Bioinformatics Laboratory Publications
Publications
2021 Publications
Gong T, Borgard H, Zhang Z, Chen S, Gao Z, Deng Y*. Analysis and Performance Assessment of the Whole Genome Bisulfite Sequencing Data Workflow: Currently Available Tools and a Practical Guide to Advance DNA Methylation Studies. Small Methods. 2022 Jan 22. doi: 10.1002/smtd.202101251. Epub ahead of print. PMID: 35064762.
Fu Y, Hu L, Ren HW, Zuo Y, Chen S, Zhang QS, Shao C, Ma Y, Wu L, Hao JJ, Wang CZ, Wang Z, Yanagihara R, Deng Y*. Prognostic Factors for COVID-19 Hospitalized Patients with Preexisting Type 2 Diabetes. Int J Endocrinol. 2022 Jan 17;2022:9322332. doi: 10.1155/2022/9322332. PMID: 35047039; PMCID: PMC8763039.
Zitello E, Hernandez B, Deng Y*. Viral Etiology of Solid Tumors and Immunotherapy. Gastroenterology. 2022 Feb;162(2):659-660. doi: 10.1053/j.gastro.2021.09.048. Epub 2021 Sep 25. PMID: 34582894.
Wu J, Danko D, Afshinnekoo E, Bezdan D, Bhattacharyya M, Castro-Nallar E, Chmielarczyk A, Hazrin-Chong NH, Deng Y, Dias-Neto E, Frolova A, Mason-Buck G, Iraola G, Jang S, ?abaj P, Lee PKH, Nieto-Caballero M, Osuolale OO, Ouzounis CA, Perlin MH, Prithiviraj B, Rascovan N, Ró?a?ska A, Schriml LM, Semmler T, Suzuki H, Ugalde JA, Young B, Werner J, Zambrano MM, Zhao Y, Mason C, Shi T; MetaSUB Consortium. Annotating unknown species of urban microorganisms on a global scale unveils novel functional diversity and local environment association. Environ Res. 2022 May 1;207:112183. doi: 10.1016/j.envres.2021.112183. Epub 2021 Oct 9. PMID: 34637759.
Zuo Y, Chen S, Yan L, Hu L, Bowler S, Zitello E, Huang G and Deng Y*. Development of a tRNA-derived small RNA diagnostic and prognostic signature in liver cancer. Genes Dis. 2021 Jan 28;9(2):393-400. doi: 10.1016/j.gendis.2021.01.006. eCollection 2022, Mar. PMID: 3522415.
Foox J, Nordlund J, Lalancette C, Gong T, Lacey M, Lent S, Langhorst BW, Ponnaluri VKC, Williams L, Padmanabhan KR, Cavalcante R, Lundmark A, Butler D, Mozsary C, Gurvitch J, Greally JM, Suzuki M, Menor M, Nasu M, Alonso A, Sheridan C, Scherer A, Bruinsma S, Golda G, Muszynska A, ?abaj PP, Campbell MA, Wos F, Raine A, Liljedahl U, Axelsson T, Wang C, Chen Z, Yang Z, Li J, Yang X, Wang H, Melnick A, Guo S, Blume A, Franke V, Ibanez de Caceres I, Rodriguez-Antolin C, Rosas R, Davis JW, Ishii J, Megherbi DB, Xiao W, Liao W, Xu J, Hong H, Ning B, Tong W, Akalin A, Wang Y, Deng Y*, Mason CE. The SEQC2 epigenomics quality control (EpiQC) study. Genome Biol. 2021 Dec 6;22(1):332. doi: 10.1186/s13059-021-02529-2. Erratum in: Genome Biol. 2021 Dec 23;22(1):350. PMID: 34872606; PMCID: PMC8650396.
Zhan S, Siu J, Wang Z, Yu H, Bezabeh T, Deng Y, Du W, Fei P. Focal Point of Fanconi Anemia Signaling. Int J Mol Sci. 2021 Nov 30;22(23):12976. doi: 10.3390/ijms222312976. PMID: 34884777; PMCID: PMC8657418.
Bartlett B, Gao Z, Schukking M, Menor M, Khadka VS, Fabbri M, Fei P, Deng Y*. The miRNA Profile of Inflammatory Colorectal Tumors Identify TGF-? as a Companion Target for Checkpoint Blockade Immunotherapy. Front Cell Dev Biol. 2021 Oct 14;9:754507. doi: 10.3389/fcell.2021.754507. PMID: 34722540; PMCID: PMC8551827.
