V., Dozmorov I., Khan S., Miyata N., Fraile G., Raj P., Xu Z., Xu Z., Ma L., Lin Z., Wang H., Yang Y., Ben-Amitai D., Orenstein N., Mussaffi H., Baselga E., Tadini G., Grunebaum E., Sarajlija A., Krzewski K., Wakeland E. K., Yan N., de la Morena M. T., Zinn A. R., & Burstein E. (2016). DNA polymerase-alpha regulates the activation of type I interferons through cytosolic RNA:DNA synthesis. Nat Immunol, 17(5): 495-504

2021

Selvaraj UM, Ujas TA, Kong X, Kumar A, Plautz EJ, Zhang S, Xing C, Sudduth TL, Wilcock DM, Turchan-Cholewo J, Goldberg MP, Stowe AM. (2021). Delayed diapedesis of CD8 T cells contributes to long-term pathology after ischemic stroke in male mice. Brain Behav Immun. 95:502-513.

Xing C, Kanchwala M, Rios JJ, Hyatt T, Wang RC, Tran A, Dougherty I, Tovar-Garza A, Purnadi C, Kumar MG, Berk D, Shinawi M, Irvine AD, Toledo-Bahena M, Agim NG, Glass DA 2nd. (2021). Biallelic variants in RNU12 cause CDAGS syndrome. Hum Mutat. [Epub ahead of print] PubMed PMID: 34085356.

Ramalingam H, Kashyap S, Cobo-Stark P, Flaten A, Chang CM, Hajarnis S, Hein KZ, Lika J, Warner GM, Espindola-Netto JM, Kumar A, Kanchwala M, Xing C, Chini EN, Patel V. (2021). A methionine-Mettl3-N⁶-methyladenosine axis promotes polycystic kidney disease. Cell Metab. 33(6):1234-1247.

Scarborough AM, Flaherty JN, Hunter OV, Liu K, Kumar A, Xing C, Tu BP, Conrad NK. (2021). SAM homeostasis is regulated by CFI_m-mediated splicing of MAT2A. Elife. 5;10.

Ni M, Afroze B, Xing C, Pan C, Shao Y, Cai L, Cantarel BL, Pei J, Grishin NV, Hewson S, Knight D, Mahida S, Michel D, Tarnopolsky M, Poduri A, Rotenberg A, Sondheimer N, DeBerardinis RJ. (2021). A pathogenic UFSP2 variant in an autosomal recessive form of pediatric neurodevelopmental anomalies and epilepsy. Genet Med. 23(5):900-908.

Ni M, Black LF, Pan C, Vu H, Pei J, Ko B, Cai L, Solmonson A, Yang C, Nugent KM, Grishin NV, Xing C, Roeder E, DeBerardinis RJ. (2021). Metabolic impact of pathogenic variants in the mitochondrial glutamyl-tRNA synthetase EARS2. J Inherit Metab Dis. [Epub ahead of print] PubMed PMID: 33855712.

Woodard DR, Xing C, Ganne P, Liang H, Mahindrakar A, Sankurathri C, Hulleman JD, Mootha VV. (2021). A novel homozygous missense mutation p.P388S in TULP1 causes protein instability and retinitis pigmentosa. Mol Vis. 27:179-190.

Chen L, Bao L, Niu Y, Wang JE, Kumar A, Xing C, Wang Y, Luo W. (2021). LncIHAT Is Induced by Hypoxia-Inducible Factor 1 and Promotes Breast Cancer Progression. Mol Cancer Res. 19(4):678-687.

Richardson TE, Sathe AA, Xing C, Mirchia K, Viapiano MS, Snuderl M, Abdullah KG, Hatanpaa KJ, Walker JM. (2021). Molecular Signatures of Chromosomal Instability Correlate With Copy Number Variation Patterns and Patient Outcome in IDH-Mutant and IDH-Wildtype Astrocytomas. J Neuropathol Exp Neurol. 80(4):354-365.

De Nisco NJ, Casey AK, Kanchwala M, Lafrance AE, Coskun FS, Kinch LN, Grishin NV, Xing C, Orth K. (2021). Manipulation of IRE1-Dependent MAPK Signaling by a Vibrio Agonist-Antagonist Effector Pair. mSystems. 6(1).

Prokai D, Pudasaini A, Kanchwala M, Moehlman AT, Waits AE, Chapman KM, Chaudhary J, Acevedo J, Keller P, Xing C, Carr BR, Hamra FK. (2021). Spermatogonial Gene Networks ively Couple to Glutathione and Pentose Phosphate Metabolism but Not Cysteine Biosynthesis. iScience. 24(1):101880.

Brosseau JP, Sathe AA, Wang Y, Nguyen T, Glass DA 2nd, Xing C, Le LQ. (2021). Human cutaneous neurofibroma matrisome revealed by single-cell RNA sequencing. Acta Neuropathol Commun. 9(1):11.

