1. Center for Informatics
  2. Translational Bioinformatics
  3. Research Collaborations
  4. Publications
  5. Publications co-authored by TBI team

Journal articles co-authored by TBI team

 

January 2017 – July 31, 2022

83  Journal  Articles


View graph of PI co-authors by Cancer Center Program

 

Legend: Bold only is Cancer Center Program PI.  Bold & Underline is TBI team member.

2022 - 10  

  1. Yi S, Yan Y, Jin M, Bhattacharya S, Wang Y, Wu Y, Yang L, Gine E, Clot G, Chen L, Yu Y, Zou D, Wang J, Phan AT, Cui R, Li F, Sun Q, Zhai Q, Wang T, Yu Z, Liu L, Liu W, Lyv R, Sui W, Huang W, Xiong W, Wang H, Li C, Xiao Z, Hao M, Wang J, Cheng T, Bea S, Herrera AF, Danilov A, Campo E, Ngo VN, Qiu L, Wang L. Genomic and transcriptomic profiling reveals distinct molecular subsets associated with outcomes in mantle cell lymphoma. J Clin Invest. 2022 Feb 1;132(3):e153283. PMID: 34882582; PMCID: PMC8803323; DOI: 1172/JCI153283.
  2. Lee JS, Yost SE, Cui Y, Frankel PH, Li SM, Yuan YC, Morse D, Wong-Toh J, Bosserman L, Mortimer J, Yuan Y. Abstract P5-13-35: Mechanisms of CDK4/6 inhibitor resistance in hormone receptor positive metastatic breast cancer: Single institution retrospective analysis. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P5-13-35. 2022 Feb 15. DOI: https://doi.org/10.1158/1538-7445.SABCS21-P5-13-35
  3. Han Z, Estephan RJ, Wu X, Su C, Yuan YC, Qin H, Kil SH, Morales C, Schmolze D, Sanchez JF, Tian L, Yu J, Kortylewski M, Rosen ST, Querfeld C. MicroRNA Regulation of T-Cell Exhaustion in Cutaneous T Cell Lymphoma. J Invest Dermatol. 2022 Mar;142(3 Pt A):603-612.e7. Epub 2021 Nov 11. PMID: 34774537; PMCID: PMC8860868. DOI: 10.1016/j.jid.2021.08.447
  4. Roy S, Zhao Y, Yuan YC, Goel A. Metformin and ICG-001 Act Synergistically to Abrogate Cancer Stem Cells-Mediated Chemoresistance in Colorectal Cancer by Promoting Apoptosis and Autophagy. Cancers (Basel). 2022 Mar 2;14(5):1281. PMID: 35267590; PMCID: PMC8908991; DOI: 10.3390/cancers14051281
  5. Wang Z, Zhang C, Warden CD, Liu Z, Yuan YC, Guo C, Wang C, Wang J, Wu X, Ermel R, Vonderfecht SL, Wang X, Brown C, Forman S, Yang Y, James You M, Chen W. Loss of SIRT1 inhibits hematopoietic stem cell aging and age-dependent mixed phenotype acute leukemia. Commun Biol. 2022 Apr 28;5(1):396. PMID: 35484199; PMCID: PMC9051098; DOI: 10.1038/s42003-022-03340-w. 
  6. Zhang Z, Yang A, Chaurasiya S, Park AK, Lu J, Kim SI, Warner SG, Yuan YC, Liu Z, Han H, Von Hoff D, Fong Y, Woo Y. CF33-hNIS-antiPDL1 virus primes pancreatic ductal adenocarcinoma for enhanced anti-PD-L1 therapy. Cancer Gene Ther. 2022 Jun;29(6):722-733. Epub 2021 Jun 9. PMID: 34108669; PMCID: PMC8896143(available on 2022-12-01); DOI: 1038/s41417-021-00350-4
  7. Han Z, Feng M, Wu X, Su C, Yuan YC; Qin H, Sanchez JF, Zain, J; Rosen ST, Querfeld C. Abstract 5196: CD47 Blockade potentiates immunotherapy of durvalumab against cutaneous T cell lymphoma. Cancer Re. Volume 82, Issue 12_Supplement: 5196. 2022 June 15. DOI: https://doi.org/10.1158/1538-7445.AM2022-5196
  8. Sullivan KM; Li H, Mahuron K, Yuan YC, Chao J, Paz IB, Han H, Fong Y, Woo Y. Abstract 6144: Novel M2 macrophage gene signature as a biomarker of poor outcomes independent of TNM stage in peritoneal liquid biopsy of gastric cancer patients. Cancer Res (2022) 82 (12_Supplement): 6144. 2022 June 15. DOI: https://doi.org/10.1158/1538-7445.AM2022-6144
  9. Lee JS, Yost SE, Li SM, Cui Y, Frankel PH, Yuan YC, Schmolze D, Egelston CA, Guo W, Murga M, Chang H, Bosserman L, Yuan Y. Genomic Markers of CDK 4/6 Inhibitor Resistance in Hormone Receptor Positive Metastatic Breast Cancer. Cancers. 28 June 2022; 14(13), 3159. DOI: https://doi.org/10.3390/cancers14133159
  10. Okuno K, Garg R, Yuan YC, Tokunaga M, Kinugasa Y, Goel A. Corrigendum: Berberine and Oligomeric Proanthocyanidins Exhibit Synergistic Efficacy Through Regulation of PI3K-Akt Signaling Pathway in Colorectal Cancer. Front Oncol. 2022 Jun 29;12:952180. Erratum for: Front Oncol. 2022 May 04;12:855860. PMID: 35847926; PMCID: PMC9278059. DOI: 10.3389/fonc.2022.952180.

