Biomedical Informatics - Research Accomplishments

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From 2018 to 2022, BISR has supported approximately 145 cancer-relevant publications. BISR Personnel have co-authored 28 cancer relevant publications and supported 16 research publications in high Impact Factor journals (IF>10) shown below. 



David J Foran, Wenjin Chen, Ying Chen, and Youyi Peng - Cancer-Relevant Publications (2018 – 2022)
 

An Expandable Informatics Framework for Enhancing Central Cancer Registries with Digital Pathology Specimens, Computational Imaging Tools, and Advanced Mining Capabilities. Foran DJ, Durbin EB, Chen Y, Sadimin E, Sharma A, Banerjee I, Kurc T, Li N, Stroup AM, Harris G, Gu A, Schymura M, Gupta R, Bremer E, Balsamo J, DiPrima T, Wang F, Abousamra S, Samaras D, Hands I, Ward K, Saltz JH. J Pathol Inform. 2022 Jan 5;13:5. doi: 10.4103/jpi.jpi_31_21.

Liver disease classification from ultrasound using multi-scale CNN. Che H, Brown LG, Foran DJ, Nosher JL, Hacihaliloglu I. Int J Comput Assist Radiol Surg. 2021 Sep;16(9):1537-1548. doi: 10.1007/s11548-021-02414-0. Epub 2021 Jun 7.

Chest X-ray image phase features for improved diagnosis of COVID-19 using convolutional neural network. Qi X, Brown LG, Foran DJ, Nosher J, Hacihaliloglu I. Int J Comput Assist Radiol Surg. 2021 Feb;16(2):197-206. doi: 10.1007/s11548-020-02305-w.

Gene expression of adipokines and adipokine receptors in the tumor microenvironment: associations of lower expression with more aggressive breast tumor features. Llanos AAM, Yao S, Singh A, Aremu JB, Khiabanian H, Lin Y, Omene C, Omilian AR, Khoury T, Hong CC, Ganesan S, Foran DJ, Higgins MJ, Ambrosone CB, Bandera EV, Demissie K. Breast Cancer Res Treat. 2021 Feb;185(3):785-798. doi: 10.1007/s10549-020-05972-0.

Immunohistochemical analysis of adipokine and adipokine receptor expression in the breast tumor microenvironment: associations of lower leptin receptor expression with estrogen receptor-negative status and triple-negative subtype. Llanos AAM, Lin Y, Chen Y, Yao S, Norin J, Chekmareva MA, Omene C, Cong L, Omilian AR, Khoury T, Hong CC, Ganesan S, Foran DJ, Higgins M, Ambrosone CB, Bandera EV, Demissie K. Breast Cancer Res. 2020 Feb 11;22(1):18. doi: 10.1186/s13058-020-1256-3.

Statistical Analysis of Survival Models Using Feature Quantification on Prostate Cancer Histopathological Images. Ren J, Singer EA, Sadimin E, Foran DJ, Qi X. J Pathol Inform. 2019 Sep 27;10:30. doi: 10.4103/jpi.jpi_85_18.

Two well-differentiated pancreatic neuroendocrine tumor mouse models. Wong C, Tang LH, Davidson C, Vosburgh E, Chen Y, Foran DJ, Notterman DA, Levine AJ, Xu EY. Cell Death Differ. 2020 Jan;27(1):269-283. doi: 10.1038/s41418-019-0355-0.

Unsupervised Domain Adaptation for Classification of Histopathology Whole-Slide Images. Ren J, Hacihaliloglu I, Singer EA, Foran DJ, Qi X. Front Bioeng Biotechnol. 2019 May 15;7:102. doi: 10.3389/fbioe.2019.00102.

Recurrence analysis on prostate cancer patients with Gleason score 7 using integrated histopathology whole-slide images and genomic data through deep neural networks. Ren J, Karagoz K, Gatza ML, Singer EA, Sadimin E, Foran DJ, Qi X. J Med Imaging (Bellingham). 2018 Oct;5(4):047501. doi: 10.1117/1.JMI.5.4.047501. Epub 2018 Nov 15.

