Farhad Kosari, PhD

  • 5915 Citations
  • 24 Scopus h-Index
19952019
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Research Output 1995 2019

  • 5915 Citations
  • 24 Scopus h-Index
  • 55 Article
  • 1 Conference contribution
  • 1 Letter
2019

A comparison of adult rhabdomyosarcoma and high-grade neuroendocrine carcinoma of the urinary bladder reveals novel PPP1R12A fusions in rhabdomyosarcoma

Gupta, S., Sosa, C. P., Kosari, F., Folpe, A., Bhinge, K. N., Yang, L., Agahi, A., Johnson, S. H., Frank, I., Boorjian, S. A., Hansel, D. E., Al-Ahmadie, H. A., Reuter, V. E., Vasmatzis, G., Jimenez, R. E., Herrera-Hernandez, L. & Cheville, J., Jun 1 2019, In : Human Pathology. 88, p. 48-59 12 p.

Research output: Contribution to journalArticle

Neuroendocrine Carcinoma
Rhabdomyosarcoma
Urinary Bladder
RNA Sequence Analysis
Alveolar Rhabdomyosarcoma
5 Citations (Scopus)

Immune Cell Infiltration May Be a Key Determinant of Long-Term Survival in Small Cell Lung Cancer

Muppa, P., Parrilha Terra, S. B. S., Sharma, A., Mansfield, A., Aubry, M. C., Bhinge, K., Asiedu, M. K., De Andrade, M., Janaki, N., Murphy, S. J., Nasir, A., Van Keulen, V., Vasmatzis, G., Wigle, D. A., Yang, P., Yi, E. S., Peikert, T. D. & Kosari, F., Jul 1 2019, In : Journal of Thoracic Oncology. 14, 7, p. 1286-1295 10 p.

Research output: Contribution to journalArticle

Open Access
Small Cell Lung Carcinoma
Tumor Microenvironment
Survival Rate
Survivors
Survival

Integration of Comprehensive Genomic Analysis and Functional Screening of Affected Molecular Pathways to Inform Cancer Therapy

Vasmatzis, G., Liu, M. C., Reganti, S., Feathers, R. W., Smadbeck, J., Johnson, S. H., Schaefer Klein, J. L., Harris, F. R., Yang, L., Kosari, F., Murphy, S. J., Borad, M. J., Thompson, E. A., Cheville, J. C. & Anastasiadis, P. Z., Jan 1 2019, (Accepted/In press) In : Mayo Clinic proceedings.

Research output: Contribution to journalArticle

Open Access
Neoplasms
Mutation
Therapeutics
Precision Medicine
Preclinical Drug Evaluations
1 Citation (Scopus)

Large Chromosomal Rearrangements Yield Biomarkers to Distinguish Low-Risk From Intermediate- and High-Risk Prostate Cancer

Vasmatzis, G., Kosari, F., Murphy, S. J., Terra, S., Kovtun, I. V., Harris, F. R., Zarei, S., Smadbeck, J., Johnson, S. H., Gaitatzes, A. G., Therneau, T. M., Rangel, L. J., Knudson, R. A., Greipp, P. T., Sukov, W. R., Knutson, D. L., Kloft-Nelson, S. M., Karnes, R. J. & Cheville, J., Jan 1 2019, In : Mayo Clinic Proceedings. 94, 1, p. 27-36 10 p.

Research output: Contribution to journalArticle

Prostatic Neoplasms
Biomarkers
Area Under Curve
Neoplasm Grading
Needle Biopsy
16 Citations (Scopus)

Neoantigenic Potential of Complex Chromosomal Rearrangements in Mesothelioma

Mansfield, A., Peikert, T. D., Smadbeck, J., Udell, J. B. M., Garcia-Rivera, E., Elsbernd, L., Erskine, C. L., Van Keulen, V. P., Kosari, F., Murphy, S. J., Ren, H., Serla, V. V., Schaefer Klein, J. L., Karagouga, G., Harris, F. R., Sosa, C., Johnson, S. H., Nevala, W., Markovic, S. N., Bungum, A. O. & 6 others, Edell, E., Dong, H. M., Cheville, J., Aubry, M. C., Jen, J. & Vasmatzis, G., Feb 1 2019, In : Journal of Thoracic Oncology. 14, 2, p. 276-287 12 p.

Research output: Contribution to journalArticle

Mesothelioma
T-Lymphocytes
Carcinogens
Atlases
Asbestos

Response to Letter to the Editor

Peikert, T. & Kosari, F., Nov 2019, In : Journal of Thoracic Oncology. 14, 11, p. e261-e262

Research output: Contribution to journalLetter

2 Citations (Scopus)

Using Genomics to Differentiate Multiple Primaries From Metastatic Lung Cancer

Murphy, S. J., Harris, F. R., Kosari, F., Barreto Siqueira Parrilha Terra, S., Nasir, A., Johnson, S. H., Serla, V., Smadbeck, J., Halling, G. C., Karagouga, G., Sukov, W. R., Leventakos, K., Yang, P., Peikert, T. D., Mansfield, A., Wigle, D. A., Yi, E. S., Kipp, B. R., Vasmatzis, G. & Aubry, M. C., Jan 1 2019, In : Journal of Thoracic Oncology.

