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2017

Cancer-associated mutations in endometriosis without cancer

Anglesio, M. S. , Papadopoulos, N. , Ayhan, A. , Nazeran, T. M. , Noë, M. , Horlings, H. M. , Lum, A. , Jones, S. , Senz, J. , Seckin, T. , Ho, J. , Wu, R. C. , Lac, V. , Ogawa, H. , Tessier-Cloutier, B. , Alhassan, R. , Wang, A. , Wang, Y. , Cohen, J. D. , Wong, F. & 20 others Hasanovic, A., Orr, N., Zhang, M., Popoli, M., McMahon, W., Wood, L. D., Mattox, A., Allaire, C., Segars, J., Williams, C., Tomasetti, C., Boyd, N., Kinzler, K. W., Gilks, C. B., Diaz, L., Wang, T. L., Vogelstein, B., Yong, P. J., Huntsman, D. G. & Shih, I. M., May 11 2017, In : New England Journal of Medicine. 376, 19, p. 1835-1848 14 p.

Research output: Contribution to journalArticle

Endometriosis
Mutation
Neoplasms
Epithelium
Exome

Cancer Implications for Patients with Endometriosis

Wilbur, M. A., Shih, I. M., Segars, J. H. & Fader, A. N., Jan 1 2017, In : Seminars in Reproductive Medicine. 35, 1, p. 110-116 7 p.

Research output: Contribution to journalArticle

Endometriosis
Neoplasms
Carcinoma
Endometrioid Carcinoma
Pelvic Pain

CINdex: A Bioconductor Package for Analysis of Chromosome Instability in DNA Copy Number Data

Song, L., Bhuvaneshwar, K., Wang, Y., Feng, Y., Shih, I. M., Madhavan, S. & Gusev, Y., Dec 13 2017, In : Cancer Informatics. 16

Research output: Contribution to journalArticle

Chromosomal Instability
Genomic Instability
DNA
Biological Phenomena
Translational Medical Research
Local Neoplasm Recurrences
DNA Mutational Analysis
Multiple Primary Neoplasms
INDEL Mutation
PTEN Phosphohydrolase

Endometriosis: Benign, malignant, or something in between?

Chui, M. H., Wang, T. L. & Shih, I. M., 2017, In : Oncotarget. 8, 45, p. 78263-78264 2 p.

Research output: Contribution to journalEditorial

Endometriosis

Epigenetic therapy activates type I interferon signaling in murine ovarian cancer to reduce immunosuppression and tumor burden

Stone, M. L., Chiappinelli, K. B., Li, H., Murphy, L. M., Travers, M. E., Topper, M. J., Mathios, D., Lim, M., Shih, I. M., Wang, T. L., Hung, C. F., Bhargava, V., Wiehagen, K. R., Cowley, G. S., Bachman, K. E., Strick, R., Strissel, P. L., Baylin, S. B. & Zahnow, C. A., Dec 19 2017, In : Proceedings of the National Academy of Sciences of the United States of America. 114, 51, p. E10981-E10990

Research output: Contribution to journalArticle

Azacitidine
Interferon Type I
Tumor Burden
Epigenomics
Ovarian Neoplasms

High grade serous ovarian carcinomas originate in the fallopian tube

Labidi-Galy, S. I. , Papp, E. , Hallberg, D. , Niknafs, N. , Adleff, V. , Noe, M. , Bhattacharya, R. , Novak, M. , Jones, S. , Phallen, J. , Hruban, C. A. , Hirsch, M. S. , Lin, D. I. , Schwartz, L. , Maire, C. L. , Tille, J. C. , Bowden, M. , Ayhan, A. , Wood, L. D. , Scharpf, R. B. & 6 others Kurman, R., Wang, T. L., Shih, I. M., Karchin, R., Drapkin, R. & Velculescu, V. E., Dec 1 2017, In : Nature Communications. 8, 1, 1093

Research output: Contribution to journalArticle

cancer
etiology
lesion
tumor
laser

Human transposon insertion profiling: Analysis, visualization and identification of somatic LINE-1 insertions in ovarian cancer