Differentiation among prostate cancer patients with Gleason score of 7 using histopathology whole-slide image and genomic data. Ren J, Karagoz K, Gatza M, Foran DJ, Qi X. Proc SPIE Int Soc Opt Eng. 2018 Feb;10579:1057904. doi: 10.1117/12.2293193.

Adversarial Domain Adaptation for Classification of Prostate Histopathology Whole-Slide Images. Ren J, Hacihaliloglu I, Singer EA, Foran DJ, Qi X. Med Image Comput Comput Assist Interv. 2018 Sep;11071:201-209. doi: 10.1007/978-3-030-00934-2_23.

Greater Body Fatness Is Associated With Higher Protein Expression of LEPR in Breast Tumor Tissues: A Cross-Sectional Analysis in the Women's Circle of Health Study. Llanos AAM, Aremu JB, Cheng TD, Chen Y, Chekmareva MA, Cespedes Feliciano EM, Qin B, Lin Y, Omene C, Khoury T, Hong CC, Yao S, Ambrosone CB, Bandera EV, Demissie K. Front Endocrinol (Lausanne). 2022 Jun 29;13:879164. doi: 10.3389/fendo.2022.879164.

Sparse Autoencoder for Unsupervised Nucleus Detection and Representation in Histopathology Images. Hou L, Nguyen V, Kanevsky AB, Samaras D, Kurc TM, Zhao T, Gupta RR, Gao Y, Chen Y, Foran D, Saltz JH. Pattern Recognit. 2019 Feb;86:188-200. doi: 10.1016/j.patcog.2018.09.007.

Analysis and Comparison of Tissue-Marking Dye Detection via Light Microscopy, Telemicroscopy, and Virtual Microscopy. Hon JD, Chen Y, Minerowicz C, Thomas S, Barnard N, Gilbert N, Fyfe B. Am J Clin Pathol. 2019 Jan 1;151(1):95-99. doi: 10.1093/ajcp/aqy117.

An Analysis of Transcriptomic Burden Identifies Biological Progression Roadmaps for Hematological Malignancies and Solid Tumors. Ravi D, Beheshti A, Burgess K, Kritharis A, Chen Y, Evens AM, Parekkadan B. Biomedicines. 2022 Oct 27;10(11):2720. doi: 10.3390/biomedicines10112720.

Oncogenic Integration of Nucleotide Metabolism via Fatty Acid Synthase in Non-Hodgkin Lymphoma. Ravi D, Beheshti A, Abermil N, Lansigan F, Kinlaw W, Matthan NR, Mokhtar M, Passero FC Jr, Puliti P, David KA, Dolnikowski GG, Su X, Chen Y, Bijan M, Varshney RR, Kim B, Dave SS, Rudolph MC, Evens AM. Front Oncol. 2021 Oct 26;11:725137. doi: 10.3389/fonc.2021.725137.

Genetic interactions among Brca1, Brca2, Palb2, and Trp53 in mammary tumor development. Huo Y, Selenica P, Mahdi AH, Pareja F, Kyker-Snowman K, Chen Y, Kumar R, Da Cruz Paula A, Basili T, Brown DN, Pei X, Riaz N, Tan Y, Huang YX, Li T, Barnard NJ, Reis-Filho JS, Weigelt B, Xia B. NPJ Breast Cancer. 2021 Apr 23;7(1):45. doi:10.1038/s41523-021-00253-5.

