Biomedical Statistics and Informatics

Research Output

2020

Combining copy number, methylation markers, and mutations as a panel for endometrial cancer detection via intravaginal tampon collection

Sangtani, A., Wang, C., Weaver, A., Hoppman, N. L., Kerr, S. E., Abyzov, A., Shridhar, V., Staub, J., Kocher, J. P. A., Voss, J. S., Podratz, K. C., Wentzensen, N., Kisiel, J. B., Sherman, M. E. & Bakkum-Gamez, J. N., Feb 2020, In : Gynecologic oncology. 156, 2, p. 387-392 6 p.

Research output: Contribution to journalArticle

2019

Ccne1 Overexpression Causes Chromosome Instability in Liver Cells and Liver Tumor Development in Mice

Aziz, K., Limzerwala, J. F., Sturmlechner, I., Hurley, E., Zhang, C., Jeganathan, K. B., Nelson, G., Bronk, S., Fierro Velasco, R. O., van Deursen, E. J., O'Brien, D. R., Kocher, J-P., Youssef, S. A., van Ree, J. H., de Bruin, A., van den Bos, H., Spierings, D. C. J., Foijer, F., van de Sluis, B., Roberts, L. R. & 3 others, Gores, G. J., Li, H. & Van Deursen, J., Jul 1 2019, In : Gastroenterology. 157, 1, p. 210-226.e12

Research output: Contribution to journalArticle

6 Scopus citations

Enhanced and controlled chromatin extraction from FFPE tissues and the application to ChIP-seq

Zhong, J., Ye, Z., Clark, C. R., Lenz, S. W., Nguyen, J. H., Yan, H., Robertson, K. D., Farrugia, G., Zhang, Z., Ordog, T. & Lee, J. H., Mar 29 2019, In : BMC genomics. 20, 1, 249.

Research output: Contribution to journalArticle

Identification of factors associated with duplicate rate in ChIP-seq data

Tian, S., Peng, S., Kalmbach, M., Gaonkar, K. S., Bhagwate, A., Ding, W. D., Eckel-Passow, J. E., Yan, H. D. & Slager, S. L., Apr 1 2019, In : PloS one. 14, 4, e0214723.

Research output: Contribution to journalArticle

Open Access

Predict drug sensitivity of cancer cells with pathway activity inference

Wang, X., Sun, Z. D., Zimmermann, M. T., Bugrim, A. & Kocher, J-P., Jan 31 2019, In : BMC Medical Genomics. 12, 15.

Research output: Contribution to journalArticle

4 Scopus citations

Prognostic subclass of intrahepatic cholangiocarcinoma by integrative molecular–clinical analysis and potential targeted approach

Ahn, K. S., O’Brien, D., Kang, Y. N., Mounajjed, T., Kim, Y. H., Kim, T. S., Kocher, J-P., Allotey, L. K., Borad, M. J., Roberts, L. R. & Kang, K. J., Jan 1 2019, In : Hepatology International.

Research output: Contribution to journalArticle

2 Scopus citations

Recurrent MSCE116K mutations in ALK-negative anaplastic large cell lymphoma

Luchtel, R. A., Zimmermann, M. T., Hu, G., Dasari, S., Jiang, M., Oishi, N., Jacobs, H. K., Zeng, Y., Hundal, T., Rech, K. L., Ketterling, R. P., Lee, J. H., Eckloff, B. W., Yan, H., Gaonkar, K. S., Tian, S., Ye, Z., Kadin, M. E., Sidhu, J., Jiang, L. & 11 others, Voss, J., Link, B. K., Syrbu, S. I., Facchetti, F., Bennani, N. N., Slager, S. L., Ordog, T., Kocher, J. P., Cerhan, J. R., Ansell, S. M. & Feldman, A. L., Jun 27 2019, In : Blood. 133, 26, p. 2776-2789 14 p.