2020

Dahl HC, Kanchwala M, Thomas-Jardin SE, Sandhu A, Kanumuri P, Nawas AF, Xing C, Lin C, Frigo DE, Delk NA. (2020). Chronic IL-1 exposure drives LNCaP cells to evolve androgen and AR independence. PLoS One. e0242970.

Wu G, Liu L, Zhou Z, Liu J, Wang B, Ruan J, Yang Q, Kanchwala M, Dai P, Zhang C, Wang D, Kang L, Wang S, Hui R, Zou Y, Xing C, Song L, Wang J. (2020). East Asian-Specific Common Variant in TNNI3 Predisposes to Hypertrophic Cardiomyopathy. Circulation. 142(21):2086-2089.

Jiang X, Shao Y, Araj FG, Amin AA, Greenberg BM, Drazner MH, Xing C, Mammen PPA. (2020). Heterozygous Cystic Fibrosis Transmembrane Regulator Gene Missense Variants Are Associated With Worse Cardiac Function in Patients With Duchenne Muscular Dystrophy. J Am Heart Assoc. 9(19):e016799.

Hussain I, Jin RR, Baum HBA, Greenfield JR, Devery S, Xing C, Hegele RA, Carranza-Leon BG, Linton MF, Vuitch F, Wu KHC, Precioso DR, Oshima J, Agarwal AK, Garg A. (2020). Multisystem Progeroid Syndrome With Lipodystrophy, Cardiomyopathy, and Nephropathy Due to an LMNA p.R349W Variant. J Endocr Soc. 4(10):bvaa104.

Richardson TE, Kumar A, Xing C, Hatanpaa KJ, Walker JM. (2020). Overcoming the Odds: Toward a Molecular Profile of Long-Term Survival in Glioblastoma. J Neuropathol Exp Neurol. 79(10):1031-1037.

Wang Y, Chen Y, Bao L, Zhang B, Wang JE, Kumar A, Xing C, Wang Y, Luo W. (2020). CHD4 Promotes Breast Cancer Progression as a Coactivator of Hypoxia-Inducible Factors. Cancer Res. 80(18):3880-3891.

Richardson TE, Williams M, Galbraith K, Mirchia K, Kumar A, Xing C, Walker JM. (2020). Total copy number variation, somatic mutation burden, and histologic grade correlate with clinical outcome in oligodendroglioma. Clin Neuropathol. 39(5):238-242.

Wang X, Sathe AA, Smith GR, Ruf-Zamojski F, Nair V, Lavine KJ, Xing C, Sealfon SC, Zhou L. (2020). Heterogeneous origins and functions of mouse skeletal muscle-resident macrophages. Proc Natl Acad Sci U S A. 117(34):20729-20740.

Ramanand SG, Chen Y, Yuan J, Daescu K, Lambros MB, Houlahan KE, Carreira S, Yuan W, Baek G, Sharp A, Paschalis A, Kanchwala M, Gao Y, Aslam A, Safdar N, Zhan X, Raj GV, Xing C, Boutros PC, de Bono J, Zhang MQ, Mani RS. (2020). The landscape of RNA polymerase II-associated chromatin interactions in prostate cancer. J Clin Invest. 130(8):3987-4005.

Galbraith K, Kumar A, Abdullah KG, Walker JM, Adams SH, Prior T, Dimentberg R, Henderson FC, Mirchia K, Sathe AA, Viapiano MS, Chin LS, Corona RJ, Hatanpaa KJ, Snuderl M, Xing C, Brem S, Richardson TE. (2020). Molecular Correlates of Long Survival in IDH-Wildtype Glioblastoma Cohorts. J Neuropathol Exp Neurol. 79(8):843-854.

Garg A, El-Shanti H, Xing C, Zhou Z, Abujbara M, Al-Rashed K, El-Khateeb M, Ajlouni K, Agarwal AK. (2020). A Novel Syndrome With Short Stature, Mandibular Hypoplasia, and Osteoporosis May Be Associated With a PRRT3 Variant. J Endocr Soc. 4(8):bvaa088.

Chu Y, Hu J, Liang H, Kanchwala M, Xing C, Beebe W, Bowman CB, Gong X, Corey DR, Mootha VV. (2020). Analyzing pre-symptomatic tissue to gain insights into the molecular and mechanistic origins of late-onset degenerative trinucleotide repeat disease. Nucleic Acids Res. 48(12):6740-6758.

Xiong N, Gao X, Zhao H, Cai F, Zhang FC, Yuan Y, Liu W, He F, Zacharias LG, Lin H, Vu HS, Xing C, Yao DX, Chen F, Luo B, Sun W, DeBerardinis RJ, Xu H, Ge WP. (2020). Using arterial-venous analysis to characterize cancer metabolic consumption in patients. Nat Commun. 11(1):3169.