 

2021 - 11 

  1. Khan A, Ituarte PHG, Raoof M, Melstrom L, Li H, Yuan YC, Lai L, Paz IB, Goel A, Fong Y, Woo Y. Disparate and Alarming Impact of Gastrointestinal Cancers in Young Adult Patients. Ann Surg Oncol. 2021 Feb;28(2):785-796. PMID: 32740736; DOI: 1245/s10434-020-08969-7
  2. Lyou Y, Dorff TB, Pal SK, Yuan YC. High-throughput global transcriptional profiling to identify the STAT3 signaling pathway as a potential biomarker for immune checkpoint inhibitor resistance in metastatic/advanced urothelial carcinoma. Journal of Clinical Oncology. Abstract | 2021 Genitourinary Cancers Symposium. 2021 Feb 20; 39(6), 2. No PMID; No PMCID; DOI: 10.1200/JCO.2021.39.6_suppl.474.
  3. Lewinsky H, Gunes EG, David K, Radomir L, Kramer MP, Pellegrino B, Perpinial M, Chen J, He TF, Mansour AG, Teng KY, Bhattacharya S, Caserta E, Troadec E, Lee P, Feng M, Keats J, Krishnan A, Rosenzweig M, Yu J, Caligiuri MA, Cohen Y, Shevetz O, Becker-Herman S, Pichiorri F, Rosen S, Shachar I. CD84 is a regulator of the immunosuppressive microenvironment in multiple myeloma. JCI Insight. 2021 Feb 22;6(4):e141683. PMID: 33465053; PMCID: PMC7934939; DOI: 1172/jci.insight.141683
  4. Wang C, Ouyang C, Cho M, Ji J, Sandhu J, Goel A, Kahn M, Fakih M. Wild-type APC Is Associated with Poor Survival in Metastatic Microsatellite Stable Colorectal Cancer. Oncologist. 2021 Mar;26(3):208-214. PMID: 33230914; PMCID: PMC7930429; DOI: 1002/onco.13607
  5. Woo Y, Behrendt CE, Yang A, Hahn M, Goel A, Li H, Yuan YC, Fong Y. Tumor Epigenetic Signature and Survival in Resected Gastric Cancer Patients. J Am Coll Surg. 2021 Apr;232(4):483-491.e1. PMID: 33465468; DOI: 1016/j.jamcollsurg.2020.12.023
  6. Bhattacharya S, Mohanty A, Achuthan S, Kotnala S, Jolly MK, Kulkarni P, Salgia R. Group Behavior and Emergence of Cancer Drug Resistance. Trends Cancer. 2021 Apr;7(4):323-334. PMID: 33622644; PMCID: PMC8500356; DOI: 1016/j.trecan.2021.01.009
  7. Courdy S, Hulse M, Nadaf S, Mao A, Pozhitkov A, Berger S, Chang J, Achuthan S, Kancharla C, Kunz I, Peddinti A, Sarmiento R, Seetharamu K, Kirkpatrick T, Dilsizian B, Morris M, Bonner JD, Gray SW, McDonnell K,  Gruber SB, The City of Hope POSEIDON enterprise-wide platform for real-world data and evidence in cancer. J Clinical Oncology, published online May 28, 2021, 39(15), suppl.e18813.
    Abstract ASCO: https://ascopubs.org/doi/abs/10.1200/JCO.2021.39.15_suppl.e18813
  8. Zhang Z, Yang A, Chaurasiya S, Park AK, Lu J, Kim SI, Warner SG, Yuan YC, Liu Z, Han H, Von Hoff D, Fong Y, Woo Y. CF33-hNIS-antiPDL1 virus primes pancreatic ductal adenocarcinoma for enhanced anti-PD-L1 therapy. Cancer Gene Ther. 2021, Jun 9. PMID: 34108669; DOI: 1038/s41417-021-00350-4
  9. Yang L, Chan A, Miyashita K, Delaney CD , Wang X, Li H, Pokharel SP, Li S, Li M, Xu X, Lu W, Liu Q, Mattson N, Chen KY, Wang J, Yuan YC, Horne D, Rosen ST, Feliciano YS , Feng Z, Hoshii T, Xiao G, Müschen M, Chen J, Armstrong SA, Chen CW. High-resolution characterization of gene function using single-cell CRISPR tiling screen. Nature Communications 12, 4063. 2021 Jul 1. PMID: 34210975; DOI: 1038/s41467-021-24324-0
  10. Singh SP, Lee J, Bose C, Li H, Yuan YC, Hindle A, Singhal SS, Kopel J, Palade PT, Jones C, Rahman RL, Awasthi S. Haploinsufficiency Interactions between RALBP1 and p53 in ERBB2 and PyVT Models of Mouse Mammary Carcinogenesis. Cancers. 2021 Jul 2;13(13):3329. PMID: 34283045; PMCID: PMC8268413; DOI: 3390/cancers13133329
  11. Di Raimondo C, Han Z, Su C, Wu X, Qin H, Sanchez JF, Yuan YC, Martinez X, Abdulla F, Zain J, Chen CW, Rosen ST, Querfeld C. Identification of a Distinct miRNA Regulatory Network in the Tumor Microenvironment of Transformed Mycosis Fungoides. Cancers (Basel). 2021 Nov 22;13(22):5854. PMID: 34831008; PMCID: PMC8616450; DOI:3390/cancers13225854