Shotgun transcriptome, spatial omics, and isothermal profiling of SARS-CoV-2 infection reveals unique host responses, viral diversification, and drug interactions. Butler D, Mozsary C, Meydan C, Foox J, Rosiene J, Shaiber A, Danko D, Afshinnekoo E, MacKay M, Sedlazeck FJ, Ivanov NA, Sierra M, Pohle D, Zietz M, Gisladottir U, Ramlall V, Sholle ET, Schenck EJ, Westover CD, Hassan C, Ryon K, Young B, Bhattacharya C, Ng DL, Granados AC, Santos YA, Servellita V, Federman S, Ruggiero P, Fungtammasan A, Chin CS, Pearson NM, Langhorst BW, Tanner NA, Kim Y, Reeves JW, Hether TD, Warren SE, Bailey M, Gawrys J, Meleshko D, Xu D, Couto-Rodriguez M, Nagy-Szakal D, Barrows J, Wells H, O'Hara NB, Rosenfeld JA, Chen Y, Steel PAD, Shemesh AJ, Xiang J, Thierry-Mieg J, Thierry-Mieg D, Iftner A, Bezdan D, Sanchez E, Campion TR Jr, Sipley J, Cong L, Craney A, Velu P, Melnick AM, Shapira S, Hajirasouliha I, Borczuk A, Iftner T, Salvatore M, Loda M, Westblade LF, Cushing M, Wu S, Levy S, Chiu C, Schwartz RE, Tatonetti N, Rennert H, Imielinski M, Mason CE. Nat Commun. 2021 Mar 12;12(1):1660. doi: 10.1038/s41467-021-21361-7.

Loss of the BRCA1-PALB2 interaction accelerates p53-associated tumor development in mice.Mahdi AH, Huo Y, Chen Y, Selenica P, Sharma A, Merritt E, Barnard N, Chan C, Ganesan S, Reis-Filho JS, Weigelt B, De S, Xia B. Genes Dis. 2020 Sep 5;9(3):807-813. doi: 10.1016/j.gendis.2020.08.012.

Interaction kinetics with transcriptomic and secretory responses of CD19-CAR natural killer-cell therapy in CD20 resistant non-hodgkin lymphoma. Ravi D, Sarkar S, Purvey S, Passero F, Beheshti A, Chen Y, Mokhtar M, David K, Konry T, Evens AM. Leukemia. 2020 May;34(5):1291-1304. doi: 10.1038/s41375-019-0663-x.

Zinc Metallochaperones Reactivate Mutant p53 Using an ON/OFF Switch Mechanism: A New Paradigm in Cancer Therapeutics. Yu X, Kogan S, Chen Y, Tsang AT, Withers T, Lin H, Gilleran J, Buckley B, Moore D, Bertino J, Chan C, Kimball SD, Loh SN, Carpizo DR. Clin Cancer Res. 2018 Sep 15;24(18):4505-4517. doi: 10.1158/1078-0432.CCR-18-0822.

Bone morphogenetic protein inhibitors and mitochondria targeting agents synergistically induce apoptosis-inducing factor (AIF) caspase-independent cell death in lung cancer cells. Mondal A, Roberge J, Gilleran J, Peng Y, Jia D, Akel M, Patel Y, Zoltowski H, Doraiswamy A, Langenfeld J. Cell Commun Signal. 2022 Jun 27;20(1):99. doi: 10.1186/s12964-022-00905-4.

Bone morphogenetic protein receptor 2 inhibition destabilizes microtubules promoting the activation of lysosomes and cell death of lung cancer cells. Mondal A, NeMoyer R, Vora M, Napoli L, Syed Z, Langenfeld E, Jia D, Peng Y, Gilleran J, Roberge J, Rongo C, Jabbour SK, Langenfeld J. Cell Commun Signal. 2021 Sep 25;19(1):97. doi: 10.1186/s12964-021-00743-w.

QSAR-Based Computational Approaches to Accelerate the Discovery of Sigma-2 Receptor (S2R) Ligands as Therapeutic Drugs. Yu Y, Dong H, Peng Y, Welsh WJ. Molecules. 2021 Aug 30;26(17):5270. doi: 10.3390/molecules26175270. 

Novel Sigma 1 Receptor Antagonists as Potential Therapeutics for Pain Management. Peng Y, Zhang Q, Welsh WJ. J Med Chem. 2021 Jan 14;64(1):890-904. doi: 10.1021/acs.jmedchem.0c01964.

Identification of an irreversible PPARγ antagonist with potent anticancer activity. Peng Y, Zhang Q, Zielinski RM, Howells RD, Welsh WJ. Pharmacol Res Perspect. 2020 Dec;8(6):e00693. doi: 10.1002/prp2.693.