Rodriguez RM, Menor M, Hernandez BY, Deng Y*, Khadka VS. Bacterial Diversity Correlates with Overall Survival in Cancers of the Head and Neck, Liver, and Stomach. Molecules. 2021 Sep 17;26(18):5659. doi: 10.3390/molecules26185659. PMID: 34577130; PMCID: PMC8468759.
Deng Y is one of co-authors in the Somatic Mutation Working Group of Sequencing Quality Control Phase II Consortium. Establishing community reference samples, data and call sets for benchmarking cancer mutation detection using whole-genome sequencing. Nat Biotechnol. 2021 Sep;39(9):1151-1160. doi: 10.1038/s41587-021-00993-6. Epub 2021 Sep 9. PMID: 34504347.
Chen Y, Zitello E, Guo R and Deng Y*. The Function of LncRNAs and Their Role in the Prediction, Diagnosis and Prognosis of Lung Cancer. Clin Transl Med. 2021 Apr;11(4). doi: 10.1002/ctm2.367. PMID: 33931980.
Chen Y, Li Y, Qi C, Zhang C, Liu D, Deng Y, Fu Y, Khadka VS, Wang DD, Tan S, Liu S, Peng Z, Gong J, Lin PP, Zhang X, Li J, Li Y, Shen L. Dysregulated KRAS gene-signaling axis and abnormal chromatin remodeling drive therapeutic resistance in heterogeneous-sized circulating tumor cells in gastric cancer patients. Cancer Lett. 2021 Oct 1;517:78-87. doi: 10.1016/j.canlet.2021.06.002. Epub 2021 Jun 11. PMID: 34126192.
Zhu Y, Chen S, Ling Z, Winnicki A, Xu L, Xu S, Gong T, Jiang B, Huang G, Deng Y*. Comprehensive Analysis of a tRNA-Derived Small RNA in Colorectal Cancer. Front Oncol. 2021 Aug 4;11:701440. doi: 10.3389/fonc.2021.701440. PMID: 34422655; PMCID: PMC8371552.
Danko D, Bezdan D, Sofia E, Deng Y, Kahles A, Mason CE, and The International MetaSUB Consortium. Global Genetic Cartography of Urban Metagenomes and Anti-Microbial Resistance. Cell. 2021 Jun 24;184(13):3376-3393.e17. doi: 10.1016/j.cell.2021.05.002. Epub 2021 May 26. PMID: 34043940.
Bartlett B, Zhu Y, Menor M, Khadka VS, Zhang J, Zheng J and Deng Y*. Development of a RNA-Seq based prognostic signature for colon cancer. Int J Comput Biol Drug Des. 2021, 13, 488-503.
Marikawa Y, Menor M, Deng Y, Alarcon VB. Regulation of endoplasmic reticulum stress and trophectoderm lineage specification by the mevalonate pathway in the mouse preimplantation embryo. Mol Hum Reprod. 2021 Mar 24;27(4). doi:10.1093/molehr/gaab015. PMID: 33677573.
Afshinnekoo E, Bhattacharya C, Burguete-García A, Castro-Nallar E, Deng Y, Desnues C, Dias-Neto E, Elhaik E, Iraola G, Jang S, ?abaj PP, Mason CE, Nagarajan N, Poulsen M, Prithiviraj B, Siam R, Shi T, Suzuki H, Werner J, Zambrano MM, Bhattacharyya M; MetaSUB Consortium. COVID-19 drug practices risk antimicrobial resistance evolution. Lancet Microbe. 2021 Feb 24. doi:10.1016/S2666-5247(21)00039-2. Epub ahead of print. PMID: 33655229; PMCID.
Ma C, Hoffmann FW, Marciel MP, Page KE, Williams-Aduja MA, Akana ENL, Gojanovich GS, Gerschenson M, Urschitz J, Moisyadi S, Khadka VS, Rozovsky S, Deng Y, Horgen FD, Hoffmann PR. Upregulated ethanolamine phospholipid synthesis via selenoprotein I is required for effective metabolic reprogramming during T cell activation. Mol Metab. 2021 Jan 20;47:101170. doi: 10.1016/j.molmet.2021.101170. Epub ahead of print. PMID: 33484950; PMCID: PMC7881273.