 

2020 - 21  

  1. Su YL, Wang X, Mann M, Adamus TP, Wang D, Moreira DF, Zhang Z, Ouyang C, He X, Zhang B, Swiderski PM, Forman SJ, Baltimore D, Li L, Marcucci G, Boldin MP, Kortylewski M. Myeloid cell-targeted miR-146a mimic inhibits NF-κB-driven inflammation and leukemia progression in vivo. Blood. 2020 Jan 16;135(3):167-180. PMID: 31805184; PMCID: 6966933.
  2. Mambetsariev I, Wang Y, Chen C, Nadaf S, Pharaon R, Fricke J, Amanam I, Amini A, Bild A, Chu P, Erhunmwunsee L, Kim JY, Munu J, Pillai R, Raz D, Sampath S, Vora L, Qiu F, Smith L, Batra SK, Massarelli E, Koczywas M, Reckamp K, Salgia R. Precision medicine and actionable alterations in lung cancer: A single institution experience. PLoS One. 2020 Feb 11;15(2):e0228188. doi: 1371/journal.pone.0228188; PMID: 32045431; PMCID: 7012442.
  3. Ramos CA, Ouyang C, Qi Y, Chung Y, Cheng CT, LaBarge MA, Seewaldt VL, Ann DK. A Non-canonical Function of BMAL1 Metabolically Limits Obesity-Promoted Triple-Negative Breast Cancer. iScience. 2020 Feb 21;23(2):100839. PMID: 32058954; PMCID: 6997869.
  4. Nardi IK, Stark JM, Larsen A, Salgia R, Raz DJ. USP22 Interacts with PALB2 and Promotes Chemotherapy Resistance via Homologous Recombination of DNA Double-Strand Breaks. Mol Cancer Res. 2020 Mar;18(3):424-435. Epub 2019 Nov 4. doi:10.1158/1541-7786.MCR-19-0053; PMID: 31685642.
  5. Yoon S, Li H, Quintanar L, Armstrong B, Rossi JJ. Uncovering Differently Expressed Markers and Heterogeneity on Human Pancreatic Cancer. Transl Oncol. 2020 Mar 01; 13(3):100749. doi: 1016/j.tranon.2020.100749; PMID: 32143178;  PMCID: 7056725
  6. Gupta R, Othman T, Chen C, Sandhu J, Ouyang C, Fakih M. Guardant360 Circulating Tumor DNA Assay Is Concordant with FoundationOne Next-Generation Sequencing in Detecting Actionable Driver Mutations in Anti-EGFR Naive Metastatic Colorectal Cancer. Oncologist. 2020 Mar;25(3):235-243. PMID: 32162812; PMCID: 7066697.
  7. Tran T, Hanse E, Habowski A, Li H, Gabra M, Yang Y, Lowman X, Ooi A, Liao S, Edwards R, Waterman M, Kong M. α-Ketoglutarate attenuates Wnt signaling and drives differentiation in colorectal cancer.  Nature Cancer. 2020 Mar;1(3):345-358. doi: 1038/s43018-020-0035-5; PMID: 32832918; PMCID: 7442208.
  8. Chao J, Bedell V, Lee J, Li MS, Chu P, Yuan YC, Zhao D, Klempner SJ, Lin RJ. Association Between Spatial Heterogeneity Within Nonmetastatic Gastroesophageal Adenocarcinomas and Survival. JAMA Netw Open. 2020 Apr 1;3(4):e203652. DOI: 1001/jamanetworkopen.2020.3652; PMID: 32338752; PMCID: 7186861.
  9. Wang C, Park J, Ouyang C, Longmate JA, Tajon M, Chao J, Lim D, Sandhu J, Yin HH, Pillai R, Gozo MC, Avalos C, Egelston CA, Lee PP, Fakih M. A Pilot Feasibility Study of MiR-16Liver Radioembolization Followed by Durvalumab and Tremelimumab in Patients with Microsatellite Stable Colorectal Cancer Liver Metastases. Oncologist. 2020 May; 25(5):382-e776. doi: 1634/theoncologist.2019-0924; PMID: 31857446; PMCID: 7216435.
  10. Che M, Kweon SM, Teo JL, Yuan YC, Melstrom LG, Waldron RT, Lugea A, Urrutia RA, Pandol SJ, Lai KKY. Targeting the CBP/β-Catenin Interaction to Suppress Activation of Cancer-Promoting Pancreatic Stellate Cells. Cancers (Basel). 2020 Jun 5;12(6):E1476. doi: 3390/cancers1206147; PMID: 32516943; PMCID: 7352534.
  11. Mirzapoiazova T, Pozhitkov A, Nam A, Mambetsariev I, Nelson MS, Tan YC, Zhang K, Raz D, Singhal S, Nasser MW, Kulkarni P, Batra SK, Sattler M, Salgia R. Effects of selected deubiquitinating enzyme inhibitors on the proliferation and motility of lung cancer and mesothelioma cell lines.  Int J Oncol. 2020 Jul;57(1):80-86. Epub 2020 Apr 1. doi: 3892/ijo.2020.5034; PMID: 32236606; PMCID: 7252467.