Chen B, Aredo B, Ding Y, Zhong X, Zhu Y, Zhao CX, Kumar A, Xing C, Gautron L, Lyon S, Russell J, Li X, Tang M, Anderton P, Ludwig S, Moresco EMY, Beutler B, Ufret-Vincenty RL. (2020). Forward genetic analysis using OCT screening identifies Sfxn3 mutations leading to progressive outer retinal degeneration in mice. Proc Natl Acad Sci U S A. 117(23):12931-12942.

Patni N, Hatab S, Xing C, Zhou Z, Quittner C, Garg A. (2020). A novel autosomal recessive lipodystrophy syndrome due to homozygous LMNA variant. J Med Genet. 57(6):422-426.

Nguyen NUN, Canseco DC, Xiao F, Nakada Y, Li S, Lam NT, Muralidhar SA, Savla JJ, Hill JA, Le V, Zidan KA, El-Feky HW, Wang Z, Ahmed MS, Hubbi ME, Menendez-Montes I, Moon J, Ali SR, Le V, Villalobos E, Mohamed MS, Elhelaly WM, Thet S, Anene-Nzelu CG, Tan WLW, Foo RS, Meng X, Kanchwala M, Xing C, Roy J, Cyert MS, Rothermel BA, Sadek HA. (2020). A calcineurin-Hoxb13 axis regulates growth mode of mammalian cardiomyocytes. Nature. 582(7811):271-276.

Suresh S, Chen B, Zhu J, Golden RJ, Lu C, Evers BM, Novaresi N, Smith B, Zhan X, Schmid V, Jun S, Karacz CM, Peyton M, Zhong L, Wen Z, Sathe AA, Xing C, Behrens C, Wistuba II, Xiao G, Xie Y, Fu YX, Minna JD, Mendell JT, O'Donnell KA. (2020). eIF5B drives integrated stress response-dependent translation of PD-L1 in lung cancer. Nat Cancer. 1(5):533-545.

Martins FH, Kumar A, Abe CM, Carvalho E, Nishiyama-Jr M, Xing C, Sperandio V, Elias WP. (2020). EspFu-Mediated Actin Assembly Enhances Enteropathogenic Escherichia coli Adherence and Activates Host Cell Inflammatory Signaling Pathways. mBio. 11(2).

Gong K, Guo G, Panchani N, Bender ME, Gerber DE, Minna JD, Fattah F, Gao B, Peyton M, Kernstine K, Mukherjee B, Burma S, Chiang CM, Zhang S, Sathe AA, Xing C, Dao KH, Zhao D, Akbay EA, Habib AA. (2020). EGFR inhibition triggers an adaptive response by co-opting antiviral signaling pathways in lung cancer. Nat Cancer. 1(4):394-409.

Esparza M, Mor A, Niederstrasser H, White K, White A, Zhang K, Gao S, Wang J, Liang J, Sho S, Sakthivel R, Sathe AA, Xing C, Muñoz-Moreno R, Shay JW, García-Sastre A, Ready J, Posner B, Fontoura BMA. (2020). Chemical intervention of influenza virus mRNA nuclear export. PLoS Pathog. 16(4):e1008407.

Yang J, Smith DK, Ni H, Wu K, Huang D, Pan S, Sathe AA, Tang Y, Liu ML, Xing C, Zhang CL, Zhuge Q. (2020). SOX4-mediated repression of specific tRNAs inhibits proliferation of human glioblastoma cells. Proc Natl Acad Sci U S A. 117(11):5782-5790.

Niu Y, Bao L, Chen Y, Wang C, Luo M, Zhang B, Zhou M, Wang JE, Fang YV, Kumar A, Xing C, Wang Y, Luo W. (2020). HIF2-Induced Long Noncoding RNA RAB11B-AS1 Promotes Hypoxia-Mediated Angiogenesis and Breast Cancer Metastasis. Cancer Res. 80(5):964-975.

Wu JL, Keller P, Kanchwala M, Xing C, Babayev SN, Carr BR, Bukulmez O, Word RA. (2020). Controlled Ovarian Stimulation Protocols Alter Endometrial Histomorphology and Gene Expression Profiles. Reprod Sci. 27(3):895-904.

Iqbal NS, Jascur TA, Harrison SM, Edwards AB, Smith LT, Choi ES, Arevalo MK, Chen C, Zhang S, Kern AJ, Scheuerle AE, Sanchez EJ, Xing C, Baker LA. (2020). Prune belly syndrome in surviving males can be caused by Hemizygous missense mutations in the X-linked Filamin A gene. BMC Med Genet. 21(1):38.