Research output: Contribution to journalArticle

5 Scopus citations

TGFβ-induced fibroblast activation requires persistent and targeted HDAC-mediated gene repression

Jones, D. L., Haak, A. J., Caporarello, N., Choi, K. M., Ye, Z., Yan, H., Varelas, X., Ordog, T., Ligresti, G. & Tschumperlin, D. J., Jan 1 2019, In : Journal of cell science. 132, 20, jcs233486.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations
2018

A Comprehensive Pan-Cancer Molecular Study of Gynecologic and Breast Cancers

The Cancer Genome Atlas Research Network, Apr 9 2018, In : Cancer cell. 33, 4, p. 690-705.e9

Research output: Contribution to journalArticle

94 Scopus citations

A data science approach for the classification of low-grade and high-grade ovarian serous carcinomas

Lin, S., Wang, C., Zarei, S., Bell, D. A., Kerr, S. E., Runger, G. C. & Kocher, J-P., Nov 27 2018, In : BMC Genomics. 19, 1, 841.

Research output: Contribution to journalArticle

1 Scopus citations

An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

The Cancer Genome Atlas Research Network, Apr 5 2018, In : Cell. 173, 2, p. 400-416.e11

Research output: Contribution to journalArticle

232 Scopus citations

A Pan-Cancer Analysis of Enhancer Expression in Nearly 9000 Patient Samples

The Cancer Genome Atlas Research Network, Apr 5 2018, In : Cell. 173, 2, p. 386-399.e12

Research output: Contribution to journalArticle

45 Scopus citations

CARM1-expressing ovarian cancer depends on the histone methyltransferase EZH2 activity

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. D., Drapkin, R., Conejo-Garcia, J. R., Speicher, D. W., Ordog, T. & Zhang, R., Dec 1 2018, In : Nature Communications. 9, 1, 631.

Research output: Contribution to journalArticle

25 Scopus citations

Cell-of-Origin Patterns Dominate the Molecular Classification of 10,000 Tumors from 33 Types of Cancer

The Cancer Genome Atlas Network, Apr 5 2018, In : Cell. 173, 2, p. 291-304.e6

Research output: Contribution to journalArticle

247 Scopus citations

Comparative analysis of de novo assemblers for variation discovery in personal genomes

Tian, S., Yan, H. D., Klee, E. W., Kalmbach, M. & Slager, S. L., Sep 28 2018, In : Briefings in Bioinformatics. 19, 5, p. 893-904 12 p.

Research output: Contribution to journalArticle

3 Scopus citations

Comparative Molecular Analysis of Gastrointestinal Adenocarcinomas

The Cancer Genome Atlas Research Network, Apr 9 2018, In : Cancer cell. 33, 4, p. 721-735.e8

Research output: Contribution to journalArticle

68 Scopus citations

Comprehensive Analysis of Alternative Splicing Across Tumors from 8,705 Patients

The Cancer Genome Atlas Research Network, Aug 13 2018, In : Cancer cell. 34, 2, p. 211-224.e6

Research output: Contribution to journalArticle

101 Scopus citations

Comprehensive Characterization of Cancer Driver Genes and Mutations

The MC3 Working Group & The Cancer Genome Atlas Research Network, Apr 5 2018, In : Cell. 173, 2, p. 371-385.e18

Research output: Contribution to journalArticle

278 Scopus citations

Comprehensive Molecular Characterization of the Hippo Signaling Pathway in Cancer

The Cancer Genome Atlas Research Network, Oct 30 2018, In : Cell reports. 25, 5, p. 1304-1317.e5

Research output: Contribution to journalArticle

29 Scopus citations

Detection and visualization of complex structural variants from long reads

Stephens, Z., Wang, C., Iyer, R. K. & Kocher, J-P., Dec 21 2018, In : BMC Bioinformatics. 19, 508.

Research output: Contribution to journalArticle

4 Scopus citations

Distinct epigenetic landscapes underlie the pathobiology of pancreatic cancer subtypes

Lomberk, G., Blum, Y., Nicolle, R., Nair, A., Gaonkar, K. S., Marisa, L., Mathison, A., Sun, Z., Yan, H., Elarouci, N., Armenoult, L., Ayadi, M., Ordog, T., Lee, J. H., Oliver, G., Klee, E., Moutardier, V., Gayet, O., Bian, B., Duconseil, P. & 13 others, Gilabert, M., Bigonnet, M., Garcia, S., Turrini, O., Delpero, J. R., Giovannini, M., Grandval, P., Gasmi, M., Secq, V., De Reyniès, A., Dusetti, N., Iovanna, J. & Urrutia, R., Dec 1 2018, In : Nature communications. 9, 1, 1978.