  12. Ishak Gabra M, Yang Y, Li H, Senapati P, Hanse E, Lowman X, Tran T, Zhang L, Doan L, Xu X, Schones D, Fruman D, Kong M. Dietary glutamine supplementation suppresses epigenetically-activated oncogenic pathways to inhibit melanoma tumour growth. Nat Commun. 2020 Jul 3;11(1):3326. doi: 10.1038/s41467-020-17181-w; PMID: 32620791; PMCID: 7335172
  13. Rockne RC, Branciamore S, Qi J, Frankhouser DE, O'Meally D, Hua WK, Cook G, Carnahan E, Zhang L, Marom A, Wu H, Maestrini D, Wu X, Yuan YC, Liu Z, Wang LD, Forman S, Carlesso N, Kuo YH, Marcucci G. State-transition analysis of time-sequential gene expression identifies critical points that predict development of acute myeloid leukemia. Cancer Res. 2020 Aug 1;80(15):3157-3169. Epub 2020 May 15. doi: 10.1158/0008-5472; PMID: 32414754; PMCID: PMC7416495 (available on 2021-02-01)
  14. Zhao D, Mambetsariev I, Li H, Chen C, Fricke J, Fann P, Kulkarni P, Xing Y, Lee PP, Bild A, Massarelli E, Koczywas M, Reckamp K, Salgia R. Association of molecular characteristics with survival in advanced non-small cell lung cancer patients treated with checkpoint inhibitors. Lung Cancer. 2020 Aug;146:174-181. ePub 2020 May 24. doi: 10.1016/j.lungcan.2020.05.025. PMID: 32554069. 
  15. Khan A, Ituarte PHG, Raoof M, Melstrom L, Li H, Yuan YC, Lai L, Benjamin Paz I, Goel A, Fong Y, Woo Y.  Disparate and Alarming Impact of Gastrointestinal Cancers in Young Adult Patients.  Ann Surg Oncol. ePub 2020 Aug 1. doi: 10.1245/s10434-020-08969-7. PMID: 32740736.
  16. Hu W, Bhattacharya S, Hong T, Wong P, Li L, Vaidehi N, Kalkum M, Shively J. Structural characterization of a dimeric complex between the short cytoplasmic domain of CEACAM1 and the pseudo tetramer of S100A10-Annexin A2 using NMR and molecular dynamics. Biochimica et Biophysica Acta (BBA)-Biomembranes. ePub 2020 Aug 21;1863(1):183451. DOI : 10.1016/j.bbamem.2020.183451. PMID: 32835655.
  17. Mohanty A, Nam A, Pozhitkov A, Yang L, Srivastava S, Nathan A, Wu X, Mambetsariev I, Nelson M, Subbalakshmi AR, Guo L, Nasser MW, Batra SK, Orban J, Jolly MK, Massarelli E, Kulkarni P, Salgia R. A Non-genetic Mechanism Involving the Integrin β4/Paxillin Axis Contributes to Chemoresistance in Lung Cancer. iScience. Epub 2020 Aug 22;23(9):101496. doi: 10.1016/j.isci.2020.101496; PMID: 32947124. PMCID: 7502350.
  18. Amanam I, Mambetsariev I, Gupta R, Achuthan S, Wang Y, Pharaon R, Massarelli E, Koczywas M, Reckamp K, Salgia R. Role of immunotherapy and co-mutations on KRAS-mutant non-small cell lung cancer survival. J Thorac Dis. 2020 Sep;12(9):5086-5095. PMID: 33145085; PMCID: PMC7578487; DOI: 10.21037/jtd.2020.04.18
  19. Pozhitkov A, Rosenzweig M, Pichiorri F, Gunes EG, Buettner R, Keats JJ, Rosen ST. Glucocorticoid receptor expression in multiple myeloma patients is a predictor of survival. Leuk Lymphoma. ePub: 2020 Sep 13:1-5. doi:1080/10428194.2020.1811860. PMID: 32921213.
  20. Hammad M, Cornejo Y, Batalla-Covello J, Majid AA, Burke C, Liu Z, Yuan YC, Li M, Dellinger T, Lu J, Chen NG, Fong Y, Aboody KS, Mooney R. Neural Stem Cells Improve the Delivery of Oncolytic Chimeric Orthopoxvirus in a Metastatic Ovarian Cancer Model. Mol Ther Oncolytics. 2020 Sep 25; 18:326-334. ePub 2020 Jul 6; doi: 10.1016/j.omto.2020.07.002. PMID: 32775617; PMCID: PMC7394740.
  21. Pathak KV, McGilvrey MI, Hu CK, Garcia-Mansfield K, Lewandoski K, Eftekhari Z, Yuan YC, Zenhausern F, Menashi E, Pirrotte P.  Molecular Profiling of Innate Immune Response Mechanisms in Ventilator-associated Pneumonia. Mol Cell Proteomics. 2020 Oct;19(10):1688-1705.  PMID: 32709677; PMCID: PMC8014993; DOI: 10.1074/mcp.RA120.002207