Research output: Contribution to journalArticle

Open Access
Genomics
Lung Neoplasms
Neoplasms
DNA
Histology
2018

Chromoanasynthesis is a common mechanism that leads to ERBB2 amplifications in a cohort of early stage HER2+ breast cancer samples

Vasmatzis, G., Wang, X., Smadbeck, J., Murphy, S. J., Geiersbach, K. B., Johnson, S. H., Gaitatzes, A. G., Asmann, Y., Kosari, F., Borad, M. J., Serie, D. J., McLaughlin, S. A., Kachergus, J. M., Necela, B. M. & Thompson, E. A., Jul 13 2018, In : BMC Cancer. 18, 1, 738.

Research output: Contribution to journalArticle

Chromosomes, Human, Pair 8
Breast Neoplasms
Chromosomes, Human, Pair 17
Transcriptome
Genome
15 Citations (Scopus)

Copy number variant analysis using genome-wide mate-pair sequencing

Smadbeck, J., Johnson, S. H., Smoley, S. A., Gaitatzes, A., Drucker, T. M., Zenka, R. M., Kosari, F., Murphy, S. J., Hoppman, N., Aypar, U., Sukov, W. R., Jenkins, R. B., Kearney, H. M., Feldman, A. L. & Vasmatzis, G., Sep 1 2018, In : Genes Chromosomes and Cancer. 57, 9, p. 459-470 12 p.

Research output: Contribution to journalArticle

Cytogenetic Analysis
Genome
Technology
Karyotyping
Human Genome
8 Citations (Scopus)

Enhanced mRNA FISH with compact quantum dots

Liu, Y., Le, P., Lim, S. J., Ma, L., Sarkar, S., Han, Z., Murphy, S. J., Kosari, F., Vasmatzis, G., Cheville, J. & Smith, A. M., Dec 1 2018, In : Nature Communications. 9, 1, 4461.

Research output: Contribution to journalArticle

Quantum Dots
Fluorescence In Situ Hybridization
Semiconductor quantum dots
Fluorescence
quantum dots
9 Citations (Scopus)

Pathways impacted by genomic alterations in pulmonary carcinoid tumors

Asiedu, M. K., Thomas, C. F., Dong, J., Schulte, S. C., Khadka, P., Sun, Z. D., Kosari, F., Jen, J., Molina, J. R., Vasmatzis, G., Kuang, R., Aubry, M. C., Yang, P. & Wigle, D. A., Apr 1 2018, In : Clinical Cancer Research. 24, 7, p. 1691-1704 14 p.

Research output: Contribution to journalArticle

Carcinoid Tumor
Lung
Neoplasm Genes
Biological Phenomena
Exome
5 Citations (Scopus)

Pixelated spatial gene expression analysis from tissue

Ganguli, A., Ornob, A., Spegazzini, N., Liu, Y., Damhorst, G., Ghonge, T., Thornton, B., Konopka, C. J., Dobrucki, W., Clare, S. E., Bhargava, R., Smith, A. M., Kosari, F. & Bashir, R., Dec 1 2018, In : Nature Communications. 9, 1, 202.

Research output: Contribution to journalArticle

gene expression
Gene expression
Tissue
Gene Expression
ribonucleic acids
2017
4 Citations (Scopus)

EGFR mediates activation of RET in lung adenocarcinoma with neuroendocrine differentiation characterized by ASCL1 expression

Bhinge, K., Yang, L., Terra, S., Nasir, A., Muppa, P., Aubry, M. C., Yi, J., Janaki, N., Kovtun, I. V., Murphy, S. J., Halling, G., Rahi, H., Mansfield, A., De Andrade, M., Yang, P., Vasmatzis, G., Peikert, T. D. & Kosari, F., 2017, In : Oncotarget. 8, 16, p. 27155-27165 11 p.

Research output: Contribution to journalArticle

Epidermal Growth Factor Receptor
Adenocarcinoma
Epidermal Growth Factor
Protein Isoforms
Phosphorylation

Prediction is "Still" Difficult when it is About the Past

Kosari, F. & Karnes, R. J., 2017, (Accepted/In press) In : European Urology.

Research output: Contribution to journalArticle

3 Citations (Scopus)

Retention of interstitial genes between TMPRSS2 and ERG is associated with low-risk prostate cancer

Murphy, S. J., Kosari, F., Karnes, R. J., Nasir, A., Johnson, S. H., Gaitatzes, A. G., Smadbeck, J., Rangel, L. J., Vasmatzis, G. & Cheville, J., Nov 15 2017, In : Cancer Research. 77, 22, p. 6157-6167 11 p.

Research output: Contribution to journalArticle

Gene Fusion
Prostatic Neoplasms
Genes
Neoplasms
Prostatectomy
2016
19 Citations (Scopus)

Integrated analysis of the genomic instability of PTEN in clinically insignificant and significant prostate cancer

Murphy, S. J., Karnes, R. J., Kosari, F., Castellar, B. E. R. P., Kipp, B. R., Johnson, S. H., Terra, S., Harris, F. R., Halling, G. C., Klein, J. L. S., Nasir, A., Bergstrahl, E., Rangel, L. J., Sukov, W. R., Vasmatzis, G. & Cheville, J. C., Feb 1 2016, In : Modern Pathology. 29, 2, p. 143-156 14 p.