Cardoso AC, Lam NT, Savla JJ, Nakada Y, Pereira AHM, Elnwasany A, Menendez-Montes I, Ensley EL, Petric UB, Sharma G, Sherry AD, Malloy CR, Khemtong C, Kinter MT, Tan WLW, Anene-Nzelu CG, Foo RS, Nguyen NUN, Li S, Ahmed MS, Elhelaly WM, Abdisalaam S, Asaithamby A, Xing C, Kanchwala M, Vale G, Eckert KM, Mitsche MA, McDonald JG, Hill JA, Huang L, Shaul PW, Szweda LI, Sadek HA. (2020). Mitochondrial Substrate Utilization Regulates Cardiomyocyte Cell Cycle Progression. Nat Metab. 2(2):167-178.

Thomas-Jardin SE, Dahl H, Kanchwala MS, Ha F, Jacob J, Soundharrajan R, Bautista M, Nawas AF, Robichaux D, Mistry R, Anunobi V, Xing C, Delk NA. (2020). RELA is sufficient to mediate interleukin-1 repression of androgen receptor expression and activity in an LNCaP disease progression model. Prostate. 80(2):133-145.

Nawas AF, Kanchwala M, Thomas-Jardin SE, Dahl H, Daescu K, Bautista M, Anunobi V, Wong A, Meade R, Mistry R, Ghatwai N, Bayerl F, Xing C, Delk NA. (2020). IL-1-conferred gene expression pattern in ERα⁺ BCa and AR⁺ PCa cells is intrinsic to ERα^- BCa and AR^- PCa cells and promotes cell survival. BMC Cancer. 20(1):46.

Xu C, Yang X, Zhou H, Li Y, Xing C, Zhou T, Zhong D, Lian C, Yan M, Chen T, Liao Z, Gao B, Su D, Wang T, Sharma S, Mohan C, Ahituv N, Malik S, Li QZ, Su P. (2020). A novel ZRS variant causes preaxial polydactyly type I by increased sonic hedgehog expression in the developing limb bud. Genet Med. 22(1):189-198.

Gotway G, Crossley E, Kozlitina J, Xing C, Fan J, Hornbuckle C, Thies J, Michel D, Quinn C, Scheuerle AE, Umana LA, Uhles CL, Park JY. (2020). Clinical Exome Studies Have Inconsistent Coverage. Clin Chem. 66(1):199-206.

2019

Babayev S. N., Kanchwala M., Xing C., Akgul Y., Carr B. R.,Word R. A. (2019). Thrombin Alters Human Endometrial Stromal Cell Differentiation During Decidualization. Reproductive Sciences 26:278-288

Bhattacharyya S., Sathe A. A., Bhakta M., Xing C.,Munshi N. V. (2019). PAN-INTACT enables direct isolation of lineage-specific nuclei from fibrous tissues. PloS one 14

Cuevas I. C., Sahoo S. S., Kumar A., Zhang H., Westcott J., Aguilar M., Cortez J. D., Sullivan S. A., Xing C., Hayes D. N., Brekken R. A., Bae-Jump V. L.,Castrillon D. H. (2019). Fbxw7 is a driver of uterine carcinosarcoma by promoting epithelial-mesenchymal transition. Proceedings of the National Academy of Sciences 116:25880-25890

Fernandez-Perez A., Sathe A. A., Bhakta M., Leggett K., Xing C.,Munshi N. V. (2019). Hand2 Selectively Reorganizes Chromatin Accessibility to Induce Pacemaker-like Transcriptional Reprogramming. Cell reports 27:2354-2369. e2357

Huang H., Zhang Y., Gallegos V., Sorrelle N., Zaid M. M., Toombs J., Du W., Wright S., Hagopian M., Wang Z., Hosein A. N., Sathe A. A., Xing C., Koay E. J., Driscoll K. E.,Brekken R. A. (2019). Targeting TGFβR2-mutant tumors exposes vulnerabilities to stromal TGFβ blockade in pancreatic cancer. EMBO Molecular Medicine 11:e10515

Liu Z., Mar K. B., Hanners N. W., Perelman S. S., Kanchwala M., Xing C., Schoggins J. W.,Alto N. M. (2019). A NIK–SIX signalling axis controls inflammation by targeted silencing of non-canonical NF-κB. Nature 568:249-253

Lu H., Sathe A. A., Xing C.,Lehrman M. A. (2019). The Lec5 glycosylation mutant links homeobox genes with cholesterol and lipid-linked oligosaccharides. Glycobiology 29:106-109

Mirchia K., Sathe A. A., Walker J. M., Fudym Y., Galbraith K., Viapiano M. S., Corona R. J., Snuderl M., Xing C., Hatanpaa K. J.,Richardson T. E. (2019). Total copy number variation as a prognostic factor in adult astrocytoma subtypes. Acta Neuropathologica Communications 7:92