Tang, Z., Steranka, J. P., Ma, S., Grivainis, M., Rodić, N., Huang, C. R. L., Shih, I. M., Wang, T. L., Boeke, J. D., Fenyö, D. & Burns, K. H., Jan 31 2017, In : Proceedings of the National Academy of Sciences of the United States of America. 114, 5, p. E733-E740

Research output: Contribution to journalArticle

Human Genome
Ovarian Neoplasms
Long Interspersed Nucleotide Elements
Retroelements
DNA Transposable Elements

Molecular analysis of high-grade serous ovarian carcinoma with and without associated serous tubal intra-epithelial carcinoma

Ducie, J., Dao, F., Considine, M., Olvera, N., Shaw, P. A., Kurman, R. J., Shih, I. M., Soslow, R. A., Cope, L. & Levine, D. A., Dec 1 2017, In : Nature Communications. 8, 1, 1217

Research output: Contribution to journalArticle

MicroRNAs
Tumors
grade
cancer
RNA

Mutation of NRAS is a rare genetic event in ovarian low-grade serous carcinoma

Xing, D., Suryo Rahmanto, Y., Zeppernick, F., Hannibal, C. G., Kjaer, S. K., Vang, R., Shih, I. M. & Wang, T. L., Oct 1 2017, In : Human Pathology. 68, p. 87-91 5 p.

Research output: Contribution to journalArticle

Carcinoma
Mutation
Neoplasms
Oncogenes
Exons

Primary cytoreductive surgery and adjuvant hormonal monotherapy in women with advanced low-grade serous ovarian carcinoma: Reducing overtreatment without compromising survival?

Fader, A. N., Bergstrom, J., Jernigan, A., Tanner, E. J., Roche, K. L., Stone, R. L., Levinson, K. L., Ricci, S., Wethingon, S., Wang, T. L., Shih, I. M., Yang, B., Zhang, G., Armstrong, D. K., Gaillard, S., Michener, C., DeBernardo, R. & Rose, P. G., 2017, (Accepted/In press) In : Gynecologic Oncology.

Research output: Contribution to journalArticle

Carcinoma
Survival
Hormones
letrozole
Therapeutics

The novel ZIP4 regulation and its role in ovarian cancer

Fan, Q., Cai, Q., Li, P., Wang, W., Wang, J., Gerry, E., Wang, T. L., Shih, I. M., Nephew, K. P. & Xu, Y., 2017, In : Oncotarget. 8, 52, p. 90090-90107 18 p.

Research output: Contribution to journalArticle

Neoplastic Stem Cells
Ovarian Neoplasms
Zinc
Carcinogenesis
Clustered Regularly Interspaced Short Palindromic Repeats

Tubal origin of ovarian cancer – the double-edged sword of haemoglobin

Lin, S. F., Gerry, E. & Shih, I. M., May 1 2017, In : Journal of Pathology. 242, 1, p. 3-6 4 p.

Research output: Contribution to journalComment/debate

Ovarian Neoplasms
Hemoglobins
Carcinoma
Cell Death
Epithelial Cells

Updates on Rare Epithelial Ovarian Carcinoma

Bergstrom, J., Shih, I. M. & Fader, A. N., Feb 22 2017, Translational Advances in Gynecologic Cancers. Elsevier Inc., p. 181-195 15 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

2016

Biologically inspired survival analysis based on integrating gene expression as mediator with genomic variants

Youssef, I., Clarke, R., Shih, I. M., Wang, Y. & Yu, G., Oct 1 2016, In : Computers in Biology and Medicine. 77, p. 231-239 9 p.

Research output: Contribution to journalArticle

Survival Analysis
Gene expression
Gene Expression
Survival
Genes

CCNE1 amplification and centrosome number abnormality in serous tubal intraepithelial carcinoma: further evidence supporting its role as a precursor of ovarian high-grade serous carcinoma

Kuhn, E., Wang, T. L., Doberstein, K., Bahadirli-Talbott, A., Ayhan, A., Sehdev, A. S., Drapkin, R., Kurman, R. J. & Shih, I. M., Jul 22 2016, (Accepted/In press) In : Modern Pathology.

