Featured publications supported by the Bioinformatics Team

Featured publications supported by the Bioinformatics Team

Year of publication: 2023

Yang WS, Caliva MJ, Khadka VS, Tiirikainen M, Matter ML, Deng Y, Ramos JW. RSK1 and RSK2 serine/threonine kinases regulate different transcription programs in cancer. Front Cell Dev Biol. 2023 Jan 4;10:1015665. doi:10.3389/fcell.2022.1015665. PMID: 36684450; PMCID: PMC9845784.

Year of publication: 2022

Chen Y, Qin Y, Fu Y, Gao Z, Deng Y. Integrated Analysis of Bulk RNA-Seq and Single-Cell RNA-Seq Unravels the Influences of SARS-CoV-2 Infections to Cancer Patients. Int J Mol Sci. 2022 Dec 10;23(24):15698. doi: 10.3390/ijms232415698. PMID: 36555339; PMCID: PMC9779348.

Awad CS, Deng Y, Kwagyan J, Roche-Lima A, Tchounwou PB, Wang Q, Idris MY. Summary of Year-One Effort of the RCMI Consortium to Enhance Research Capacity and Diversity with Data Science. Int J Environ Res Public Health. 2022 Dec 24;20(1):279. doi: 10.3390/ijerph20010279. PMID: 36612607; PMCID: PMC9819075.

Yu Z, Chen S, Tang Z, Yang Y, Ling Z, Wang H, Gong T, Gao Z, Devendra G, Hang G, Chen W and Deng Y. Mitochondria-derived small RNAs as diagnostic biomarkers in lung cancer patients through a novel ratio-based expression analysis methodology, 2022, https://doi.org/10.1016/j.gendis.2022.07.013 Genes and Diseases, in Press

Gao Z, Jijiwa M, Nasu M, Borgard H, Gong T, Xu J, Chen S, Fu Y, Chen Y, Hu X, Huang G, Deng Y. Comprehensive landscape of tRNA-derived fragments in lung cancer. Mol Ther Oncolytics. 2022 Jul 6;26:207-225. doi:10.1016/j.omto.2022.07.002. PMID: 35892120; PMCID: PMC9307607.

Genomic Data Science Community Network (Deng Y is one of co-authors). Diversifying the genomic data science research community. Genome Res. 2022 Jul 20. doi: 10.1101/gr.276496.121. Epub ahead of print. PMID: 35858750.

Kumar R, Deng Y, Fan JB, Wei L. Editorial: Early Detection and Diagnosis of Cancer. Front Genet. 2022 Mar 14;13:875421. doi: 10.3389/fgene.2022.875421.PMID: 35360854; PMCID: PMC8963914.

Urena F, Ma C, Hoffmann FW, Nunes LGA, Urschitz J, Moisyadi S, Khadka VS, Deng Y, Hoffmann PR. T cell activation decreases microRNA-15a/16 levels to promote MEK1-ERK1/2-Elk1 signaling and promote proliferative capacity. J Biol Chem. 2022 Jan 24:101634. doi: 10.1016/j.jbc.2022.101634. Epub ahead of print. PMID: 35085550.

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:e2101251. doi: 10.1002/smtd.202101251. Epub ahead of print. PMID: 35064762.

Wang J, Katsaros D, Biglia N, Fu Y, Benedetto C, Loo L, Wang Z, Yu H. LncRNA NF582-AS1 Expression and Methylation in Breast Cancer and Its Biological and Clinical Implications. Cancers (Basel). 2022 Jun 4;14(11):2788. doi:10.3390/cancers14112788. PMID: 35681777; PMCID: PMC9179509.

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

Year of publication: 2021

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, Łabaj 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. 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-β 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, Clinical and Translational Medicine, 2021 Apr;11(4):e367. 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.

