Biomedical Statistics and Informatics

Research Output 2007 2019

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2019

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. D., 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

Paraffin
Formaldehyde
Chromatin
Epigenomics
Temperature

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
Chromatin Immunoprecipitation
Polymerase chain reaction
Chromatin
chromatin
polymerase chain reaction
1 Citation (Scopus)

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

Pharmaceutical Preparations
Neoplasms
Encyclopedias
Genes
Cell Line
2018
23 Citations (Scopus)

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

Breast Neoplasms
Atlases
Long Noncoding RNA
Decision Trees
Genome

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

Carcinoma
Neoplasms
Dermatoglyphics
Aneuploidy
Genomics
42 Citations (Scopus)

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

Atlases
Genes
Genome
Survival
Neoplasms
15 Citations (Scopus)

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

Genes
Tumors
Neoplasms
Computational methods
Chromatin
8 Citations (Scopus)

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

Ovarian Neoplasms
tumor suppressor genes
cancer
tumors
Tumors
62 Citations (Scopus)

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

Tumors
Tissue
Histology
Methylation
Oncology

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

Exome
Genes
Genome
Antigens
HLA Antigens
25 Citations (Scopus)

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

Adenocarcinoma
Neoplasms
Genome
Chromosomal Instability
Rectum
15 Citations (Scopus)

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

Alternative Splicing
Neoplasms
Exons
Exome
Peptides
77 Citations (Scopus)

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

Neoplasm Genes
Tumors
Genes
Mutation
Neoplasms

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

Genes
Neoplasms
Squamous Cell Neoplasms
Tumors
Atlases

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

Labels
Visualization
Genes
Rearrangement
Graph Search
8 Citations (Scopus)

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. D., Yan, H. D., Elarouci, N., Armenoult, L., Ayadi, M., Ordog, T., Lee, J. H., Oliver, G., Klee, E. W., Moutardier, V., Gayet, O., Bian, B., Duconseil, P. & 13 othersGilabert, 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

Pancreatic Neoplasms
Epigenomics
Adenocarcinoma
sequencing
cancer
21 Citations (Scopus)

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

Human Development
Phosphotransferases
Genes
Gene expression
Tumors
14 Citations (Scopus)

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

Squamous Cell Carcinoma
MicroRNAs
Mutation
Epithelial Cells
Squamous Cell Neoplasms
27 Citations (Scopus)

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

Aneuploidy
Chromosomes
Neoplasms
Genome
Mutation Rate
39 Citations (Scopus)

Genomic and Molecular Landscape of DNA Damage Repair Deficiency across The Cancer Genome Atlas

The Cancer Genome Atlas Research Network, Apr 3 2018, In : Cell Reports. 23, 1, p. 239-254.e6

Research output: Contribution to journalArticle

DNA Repair-Deficiency Disorders
Atlases
DNA Damage
Repair
Genes
Gene transfer
Horizontal Gene Transfer
Workflow
Sequencing
Work Flow
1 Citation (Scopus)
Bayesian Hierarchical Model
Single nucleotide Polymorphism
Nucleotides
Plasma Cells
Polymorphism
RNA Sequence Analysis
Precision Medicine
Biological Science Disciplines
RNA
Mutation
6 Citations (Scopus)

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

Ubiquitin
Genes
Neoplasms
Tumors
Amplification
43 Citations (Scopus)

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

Long Noncoding RNA
Epigenomics
Cell Cycle
Genes
Neoplasms
12 Citations (Scopus)

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

Atlases
Learning systems
Tumors
Genes
Chemical activation
39 Citations (Scopus)

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

Learning systems
Tumors
Neoplasms
Stem cells
Logistics
5 Citations (Scopus)

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

Amyloid
Tauopathies
Alzheimer Disease
Amyloidosis
Disease Susceptibility
13 Citations (Scopus)

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

Tumors
Carbohydrates
Oncology
Metabolism
Vitamins

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

Genome-Wide Association Study
Drug-Related Side Effects and Adverse Reactions
Drug Interactions
Pharmaceutical Preparations
Databases
82 Citations (Scopus)

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

Atlases
Tumors
Genes
Genome
Neoplasms
17 Citations (Scopus)

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

Atlases
Oncogenes
Genome
Neoplasms
Neoplasm Genes
30 Citations (Scopus)

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

Long Noncoding RNA
Neoplasm Genes
Tumors
Genes
Neoplasms
33 Citations (Scopus)

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

Gene expression
Automatic teller machines
Tumors
Neoplasms
Genes
23 Citations (Scopus)

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

Genomics
Tumors
Genes
Neoplasms
Atlases
2 Citations (Scopus)

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

Defensins
Immunotherapy
Interferons
Genes
Neoplasms
29 Citations (Scopus)

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

Exome
Mutation
Atlases
Neoplasms
Genomics
17 Citations (Scopus)

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

Genes
Mutation
Neoplasms
Tumors
RNA
32 Citations (Scopus)

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

Tumor-Infiltrating Lymphocytes
Lymphocytes
Pathology
Tumors
Learning
10 Citations (Scopus)

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

Tumors
Mutation
Neoplasms
Bioelectric potentials
Bioinformatics
29 Citations (Scopus)

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

Atlases
Renal Cell Carcinoma
Genes
Cells
Genome
127 Citations (Scopus)

The Immune Landscape of Cancer

The Cancer Genome Atlas Research Network, Apr 17 2018, In : Immunity. 48, 4, p. 812-830.e14

Research output: Contribution to journalArticle

Neoplasms
Genetic Epigenesis
Lymphocytes
Th2 Cells
Th1 Cells
1 Citation (Scopus)

The impact of pharmacokinetic gene profiles across human cancers

Zimmermann, M. T., Therneau, T. M. & Kocher, J-P., May 21 2018, In : BMC Cancer. 18, 1, 577.