Research output: Contribution to journalArticle

Centrosome
Carcinoma in Situ
Cyclins
Carcinoma
Chromosomal Instability

CCNE1 copy-number gain and overexpression identify ovarian clear cell carcinoma with a poor prognosis

Ayhan, A., Kuhn, E., Wu, R. C., Ogawa, H., Bahadirli-Talbott, A., Mao, T. L., Sugimura, H., Shih, I. M. & Wang, T. L., Oct 21 2016, (Accepted/In press) In : Modern Pathology.

Research output: Contribution to journalArticle

Cyclins
Endometriosis
Carcinoma
Mutation
Ovarian Neoplasms

Correction: Expression of cell competition markers at the interface between p53 signature and normal epithelium in the human fallopian tube

Kito, M., Maeda, D., Kudo-Asabe, Y., Sato, N., Shih, I. M., Wang, T. L., Tanaka, M., Terada, Y. & Goto, A., Jul 1 2016, In : PLoS One. 11, 7, e0160136

Research output: Contribution to journalComment/debate

fallopian tubes
Fallopian Tubes
epithelium
Epithelium
Cells

Diagnostic potential of tumor DNA from ovarian cyst fluid

Wang, Y., Sundfeldt, K., Mateoiu, C., Shih, I. M., Kurman, R. J., Schaefer, J., Silliman, N., Kinde, I., Springer, S., Foote, M., Kristjansdottir, B., James, N., Kinzler, K. W., Papadopoulos, N., Diaz, L. A. & Vogelstein, B., Jul 15 2016, In : eLife. 5, 2016JULY, e15175

Research output: Contribution to journalArticle

Cyst Fluid
Ovarian Cysts
Tumors
Fluids
DNA

Expression of cell competition markers at the interface between p53 signature and normal epithelium in the human fallopian tube

Kito, M., Maeda, D., Kudo-Asabe, Y., Sato, N., Shih, I. M., Wang, T. L., Tanaka, M., Terada, Y. & Goto, A., Jun 1 2016, In : PLoS One. 11, 6, e0156069

Research output: Contribution to journalArticle

fallopian tubes
Fallopian Tubes
Vimentin
epithelium
Epithelium

Inactivating ARID1A tumor suppressor enhances TERT transcription and maintains telomere length in cancer cells

Rahmanto, Y. S., Jung, J. G., Wu, R. C., Kobayashi, Y., Heaphy, C. M., Meeker, A. K., Wang, T. L. & Shih, I. M., 2016, In : Journal of Biological Chemistry. 291, 18, p. 9690-9699 10 p.

Research output: Contribution to journalArticle

Telomerase
Telomere
Transcription
Reverse Transcription
Tumors

Integrated Proteogenomic Characterization of Human High-Grade Serous Ovarian Cancer

the CPTAC Investigators, Jul 28 2016, In : Cell. 166, 3, p. 755-765 11 p.

Research output: Contribution to journalArticle

Ovarian Neoplasms
Genes
Genome
Proteome
Proteomics
Atlases
Genome
Carcinoma
Mutation
Neoplasms

Ovarian cancer chemoresistance relies on the stem cell reprogramming factor PBX1

Jung, J. G., Shih, I. M., Park, J. T., Gerry, E., Kim, T. H., Ayhan, A., Handschuh, K., Davidson, B., Fader, A. N., Selleri, L. & Wang, T. L., Nov 1 2016, In : Cancer Research. 76, 21, p. 6351-6361 11 p.

Research output: Contribution to journalArticle

Stem Cell Factor
Platinum
Ovarian Neoplasms
Neoplasms
Neoplastic Stem Cells

PD-L1 Expression in Human Placentas and Gestational Trophoblastic Diseases

Veras, E., Kurman, R. J., Wang, T. L. & Shih, I. M., Jun 29 2016, (Accepted/In press) In : International Journal of Gynecological Pathology.

Research output: Contribution to journalArticle

Gestational Trophoblastic Disease
Trophoblastic Neoplasms
Placenta
Trophoblasts
Choriocarcinoma

Rationale for developing a specimen bank to study the pathogenesis of high-grade serous carcinoma: A review of the evidence

Sherman, M. E., Drapkin, R. I., Horowitz, N. S., Crum, C. P., Friedman, S., Kwon, J. S., Levine, D. A., Shih, I. M., Shoupe, D., Swisher, E. M., Walker, J., Trabert, B., Greene, M. H., Samimi, G., Temkin, S. M. & Minasian, L. M., Sep 1 2016, In : Cancer Prevention Research. 9, 9, p. 713-720 8 p.