Fu Y, Katsaros D, Biglia N, Wang Z, Pagano I, Tius M, Tiirikainen M, Rosser C, Yang H, Yu H. Vitamin D receptor upregulates lncRNA TOPORS-AS1 which inhibits the Wnt/β-catenin pathway and associates with favorable prognosis of ovarian cancer. Sci Rep. 2021 Apr 5;11(1):7484. doi: 10.1038/s41598-021-86923-7. PMID:33820921; PMCID: PMC8021562.

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. Computational Biology and Drug Design, 2021, 13, 488-503

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.

Year of publication: 2020

Wen Z, Huang Y, Ling Z, Chen J, Wei X, Su R, Tang Z, Wen Z, Deng Y, Hu Z. Lack of Efficacy of Combined Carbohydrate Antigen Markers for Lung Cancer Diagnosis. Dis Markers. 2020 Dec 10;2020:4716793. doi: 10.1155/2020/4716793. PMID: 33488842; PMCID: PMC7787803.

Zhang F, Wu X, Chen W, Deng Y. Editorial: Cancer Informatics Toward Precision Medicine. Front Med (Lausanne). 2020 Nov 25;7:576611. doi:10.3389/fmed.2020.576611. PMID: 33330533; PMCID: PMC7732532.

Rodriguez RM, Khadka VS, Menor M, Hernandez BY, Deng Y. Tissue-associated microbial detection in cancer using human sequencing data. BMC Bioinformatics. 2020 Dec 3;21(Suppl 9):523. doi: 10.1186/s12859-020-03831-9. PMID: 33272199; PMCID: PMC7713026.

Fu Y, Ling Z, Arabnia H, Deng Y. Current trend and development in bioinformatics research. BMC Bioinformatics. 2020 Dec 3;21(Suppl 9):538. doi:10.1186/s12859-020-03874-y. PMID: 33272214; PMCID: PMC7713158.

Guo R, Chen Y, Borgard H, Jijiwa M, Nasu M, He M, Deng Y. The Function and Mechanism of Lipid Molecules and Their Roles in The Diagnosis and Prognosis of Breast Cancer. Molecules. 2020 Oct 21;25(20):4864. doi:10.3390/molecules25204864. PMID: 33096860; PMCID: PMC7588012.

Chen X, Zhu Y, Jijiwa M, Nasu M, Ai J, Dai S, Jiang B, Zhang J, Huang G, Deng Y. Identification of plasma lipid species as promising diagnostic markers for prostate cancer. BMC Med Inform Decis Mak. 2020 Sep 24;20(Suppl 9):223. doi:10.1186/s12911-020-01242-7. PMID: 32967667; PMCID: PMC7513490.

Zhao T, Khadka VS, Deng Y. Identification of lncRNA biomarkers for lung cancer through integrative cross-platform data analyses. Aging (Albany NY). 2020 Jul 16;12. doi: 10.18632/aging.103496. Epub ahead of print. PMID: 32675385.

Xie G, Wang X, Wei R, Wang J, Zhao A, Chen T, Wang Y, Zhang H, Xiao Z, Liu X, Deng Y, Wong L, Rajani C, Kwee S, Bian H, Gao X, Liu P, Jia W. Serum metabolite profiles are associated with the presence of advanced liver fibrosis in Chinese patients with chronic hepatitis B viral infection. BMC Med. 2020 Jun 5;18(1):144. doi: 10.1186/s12916-020-01595-w. PMID: 32498677.

Rodriguez RM, Hernandez BY, Menor M, Deng Y, Khadka VS. The landscape of bacterial presence in tumor and adjacent normal tissue across 9 major cancer types using TCGA exome sequencing. Comput Struct Biotechnol J. 2020 Mar 13;18:631-641. doi: 10.1016/j.csbj.2020.03.003. eCollection 2020. PubMed PMID:32257046; PubMed Central PMCID: PMC7109368.