Research output: Contribution to journalArticle

Genomic Instability
Prostatic Neoplasms
Neoplasm Grading
Neoplasms
Fluorescence In Situ Hybridization
15 Citations (Scopus)

Integrated genomic analysis of pancreatic ductal adenocarcinomas reveals genomic rearrangement events as significant drivers of disease

Murphy, S. J., Hart, S., Halling, G. C., Johnson, S. H., Smadbeck, J., Drucker, T., Lima, J. F., Rohakhtar, F. R., Harris, F. R., Kosari, F., Subramanian, S., Petersen, G. M., Wiltshire, T. D., Kipp, B. R., Truty, M., Mc Williams, R. R., Couch, F. J. & Vasmatzis, G., Feb 1 2016, In : Cancer Research. 76, 3, p. 749-761 13 p.

Research output: Contribution to journalArticle

Adenocarcinoma
Disease Progression
Genes
Exome
Gene Dosage
5 Citations (Scopus)

Magnetophoretic-based microfluidic device for DNA Concentration

Shim, S., Shim, J., Taylor, W. R., Kosari, F., Vasmatzis, G., Ahlquist, D. A. & Bashir, R., Apr 1 2016, In : Biomedical Microdevices. 18, 2, p. 1-8 8 p., 28.

Research output: Contribution to journalArticle

Lab-On-A-Chip Devices
Microfluidics
DNA
Nanofluidics
Nucleic acids
2 Citations (Scopus)

Mapping lung tumor cell drug responses as a function of matrix context and genotype using cell microarrays

Kaylan, K. B., Gentile, S. D., Milling, L. E., Bhinge, K. N., Kosari, F. & Underhill, G. H., Dec 1 2016, In : Integrative Biology (United Kingdom). 8, 12, p. 1221-1231 11 p.

Research output: Contribution to journalArticle

Microarrays
Tumors
Genotype
Cells
Extracellular Matrix Proteins
21 Citations (Scopus)

Quantification of Somatic Chromosomal Rearrangements in Circulating Cell-Free DNA from Ovarian Cancers

Harris, F. R., Kovtun, I. V., Smadbeck, J., Multinu, F., Jatoi, A., Kosari, F., Kalli, K. R., Murphy, S. J., Halling, G. C., Johnson, S. H., Liu, M. C., Mariani, A. & Vasmatzis, G., Jul 20 2016, In : Scientific Reports. 6, 29831.

Research output: Contribution to journalArticle

Ovarian Neoplasms
DNA
Neoplasms
Polymerase Chain Reaction
Tumor Burden
2015
22 Citations (Scopus)

MicroRNA and mRNA features of malignant pleural mesothelioma and benign asbestos-related pleural effusion

Ak, G., Tomaszek, S. C., Kosari, F., Metintas, M., Jett, J. R., Metintas, S., Yildirim, H., Dundar, E., Dong, J., Aubry, M. C., Wigle, D. A. & Thomas, C. F., 2015, In : BioMed Research International. 2015, 635748.

Research output: Contribution to journalArticle

Asbestos
Pleural Effusion
MicroRNAs
Messenger RNA
Tissue
49 Citations (Scopus)

Nanopore-based assay for detection of methylation in double-stranded DNA fragments

Shim, J., Kim, Y., Humphreys, G. I., Nardulli, A. M., Kosari, F., Vasmatzis, G., Taylor, W. R., Ahlquist, D. A., Myong, S. & Bashir, R., Jan 27 2015, In : ACS Nano. 9, 1, p. 290-300 11 p.

Research output: Contribution to journalArticle

methylation
Methylation
Nanopores
Assays
DNA
31 Citations (Scopus)

The cistrome and gene signature of androgen receptor splice variants in castration resistant prostate cancer cells

Lu, J., Lonergan, P. E., Nacusi, L. P., Wang, L., Schmidt, L. J., Sun, Z. D., Van Der Steen, T., Boorjian, S. A., Kosari, F., Vasmatzis, G., Klee, G. G., Balk, S. P., Huang, H., Wang, C. & Tindall, D. J., Feb 1 2015, In : Journal of Urology. 193, 2, p. 690-698 9 p.

Research output: Contribution to journalArticle

Castration
Androgen Receptors
Prostatic Neoplasms
Genes
Androgens
2014
28 Citations (Scopus)

ASCL1 and RET expression defines a clinically relevant subgroup of lung adenocarcinoma characterized by neuroendocrine differentiation

Kosari, F., Ida, C. M., Aubry, M. C., Yang, L., Kovtun, I. V., Klein, J. L. S., Li, Y., Erdogan, S., Tomaszek, S. C., Murphy, S. J., Bolette, L. C., Kolbert, C. P., Yang, P., Wigle, D. A. & Vasmatzis, G., Jul 17 2014, In : Oncogene. 33, 29, p. 3776-3783 8 p.

