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Andrew Kossenkov, Ph.D.

Laboratory

The Kossenkov Laboratory

Contact

215-495-6898
akossenkov@wistar.org

Assistant Professor, Bioinformatics

About the Scientist

Kossenkov applies computational approaches to the analysis of various kinds of biomedical high-throughput data in effort to interpret results and visualize complex data.

He obtained his bachelor’s and master’s degrees in computer science and bioinformatics from Moscow Engineering Physics Institute in Russia, and his Ph.D. in biomedical science from Drexel University in Philadelphia. In 2007, Kossenkov joined The Wistar Institute as a postdoctoral fellow in the Showe lab and later became managing director of the Bioinformatics Facility.  He was appointed assistant professor in 2019.
 

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The Kossenkov Laboratory

The Kossenkov laboratory collaborates with several other Wistar labs on research projects in cancer, infectious diseases and basic biological questions, including regeneration and stem cell biology, mitochondrial proteins, transcriptional regulation, synapse biology, blood development, and global epigenetic gene silencing. The lab uses bioinformatics, biostatistics and computational biology approaches in a variety of models. They rely heavily on bioinformatics analysis of drug screen results, next-generation sequencing data and proteomics.

Research

Through a network of internal and external collaborations, the Kossenkov lab provides bioinformatics expertise for high throughput data support, analysis and annotation and complex results visualization. Thanks to Kossenkov’s experience in development of database-oriented gene annotation pipelines and algorithms to visualize highly specific and intricate results, the lab provides flexible and customizable support for a wide range of experiments. 

Research collaborations outside of Wistar include teams at Fox Chase Cancer Center, The Children's Hospital of Philadelphia, the University of Pennsylvania, Drexel University, New York University, Weill Cornell, Harvard, and others.

Selected Publications

Kossenkov, A.V., Qureshi, R., Showe, L.C., et al. “A Gene Expression Classifier from Whole Blood Distinguishes Benign from Malignant Lung Nodules Detected by Low-Dose CT”. Cancer Res. 2019 Jan 1;79(1):263-273. doi: 10.1158/0008-5472.CAN-18-2032. Epub 2018 Nov 28.

Patel, S., Fu, S., Mastio,  J., Dominguez, G.A., Purohit, A., Kossenkov, A., Lin, C., Alicea-Torres, K., Sehgal, M., Nefedova, Y., Zhou, J., Languino, L.R., Clendenin, C., Vonderheide, R.H., Mulligan, C., Nam, B., Hockstein, N., Masters, G., Guarino, M., Schug, Z.T., Altieri, D.C., Gabrilovich, D.I. “Unique pattern of neutrophil migration and function during tumor progression.” Nat Immunol. 2018 Nov;19(11):1236-1247. doi: 10.1038/s41590-018-0229-5. Epub 2018 Oct 15

Song, M., Sandoval, T.A., Chae, C.S., Chopra, S., Tan, C., Rutkowski, M.R., Raundhal, M., Chaurio, R.A., Payne, K.K., Konrad, C., Bettigole, S.E., Shin, H.R., Crowley, M.J.P., Cerliani, J.P., Kossenkov, A.V., Motorykin, I., Zhang, S., Manfredi, G., Zamarin, D., Holcomb, K., Rodriguez, P.C., Rabinovich, G.A., Conejo-Garcia, J.R., Glimcher, L.H., Cubillos-Ruiz, J.R. “IRE1α-XBP1 controls T cell function in ovarian cancer by regulating mitochondrial activity.” Nature. 2018 Oct;562(7727):423-428. doi: 10.1038/s41586-018-0597-x. Epub 2018 Oct 10.

Karakashev, S., Zhu, H., Wu, S., Yokoyama, Y., Bitler, B.G., Park, P.H., Lee, J.H., Kossenkov, A.V., Gaonkar, K.S., Yan, H., Drapkin, R., Conejo-Garcia, J.R., Speicher, D.W., Ordog, T., Zhang, R. "CARM1-expressing ovarian cancer depends on the histone methyltransferase EZH2 activity." Nat Commun. 2018 Feb 12;9(1):631. doi: 10.1038/s41467-018-03031-3.

Tso, F.Y., Kossenkov, A.V., Wood, C., et al. “RNA-Seq of Kaposi's sarcoma reveals alterations in glucose and lipid metabolism.” PLoS Pathog. 2018 Jan 19;14(1):e1006844. doi: 10.1371/journal.ppat.1006844. eCollection 2018 Jan.

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