Research output: Contribution to journalArticle

34 Scopus citations

Driver Fusions and Their Implications in the Development and Treatment of Human Cancers

The Fusion Analysis Working Group & The Cancer Genome Atlas Research Network, Apr 3 2018, In : Cell reports. 23, 1, p. 227-238.e3

Research output: Contribution to journalArticle

85 Scopus citations

Erratum: Comprehensive Characterization of Cancer Driver Genes and Mutations (ARTICLE (2018) 173(2) (371–385), (S009286741830237X), (10.1016/j.cell.2018.02.060))

The MC3 Working Group & The Cancer Genome Atlas Research Network, Aug 9 2018, In : Cell. 174, 4, p. 1034-1035 2 p.

Research output: Contribution to journalComment/debate

57 Scopus citations
25 Scopus citations

Erratum: Author Correction: UClncR: Ultrafast and comprehensive long non-coding RNA detection from RNA-seq (Scientific reports (2017) 7 1 (14196))

Sun, Z., Nair, A., Chen, X., Prodduturi, N., Wang, J. & Kocher, J. P., Mar 20 2018, In : Scientific reports. 8, 1, 1 p.

Research output: Contribution to journalComment/debate

Open Access
1 Scopus citations

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

The Cancer Genome Atlas Research Network, Apr 3 2018, In : Cell reports. 23, 1, p. 194-212.e6

Research output: Contribution to journalArticle

51 Scopus citations

Genomic and Functional Approaches to Understanding Cancer Aneuploidy

The Cancer Genome Atlas Research Network, Apr 9 2018, In : Cancer cell. 33, 4, p. 676-689.e3

Research output: Contribution to journalArticle

88 Scopus citations
1 Scopus citations

Hybrid-denovo: A de novo OTU-picking pipeline integrating single-end and paired-end 16S sequence tags

Chen, X., Johnson, S., Jeraldo, P., Wang, J., Chia, N., Kocher, J. P. A. & Chen, J., Mar 1 2018, In : GigaScience. 7, 3, p. 1-7 7 p.

Research output: Contribution to journalComment/debate

21 Scopus citations

Improving Single-Nucleotide Polymorphism-Based Fetal Fraction Estimation of Maternal Plasma Circulating Cell-Free DNA Using Bayesian Hierarchical Models

Larson, N., Wang, C., Na, J., Rowsey, R. A., Highsmith, W. E. J., Hoppman, N. L., Kocher, J-P. & Klee, E. W., Sep 1 2018, In : Journal of Computational Biology. 25, 9, p. 1040-1049 10 p.

Research output: Contribution to journalArticle

2 Scopus citations

Integrated Genomic Analysis of the Ubiquitin Pathway across Cancer Types

The Cancer Genome Atlas Research Network, Apr 3 2018, In : Cell reports. 23, 1, p. 213-226.e3

Research output: Contribution to journalArticle

20 Scopus citations

lncRNA Epigenetic Landscape Analysis Identifies EPIC1 as an Oncogenic lncRNA that Interacts with MYC and Promotes Cell-Cycle Progression in Cancer

The Cancer Genome Atlas Research Network, Apr 9 2018, In : Cancer cell. 33, 4, p. 706-720.e9

Research output: Contribution to journalArticle

121 Scopus citations

Machine Learning Detects Pan-cancer Ras Pathway Activation in The Cancer Genome Atlas

The Cancer Genome Atlas Research Network, Apr 3 2018, In : Cell reports. 23, 1, p. 172-180.e3

Research output: Contribution to journalArticle

25 Scopus citations

Machine Learning Identifies Stemness Features Associated with Oncogenic Dedifferentiation

The Cancer Genome Atlas Research Network, Apr 5 2018, In : Cell. 173, 2, p. 338-354.e15

Research output: Contribution to journalArticle

136 Scopus citations

Microglial translational profiling reveals a convergent APOE pathway from aging, amyloid, and tau

Kang, S., Ebbert, M. T. W., Baker, K. E., Cook, C., Wang, X., Sens, J. P., Kocher, J-P., Petrucelli, L. & Fryer, J. D., Jan 1 2018, In : Journal of Experimental Medicine. 215, 9, p. 2235-2245 11 p.