 

2019 - 20 

  1. Hewelt B, Li H, Jolly M, Kulkarni P, Mambetsariev I, Salgia R. The DNA Walk and its Demonstration of Deterministic Chaos—Relevance to Genomic Alterations in Lung Cancer.  2019 Jan 7.  PMID: 30615123 PMCID: PMCID 6691335.
  2. Zhao ZM, Yost SE, Hutchinson KE, Li SM, Yuan YC, Noorbakhsh J, Liu Z, Warden C, Johnson RM, Wu X, Chuang JH, Yuan Y. CCNE1 amplification is associated with poor prognosis in patients with triple negative breast cancer. BMC Cancer. 2019 Jan 21;19(1):96. PubMed PMID: 30665374; PubMed Central PMCID: PMC6341717.
  3. Jayathilake B, Bhattacharya S, Vaidehi N, Narayanan S. Efficient and selective electrochemically driven enzyme-catalyzed reduction of carbon dioxide to formate using formate dehydrogenase and an artificial cofactor. Accounts of chemical research. 2019 Feb 11;52 (3):676-685. doi/10.1021. PMID: 30741524.
  4. Yang Y, Ishak Gabra MB, Hanse EA, Lowman XH, Tran TQ, Li H, Milman N, Liu J, Reid MA, Locasale JW, Gil Z, Kong M. MiR-135 suppresses glycolysis and promotes pancreatic cancer cell adaptation to metabolic stress by targeting phosphofructokinase-1. Nature communications.  2019 Feb 18; 10(1), 809.  PMID:  PMCID: PMC6379428.
  5. Lowman XH, Hanse EA, Yang Y, Ishak Gabra MB, Tran TQ, Li H, Kong M. p53 Promotes Cancer Cell Adaptation to Glutamine Deprivation by Upregulating Slc7a3 to Increase Arginine Uptake.  Cell Reports, 2019 Mar 12; 26: 3051-3060.e4.. PMID 30865893.  PMCID:
  6. Gupta R, Amanam I, Rahmanuddin S, Mambetsariev I, Wang Y, Huang C, Reckamp K, Vora L, Salgia R. Anaplastic Lymphoma Kinase (ALK)-positive Tumors: Clinical,Radiographic and Molecular Profiles, and Uncommon Sites of Metastases in Patients With Lung Adenocarcinoma. Am J Clin Oncol. 2019 Apr;42(4):337-344. PubMed PMID: 30741758.
  7. Ghazarian H, Hu W, Mao A, Nguyen T, Vaidehi N, Sligar S, Shively JE. NMR analysis of free and lipid nanodisc anchored CEACAM1 membrane proximal peptides with Ca2+/CaM. Biochim Biophys Acta Biomembr. 2019 Apr 1;1861(4):787-797. PMID: 30639287; PMCID: PMC6524640; DOI: 10.1016/j.bbamem.2019.01.004
  8. Buettner R, Morales C, Caserta E, Troadec E, Gunes EG, Viola D, Khalife J, Li H, Keats JJ, Christofferson A, Wu XW, Synold TW, Palmer JM, Sanchez JF, Pozhitkov A, Vaidehi N, Marcucci G, Krishnan A, Rosenzweig MA, Pichiorri F, Rosen ST. Leflunomide regulates c-Myc expression in myeloma cells through PIM targeting. Blood Adv. 2019 Apr 9;3(7):1027-1032. PubMed PMID: 30940637; PubMed Central PMCID: PMC6457239.
  9. Bhattacharya S, Lin X. Recent Advances in Computational Protocols Addressing Intrinsically Disordered Proteins. Biomolecules. 2019 Apr 11;9(4). Review. PubMed PMID: 30979035; PubMed Central PMCID:PMC6523529.
  10. Schrock AB*, Ouyang C*, Sandhu J, Sokol E, Jin D, Ross JS, Miller VA, Lim D, Amanam I, Chao J, Catenacci D, Cho M, Braiteh F, Klempner SJ, Ali SM, Fakih M. Tumor mutational burden is predictive of response to immune checkpoint inhibitors in MSI-high metastatic colorectal cancer. Ann Oncol. 2019 Jul 1;30(7):1096-1103. PubMed PMID: 31038663. *contributed equally