Targeting bone morphogenetic protein receptor 2 sensitizes lung cancer cells to TRAIL by increasing cytosolic Smac/DIABLO and the downregulation of X-linked inhibitor of apoptosis protein. NeMoyer R, Mondal A, Vora M, Langenfeld E, Glover D, Scott M, Lairson L, Rongo C, Augeri DJ, Peng Y, Jabbour SK, Langenfeld J. Cell Commun Signal. 2019 Nov 19;17(1):150. doi: 10.1186/s12964-019-0469-5.

Comprehensive 3D-QSAR Model Predicts Binding Affinity of Structurally Diverse Sigma 1 Receptor Ligands. Peng Y, Dong H, Welsh WJ. J Chem Inf Model. 2019 Jan 28;59(1):486-497. doi: 10.1021/acs.jcim.8b00521.

 

BISR-Supported high Impact Factor (IF >10) cancer relevant publications (2018 – 2022)
 

Ravi D, Sarkar S, Purvey S, Passero F, Beheshti A, Chen Y, Mokhtar M, David K, Konry T, Evens AM. Interaction kinetics with transcriptomic and secretory responses of CD19-CAR natural killer-cell therapy in CD20 resistant non-hodgkin lymphoma. Leukemia. 2020 MAY 01; 34(5):1291-1304. DOI: 10.1038/s41375-019-0663-x.

Severson EA, Riedlinger GM, Connelly CF, Vergilio JA, Goldfinger M, Ramkissoon S, Frampton GM, Ross JS, Fratella-Calabrese A, Gay L, Ali S, Miller V, Elvin J, Hadigol M, Hirshfield KM, Rodriguez-Rodriguez L, Ganesan S, Khiabanian H. Detection of clonal hematopoiesis of indeterminate potential in clinical sequencing of solid tumor specimens. Blood. 2018;131(22):2501-5. doi: 10.1182/blood-2018-03-840629.

Yu X, Kogan S, Chen Y, Tsang AT, Withers T, Lin H, Gilleran J, Buckley B, Moore D, Bertino J, Chan C, Kimball SD, Loh SN, Carpizo DR. Zinc Metallochaperones Reactivate Mutant p53 Using an ON/OFF Switch Mechanism: A New Paradigm in Cancer Therapeutics. Clin Cancer Res. 2018 SEP 15; 24(18):4505-4517. DOI: 10.1158/1078-0432.CCR-18-0822.

Bhatt V, Khayati K, Hu ZS, Lee A, Kamran W, Su X, Guo JY. Autophagy modulates lipid metabolism to maintain metabolic flexibility for Lkb1-deficient Kras-driven lung tumorigenesis. Genes Dev. 2019 FEB 01; 33(3-4):150-165. DOI: 10.1101/gad.320481.118..

Riedlinger G, Hadigol M, Khiabanian H, Ganesan S. Association of JAK2-V617F Mutations Detected by Solid Tumor Sequencing With Coexistent Myeloproliferative Neoplasms. JAMA Oncol. 2019 FEB 01; 5(2):265-267. DOI: 10.1001/jamaoncol.2018.6286.

Esposito M, Mondal N, Greco TM, Wei Y, Spadazzi C, Lin SC, Zheng H, Cheung C, Magnani JL, Lin SH, Cristea IM, Sackstein R, Kang Y. Bone vascular niche E-selectin induces mesenchymal-epithelial transition and Wnt activation in cancer cells to promote bone metastasis. Nat Cell Biol. 2019 MAY 01; 21(5):627-639. DOI: 10.1038/s41556-019-0309-2.

Wong C, Tang LH, Davidson C, Vosburgh E, Chen W, Foran DJ, Notterman DA, Levine AJ, Xu EY. Two well-differentiated pancreatic neuroendocrine tumor mouse models. Cell Death Differ. 2020 JAN 01; 27(1):269-283. DOI: 10.1038/s41418-019-0355-0.