Research output: Contribution to journalArticle

26 Scopus citations

Molecular Characterization and Clinical Relevance of Metabolic Expression Subtypes in Human Cancers

The Cancer Genome Atlas Research Network, Apr 3 2018, In : Cell reports. 23, 1, p. 255-269.e4

Research output: Contribution to journalArticle

30 Scopus citations

Novel Neural Network Approach to Predict Drug-Target Interactions Based on Drug Side Effects and Genome-Wide Association Studies

Prinz, J., Koohi-Moghadam, M., Sun, H., Kocher, J-P. & Wang, J., Jan 1 2018, (Accepted/In press) In : Human Heredity. p. 79-91 13 p.

Research output: Contribution to journalArticle

Oncogenic Signaling Pathways in The Cancer Genome Atlas

The Cancer Genome Atlas Research Network, Apr 5 2018, In : Cell. 173, 2, p. 321-337.e10

Research output: Contribution to journalArticle

306 Scopus citations

Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas

The Cancer Genome Atlas Network, Mar 28 2018, In : Cell Systems. 6, 3, p. 282-300.e2

Research output: Contribution to journalArticle

48 Scopus citations

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

The Cancer Genome Atlas Research Network, Apr 3 2018, In : Cell reports. 23, 1, p. 297-312.e12

Research output: Contribution to journalArticle

83 Scopus citations

Pathogenic Germline Variants in 10,389 Adult Cancers

The Cancer Genome Atlas Research Network, Apr 5 2018, In : Cell. 173, 2, p. 355-370.e14

Research output: Contribution to journalArticle

127 Scopus citations

Perspective on Oncogenic Processes at the End of the Beginning of Cancer Genomics

The Cancer Genome Atlas Research Network, Apr 5 2018, In : Cell. 173, 2, p. 305-320.e10

Research output: Contribution to journalArticle

67 Scopus citations

Prevalent homozygous deletions of type i interferon and defensin genes in human cancers associate with immunotherapy resistance

Ye, Z., Dong, H. M., Li, Y., Ma, T., Huang, H., Leong, H. S., Eckel-Passow, J. E., Kocher, J-P., Liang, H. & Wang, L., Jul 15 2018, In : Clinical Cancer Research. 24, 14, p. 3299-3308 10 p.

Research output: Contribution to journalArticle

9 Scopus citations

Scalable Open Science Approach for Mutation Calling of Tumor Exomes Using Multiple Genomic Pipelines

MC3 Working Group & The Cancer Genome Atlas Research Network, Mar 28 2018, In : Cell Systems. 6, 3, p. 271-281.e7

Research output: Contribution to journalArticle

97 Scopus citations

Somatic Mutational Landscape of Splicing Factor Genes and Their Functional Consequences across 33 Cancer Types

The Cancer Genome Atlas Research Network, Apr 3 2018, In : Cell reports. 23, 1, p. 282-296.e4

Research output: Contribution to journalArticle

69 Scopus citations

Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images

The Cancer Genome Atlas Research Network, Apr 3 2018, In : Cell reports. 23, 1, p. 181-193.e7

Research output: Contribution to journalArticle

97 Scopus citations

Systematic Analysis of Splice-Site-Creating Mutations in Cancer

The Cancer Genome Atlas Research Network, Apr 3 2018, In : Cell reports. 23, 1, p. 270-281.e3

Research output: Contribution to journalArticle

39 Scopus citations

The Cancer Genome Atlas Comprehensive Molecular Characterization of Renal Cell Carcinoma

The Cancer Genome Atlas Research Network, Apr 3 2018, In : Cell reports. 23, 1, p. 313-326.e5

Research output: Contribution to journalArticle

99 Scopus citations