  11. Lin FM, Yost SE, Wen W, Frankel PH, Schmolze D, Chu PG, Yuan YC, Liu Z, Yim J, Chen Z, Yuan Y. Differential gene expression and AKT targeting in triple negative breast cancer. Oncotarget. 2019 Jul 8;10(43):4356-4368. 2019 Jul 8. PubMed PMID: 31320990; PubMed Central PMCID: PMC6633890.
  12. Mambetsariev I, Mirzapoiazova T, Lennon F, Jolly MK, Li H, Nasser MW, Salgia R. Small Cell Lung Cancer Therapeutic Responses Through Fractal Measurements: From Radiology to Mitochondrial Biology. J Clin Med. 2019 Jul 16; 8(7), 1038.  PMID: 31315252
  13. Warden CD, Lee H, Tompkins JD, Li X, Wang C, Riggs AD, Yu H, Jove R, Yuan YC. COHCAP: an integrative genomic pipeline for single-nucleotide resolution DNA methylation analysis. Nucleic Acids Res. 2019 Sep 5;47(15):8335-8336. PubMed PMID: 31340028; PubMed Central PMCID: PMC6735849.
  14. Kujawski, M., Li, L., Bhattacharya, S., Wong P, Lee WH, Williams L, Li H, Chea J, Poku K, Bowles N, Vaidehi N, Yazaki P, Shively JE. Generation of dual specific bivalent BiTEs (dbBIspecific T-cell engaging antibodies) for cellular immunotherapy. BMC Cancer.2019 Sep 5;19(1):882. PMID: 31488104 . PMCID: PMC6727398 
  15. Fakih M*, Ouyang C*, Wang C, Tu TY, Gozo MC, Cho M, Sy M, Longmate JA, Lee PP. Immune overdrive signature in colorectal tumor subset predicts poor clinical outcome. J Clin Invest. 2019 Oct 1;129(10):4464-4476. PubMed PMID: 31524634; PubMed Central PMCID: PMC6763253.
    *contributed equally
  16. Mirzapoiazova T, Li H, Nathan A, Srivstava S, Nasser MW, Lennon F, Armstrong B, Mambetsariev I, Chu PG, Achuthan S, Batra SK, Kulkarni P, Salgia R. Monitoring and Determining Mitochondrial Network Parameters in Live Lung Cancer Cells. J Clin Med. 2019 Oct 18;8(10). PubMed PMID: 31635288; PubMed Central PMCID: PMC6832496
  17. Kalvala A, Wallet P, Yang L, Wang C, Li H, Nam A, Nathan A, Mambetsariev I, Poroyko V, Gao H, Chu P, Sattler M, Bild A, Manuel ER, Lee PP, Jolly MK, Kulkarni P, Salgia R. Phenotypic Switching of Naïve T Cells to Immune-Suppressive Treg-Like Cells by Mutant KRAS. J Clin Med. 2019 Oct 18;8(10). PubMed PMID: 31635338.
  18. Khalife J, Ghose J, Martella M, Viola D, Rocci A, Troadec E, Terrazas C, Satoskar AR, Gunes EG, Dona A, Sanchez JF, Bergsagel PL, Chesi M, Pozhitkov A, Rosen S, Marcucci G, Keats JJ, Hofmeister CC, Krishnan A, Caserta E, Pichiorri F. MiR-16 regulates crosstalk in NF-κB tolerogenic inflammatory signaling between myeloma cells and bone marrow macrophages. JCI Insight. 2019 Nov 1;4(21). PubMed PMID: 31593552.
  19. Slavin TP, Teh JB, Weitzel JN, Peng K, Wong FL, Qin H, Wang J, Wu X, Mei M, Pillai R, Wang Y, Tsang KK, Pozhitkov A, Krishnan A, Forman SJ, Armenian SH. Association between Clonal Hematopoiesis and Late Nonrelapse Mortality after Autologous Hematopoietic Cell Transplantation.  Biol Blood Marrow Transplant. 2019 Dec;25(12):2517-2521. PMID: 31445185.
  20. Muk S, Ghosh S, Achuthan S, Chen X, Yao X, Sandhu M, Griffor MC, Fennell KF, Che Y, Shanmugasundaram V, Qiu X, Tate CG, Vaidehi N. Machine Learning for Prioritization of Thermostabilizing Mutations for G-Protein Coupled Receptors. Biophys J. 2019 Dec 3;117(11):2228-2239. PMID: 31703801; PMCID: PMC6895739;DOI: 10.1016/j.bpj.2019.10.023