Research output: Contribution to journalReview article

Ovary
Carcinoma
Mutation
Fallopian Tubes
Epithelium

Seromucinous tumors of the ovary. What's in a name?

Kurman, R. J. & Shih, I. M., Jan 1 2016, In : International Journal of Gynecological Pathology. 35, 1, p. 78-81 4 p.

Research output: Contribution to journalArticle

Names
Ovary
Neoplasms
Mullerian Mixed Tumor
Epithelium

The dualistic model of ovarian carcinogenesis revisited, revised, and expanded

Kurman, R. J. & Shih, I. M., Apr 1 2016, In : American Journal of Pathology. 186, 4, p. 733-747 15 p.

Research output: Contribution to journalArticle

Carcinogenesis
Carcinoma
Neoplasms
Ovary
Brenner Tumor
2015

ARID1A Deficiency Impairs the DNA Damage Checkpoint and Sensitizes Cells to PARP Inhibitors

Shen, J., Peng, Y., Wei, L., Zhang, W., Yang, L., Lan, L., Kapoor, P., Ju, Z., Mo, Q., Shih, I. M., Uray, I. P., Wu, X., Brown, P. H., Shen, X., Mills, G. B. & Peng, G., Jul 1 2015, In : Cancer Discovery. 5, 7, p. 752-767 16 p.

Research output: Contribution to journalArticle

DNA Damage
Neoplasms
Chromatin Assembly and Disassembly
Double-Stranded DNA Breaks
Poly(ADP-ribose) Polymerase Inhibitors

BACOM2.0 facilitates absolute normalization and quantification of somatic copy number alterations in heterogeneous tumor

Fu, Y., Yu, G., Levine, D. A., Wang, N., Shih, I. M., Zhang, Z., Clarke, R. & Wang, Y., Sep 9 2015, In : Scientific Reports. 5, 13955

Research output: Contribution to journalArticle

Neoplasms
Ploidies
Ovarian Neoplasms
Alleles
Datasets

ChIP-BIT: Bayesian inference of target genes using a novel joint probabilistic model of ChIP-seq profiles

Chen, X., Jung, J. G., Shajahan-Haq, A. N., Clarke, R., Shih, I. M., Wang, Y., Magnani, L., Wang, T. L. & Xuan, J., Dec 23 2015, In : Nucleic Acids Research. 44, 7, e65

Research output: Contribution to journalArticle

Statistical Models
Joints
Genes
Transcription Factors
Binding Sites

Clonality analysis of combined Brenner and mucinous tumours of the ovary reveals their monoclonal origin

Wang, Y., Wu, R. C., Shwartz, L. E., Haley, L., Lin, M. T., Shih, I. M. & Kurman, R. J., Oct 1 2015, In : Journal of Pathology. 237, 2, p. 146-151 6 p.

Research output: Contribution to journalArticle

Brenner Tumor
Neoplasms
X Chromosome Inactivation
Fallopian Tubes
Teratoma

Expression patterns of VEGF and Flk-1 in human endometrium during the menstrual cycle

Lai, T. H., Vlahos, N., Shih, I. M. & Zhao, Y., Jan 1 2015, In : Journal of Reproduction and Infertility. 16, 1, p. 3-9 7 p.

Research output: Contribution to journalArticle

Menstrual Cycle
Endometrium
Vascular Endothelial Growth Factor A
Vascular Endothelial Growth Factor Receptor
Paraffin

GATA-3 expression in trophoblastic tissues: An immunohistochemical study of 445 cases, including diagnostic utility

Banet, N., Gown, A. M., Shih, I. M., Li, Q. K., Roden, R. B. S., Nucci, M. R., Cheng, L., Przybycin, C. G., Nasseri-Nik, N., Wu, L. S. F., Netto, G. J., Ronnett, B. M. & Vang, R., Jan 20 2015, In : American Journal of Surgical Pathology. 39, 1, p. 101-108 8 p.

