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1

Personalized Oncology Through Integrative High-Throughput Sequencing: A Pilot Study

Roychowdhury, S., Iyer, M. K., Robinson, D. R., Lonigro, R. J., Wu, Y.-M., Cao, X., Kalyana-Sundaram, S., Sam, L., Balbin, O. A., Quist, M. J.

Journal:

Science Translational Medicine

Year:

2011

Language:

english

File:

PDF, 7.42 MB

english, 2011

2

Activating ESR1 mutations in hormone-resistant metastatic breast cancer

Robinson, Dan R, Wu, Yi-Mi, Vats, Pankaj, Su, Fengyun, Lonigro, Robert J, Cao, Xuhong, Kalyana-Sundaram, Shanker, Wang, Rui, Ning, Yu, Hodges, Lynda, Gursky, Amy, Siddiqui, Javed, Tomlins, Scott A, Ro

Journal:

Nature Genetics

Year:

2013

Language:

english

File:

PDF, 745 KB

english, 2013

3

Transcriptome sequencing to detect gene fusions in cancer

Maher, Christopher A., Kumar-Sinha, Chandan, Cao, Xuhong, Kalyana-Sundaram, Shanker, Han, Bo, Jing, Xiaojun, Sam, Lee, Barrette, Terrence, Palanisamy, Nallasivam, Chinnaiyan, Arul M.

Journal:

Year:

2009

Language:

english

File:

PDF, 418 KB

english, 2009

4

Probabilistic model of the human protein-protein interaction network

Rhodes, Daniel R, Tomlins, Scott A, Varambally, Sooryanarayana, Mahavisno, Vasudeva, Barrette, Terrence, Kalyana-Sundaram, Shanker, Ghosh, Debashis, Pandey, Akhilesh, Chinnaiyan, Arul M

Journal:

Nature Biotechnology

Year:

2005

Language:

english

File:

PDF, 1.37 MB

english, 2005

5

Mining for regulatory programs in the cancer transcriptome

Rhodes, Daniel R, Kalyana-Sundaram, Shanker, Mahavisno, Vasudeva, Barrette, Terrence R, Ghosh, Debashis, Chinnaiyan, Arul M

Journal:

Nature Genetics

Year:

2005

Language:

english

File:

PDF, 223 KB

english, 2005

6

Integrative molecular concept modeling of prostate cancer progression

Tomlins, Scott A, Mehra, Rohit, Rhodes, Daniel R, Cao, Xuhong, Wang, Lei, Dhanasekaran, Saravana M, Kalyana-Sundaram, Shanker, Wei, John T, Rubin, Mark A, Pienta, Kenneth J

Journal:

Nature Genetics

Year:

2006

Language:

english

File:

PDF, 597 KB

english, 2006

7

Rearrangements of the RAF kinase pathway in prostate cancer, gastric cancer and melanoma

Han, Bo, Cao, Qi, Cao, Xuhong, Suleman, Khalid, Palanisamy, Nallasivam, Ateeq, Bushra, Kalyana-Sundaram, Shanker, Pflueger, Dorothee, Ramnarayanan, Kalpana, Shankar, Sunita

Journal:

Nature Medicine

Year:

2010

Language:

english

File:

PDF, 656 KB

english, 2010

8

Expressed Pseudogenes in the Transcriptional Landscape of Human Cancers

Shanker Kalyana-Sundaram, Chandan Kumar-Sinha, Sunita Shankar, Dan R. Robinson, Yi-Mi Wu, Xuhong Cao, Irfan A. Asangani, Vishal Kothari, John R. Prensner, Robert J. Lonigro, Matthew K. Iyer, Terrence

Journal:

Year:

2012

Language:

english

File:

PDF, 101 KB

english, 2012

9

HPeak: an HMM-based algorithm for defining read-enriched regions in ChIP-Seq data

Zhaohui S Qin, Jianjun Yu, Jincheng Shen, Christopher A Maher, Ming Hu, Shanker Kalyana-Sundaram, Jindan Yu, Arul M Chinnaiyan

Journal:

BMC Bioinformatics

Year:

2010

Language:

english

File:

PDF, 874 KB

english, 2010

10

Gene Fusion Markup Language: a prototype for exchanging gene fusion data

Shanker Kalyana-Sundaram, Achiraman Shanmugam, Arul M Chinnaiyan

Journal:

BMC Bioinformatics

Year:

2012

Language:

english

File:

PDF, 224 KB

english, 2012

11

miRConnect 2.0: identification of oncogenic, antagonistic miRNA families in three human cancers

Youjia Hua, Niels Larsen, Shanker Kalyana-Sundaram, Jørgen Kjems…

Journal:

Year:

2013

Language:

english

File:

PDF, 611 KB

english, 2013

12

Identification of Targetable FGFR Gene Fusions in Diverse Cancers

Wu, Y.-M., Su, F., Kalyana-Sundaram, S., Khazanov, N., Ateeq, B., Cao, X., Lonigro, R. J., Vats, P., Wang, R., Lin, S.-F., Cheng, A.-J., Kunju, L. P., Siddiqui, J., Tomlins, S. A., Wyngaard, P., Sadis

Journal:

Cancer Discovery

Year:

2013

Language:

english

File:

PDF, 2.27 MB

english, 2013

13

Identification of recurrent NAB2-STAT6 gene fusions in solitary fibrous tumor by integrative sequencing

Robinson, Dan R, Wu, Yi-Mi, Kalyana-Sundaram, Shanker, Cao, Xuhong, Lonigro, Robert J, Sung, Yun-Shao, Chen, Chun-Liang, Zhang, Lei, Wang, Rui, Su, Fengyun, Iyer, Matthew K, Roychowdhury, Sameek, Sidd

Journal:

Nature Genetics

Year:

2013

Language:

english

File:

PDF, 929 KB

english, 2013

14

Primary Urethral Clear-Cell Adenocarcinoma

Mehra, Rohit, Vats, Pankaj, Kalyana-Sundaram, Shanker, Udager, Aaron M., Roh, Michael, Alva, Ajjai, Pan, Jincheng, Lonigro, Robert J., Siddiqui, Javed, Weizer, Alon, Lee, Cheryl, Cao, Xuhong, Wu, Yi-M

Journal:

The American Journal of Pathology

Year:

2014

Language:

english

File:

PDF, 1.49 MB

english, 2014

15

Gene Fusions Associated with Recurrent Amplicons Represent a Class of Passenger Aberrations in Breast Cancer

Kalyana-Sundaram, Shanker, Shankar, Sunita, DeRoo, Scott, Iyer, Matthew K., Palanisamy, Nallasivam, Chinnaiyan, Arul M., Kumar-Sinha, Chandan

Journal:

Year:

2012

Language:

english

File:

PDF, 2.38 MB

english, 2012

16

Molecular Concepts Analysis Links Tumors, Pathways, Mechanisms, and Drugs

Rhodes, Daniel R., Kalyana-Sundaram, Shanker, Tomlins, Scott A., Mahavisno, Vasudeva, Kasper, Nicole, Varambally, Radhika, Barrette, Terrence R., Ghosh, Debashis, Varambally, Sooryanarayana, Chinnaiya

Journal:

Year:

2007

Language:

english

File:

PDF, 1.47 MB

english, 2007

17

Characterization of the Pancreatic Adenocarcinoma Transcriptome by RNA Sequencing

Wei, I.H., Kalyana-Sundaram, S., Grasso, C., Robinson, D., Simeone, D.M., Chinnaiyan, A.M., Kumar-Sinha, C.

Journal:

Journal of Surgical Research

Year:

2013

Language:

english

File:

PDF, 62 KB

english, 2013

18

Oncomine 3.0: Genes, Pathways, and Networks in a Collection of 18,000 Cancer Gene Expression Profiles

Rhodes, Daniel R., Kalyana-Sundaram, Shanker, Mahavisno, Vasudeva, Varambally, Radhika, Yu, Jianjun, Briggs, Benjamin B., Barrette, Terrence R., Anstet, Matthew J., Kincead-Beal, Colleen, Kulkarni, Pr

Journal:

Year:

2007

Language:

english

File:

PDF, 2.48 MB

english, 2007

19

Functionally recurrent rearrangements of the MAST kinase and Notch gene families in breast cancer