Barz MJ, Hof J, Groeneveld-Krentz S, Loh JW, Szymansky A, Astrahantseff K, von Stackelberg A, Khiabanian H, Ferrando AA, Eckert C, Kirschner-Schwabe R. Subclonal NT5C2 mutations are associated with poor outcomes after relapse of pediatric acute lymphoblastic leukemia. Blood. 2020 MAR 19; 135(12):921-933. DOI: 10.1182/blood.2019002499.

Panda A, Yadav A, Yeerna H, Singh A, Biehl M, Lux M, Schulz A, Klecha T, Doniach S, Khiabanian H, Ganesan S, Tamayo P, Bhanot G. Tissue- and development-stage-specific mRNA and heterogeneous CNV signatures of human ribosomal proteins in normal and cancer samples. Nucleic Acids Res. 2020 JUL 27; 48(13):7079-7098. DOI: 10.1093/nar/gkaa485.

Ghergurovich JM, Esposito M, Chen Z, Wang JZ, Bhatt V, Lan T, White E, Kang Y, Guo JY, Rabinowitz JD. Glucose-6-Phosphate Dehydrogenase Is Not Essential for K-Ras-Driven Tumor Growth or Metastasis. Cancer Res. 2020 SEP 15; 80(18):3820-3829. DOI: 10.1158/0008-5472.CAN-19-2486. 2020 July 13.

Clements KE, Schleicher EM, Thakar T, Hale A, Dhoonmoon A, Tolman NJ, Sharma A, Liang X, Imamura Kawasawa Y, Nicolae CM, Wang HG, De S, Moldovan GL. Identification of regulators of poly-ADP-ribose polymerase inhibitor response through complementary CRISPR knockout and activation screens. Nat Commun. 2020 NOV 30; 11(1):6118. DOI: 10.1038/s41467-020-19961-w.

Sharafeldin N, Bates B, Song Q, Madhira V, Yan Y, Dong S, Lee E, Kuhrt N, Shao YR, Liu F, Bergquist T, Guinney J, Su J, Topaloglu U. Outcomes of COVID-19 in Patients With Cancer: Report From the National COVID Cohort Collaborative (N3C). J Clin Oncol. 2021 JUL 10; 39(20):2232-2246. DOI: 10.1200/JCO.21.01074. 2021 June 4.

da Silva-Diz V, Cao B, Lancho O, Chiles E, Alasadi A, Aleksandrova M, Luo S, Singh A, Tao H, Augeri D, Minuzzo S, Indraccolo S, Khiabanian H, Su X, Jin S, Herranz D. A novel and highly effective mitochondrial uncoupling drug in T-cell leukemia. Blood. 2021 OCT 14; 138(15):1317-1330. DOI: 10.1182/blood.2020008955.

Song Q, Bates B, Shao YR, Hsu FC, Liu F, Madhira V, Mitra AK, Bergquist T, Kavuluru R, Li X, Sharafeldin N, Su J, Topaloglu U. Risk and Outcome of Breakthrough COVID-19 Infections in Vaccinated Patients With Cancer: Real-World Evidence From the National COVID Cohort Collaborative. J Clin Oncol. 2022 MAY 01; 40(13):1414-1427. DOI: 10.1200/JCO.21.02419.

Yang Y, Karsli-Uzunbas G, Poillet-Perez L, Sawant A, Hu ZS, Zhao Y, Moore D, Hu W, White E. Autophagy promotes mammalian survival by suppressing oxidative stress and p53. Genes Dev. 2020 MAY 01; 34(9-10):688-700. DOI: 10.1101/gad.335570.119.

Castellano GM, Aisner J, Burley SK, Vallat B, Yu HA, Pine SR, Ganesan S. A Novel Acquired Exon 20 EGFR M766Q Mutation in Lung Adenocarcinoma Mediates Osimertinib Resistance but is Sensitive to Neratinib and Poziotinib. J Thorac Oncol. 2019 NOV 01; 14(11):1982-1988. DOI: 10.1016/j.jtho.2019.06.015.