Pelusi S., Baselli G., Pietrelli A., Dongiovanni P., Donati B., McCain M. V., Meroni M., Fracanzani A. L., Romagnoli R., Petta S., Grieco A., Miele L., Soardo G., Bugianesi E., Fargion S., Aghemo A., D’Ambrosio R., Xing C., Romeo S., De Francesco R., Reeves H. L.,Valenti L. V. C. (2019). Rare Pathogenic Variants Predispose to Hepatocellular Carcinoma in Nonalcoholic Fatty Liver Disease. Scientific Reports 9:3682

Richardson T. E., Patel S., Serrano J., Sathe A. A., Daoud E. V., Oliver D., Maher E. A., Madrigales A., Mickey B. E., Taxter T., Jour G., White C. L., Raisanen J. M., Xing C., Snuderl M.,Hatanpaa K. J. (2019). Genome-Wide Analysis of Glioblastoma Patients with Unexpectedly Long Survival. Journal of Neuropathology & Experimental Neurology 78:501-507

Zhang D., Zhou Z., Abu-Hijleh M., Batra K., Xing C.,Garcia C. K. (2019). Homozygous rare Parn missense mutation in familial pulmonary fibrosis. American journal of respiratory and critical care medicine 199:797-799

Zhang Z., Shao M., Hepler C., Zi Z., Zhao S., An Y. A., Zhu Y., Ghaben A. L., Wang M.-y., Li N., Onodera T., Joffin N., Crewe C., Zhu Q., Vishvanath L., Kumar A., Xing C., Wang Q. A., Gautron L., Deng Y., Gordillo R., Kruglikov I., Kusminski C. M., Gupta R. K.,Scherer P. E. (2019). Dermal adipose tissue has high plasticity and undergoes reversible dedifferentiation in mice. The Journal of Clinical Investigation 129:5327-5342

2018

Zhang, D., Zhou, Z., Abu-Hijleh, M., Batra, K., Xing C., Garcia, C.K., 2018. Homozygous Rare PARN Missense Mutation in Familial Pulmonary Fibrosis. Am. J. Respir. Crit. Care Med. rccm.201809-1632LE.

Wambach, J.A., Wegner, D.J., Patni, N., Kircher, M., Willing, M.C., Baldridge, D., Xing C., Agarwal, A.K., Vergano, S.A.S., Patel, C., Grange, D.K., Kenney, A., Najaf, T., Nickerson, D.A., Bamshad, M.J., Cole, F.S., Garg, A., 2018. Bi-allelic POLR3A Loss-of-Function Variants Cause Autosomal-Recessive Wiedemann-Rautenstrauch Syndrome. Am. J. Hum. Genet. 103, 968–975.

Zhou, Z., Ku, H.-C., Xing, G., Xing, C., 2018. Decomposing Pearson’s χ2 test: A linear regression and its departure from linearity. Ann. Hum. Genet. 82, 318–324.

Richardson, R.B., Ohlson, M.B., Eitson, J.L., Kumar, A., McDougal, M.B., Boys, I.N., Mar, K.B., De La Cruz-Rivera, P.C., Douglas, C., Konopka, G., Xing C., Schoggins, J.W., 2018. A CRISPR screen identifies IFI6 as an ER-resident interferon effector that blocks flavivirus replication. Nat. Microbiol. 3, 1214–1223.

Saade, J.S., Xing C., Gong, X., Zhou, Z., Mootha, V.V., 2018. Instability of TCF4 triplet repeat expansion with parent– child transmission in Fuchs’ endothelial corneal dystrophy. Investig. Ophthalmol. Vis. Sci. 59, 4065–4070.

Richardson, T.E.*, Sathe, A.A.*, Kanchwala, M., Jia, G., Habib, A.A., Xiao, G., Snuderl, M., Xing, C†., Hatanpaa, K.J†., 2018. Genetic and Epigenetic Features of Rapidly Progressing IDH-Mutant Astrocytomas. J. Neuropathol. Exp. Neurol. 77, 542–548. [* = equal contribution; †=corresponding author]

Aboudehen, K., Farahani, S., Kanchwala, M., Chan, S.C., Avdulov, S., Mickelson, A., Lee, D., Gearhart, M.D., Patel, V., Xing, C., Igarashi, P., 2018. Long noncoding RNA Hoxb3os is dysregulated in autosomal dominant polycystic kidney disease and regulates mTOR signaling. J. Biol. Chem. 293, 9388–9398.

Thomas-Jardin, S.E., Kanchwala, M.S., Jacob, J., Merchant, S., Meade, R.K., Gahnim, N.M., Nawas, A.F., Xing C., Delk, N.A., 2018. Identification of an IL-1-induced gene expression pattern in AR+PCa cells that mimics the molecular phenotype of AR−PCa cells. Prostate 78, 595–606.

Chen, Y., Zhang, B., Bao, L., Jin, L., Yang, M., Peng, Y., Kumar, A., Wang, J.E., Wang, C., Zou, X., Xing C., Wang, Y., Luo, W., 2018. ZMYND8 acetylation mediates HIF-dependent breast cancer progression and metastasis. J. Clin. Invest. 128, 1937–1955.