Robinson, Dan R, Kalyana-Sundaram, Shanker, Wu, Yi-Mi, Shankar, Sunita, Cao, Xuhong, Ateeq, Bushra, Asangani, Irfan A, Iyer, Matthew, Maher, Christopher A, Grasso, Catherine S, Lonigro, Robert J, Quis

Journal:

Nature Medicine

Year:

2011

Language:

english

File:

PDF, 818 KB

english, 2011

20

Transcriptome meta-analysis of lung cancer reveals recurrent aberrations in NRG1 and Hippo pathway genes

Dhanasekaran, Saravana M., Alejandro Balbin, O, Chen, Guoan, Nadal, Ernest, Kalyana-Sundaram, Shanker, Pan, Jincheng, Veeneman, Brendan, Cao, Xuhong, Malik, Rohit, Vats, Pankaj, Wang, Rui, Huang, Step

Journal:

Nature Communications

Year:

2014

Language:

english

File:

PDF, 930 KB

english, 2014

21

Recurrent reciprocal RNA chimera involving YPEL5 and PPP1CB in chronic lymphocytic leukemia

Velusamy, T., Palanisamy, N., Kalyana-Sundaram, S., Sahasrabuddhe, A. A., Maher, C. A., Robinson, D. R., Bahler, D. W., Cornell, T. T., Wilson, T. E., Lim, M. S., Chinnaiyan, A. M., Elenitoba-Johnson,

Journal:

Proceedings of the National Academy of Sciences

Year:

2013

Language:

english

File:

PDF, 1.22 MB

english, 2013

22

Chimeric transcript discovery by paired-end transcriptome sequencing

Maher, C. A., Palanisamy, N., Brenner, J. C., Cao, X., Kalyana-Sundaram, S., Luo, S., Khrebtukova, I., Barrette, T. R., Grasso, C., Yu, J., Lonigro, R. J., Schroth, G., Kumar-Sinha, C., Chinnaiyan, A.

Journal:

Proceedings of the National Academy of Sciences

Year:

2009

Language:

english

File:

PDF, 793 KB

english, 2009

23

Quantitative Proteomic Profiling of Prostate Cancer Reveals a Role for miR-128 in Prostate Cancer

Khan, A. P., Poisson, L. M., Bhat, V. B., Fermin, D., Zhao, R., Kalyana-Sundaram, S., Michailidis, G., Nesvizhskii, A. I., Omenn, G. S., Chinnaiyan, A. M., Sreekumar, A.

Journal:

Molecular & Cellular Proteomics

Year:

2010

Language:

english

File:

PDF, 1.64 MB

english, 2010

24

SLC45A3-ELK4 Chimera in Prostate Cancer: Spotlight on cis-Splicing

Kumar-Sinha, C., Kalyana-Sundaram, S., Chinnaiyan, A. M.

Journal:

Cancer Discovery

Year:

2012

Language:

english

File:

PDF, 566 KB

english, 2012

25

AGTR1 overexpression defines a subset of breast cancer and confers sensitivity to losartan, an AGTR1 antagonist

Rhodes, D. R., Ateeq, B., Cao, Q., Tomlins, S. A., Mehra, R., Laxman, B., Kalyana-Sundaram, S., Lonigro, R. J., Helgeson, B. E., Bhojani, M. S., Rehemtulla, A., Kleer, C. G., Hayes, D. F., Lucas, P. C

Journal:

Proceedings of the National Academy of Sciences

Year:

2009

Language:

english

File:

PDF, 1.33 MB

english, 2009

26

Deep sequencing reveals distinct patterns of DNA methylation in prostate cancer

Kim, J. H., Dhanasekaran, S. M., Prensner, J. R., Cao, X., Robinson, D., Kalyana-Sundaram, S., Huang, C., Shankar, S., Jing, X., Iyer, M., Hu, M., Sam, L., Grasso, C., Maher, C. A., Palanisamy, N., Me

Journal:

Genome Research

Year:

2011

Language:

english

File:

PDF, 2.50 MB

english, 2011

27

Outlier Kinase Expression by RNA Sequencing as Targets for Precision Therapy

Kothari, V., Wei, I., Shankar, S., Kalyana-Sundaram, S., Wang, L., Ma, L. W., Vats, P., Grasso, C. S., Robinson, D. R., Wu, Y.-M., Cao, X., Simeone, D. M., Chinnaiyan, A. M., Kumar-Sinha, C.