Research output: Contribution to journalArticle

Adenocarcinoma
Oncogenes
Lung Neoplasms
Biomarkers
Chromogranins
1963 Citations (Scopus)

Comprehensive molecular profiling of lung adenocarcinoma: The cancer genome atlas research network

Collisson, E. A., Campbell, J. D., Brooks, A. N., Berger, A. H., Lee, W., Chmielecki, J., Beer, D. G., Cope, L., Creighton, C. J., Danilova, L., Ding, L., Getz, G., Hammerman, P. S., Hayes, D. N., Hernandez, B., Herman, J. G., Heymach, J. V., Jurisica, I., Kucherlapati, R., Kwiatkowski, D. & 290 others, Ladanyi, M., Robertson, G., Schultz, N., Shen, R., Sinha, R., Sougnez, C., Tsao, M. S., Travis, W. D., Weinstein, J. N., Wigle, D. A., Wilkerson, M. D., Chu, A., Cherniack, A. D., Hadjipanayis, A., Rosenberg, M., Weisenberger, D. J., Laird, P. W., Radenbaugh, A., Ma, S., Stuart, J. M., Byers, L. A., Baylin, S. B., Govindan, R., Meyerson, M., Gabriel, S. B., Cibulskis, K., Kim, J., Stewart, C., Lichtenstein, L., Lander, E. S., Lawrence, M. S., Getz, E., Fulton, R., Fulton, L. L., McLellan, M. D., Wilson, R. K., Ye, K., Fronick, C. C., Maher, C. A., Miller, C. A., Wendl, M. C., Cabanski, C., Mardis, E., Wheeler, D., Balasundaram, M., Butterfield, Y. S. N., Carlsen, R., Chuah, E., Dhalla, N., Guin, R., Hirst, C., Lee, D., Li, H. I., Mayo, M., Moore, R. A., Mungall, A. J., Schein, J. E., Sipahimalani, P., Tam, A., Varhol, R., Robertson, A. G., Wye, N., Thiessen, N., Holt, R. A., Jones, S. J. M., Marra, M. A., Imielinski, M., Onofrio, R. C., Hodis, E., Zack, T., Helman, E., Pedamallu, C. S., Mesirov, J., Saksena, G., Schumacher, S. E., Carter, S. L., Garraway, L., Beroukhim, R., Lee, S., Mahadeshwar, H. S., Pantazi, A., Protopopov, A., Ren, X., Seth, S., Song, X., Tang, J., Yang, L., Zhang, J., Chen, P. C., Parfenov, M., Xu, A. W., Santoso, N., Chin, L., Park, P. J., Hoadley, K. A., Auman, J. T., Meng, S., Shi, Y., Buda, E., Waring, S., Veluvolu, U., Tan, D., Mieczkowski, P. A., Jones, C. D., Simons, J. V., Soloway, M. G., Bodenheimer, T., Jefferys, S. R., Roach, J., Hoyle, A. P., Wu, J., Balu, S., Singh, D., Prins, J. F., Marron, J. S., Parker, J. S., Perou, C. M., Liu, J., Maglinte, D. T., Lai, P. H., Bootwalla, M. S., Van Den Berg, D. J., Triche, T., Cho, J., DiCara, D., Heiman, D., Lin, P., Mallard, W., Voet, D., Zhang, H., Zou, L., Noble, M. S., Gehlenborg, N., Thorvaldsdottir, H., Nazaire, M. D., Robinson, J., Aksoy, B. A., Ciriello, G., Taylor, B. S., Dresdner, G., Gao, J., Gross, B., Seshan, V. E., Reva, B., Sumer, S. O., Weinhold, N., Sander, C., Ng, S., Zhu, J., Benz, C. C., Yau, C., Haussler, D., Spellman, P. T., Kimes, P. K., Broom, B. M., Wang, J., Lu, Y., Ng, P. K. S., Diao, L., Liu, W., Amos, C. I., Akbani, R., Mills, G. B., Curley, E., Paulauskis, J., Lau, K., Morris, S., Shelton, T., Mallery, D., Gardner, J., Penny, R., Saller, C., Tarvin, K., Richards, W. G., Cerfolio, R., Bryant, A., Raymond, D. P., Pennell, N. A., Farver, C., Czerwinski, C., Huelsenbeck-Dill, L., Iacocca, M., Petrelli, N., Rabeno, B., Brown, J., Bauer, T., Dolzhanskiy, C. O., Potapova, O., Rotin, D., Voronina, O., Nemirovich-Danchenko, E., Fedosenko, K. V., Gal, A., Behera, M., Ramalingam, S. S., Sica, G., Flieder, D., Boyd, J., Weaver, J. E., Kohl, B., Thinh, D. H. Q., Sandusky, G., Juhl, H., Duhig, E., Illei, P., Gabrielson, E., Shin, J., Lee, B., Rogers, K., Trusty, D., Brock, M. V., Williamson, C., Burks, E., Rieger-Christ, K., Holway, A., Sullivan, T., Asiedu, M. K., Kosari, F., Rekhtman, N., Zakowski, M., Rusch, V. W., Zippile, P., Suh, J., Pass, H., Goparaju, C., Owusu-Sarpong, Y., Bartlett, J. M. S., Kodeeswaran, S., Parfitt, J., Sekhon, H., Albert, M., Eckman, J., Myers, J. B., Morrison, C., Gaudioso, C., Borgia, J. A., Bonomi, P., Pool, M., Liptay, M. J., Moiseenko, F., Zaytseva, I., Dienemann, H., Meister, M., Schnabel, P. A., Muley, T. R., Peifer, M., Gomez-Fernandez, C., Herbert, L., Egea, S., Huang, M., Thorne, L. B., Boice, L., Salazar, A. H., Funkhouser, W. K., Rathmell, W. K., Dhir, R., Yousem, S. A., Dacic, S., Schneider, F., Siegfried, J. M., Hajek, R., Watson, M. A., McDonald, S., Meyers, B., Clarke, B., Yang, I. A., Fong, K. M., Hunter, L., Windsor, M., Bowman, R. V., Peters, S., Letovanec, I., Khan, K. Z., Jensen, M. A., Snyder, E. E., Srinivasan, D., Kahn, A. B., Baboud, J., Pot, D. A., Shaw, K. R. M., Sheth, M., Davidsen, T., Demchok, J. A., Yang, L., Wang, Z., Tarnuzzer, R., Zenklusen, J. C., Ozenberger, B. A., Sofia, H. J. & Cheney, R., 2014, In : Nature. 511, 7511, p. 543-550 8 p.