Zheng, G., Kanchwala, M., Xing C., Yu, H., 2018. MCM2–7-dependent cohesin loading during S phase promotes sister-chromatid cohesion. Elife 7.

Hu, J., Rong, Z., Gong, X., Zhou, Z., Sharma, V.K., Xing C., Watts, J.K., Corey, D.R., Mootha, V.V., 2018. Oligonucleotides targeting TCF4 triplet repeat expansion inhibit RNA foci and mis-splicing in Fuchs’ dystrophy. Hum. Mol. Genet. 27, 1015–1026.

Li, X., Baek, G., Ramanand, S.G., Sharp, A., Gao, Y., Yuan, W., Welti, J., Rodrigues, D.N., Dolling, D., Figueiredo, I., Sumanasuriya, S., Crespo, M., Aslam, A., Li, R., Yin, Y., Mukherjee, B., Kanchwala, M., Hughes, A.M., Halsey, W.S., Chiang, C.-M., Xing C., Raj, G. V., Burma, S., de Bono, J., Mani, R.S., 2018. BRD4 Promotes DNA Repair and Mediates the Formation of TMPRSS2-ERG Gene Rearrangements in Prostate Cancer. Cell Rep. 22, 796–808.

Babayev, S.N., Kanchwala, M., Xing C., Akgul, Y., Carr, B.R., Word, R.A., 2018. Thrombin Alters Human Endometrial Stromal Cell Differentiation During Decidualization. Reprod. Sci. 193371911876870.

De La Cruz-Rivera, P.C., Kanchwala, M., Liang, H., Kumar, A., Wang, L.-F., Xing C., Schoggins, J.W., 2018. The IFN Response in Bats Displays Distinctive IFN-Stimulated Gene Expression Kinetics with Atypical RNASEL Induction. J. Immunol. 200, 209–217.

2017

Nakada, Y., Canseco, D.C., Thet, S., Abdisalaam, S., Asaithamby, A., Santos, C.X., Shah, A.M., Zhang, H., Faber, J.E., Kinter, M.T., Szweda, L.I., Xing C., Hu, Z., Deberardinis, R.J., Schiattarella, G., Hill, J.A., Oz, O., Lu, Z., Zhang, C.C., Kimura, W., Sadek, H.A., 2017. Hypoxia induces heart regeneration in adult mice. Nature 541, 222–227.

Kishore, A.H., Liang, H., Kanchwala, M., Xing C., Ganesh, T., Akgul, Y., Posner, B., Ready, J.M., Markowitz, S.D., Word, R.A., 2017. Prostaglandin dehydrogenase is a target for successful induction of cervical ripening. Proc. Natl. Acad. Sci. U. S. A. 114, E6427–E6436.

De Nisco, N.J., Kanchwala, M., Li, P., Fernandez, J., Xing C., Orth, K., 2017. The cytotoxic type 3 secretion system 1 of Vibrio rewires host gene expression to subvert cell death and activate cell survival pathways. Sci. Signal. 10.

Suresh, S., Durakoglugil, D., Zhou, X., Zhu, B., Comerford, S.A., Xing C., Xie, X.-J., York, B., O’Donnell, K.A., 2017. SRC-2-mediated coactivation of anti-tumorigenic target genes suppresses MYC-induced liver cancer. PLoS Genet. 13, e1006650.

Yin, Y., Li, R., Xu, K., Ding, S., Li, J., Baek, G., Ramanand, S.G., Ding, S., Liu, Z., Gao, Y., Kanchwala, M.S., Li, X., Hutchinson, R., Liu, X., Woldu, S.L., Xing C., Desai, N.B., Feng, F.Y., Burma, S., de Bono, J.S., Dehm, S.M., Mani, R.S., Chen, B.P.C., Raj, G. V, 2017. Androgen Receptor Variants Mediate DNA Repair after Prostate Cancer Irradiation. Cancer Res. 77, 4745–4754.

Gao, W., Chen, C., Zhou, T., Yang, S., Gao, B., Zhou, H., Lian, C., Wu, Z., Qiu, X., Yang, X., Alattar, E., Liu, W., Su, D., Sun, S., Chen, Y., Cheung, K.M.C., Song, Y., Luk, K.K.D., Chan, D., Sham, P.C., Xing C., Khor, C.C., Liu, G., Yang, J., Deng, Y., Hao, D., Huang, D., Li, Q.-Z., Xu, C., Su, P., 2017. Rare coding variants in MAPK7 predispose to adolescent idiopathic scoliosis. Hum. Mutat. 38, 1500–1510.

Saboo, U.S., Penke, D., Mahindrakar, A., Uddaraju, M., Sankurathri, C., Gong, X., Xing C., Mootha, V.V., 2017. Exome sequencing reveals novel homozygous FOXE3 mutation in microphthalmos with staphylomatous malformation. Ophthalmic Genet. 38, 295–297.