Journal:

Cancer Discovery

Year:

2013

Language:

english

File:

PDF, 3.26 MB

english, 2013

28

Humoral Response Profiling Reveals Pathways to Prostate Cancer Progression

Taylor, B. S., Pal, M., Yu, J., Laxman, B., Kalyana-Sundaram, S., Zhao, R., Menon, A., Wei, J. T., Nesvizhskii, A. I., Ghosh, D., Omenn, G. S., Lubman, D. M., Chinnaiyan, A. M., Sreekumar, A.

Journal:

Molecular & Cellular Proteomics

Year:

2007

Language:

english

File:

PDF, 1.14 MB

english, 2007

29

Landscape of gene fusions in epithelial cancers: seq and ye shall find

Kumar-Sinha, Chandan, Kalyana-Sundaram, Shanker, Chinnaiyan, Arul M.

Journal:

Genome Medicine

Year:

2015

Language:

english

File:

PDF, 877 KB

english, 2015

30

Inflammation-Induced Oxidative Stress Mediates Gene Fusion Formation in Prostate Cancer

Mani, Ram S., Amin, Mohammad A., Li, Xiangyi, Kalyana-Sundaram, Shanker, Veeneman, Brendan A., Wang, Lei, Ghosh, Aparna, Aslam, Adam, Ramanand, Susmita G., Rabquer, Bradley J., Kimura, Wataru, Tran, M

Journal:

Year:

2016

Language:

english

File:

PDF, 2.93 MB

english, 2016

31

Characterization of Gene Expression Phenotype in Amyotrophic Lateral Sclerosis Monocytes

Zhao, Weihua, Beers, David R., Hooten, Kristopher G., Sieglaff, Douglas H., Zhang, Aijun, Kalyana-Sundaram, Shanker, Traini, Christopher M., Halsey, Wendy S., Hughes, Ashley M., Sathe, Ganesh M., Livi

Journal:

Year:

2017

Language:

english

File:

PDF, 1011 KB

english, 2017

32

Renal Cell Carcinoma With Chromosome 6p Amplification Including the TFEB Gene

Williamson, Sean R., Grignon, David J., Cheng, Liang, Favazza, Laura, Gondim, Dibson D., Carskadon, Shannon, Gupta, Nilesh S., Chitale, Dhananjay A., Kalyana-Sundaram, Shanker, Palanisamy, Nallasivam

Journal:

American Journal of Surgical Pathology

Year:

2017

Language:

english

File:

PDF, 1.27 MB

english, 2017

33

A first-time-in-human study of GSK2636771, a phosphoinositide 3 kinase beta-selective inhibitor, in patients with advanced solid tumors

Mateo, Joaquin, Ganji, Gopinath, Lemech, Charlotte, Burris, Howard A., Han, Sae-Won, Swales, Karen E, Decordova, Shaun, DeYoung, Maurice P, Smith, Deborah A, Kalyana-Sundaram, Shanker, Wu, Jiuhua, Mot

Journal:

Clinical Cancer Research

Year:

2017

Language:

english

File:

PDF, 1.04 MB

english, 2017

34

Renal cell tumors with clear cell histology and intact VHL and chromosome 3p: a histological review of tumors from the Cancer Genome Atlas database

Favazza, Laura, Chitale, Dhananjay A, Barod, Ravi, Rogers, Craig G, Kalyana-Sundaram, Shanker, Palanisamy, Nallasivam, Gupta, Nilesh S, Williamson, Sean R

Journal:

Modern Pathology

Year:

2017

Language:

english

File:

PDF, 11.76 MB

english, 2017

35

Heat Shock Protein Beta-1 Modifies Anterior to Posterior Purkinje Cell Vulnerability in a Mouse Model of Niemann-Pick Type C Disease

Chung, Chan, Elrick, Matthew J., Dell’Orco, James M., Qin, Zhaohui S., Kalyana-Sundaram, Shanker, Chinnaiyan, Arul M., Shakkottai, Vikram G., Lieberman, Andrew P., Orr, Harry T.

Journal:

Year:

2016

Language:

english

File:

PDF, 8.55 MB

english, 2016