Research output: Contribution to journalArticle

Atlases
Genome
Mutation
Research
Neoplasms
16 Citations (Scopus)

Genomic rearrangements define lineage relationships between adjacent lepidic and invasive components in lung adenocarcinoma

Murphy, S. J., Wigle, D. A., Lima, J. F., Harris, F. R., Johnson, S. H., Halling, G., Asiedu, M. K., Seto, C. T., Terra, S., Kosari, F., Peikert, T. D., Yang, P., Aubry, M. C. & Vasmatzis, G., Jun 1 2014, In : Cancer Research. 74, 11, p. 3157-3167 11 p.

Research output: Contribution to journalArticle

Adenocarcinoma
Growth
Neoplasms
DNA Sequence Analysis
Lasers
2013
110 Citations (Scopus)

Detection and quantification of methylation in DNA using solid-state nanopores

Shim, J., Humphreys, G. I., Venkatesan, B. M., Munz, J. M., Zou, X., Sathe, C., Schulten, K., Kosari, F., Nardulli, A. M., Vasmatzis, G. & Bashir, R., 2013, In : Scientific Reports. 3, 1389.

Research output: Contribution to journalArticle

Nanopores
DNA Methylation
Methylation
Epigenomics
5-Methylcytosine
37 Citations (Scopus)

Lineage relationship of gleason patterns in gleason score 7 prostate cancer

Kovtun, I. V., Cheville, J. C., Murphy, S. J., Johnson, S. H., Zarei, S., Kosari, F., Sukov, W. R., Karnes, R. J. & Vasmatzis, G., Jun 1 2013, In : Cancer Research. 73, 11, p. 3275-3284 10 p.

Research output: Contribution to journalArticle

Neoplasm Grading
Prostatic Neoplasms
Neoplasms
Laser Capture Microdissection
DNA
13 Citations (Scopus)

Prognostic value of discs large homolog 7 transcript levels in prostate cancer

Gomez, C. R., Kosari, F., Munz, J. M., Schreiber, C. A., Knutson, G. J., Ida, C. M., El Khattouti, A., Karnes, R. J., Cheville, J. C., Vasmatzis, G. & Vuk-Pavlović, S., Dec 9 2013, In : PLoS One. 8, 12, e82833.

Research output: Contribution to journalArticle

Cyclin B1
prostatic neoplasms
hypoxia
hyaluronic acid
Prostatic Neoplasms
2012
2057 Citations (Scopus)