Patni, N., Xing C., Agarwal, A.K., Garg, A., 2017. Juvenile-onset generalized lipodystrophy due to a novel heterozygous missense LMNA mutation affecting lamin C. Am. J. Med. Genet. A 173, 2517–2521.

Richardson, T.E., Shen, Z.-J., Kanchwala, M., Xing C., Filatenkov, A., Shang, P., Barnett, S., Abedin, Z., Malter, J.S., Raisanen, J.M., Burns, D.K., White, C.L., Hatanpaa, K.J., 2017. Aggressive Behavior in Silent Subtype III Pituitary Adenomas May Depend on Suppression of Local Immune Response: A Whole Transcriptome Analysis. J. Neuropathol. Exp. Neurol. 76, 874–882.

Zhu, Y., Zhao, S., Deng, Y., Gordillo, R., Ghaben, A.L., Shao, M., Zhang, F., Xu, P., Li, Y., Cao, H., Zagnitko, O., Scott, D.A., Gupta, R.K., Xing C., Zhang, B.B., Lin, H. V, Scherer, P.E., 2017. Hepatic GALE Regulates Whole-Body Glucose Homeostasis by Modulating Tff3 Expression. Diabetes 66, 2789–2799.

Mootha, V.V., Hansen, B., Rong, Z., Mammen, P.P., Zhou, Z., Xing C., Gong, X., 2017. Fuchs’ Endothelial Corneal Dystrophy and RNA Foci in Patients With Myotonic Dystrophy. Invest. Ophthalmol. Vis. Sci. 58, 4579–4585.

Zolotov, S., Xing, C., Mahamid, R., Shalata, A., Sheikh-Ahmad, M., Garg, A., 2017. Homozygous LIPE mutation in siblings with multiple symmetric lipomatosis, partial lipodystrophy, and myopathy. Am. J. Med. Genet. A 173, 190–194.

Zhou, Z., Ku, H.-C., Huang, Z., Xing, G., Xing C., 2017. Differentiating the Cochran-Armitage Trend Test and Pearson’s χ(2) Test: Location and Dispersion. Ann. Hum. Genet. 81, 184–189.

Thu, K.L., Papari-Zareei, M., Stastny, V., Song, K., Peyton, M., Martinez, V.D., Zhang, Y.-A., Castro, I.B., Varella-Garcia, M., Liang, H., Xing C., Kittler, R., Milchgrub, S., Castrillon, D.H., Davidson, H.L., Reynolds, C.P., Lam, W.L., Lea, J., Gazdar, A.F., 2017. A comprehensively characterized cell line panel highly representative of clinical ovarian high-grade serous carcinomas. Oncotarget 8, 50489–50499.

2016

Choi, E., Zhang, X., Xing C., Yu, H., 2016. Mitotic Checkpoint Regulators Control Insulin Signaling and Metabolic Homeostasis. Cell 166, 567–581.

Shetty, S., Xing C., Garg, A., 2016. Type 1 Hyperlipoproteinemia Due to Compound Heterozygous Rare Variants in GCKR. J. Clin. Endocrinol. Metab. 101, 3884–3887.

Lakhia, R., Hajarnis, S., Williams, D., Aboudehen, K., Yheskel, M., Xing C., Hatley, M.E., Torres, V.E., Wallace, D.P., Patel, V., 2016. MicroRNA-21 Aggravates Cyst Growth in a Model of Polycystic Kidney Disease. J. Am. Soc. Nephrol. 27, 2319–30.

Patni, N., Brothers, J., Xing C., Garg, A., 2016. Type 1 hyperlipoproteinemia in a child with large homozygous deletion encompassing GPIHBP1. J. Clin. Lipidol. 10, 1035–1039.e2.

Garg, A., Sankella, S., Xing C., Agarwal, A.K., 2016. Whole-exome sequencing identifies ADRA2A mutation in atypical familial partial lipodystrophy. JCI insight 1.

Dang, T.T., Westcott, J.M., Maine, E.A., Kanchwala, M., Xing, C., Pearson, G.W., 2016. ΔNp63α induces the expression of FAT2 and Slug to promote tumor invasion. Oncotarget 7, 28592–611.

Xing C., Garcia, C.K., 2016. Epigenetic inheritance of telomere length obscures identification of causative PARN locus. J. Med. Genet. 53, 356–8.

Starokadomskyy, P., Gemelli, T., Rios, J.J., Xing C., Wang, R.C., Li, H., Pokatayev, V., Dozmorov, I., Khan, S., Miyata, N., Fraile, G., Raj, P., Xu, Z., Xu, Z., Ma, L., Lin, Z., Wang, H., Yang, Y., Ben-Amitai, D., Orenstein, N., Mussaffi, H., Baselga, E., Tadini, G., Grunebaum, E., Sarajlija, A., Krzewski, K., Wakeland, E.K., Yan, N., de la Morena, M.T., Zinn, A.R., Burstein, E., 2016. DNA polymerase-α regulates the activation of type I interferons through cytosolic RNA:DNA synthesis. Nat. Immunol. 17, 495–504.