 

2018 - 15  

  1. Zhang K, Keymeulen S, Nelson R, Tong TR, Yuan YC, Yun X, Liu Z, Lopez J, Raz DJ, Kim JY. Overexpression of Flap Endonuclease 1 Correlates with Enhanced Proliferation and Poor Prognosis of Non-Small-Cell Lung Cancer. Am J Pathol. 2018 Jan;188(1):242-251. Epub 2017 Oct 14. PMID: 29037854; PMCID: PMC5745529.
  2. Jandial R, Neman J, Lim PP, Tamae D, Kowolik CM, Wuenschell GE, Shuck SC, Ciminera AK, De Jesus LR, Ouyang C, Chen MY, Termini J. Inhibition of GLO1 in Glioblastoma Multiforme Increases DNA-AGEs, Stimulates RAGE Expression, and Inhibits Brain Tumor Growth in Orthotopic Mouse Models. Int J Mol Sci. 2018 Jan 30;19(2). PMID: 29385725; PMCID: PMC5855628.
  3. Nivedha AK, Tautermann CS, Bhattacharya S, Lee S, Casarosa P, Kollak I, Kiechle T, Vaidehi N. Identifying Functional Hotspot Residues for Biased Ligand Design in G-Protein-Coupled Receptors. Mol Pharmacol. 2018 Apr;93(4):288-296. Epub 2018 Jan 24. PubMed PMID: 29367258; PubMed Central PMCID: PMC5832328.
  4. Awasthi S, Tompkins J, Singhal J, Riggs AD, Yadav S, Wu X, Singh S, Warden C, Liu Z, Wang J, Slavin TP, Weitzel JN, Yuan YC, Awasthi M, Srivastava SK, Awasthi YC, Singhal SS. Rlip depletion prevents spontaneous neoplasia in TP53 null mice. Proc Natl Acad Sci U S A. 2018 Apr 10, Epub PMID: 29572430.  PMCID: PMC5899455
  5. Chen SF, Liu Z, Chaurasiya S, Dellinger TH, Lu J, Wu X, Qin H, Wang J, Fong Y, Yuan YC. Identification of core aberrantly expressed microRNAs in serous ovarian carcinoma. Oncotarget. 2018 Apr 17;9(29):20451-20466. PubMed PMID: 29755664; PMCID: PMC5945511.
  6. Zhang XH, Nam S, Wu J, Chen CH, Liu X, Li H, McKeithan T, Gong Q, Chan WC, Yin HH, Yuan YC, Pillai R, Querfeld C, Horne D, Chen Y, Rosen ST. Multi-kinase inhibitor with anti-p38γ activity in cutaneous T cell lymphoma. J Invest Dermatol. 2018 May. Epub 2018m/05/15. pii: S0022-202X(18)31967-5. doi: 1016/j.jid.2018.04.030; PubMed PMID: 29758280; PMCID: PMC7269016.
  7. Zhang B, Nguyen LXT, Li L, Zhao D, Kumar B, Wu H, Lin A, Pellicano F, Hopcroft L, Su YL, Copland M, Holyoake TL, Kuo CJ, Bhatia R, Snyder DS, Ali H, Stein AS, Brewer C, Wang H, McDonald T, Swiderski P, Troadec E, Chen CC, Dorrance A, Pullarkat V, Yuan YC, Perrotti D, Carlesso N, Forman SJ, Kortylewski M, Kuo YH, Marcucci G. Bone marrow niche trafficking of miR-126 controls the self-renewal of leukemia stem cells in chronic myelogenous leukemia. Nat Med. 2018 May; 24(4):450-462. Epub 2018 Mar 5. PMID: 29505034. PMCID: PMC5965294. 
  8. Salgia, R., Mambetsariev, I., Hewelt, B., Achuthan, S., Li, H., Poroyko, V., Wang, Y., & Sattler, M. (May 2018). Modeling small cell lung cancer (SCLC) biology through deterministic and stochastic mathematical models. Oncotarget, 2018 May 25; 9(40), 26226-42. PMID: 29899855. PMCID: PMC5995226. 
  9. Lin HH, Chung Y, Cheng CT, Ouyang C, Fu Y, Kuo CY, Chi KK, Sadeghi M, Chu P, Kung HJ, Li CF, Limesand KH, Ann DK. Autophagic reliance promotes metabolic reprogramming in oncogenic KRAS-driven tumorigenesis. Autophagy. 2018;14(9):1481-1498. Epub 2018 Aug 21. PMID: 29956571; PMCID: PMC6135591.
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2017 - 6 