Comprehensive genomic characterization of squamous cell lung cancers

Hammerman, P. S., Voet, D., Lawrence, M. S., Voet, D., Jing, R., Cibulskis, K., Sivachenko, A., Stojanov, P., McKenna, A., Lander, E. S., Gabriel, S., Getz, G., Imielinski, M., Helman, E., Hernandez, B., Pho, N. H., Meyerson, M., Chu, A., Hye-Chun, J. E., Mungall, A. J. & 320 others, Pleasance, E., Robertson, A. G., Sipahimalani, P., Stoll, D., Balasundaram, M., Birol, I., Butterfield, Y. S. N., Chuah, E., Coope, R. J. N., Corbett, R., Dhalla, N., Guin, R., He, A., Hirst, C., Hirst, M., Holt, R. A., Lee, D., Li, H. I., Mayo, M., Moore, R. A., Mungall, K., Nip, K. M., Olshen, A., Schein, J. E., Slobodan, J. R., Tam, A., Thiessen, N., Varhol, R., Zeng, T., Zhao, Y., Jones, S. J. M., Marra, M. A., Saksena, G., Cherniack, A. D., Schumacher, S. E., Tabak, B., Carter, S. L., Nguyen, H., Onofrio, R. C., Crenshaw, A., Ardlie, K., Beroukhim, R., Winckler, W., Protopopov, A., Zhang, J., Hadjipanayis, A., Lee, S., Xi, R., Yang, L., Ren, X., Zhang, H., Shukla, S., Chen, P. C., Haseley, P., Lee, E., Chin, L., Park, P. J., Kucherlapati, R., Socci, N. D., Liang, Y., Schultz, N., Borsu, L., Lash, A. E., Viale, A., Sander, C., Ladanyi, M., Auman, J. T., Hoadley, K. A., Wilkerson, M. D., Shi, Y., Liquori, C., Meng, S., Li, L., Turman, Y. J., Topal, M. D., Tan, D., Waring, S., Buda, E., Walsh, J., Jones, C. D., Mieczkowski, P. A., Singh, D., Wu, J., Gulabani, A., Dolina, P., Bodenheimer, T., Hoyle, A. P., Simons, J. V., Soloway, M. G., Stuart, J., Mose, L. E., Jefferys, S. R., Balu, S., O'Connor, B. D., Chiang, D., Liu, J., Chiang, D. Y., Hayes, D. N., Perou, C. M., Cope, L., Weisenberger, D., Danilova, L., Weisenberger, D. J., Maglinte, D. T., Pan, F., Van Den Berg, D. J., Triche, T., Herman, J. G., Baylin, S. B., Laird, P. W., Noble, M., Gehlenborg, N., DiCara, D., Zhang, J., Wu, C. J., Liu, S. Y., Zou, L., Lin, P., Cho, J., Nazaire, M. D., Robinson, J., Thorvaldsdottir, H., Mesirov, J., Sinha, R., Ciriello, G., Cerami, E., Gross, B., Jacobsen, A., Gao, J., Aksoy, B. A., Weinhold, N., Ramirez, R., Taylor, B. S., Antipin, Y., Reva, B., Mo, Q., Seshan, V., Paik, P. K., Akbani, R., Zhang, N., Broom, B. M., Casasent, T., Unruh, A., Wakefield, C., Cason, R. C., Baggerly, K. A., Weinstein, J. N., Haussler, D., Benz, C. C., Stuart, J. M., Zhu, J., Szeto, C., Scott, G. K., Yau, C., Ng, S., Goldstein, T., Waltman, P., Sokolov, A., Collisson, E., Ellrott, K., Collisson, E. A., Zerbino, D., Ma, S., Craft, B., Du, Y., Cabanski, C., Walter, V., Marron, J. S., Liu, Y., Wang, K., Prins, J. F., Creighton, C. J., Zhang, Y., Travis, W. D., Rekhtman, N., Yi, J., Aubry, M. C., Cheney, R., Dacic, S., Flieder, D., Funkhouser, W., Illei, P., Myers, J., Tsao, M. S., Penny, R., Mallery, D., Shelton, T., Hatfield, M., Morris, S., Yena, P., Shelton, C., Sherman, M., Paulauskis, J., Govindan, R., Azodo, I., Beer, D., Bose, R., Byers, L. A., Carbone, D., Chang, L. W., Chun, E., Ding, L., Heymach, J., Ida, C., Johnson, B., Jurisica, I., Kaufman, J., Kosari, F., Kwiatkowski, D., Maher, C. A., Mungall, A., Pao, W., Peifer, M., Robertson, G., Rusch, V., Siegfried, J., Sougnez, C., Thomas, R. K., Tomaszek, S., Vaske, C., Wigle, D. A., Wigle, D. A., Wilks, C., Zhang, J. J., Jensen, M. A., Sfeir, R., Kahn, A. B., Chu, A. L., Kothiyal, P., Wang, Z., Snyder, E. E., Pontius, J., Pihl, T. D., Ayala, B., Backus, M., Walton, J., Baboud, J., Berton, D. L., Nicholls, M. C., Srinivasan, D., Raman, R., Girshik, S., Kigonya, P. A., Alonso, S., Sanbhadti, R. N., Barletta, S. P., Greene, J. M., Pot, D. A., Bandarchi-Chamkhaleh, B., Boyd, J., Weaver, J., Yang, P., Tomaszek, S. C., Aubry, M. C., Ida, C. M., Yang, P., Brock, M. V., Rogers, K., Rutledge, M., Brown, T., Lee, B., Shin, J., Trusty, D., Dhir, R., Siegfried, J. M., Potapova, O., Fedosenko, K. V., Nemirovich-Danchenko, E., Zakowski, M., Iacocca, M. V., Brown, J., Rabeno, B., Czerwinski, C., Petrelli, N., Fan, Z., Todaro, N., Eckman, J., Rathmell, W. K., Thorne, L. B., Huang, M., Boice, L., Hill, A., Curley, E., Morrison, C., Gaudioso, C., Bartlett, J. M. S., Kodeeswaran, S., Zanke, B., Sekhon, H., David, K., Juhl, H., Le, X. V., Kohl, B., Thorp, R., Tien, N. V., Bang, N. V., Sussman, H., Phu, B. D., Hajek, R., Hung, N. P., Khan, K. Z., Muley, T., Mills Shaw, K. R., Sheth, M., Yang, L., Buetow, K., Davidsen, T., Demchok, J. A., Eley, G., Ferguson, M., Dillon, L. A. L., Schaefer, C., Guyer, M. S., Ozenberger, B. A., Palchik, J. D., Peterson, J., Sofia, H. J., Thomson, E., Johnson, B. E. & Shen, R., Sep 27 2012, In : Nature. 489, 7417, p. 519-525 7 p.