Sun, X., Chuang, J.-C., Kanchwala, M., Wu, L., Celen, C., Li, L., Liang, H., Zhang, S., Maples, T., Nguyen, L.H., Wang, S.C., Signer, R.A.J., Sorouri, M., Nassour, I., Liu, X., Xu, J., Wu, M., Zhao, Y., Kuo, Y.-C., Wang, Z., Xing C., Zhu, H., 2016. Suppression of the SWI/SNF Component Arid1a Promotes Mammalian Regeneration. Cell Stem Cell 18, 456–466.

2015 and Previous

Stender, S., Chakrabarti, R.S., Xing C., Gotway, G., Cohen, J.C., Hobbs, H.H., 2015. Adult-onset liver disease and hepatocellular carcinoma in S-adenosylhomocysteine hydrolase deficiency. Mol. Genet. Metab. 116, 269–74.

Soliman, A.Z., Xing C., Radwan, S.H., Gong, X., Mootha, V.V., 2015. Correlation of Severity of Fuchs Endothelial Corneal Dystrophy With Triplet Repeat Expansion in TCF4. JAMA Ophthalmol. 133, 1386.

Kimura, W., Xiao, F., Canseco, D.C., Muralidhar, S., Thet, S., Zhang, H.M., Abderrahman, Y., Chen, R., Garcia, J.A., Shelton, J.M., Richardson, J.A., Ashour, A.M., Asaithamby, A., Liang, H., Xing C., Lu, Z., Zhang, C.C., Sadek, H.A., 2015. Hypoxia fate mapping identifies cycling cardiomyocytes in the adult heart. Nature 523, 226–230.

Hong, C., Wang, J., Xing C., Hwang, T.H., Park, J.Y., 2015. Intersection of DNA Privacy and Whole-Genome Sequencing. Clin. Chem. 61, 900–902.

Stuart, B.D., Choi, J., Zaidi, S., Xing C., Holohan, B., Chen, R., Choi, M., Dharwadkar, P., Torres, F., Girod, C.E., Weissler, J., Fitzgerald, J., Kershaw, C., Klesney-Tait, J., Mageto, Y., Shay, J.W., Ji, W., Bilguvar, K., Mane, S., Lifton, R.P., Garcia, C.K., 2015. Exome sequencing links mutations in PARN and RTEL1 with familial pulmonary fibrosis and telomere shortening. Nat. Genet. 47, 512–7.

Mootha, V.V., Hussain, I., Cunnusamy, K., Graham, E., Gong, X., Neelam, S., Xing C., Kittler, R., Petroll, W.M., 2015. TCF4 Triplet Repeat Expansion and Nuclear RNA Foci in Fuchs’ Endothelial Corneal Dystrophy. Investig. Ophthalmology Vis. Sci. 56, 2003.

Dongiovanni, P., Petta, S., Maglio, C., Fracanzani, A.L., Pipitone, R., Mozzi, E., Motta, B.M., Kaminska, D., Rametta, R., Grimaudo, S., Pelusi, S., Montalcini, T., Alisi, A., Maggioni, M., Kärjä, V., Borén, J., Käkelä, P., Di Marco, V., Xing C., Nobili, V., Dallapiccola, B., Craxi, A., Pihlajamäki, J., Fargion, S., Sjöström, L., Carlsson, L.M., Romeo, S., Valenti, L., 2015. Transmembrane 6 superfamily member 2 gene variant disentangles nonalcoholic steatohepatitis from cardiovascular disease. Hepatology 61, 506–514.

Xing C., Gong, X., Hussain, I., Khor, C.-C., Tan, D.T.H., Aung, T., Mehta, J.S., Vithana, E.N., Mootha, V.V., 2014. Transethnic replication of association of CTG18.1 repeat expansion of TCF4 gene with Fuchs’ corneal dystrophy in Chinese implies common causal variant. Invest. Ophthalmol. Vis. Sci. 55, 7073–8.

Garg, A., Xing C., 2014. De novo heterozygous FBN1 mutations in the extreme C-terminal region cause progeroid fibrillinopathy. Am. J. Med. Genet. A 164A, 1341–5.

Gazdar, A., Robinson, L., Oliver, D., Xing C., Travis, W.D., Soh, J., Toyooka, S., Watumull, L., Xie, Y., Kernstine, K., Schiller, J.H., 2014. Hereditary lung cancer syndrome targets never smokers with germline EGFR gene T790M mutations. J. Thorac. Oncol. 9, 456–63.