Itami Y, Miyake M, Ohnishi S, Tatsumi Y, Gotoh D, Hori S, Morizawa Y, Iida K, Ohnishi K, Nakai Y, Inoue T, Anai S, Tanaka N, Fujii T, Shimada K, Furuya H, Khadka VS, Deng Y, Fujimoto K. Disabled Homolog 2 (DAB2) Protein in Tumor Microenvironment Correlates with Aggressive Phenotype in Human Urothelial Carcinoma of the Bladder. Diagnostics (Basel). 2020 Jan 20;10(1). pii: E54. doi: 10.3390/diagnostics10010054. PubMed PMID: 31968685.

Year of publication: 2019

Wang SM, Jiang B, Deng Y, Huang SL, Fang MZ, Wang Y. Clinical significance of MLH1/MSH2 for stage II/III sporadic colorectal cancer. World J Gastrointest Oncol. 2019 Nov 15;11(11):1065-1080. doi: 10.4251/wjgo.v11.i11.1065. PubMed PMID: 31798786; PubMed Central PMCID: PMC6883179.

Seale LA, Khadka VS, Menor M, Xie G, Watanabe LM, Sasuclark A, Guirguis K, Ha HY, Hashimoto AC, Peplowska K, Tiirikainen M, Jia W, Berry MJ, Deng Y. Combined Omics Reveals That Disruption of the Selenocysteine Lyase Gene Affects Amino Acid Pathways in Mice. Nutrients. 2019 Oct 26;11(11). pii: E2584. doi: 10.3390/nu11112584. PubMed PMID: 31717805; PubMed Central PMCID: PMC6893568.

Hoffmann PR, Hoffmann FW, Premeaux TA, Fujita T, Soprana E, Panigada M, Chew GM, Richard G, Hindocha P, Menor M, Khadka VS, Deng Y, Moise L, Ndhlovu LC, Siccardi A, Weinberg AD, De Groot AS, Bertino P. Multi-antigen Vaccination With Simultaneous Engagement of the OX40 Receptor Delays Malignant Mesothelioma Growth and Increases Survival in Animal Models. Front Oncol. 2019 Aug 2;9:720. doi: 10.3389/fonc.2019.00720. eCollection 2019. PubMed PMID: 31428586; PubMed Central PMCID: PMC6688537.

Zhang R, Zhu Y, Huang XB, Deng C, Li M, Shen GS, Huang SL, Huangfu SH, Liu YN, Zhou CG, Wang L, Zhang Q, Deng Y, Jiang B. Primary neuroendocrine tumor in the presacral region: A case report. World J Clin Cases. 2019 Jul 26;7(14):1884-1891. doi: 10.12998/wjcc.v7.i14.1884. PubMed PMID: 31417935; PubMed Central PMCID: PMC6692270.

Wang Z, Katsaros D, Biglia N, Shen Y, Fu Y, Tiirikainen M, Yu H. Low expression of WWC1, a tumor suppressor gene, is associated with aggressive breast cancer and poor survival outcome. FEBS Open Bio. 2019 Jul;9(7):1270-1280. doi: 10.1002/2211-5463.12659. Epub 2019 Jun 1. PMID: 31102318; PMCID: PMC6609559.

Wang Z, Katsaros D, Biglia N, Shen Y, Loo L, Yu X, Lin H, Fu Y, Chu WM, Fei P, Ni Y, Jia W, Deng X, Qian B, Yu H. ERα upregulates the expression of long non-coding RNA LINC00472 which suppresses the phosphorylation of NF-κB in breast cancer. Breast Cancer Res Treat. 2019 Jun;175(2):353-368. doi:10.1007/s10549-018-05108-5. Epub 2019 Mar 4. PMID: 30830488; PMCID: PMC6534447.

Deng Y, Zhu Y, Wang H, Khadka VS, Hu L, Ai J, Dou Y, Li Y, Dai S, Mason CE, Wang Y, Jia W, Zhang J, Huang G, Jiang B. Ratio-Based Method To Identify True Biomarkers by Normalizing Circulating ncRNA Sequencing and Quantitative PCR Data. Anal Chem. 2019 May 21;91(10):6746-6753. doi: 10.1021/acs.analchem.9b00821. PubMed PMID: 31002238.