Research output: Contribution to journalArticle

Squamous Cell Neoplasms
Lung Neoplasms
Mutation
Neoplasms
Genes
45 Citations (Scopus)

Mate pair sequencing of whole-genome-amplified DNA following laser capture microdissection of prostate

Murphy, S. J., Cheville, J. C., Zarei, S., Johnson, S. H., Sikkink, R. A., Kosari, F., Feldman, A. L., Eckloff, B. W., Karnes, R. J. & Vasmatzis, G., Oct 2012, In : DNA Research. 19, 5, p. 395-406 12 p.

Research output: Contribution to journalArticle

Laser Capture Microdissection
Prostate
Genome
DNA
Neoplasms
14 Citations (Scopus)

Shared gene expression alterations in prostate cancer and histologically benign prostate from patients with prostate cancer

Kosari, F., Cheville, J. C., Ida, C. M., Karnes, R. J., Leontovich, A. A., Sebo, T. J., Erdogan, S., Rodriguez, E., Murphy, S. J. & Vasmatzis, G., Jul 2012, In : American Journal of Pathology. 181, 1, p. 34-42 9 p.

Research output: Contribution to journalArticle

Prostate
Prostatic Neoplasms
Gene Expression
Biomarkers
Platelet-Derived Growth Factor Receptors
80 Citations (Scopus)

USP44 regulates centrosome positioning to prevent aneuploidy and suppress tumorigenesis

Zhang, Y., Foreman, O., Wigle, D. A., Kosari, F., Vasmatzis, G., Salisbury, J. L., Van Deursen, J. & Galardy, P. J., Dec 3 2012, In : Journal of Clinical Investigation. 122, 12, p. 4362-4373 12 p.

Research output: Contribution to journalArticle

Centrosome
Aneuploidy
M Phase Cell Cycle Checkpoints
Carcinogenesis
Anaphase-Promoting Complex-Cyclosome
2010
47 Citations (Scopus)

The ability of biomarkers to predict systemic progression in men with high-risk prostate cancer treated surgically is dependent on ERG status

Karnes, R. J., Cheville, J. C., Ida, C. M., Sebo, T. J., Nair, A. A., Tang, H., Munz, J. M., Kosari, F. & Vasmatzis, G., Nov 15 2010, In : Cancer Research. 70, 22, p. 8994-9002 9 p.

Research output: Contribution to journalArticle

Prostatic Neoplasms
Biomarkers
Prostatectomy
Area Under Curve
ROC Curve
2009
22 Citations (Scopus)
Laser Capture Microdissection
Gene Expression Profiling
Dissection
Lasers
Adenocarcinoma of lung
52 Citations (Scopus)

The role of desmoglein-3 in the diagnosis of squamous cell carcinoma of the lung

Savci-Heijink, C. D., Kosari, F., Aubry, M. C., Caron, B. L., Sun, Z. D., Yang, P. & Vasmatzis, G., May 2009, In : American Journal of Pathology. 174, 5, p. 1629-1637 9 p.

Research output: Contribution to journalArticle

Desmoglein 3
Squamous Cell Carcinoma
Lung
Sensitivity and Specificity
Lung Neoplasms
2008
65 Citations (Scopus)

Gene panel model predictive of outcome in men at high-risk of systemic progression and death from prostate cancer after radical retropubic prostatectomy

Cheville, J. C., Karnes, R. J., Therneau, T. M., Kosari, F., Munz, J. M., Tillmans, L., Basal, E., Rangel, L. J., Bergstralh, E., Kovtun, I. V., Savci-Heijink, C. D., Klee, E. W. & Vasmatzis, G., 2008, In : Journal of Clinical Oncology. 26, 24, p. 3930-3936 7 p.

Research output: Contribution to journalArticle

Prostatectomy
Prostatic Neoplasms
Neoplasm Grading
Gene Expression
Genes
44 Citations (Scopus)

Identification of prognostic biomarkers for prostate cancer

Kosari, F., Munz, J. M. A., Savci-Heijink, C. D., Spiro, C., Klee, E. W., Kube, D. M., Tillmans, L., Slezak, J., Karnes, R. J., Cheville, J. C. & Vasmatzis, G., Mar 15 2008, In : Clinical Cancer Research. 14, 6, p. 1734-1743 10 p.

Research output: Contribution to journalArticle

Prostatic Neoplasms
Biomarkers
Genes
Case-Control Studies
Laser Capture Microdissection
2007
51 Citations (Scopus)

Non-random inactivation of large common fragile site genes in different cancers

McAvoy, S., Ganapathiraju, S. C., Ducharme-Smith, A. L., Pritchett, J. R., Kosari, F., Perez, D. S., Zhu, Y., James, C. D. & Smith, D. I., Nov 2007, In : Cytogenetic and Genome Research. 118, 2-4, p. 260-269 10 p.