Research output: Contribution to journalArticle

Pharmacokinetics
Genes
Neoplasms
Survival
Therapeutics
1 Citation (Scopus)

Two high-risk susceptibility loci at 6p25.3 and 14q32.13 for Waldenström macroglobulinemia

McMaster, M. L., Berndt, S. I., Zhang, J., Slager, S. L., Li, S. A., Vajdic, C. M., Smedby, K. E., Yan, H. D., Birmann, B. M., Brown, E. E., Smith, A., Kleinstern, G., Fansler, M. M., Mayr, C., Zhu, B., Chung, C. C., Park, J. H., Burdette, L., Hicks, B. D., Hutchinson, A. & 61 othersTeras, L. R., Adami, H. O., Bracci, P. M., McKay, J., Monnereau, A., Link, B. K., Vermeulen, R. C. H., Ansell, S. M., Maria, A., Diver, W. R., Melbye, M., Ojesina, A. I., Kraft, P., Boffetta, P., Clavel, J., Giovannucci, E., Besson, C. M., Canzian, F., Travis, R. C., Vineis, P., Weiderpass, E., Montalvan, R., Wang, Z., Yeager, M., Becker, N., Benavente, Y., Brennan, P., Foretova, L., Maynadie, M., Nieters, A., de Sanjose, S., Staines, A., Conde, L., Riby, J., Glimelius, B., Hjalgrim, H., Pradhan, N., Feldman, A. L., Novak, A. J., Lawrence, C., Bassig, B. A., Lan, Q., Zheng, T., North, K. E., Tinker, L. F., Cozen, W., Severson, R. K., Hofmann, J. N., Zhang, Y., Jackson, R. D., Morton, L. M., Purdue, M. P., Chatterjee, N., Offit, K., Cerhan, J. R., Chanock, S. J., Rothman, N., Vijai, J., Goldin, L. R., Skibola, C. F. & Caporaso, N. E., Dec 1 2018, In : Nature Communications. 9, 1, 4182.

Research output: Contribution to journalArticle

Waldenstrom Macroglobulinemia
loci
magnetic permeability
Lymphoma
Alleles
2017
6 Citations (Scopus)

A comprehensive analysis of breast cancer microbiota and host gene expression

Thompson, K. J., Ingle, J. N., Tang, X., Chia, N. D., Jeraldo, P. R., Walther-Antonio, M., Kandimalla, K. K., Johnson, S., Yao, J. Z., Harrington, S. C., Suman, V. J., Wang, L. M., Weinshilboum, R. M., Boughey, J. C., Kocher, J-P., Nelson, H., Goetz, M. P. & Kalari, K. R., Nov 1 2017, In : PLoS One. 12, 11, e0188873.

Research output: Contribution to journalArticle

Microbiota
Gene expression
breast neoplasms
Tumors
Breast Neoplasms
1 Citation (Scopus)

Adipose tissue DNA methylome changes in development of new-onset diabetes after kidney transplantation

Baheti, S., Singh, P., Zhang, Y., Evans, J., Jensen, M. D., Somers, V., Kocher, J-P., Sun, Z. D. & Chakkera, H. M., Nov 1 2017, In : Epigenomics. 9, 11, p. 1423-1435 13 p.

Research output: Contribution to journalArticle

Kidney Transplantation
Adipose Tissue
DNA Methylation
Kidney
DNA
11 Citations (Scopus)

Cepip: Context-dependent epigenomic weighting for prioritization of regulatory variants and disease-associated genes

Li, M. J., Li, M., Liu, Z., Yan, B., Pan, Z., Huang, D., Liang, Q., Ying, D., Xu, F., Yao, H., Wang, P., Kocher, J-P., Xia, Z., Sham, P. C., Liu, J. S. & Wang, J., Mar 16 2017, In : Genome Biology. 18, 1, 52.

Research output: Contribution to journalArticle

prioritization
Epigenomics
epigenetics
Genome-Wide Association Study
gene

CircularLogo: A lightweight web application to visualize intra-motif dependencies

Ye, Z., Ma, T., Kalmbach, M. T., Dasari, S., Kocher, J-P. & Wang, L., May 22 2017, In : BMC Bioinformatics. 18, 1, 269.

Research output: Contribution to journalArticle

Nucleotide Motifs
Nucleotides
Position-Specific Scoring Matrices
Web Application
Binding sites
201 Citations (Scopus)

Comprehensive and Integrative Genomic Characterization of Hepatocellular Carcinoma

The Cancer Genome Atlas Research Network & Chandan, V. S., Jun 15 2017, In : Cell. 169, 7, p. 1327-1341.e23

Research output: Contribution to journalArticle

Hepatocellular Carcinoma
Genes
DNA
MicroRNAs
Gene expression
1 Citation (Scopus)

Comprehensive genomic profiling of a rare thyroid follicular dendritic cell sarcoma

Davila, J. I., Starr, J. S., Attia, S., Wang, C., Knudson, R. A., Necela, B. M., Sarangi, V., Sun, Z. D., Ren, Y., Casler, J. D., Menke, D. M., Oliver, G. R., Joseph, R. W., Copland, J. A. III., Parker, A., Kocher, J-P., Thompson, E. A., Smallridge, R. C. & Asmann, Y., Sep 15 2017, In : Rare Tumors. 9, 2, p. 50-53 4 p., 6834.

Research output: Contribution to journalArticle

Follicular Dendritic Cell Sarcoma
Missense Mutation
Mutation
Gene Fusion
Neoplasms