Research output: Contribution to journalArticle

Trophoblasts
Trophoblastic Neoplasms
Placental Site Trophoblastic Tumor
Smooth Muscle Tumor
Hydatidiform Mole

Gestational trophoblastic disease

Shih, I. M., Mazur, M. T. & Kurman, R. J., Jan 21 2015, Sternberg's Diagnostic Surgical Pathology: Sixth Edition. Wolters Kluwer Health Adis (ESP), Vol. 2-2

Research output: Chapter in Book/Report/Conference proceedingChapter

Gestational Trophoblastic Disease

Immunohistochemical expression of ARID1A in penile squamous cell carcinomas: A tissue microarray study of 112 cases

Faraj, S. F., Chaux, A., Gonzalez-Roibon, N., Munari, E., Cubilla, A. L., Shih, I. M. & Netto, G. J., May 1 2015, In : Human Pathology. 46, 5, p. 761-766 6 p.

Research output: Contribution to journalArticle

Squamous Cell Carcinoma
Neoplasms
Paraguay
Penile Neoplasms
Chromatin Assembly and Disassembly

Inhibition of Spleen Tyrosine Kinase Potentiates Paclitaxel-Induced Cytotoxicity in Ovarian Cancer Cells by Stabilizing Microtubules

Yu, Y., Gaillard, S., Phillip, J., Huang, T. C., Pinto, S., Tessarollo, N., Zhang, Z., Pandey, A., Wirtz, D., Ayhan, A., Davidson, B., Wang, T. L. & Shih, I. M., Jul 13 2015, In : Cancer Cell. 28, 1, p. 82-96 15 p.

Research output: Contribution to journalArticle

Paclitaxel
Microtubules
Ovarian Neoplasms
Gene Knockdown Techniques
Syk Kinase

KDDN: An open-source Cytoscape app for constructing differential dependency networks with significant rewiring

Tian, Y., Zhang, B., Hoffman, E. P., Clarke, R., Zhang, Z., Shih, I. M., Xuan, J., Herrington, D. M. & Wang, Y., Jan 15 2015, In : Bioinformatics. 31, 2, p. 287-289 3 p.

Research output: Contribution to journalArticle

Application programs
Gene expression
Open Source
Microarrays
Parallel processing systems

Laminin C1 expression by uterine carcinoma cells is associated with tumor progression

Kashima, H., Wu, R. C., Wang, Y., Sinno, A. K., Miyamoto, T., Shiozawa, T., Wang, T. L., Fader, A. N. & Shih, I. M., 2015, In : Gynecologic Oncology. 139, 2, p. 338-344 7 p.

Research output: Contribution to journalArticle

Laminin
Endometrioid Carcinoma
Carcinoma
Neoplasms
Atlases

Loss of ALDH1A1 expression is an early event in the pathogenesis of ovarian high-grade serous carcinoma

Chui, M. H., Wang, Y., Wu, R. C., Seidman, J., Kurman, R. J., Wang, T. L. & Shih, I. M., Mar 1 2015, In : Modern Pathology. 28, 3, p. 437-445 9 p.

Research output: Contribution to journalArticle

Aldehyde Dehydrogenase
Protein Isoforms
Epithelium
Carcinoma
Stem Cells

Mevalonate pathway antagonist suppresses formation of serous tubal intraepithelial carcinoma and ovarian carcinoma in mouse models

Kobayashi, Y., Kashima, H., Wu, R. C., Jung, J. G., Kuan, J. C., Gu, J., Xuan, J., Sokoll, L., Visvanathan, K., Shih, I. M. & Wang, T. L., Oct 15 2015, In : Clinical Cancer Research. 21, 20, p. 4652-4662 11 p.

Research output: Contribution to journalArticle

Mevalonic Acid
Carcinoma in Situ
Hydroxymethylglutaryl-CoA Reductase Inhibitors
Lovastatin
Ovarian Neoplasms

Molecular analysis of ovarian mucinous carcinoma reveals different cell of origins

Wang, Y., Shwartz, L. E., Anderson, D., Lin, M. T., Haley, L., Wu, R. C., Vang, R., Shih, I. M. & Kurman, R. J., 2015, In : Oncotarget. 6, 26, p. 22949-22958 10 p.