  1. Hu W, Mao A, Wong P, Larsen A, Yazaki PJ, Wong JYC, Shively JE. Characterization of 1,2-Distearoyl-sn-glycero-3-phosphoethanolamine-N-[Methoxy(polyethylene glycerol)-2000] and Its Complex with Doxorubicin Using Nuclear Magnetic Resonance Spectroscopy and Molecular Dynamics. Bioconjug Chem. 2017 Jun 21;28(6):1777-1790. PubMed PMID: 28520406.
  2. Won H, Moreira D, Gao C, Duttagupta P, Zhao X, Manuel E, Diamond D, Yuan YC, Liu Z, Jones J, D'Apuzzo M, Pal S, and Kortylewski M. TLR9 expression and secretion of LIF by prostate cancer cells stimulates accumulation and activity of polymorphonuclear MDSCs" J Leukoc Biol. 2017 Aug;102(2):423-436. PMID: 28533357; PMCID: PMC5505743.
  3. Zhang K, Wang J, Tong T, Wu XW, Nelson R, Yuan YC, Liu Z, Kim JY, Salgia R and Raz D. Loss of H2B monoubiquitination is associated with poor-differentiation and enhanced malignancy of lung adenocarcinoma" Int J Cancer. 2017 Aug 15;141(4):766-777. PMID: 28481029; PMCID: PMC5527746.
  4. Yuan Y, Yost SE, Yuan YC, Solomon NM, Mambetsariev I, Pal S, Frankel P, Salgia R, Neuhausen SL, Mortimer J. Genomic mutation-driven metastatic breast cancer therapy: A single center experience. Oncotarget. 2017 Sep 22; 8(37), 62817. PubMed PMID: 28061482; PMCID: PMC5617552.
  5. Lee S, Devamani T, Song HD, Sandhu M, Larsen A, Sommese R, Jain A, Vaidehi N, Sivaramakrishnan S. Distinct structural mechanisms determine substrate affinity and kinase activity of protein kinase Cα. J Biol Chem. 2017 Sep 29;292(39):16300-16309. Epub 2017 Aug 15. PubMed. PMID: 28821615; PubMed Central PMCID: PMC5625059.
  6. Slavin T, Neuhausen SL, Rybak C, Solomon I, Nehoray B, Blazer K, Niell-Swiller M, Adamson AW, Yuan YC, Yang K, Sand S, Castillo D, Herzog J, Wu X, Tao S, Chavez T, Woo Y, Chao J, Mora P, Horcasitas D, Weitzel J. Genetic Gastric Cancer Susceptibility in the International Clinical Cancer Genomics Community Research Network. Cancer Genet. 2017 Oct;216-217:111-119. Epub 2017 Aug 17. PMID: 29025585. PMCID: PMC5659836.

 

2013

This article from 2013 is included for reference, because it relates directly to an application TBI includes in its Software Catalog:  
https://centerforinformatics.cityofhope.org/translational-bioinformatics/software-and-resources/software-catalog/     (scroll down to “BD-Func” in the Catalog)

Warden CD, Kanaya N, Chen S, Yuan YC. BD-Func: a streamlined algorithm for predicting activation and inhibition of pathways. PeerJ.  2013 1: e159. PubMed PMID: 24058887; PubMed Central PMCID: PMC3775632.


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