Menor M, Zhu Y, Wang Y, Zhang J, Jiang B, Deng Y. Development of somatic mutation signatures for risk stratification and prognosis in lung and colorectal adenocarcinomas. BMC Med Genomics. 2019 Jan 31;12(Suppl 1):24. doi: 10.1186/s12920-018-0454-7. PubMed PMID: 30704450.

Fang R, Zhu Y, Hu L, Khadka VS, Ai J, Zou H, Ju D, Jiang B, Deng Y, Hu X. Plasma MicroRNA Pair Panels as Novel Biomarkers for Detection of Early Stage Breast Cancer. Front Physiol. 2019 Jan 8;9:1879. doi: 10.3389/fphys.2018.01879. eCollection 2018. PubMed PMID: 30670982; PubMed Central PMCID: PMC6331533.

Siriwardhana C, Khadka VS, Chen JJ, Deng Y. Development of a miRNA-seq based prognostic signature in lung adenocarcinoma. BMC Cancer. 2019 Jan 8;19(1):34. PMID: 30621620.

Year of publication: 2018

Fang R, Zhu Y, Khadka VS, Zhang F, Jiang B, Deng Y. The Evaluation of Serum Biomarkers for Non-small Cell Lung Cancer (NSCLC) Diagnosis. Front Physiol. 2018 Nov 29;9:1710. PMID: 30555348;

Guo M, Lu S, Huang H, Wang Y, Yang MQ, Yang Y, Fan Z, Jiang B, Deng Y. Increased AURKA promotes cell proliferation and predicts poor prognosis in bladder cancer. BMC Syst Biol. 2018 Dec 14;12(Suppl 7):118. PMID: 30547784;

Dou Y, Zhu Y, Ai J, Chen H, Liu H, Borgia JA, Li X, Yang F, Jiang B, Wang J, Deng Y. Plasma small ncRNA pair panels as novel biomarkers for early-stage lung adenocarcinoma screening. BMC Genomics. 2018 Jul 20;19(1):545. PubMed PMID: 30029594.

Yu Z, Chen H, Zhu Y, Ai J, Li Y, Gu W, Borgia JA, Zhang J, Jiang B, Chen W, Deng Y. Global lipidomics reveals two plasma lipids as novel biomarkers for the detection of squamous cell lung cancer: A pilot study. Oncol Lett. 2018, Jul;16(1):761-768. PubMed PMID: 29963143; PubMed Central PMCID: PMC6019901.

Marciel MP, Khadka VS, Deng Y, Kilicaslan P, Pham A, Bertino P, Lee K, Chen S, Glibetic N, Hoffmann FW, Matter ML, Hoffmann PR. Selenoprotein K deficiency inhibits melanoma by reducing calcium flux required for tumor growth and metastasis. Oncotarget. 2018 Feb 3;9(17):13407-13422. PubMed PMID: 29568366; PubMed Central PMCID: PMC5862587.

Chen T, You Y, Xie G, Zheng X, Zhao A, Liu J, Zhao Q, Wang S, Huang F, Rajani C, Wang C, Chen S, Ni Y, Yu H, Deng Y, Wang X, Jia W. Strategy for an Association Study of the Intestinal Microbiome and Brain Metabolome Across the Lifespan of Rats. Anal Chem. 2018 PubMed PMID: 29353471.

Jiang Z, Jiang J, Zhao B, Yang H, Wang Y, Guo S, Deng Y, Lu D, Ma T, Wang H, Wang J. CPNE1 silencing inhibits the proliferation, invasion and migration of human osteosarcoma cells. Oncol Rep. 2018 39(2):643-650. PubMed PMID: 29207139.