Research output: Contribution to journalArticle

Mucinous Adenocarcinoma
Teratoma
Neoplasms
Microsatellite Repeats
Mucinous Cystadenoma

Precursors of ovarian cancer in the fallopian tube: Serous tubal intraepithelial carcinoma - An update

Zeppernick, F., Meinhold-Heerlein, I. & Shih, I. M., Jan 1 2015, In : Journal of Obstetrics and Gynaecology Research. 41, 1, p. 6-11 6 p.

Research output: Contribution to journalArticle

Fallopian Tube Neoplasms
Carcinoma in Situ
Ovarian Neoplasms
Carcinoma
Neoplasms

Synthetic lethality by targeting EZH2 methyltransferase activity in ARID1A-mutated cancers

Bitler, B. G., Aird, K. M., Garipov, A., Li, H., Amatangelo, M., Kossenkov, A. V., Schultz, D. C., Liu, Q., Shih, I. M., Conejo-Garcia, J. R., Speicher, D. W. & Zhang, R., 2015, In : Nature Medicine. 21, 3, p. 231-238 8 p.

Research output: Contribution to journalArticle

Methyltransferases
Cells
Gene encoding
Phosphatidylinositol 3-Kinases
Chromatin

UNDO: A Bioconductor R package for unsupervised deconvolution of mixed gene expressions in tumor samples

Wang, N., Gong, T., Clarke, R., Chen, L., Shih, I. M., Zhang, Z., Levine, D. A., Xuan, J. & Wang, Y., Jan 1 2015, In : Bioinformatics. 31, 1, p. 137-139 3 p.

Research output: Contribution to journalArticle

Deconvolution
Gene expression
Gene Expression
Tumors
Tumor
Tumor Biomarkers
Early Detection of Cancer
Ovarian Neoplasms
2014

A genetically engineered ovarian cancer mouse model based on fallopian tube transformation mimics human high-grade serous carcinoma development

Sherman-Baust, C. A., Kuhn, E., Valle, B. L., Shih, I. M., Kurman, R. J., Wang, T. L., Amano, T., Ko, M. S., Miyoshi, I., Araki, Y., Lehrmann, E., Zhang, Y., Becker, K. G. & Morin, P. J., 2014, In : Journal of Pathology. 233, 3, p. 228-237 10 p.

Research output: Contribution to journalArticle

Fallopian Tubes
Ovarian Neoplasms
Carcinoma
Viral Tumor Antigens
Epithelium

AISAIC: A software suite for accurate identification of significant aberrations in cancers

Zhang, B., Hou, X., Yuan, X., Shih, I. M., Zhang, Z., Clarke, R., Wang, R. R., Fu, Y., Madhavan, S., Wang, Y. & Yu, G., Feb 1 2014, In : Bioinformatics. 30, 3, p. 431-433 3 p.

Research output: Contribution to journalArticle

Aberrations
Aberration
Cancer
Software
Neoplasms

ARID1A immunohistochemistry improves outcome prediction in invasive urothelial carcinoma of urinary bladder

Faraj, S. F., Chaux, A., Gonzalez-Roibon, N., Munari, E., Ellis, C., Driscoll, T., Schoenberg, M. P., Bivalacqua, T. J., Shih, I. M. & Netto, G. J., Nov 1 2014, In : Human Pathology. 45, 11, p. 2233-2239 7 p.

Research output: Contribution to journalArticle

Urinary Bladder
Immunohistochemistry
Carcinoma
Neoplasms
Chromatin Assembly and Disassembly

ARID1A loss correlates with mismatch repair deficiency and intact p53 expression in high-grade endometrial carcinomas

Allo, G., Bernardini, M. Q., Wu, R. C., Shih, I. M., Kalloger, S., Pollett, A., Gilks, C. B. & Clarke, B. A., Feb 2014, In : Modern Pathology. 27, 2, p. 255-261 7 p.

Research output: Contribution to journalArticle

DNA Mismatch Repair
Endometrial Neoplasms
Endometrioid Carcinoma
Carcinosarcoma
Stomach Neoplasms