Research output: Contribution to journalArticle

Genes
Neoplasms
Endometrial Neoplasms
Brain Neoplasms
Ovarian Neoplasms
61 Citations (Scopus)

Optimization of laser capture microdissection and RNA amplification for gene expression profiling of prostate cancer

Kube, D. M., Savci-Heijink, C. D., Lamblin, A. F., Kosari, F., Vasmatzis, G., Cheville, J. C., Connelly, D. P. & Klee, G. G., Mar 21 2007, In : BMC Molecular Biology. 8, 25.

Research output: Contribution to journalArticle

Microdissection
Laser Capture Microdissection
Gene Expression Profiling
Gene expression
Amplification
12 Citations (Scopus)

Quantitating tissue specificity of human genes to facilitate biomarker discovery

Vasmatzis, G., Klee, E. W., Kube, D. M., Therneau, T. M. & Kosari, F., Jun 2007, In : Bioinformatics. 23, 11, p. 1348-1355 8 p.

Research output: Contribution to journalArticle

Organ Specificity
Biomarkers
Specificity
Genes
Tissue
2006
1 Citation (Scopus)
Epithelial Sodium Channels
Xenopus laevis
Oocytes
Voltage-Gated Potassium Channels
Amiloride
42 Citations (Scopus)

DNA counterion current and saturation examined by a MEMS-based solid state nanopore sensor

Chang, H., Venkatesan, B. M., Iqbal, S. M., Andreadakis, G., Kosari, F., Vasmatzis, G., Peroulis, D. & Bashir, R., Sep 2006, In : Biomedical Microdevices. 8, 3, p. 263-269 7 p.

Research output: Contribution to journalArticle

Nanopores
Micro-Electrical-Mechanical Systems
MEMS
DNA
Sensors
77 Citations (Scopus)

High expression levels of survivin protein independently predict a poor outcome for patients who undergo surgery for clear cell renal cell carcinoma

Parker, A., Kosari, F., Lohse, C. M., Thompson, R. H., Kwon, E. D., Murphy, L., Riehle, D. L., Blute, M. L., Leibovich, B. C., Vasmatzis, G. & Cheville, J. C., Jul 1 2006, In : Cancer. 107, 1, p. 37-45 9 p.

Research output: Contribution to journalArticle

Renal Cell Carcinoma
Neoplasms
Proteins
Odds Ratio
Disease Progression
2005
115 Citations (Scopus)

Clear cell renal cell carcinoma: Gene expression analyses identify a potential signature for tumor aggressiveness

Kosari, F., Parker, A., Kube, D. M., Lohse, C. M., Leibovich, B. C., Blute, M. L., Cheville, J. C. & Vasmatzis, G., Jul 15 2005, In : Clinical Cancer Research. 11, 14, p. 5128-5139 12 p.

Research output: Contribution to journalArticle

Renal Cell Carcinoma
Gene Expression
Neoplasms
Reverse Transcription
Polymerase Chain Reaction
2004
26 Citations (Scopus)
Gene Expression Profiling
Gene expression
Squamous Cell Carcinoma
Genes
Lung Neoplasms
289 Citations (Scopus)

DNA-mediated fluctuations in ionic current through silicon oxide nanopore channels

Chang, H., Kosari, F., Andreadakis, G., Alam, M. A., Vasmatzis, G. & Bashir, R., Aug 2004, In : Nano Letters. 4, 8, p. 1551-1556 6 p.

Research output: Contribution to journalArticle

Nanopores
Silicon oxides
silicon oxides
DNA
deoxyribonucleic acid
13 Citations (Scopus)

Study design considerations in clinical outcome research of lung cancer using microarray analysis

Yang, P., Sun, Z. D., Aubry, M. C., Kosari, F., Bamlet, W., Endo, C., Molina, J. R. & Vasmatzis, G., Nov 2004, In : Lung Cancer. 46, 2, p. 215-226 12 p.

Research output: Contribution to journalArticle

Microarray Analysis
Lung Neoplasms
Outcome Assessment (Health Care)
Genes
Squamous Cell Neoplasms
2002
55 Citations (Scopus)

Cysteine-rich secretory protein-3: A potential biomarker for prostate cancer

Kosari, F., Asmann, Y., Cheville, J. C. & Vasmatzis, G., Nov 1 2002, In : Cancer Epidemiology Biomarkers and Prevention. 11, 11, p. 1419-1426 8 p.

Research output: Contribution to journalArticle

Cysteine
Prostatic Neoplasms
Biomarkers
Prostate
Proteins
18 Citations (Scopus)

Electrical characterization of micro-organisms using microfabricated devices

Chang, H., Ikram, A., Kosari, F., Vasmatzis, G., Bhunia, A. & Bashir, R., Sep 2002, In : Journal of Vacuum Science and Technology B: Microelectronics and Nanometer Structures. 20, 5, p. 2058-2064 7 p.

Research output: Contribution to journalArticle

Electrophoretic mobility
Surface charge
organisms
Bacteria
Electric properties