Institute for Personalized Medicine

  • 500 University Drive

    17033 Hershey

    United States

Research Output 1975 2019

2017
5 Citations (Scopus)

Endophilin B2 facilitates endosome maturation in response to growth factor stimulation, autophagy induction, and influenza A virus infection

Serfass, J. M., Takahashi, Y., Zhou, Z., Imamura, Y., Liu, Y., Tsotakos, N., Young, M. M., Tang, Z., Yang, L., Xavier, J., Chroneos, Z. & Wang, H-G., Jun 16 2017, In : Journal of Biological Chemistry. 292, 24, p. 10097-10111 15 p.

Research output: Contribution to journal › Article

Endosomes
Influenza A virus
Autophagy
Virus Diseases
Viruses

Expansion of C9ORF72 in amyotrophic lateral sclerosis correlates with brain-computer interface performance

Geronimo, A., Sheldon, K. E., Broach, J. R., Simmons, Z. & Schiff, S. J., Dec 1 2017, In : Scientific reports. 7, 1, 8875.

Research output: Contribution to journal › Article

Brain-Computer Interfaces
Amyotrophic Lateral Sclerosis
Evoked Potentials
Neurodegenerative Diseases
Alleles
26 Citations (Scopus)

Genetic evolution of uveal melanoma guides the development of an inflammatory microenvironment

Gezgin, G., Dogrusöz, M., van Essen, T. H., Kroes, W. G. M., Luyten, G. P. M., van der Velden, P. A., Walter, V., Verdijk, R. M., van Hall, T., van der Burg, S. H. & Jager, M. J., Jul 1 2017, In : Cancer Immunology, Immunotherapy. 66, 7, p. 903-912 10 p.

Research output: Contribution to journal › Article

Molecular Evolution
T-Lymphocytes
Chromosomes, Human, Pair 3
Chromosomes
Macrophages

Genome-wide profiling of differentially spliced mRNAs in human fetal cortical tissue exposed to alcohol

Imamura, Y., Mohammad, S., Son, A. I., Morizono, H., Basha, A., Salzberg, A. C., Torii, M. & Hashimoto-Torii, K., Aug 1 2017, In : Alcohol. 62, p. 1-9 9 p.

Research output: Contribution to journal › Article

alcohol consumption
Protein Isoforms
Fetus
Ethanol
Genes

HiCComp: Multiple-level comparative analysis of Hi-C data by triplet network

Zhang, Y., Zhang, B., Zheng, W. J., Tang, J. & Yue, F., Dec 15 2017, Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017. Yoo, I., Zheng, J. H., Gong, Y., Hu, X. T., Shyu, C-R., Bromberg, Y., Gao, J. & Korkin, D. (eds.). Institute of Electrical and Electronics Engineers Inc., p. 92-96 5 p. (Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017; vol. 2017-January).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Genes
Tissue
Neural networks
Transcription factors
Binding sites
31 Citations (Scopus)

HiCRep: assessing the reproducibility of Hi-C data using a stratum-adjusted correlation coefficient

Yang, T., Zhang, F., Yardımci, G. G., Song, F., Hardison, R. C., Noble, W. S., Yue, F. & Li, Q., Nov 2017, In : Genome research. 27, 11, p. 1939-1949 11 p.

Research output: Contribution to journal › Article

Cell Lineage
Quality Control
Chromatin
Genome
Technology
5 Citations (Scopus)

Hypomethylated Fgf3 is a potential biomarker for early detection of oral cancer in mice treated with the tobacco carcinogen dibenzo[def,p]chrysene

Sun, Y. W., Chen, K. M., Kawasawa, Y. I., Salzberg, A. C., Cooper, T. K., Caruso, C., Aliaga, C., Zhu, J., Gowda, K., Amin, S. & El-Bayoumy, K., Oct 2017, In : PloS one. 12, 10, e0186873.

Research output: Contribution to journal › Article

Tobacco
Mouth Neoplasms
Biomarkers
carcinogens
Early Detection of Cancer
9 Citations (Scopus)

Identification of a rare LAMB4 variant associated with familial diverticulitis through exome sequencing

Coble, J. L., Yue, F., Salameh, T. J., Harris, L. R., Deiling, S., Ruggiero, F. M., Eshelman, M. A., Yochum, G. S., Koltun, W. A., Gerhard, G. S. & Broach, J. R., Aug 15 2017, In : Human Molecular Genetics. 26, 16, p. 3212-3220 9 p., ddx204.

Research output: Contribution to journal › Article

Exome
Diverticulitis
Enteric Nervous System
Laminin
Genes
21 Citations (Scopus)

Immunohistochemical Characterization of the Origins of Metastatic Well-differentiated Neuroendocrine Tumors to the Liver

Yang, Z., Klimstra, D. S., Hruban, R. H. & Tang, L. H., Jan 1 2017, In : American Journal of Surgical Pathology. 41, 7, p. 915-922 8 p.

Research output: Contribution to journal › Article

Neuroendocrine Tumors
Liver
Bile Ducts
Rectum
Lung
76 Citations (Scopus)

Integrated Molecular Characterization of Uterine Carcinosarcoma

Cherniack, A. D., Shen, H., Walter, V., Stewart, C., Murray, B. A., Bowlby, R., Hu, X., Ling, S., Soslow, R. A., Broaddus, R. R., Zuna, R. E., Robertson, G., Laird, P. W., Kucherlapati, R., Mills, G. B., Akbani, R., Ally, A., Auman, J. T., Balasundaram, M., Balu, S. & 130 others, Baylin, S. B., Beroukhim, R., Bodenheimer, T., Bogomolniy, F., Boice, L., Bootwalla, M. S., Bowen, J., Broaddus, R., Brooks, D., Carlsen, R., Cho, J., Chuah, E., Chudamani, S., Cibulskis, K., Cline, M., Dao, F., David, M., Demchok, J. A., Dhalla, N., Dowdy, S., Felau, I., Ferguson, M. L., Frazer, S., Frick, J., Gabriel, S., Gastier-Foster, J. M., Gehlenborg, N., Gerken, M., Getz, G., Gupta, M., Haussler, D., Hayes, D. N., Heiman, D. I., Hess, J., Hoadley, K. A., Hoffmann, R., Holt, R. A., Hoyle, A. P., Huang, M., Hutter, C. M., Jefferys, S. R., Jones, S. J. M., Jones, C. D., Kanchi, R. S., Kandoth, C., Kasaian, K., Kerr, S., Kim, J., Lai, P. H., Lander, E., Lawrence, M. S., Lee, D., Leraas, K. M., Leshchiner, I., Levine, D. A., Lichtenberg, T. M., Lin, P., Liu, J., Liu, W., Liu, Y., Lolla, L., Lu, Y., Ma, Y., Maglinte, D. T., Marra, M. A., Mayo, M., Meng, S., Meyerson, M., Mieczkowski, P. A., Moore, R. A., Mose, L. E., Mungall, A. J., Mungall, K., Naresh, R., Noble, M. S., Olvera, N., Parker, J. S., Perou, C. M., Perou, A. H., Pihl, T., Radenbaugh, A. J., Ramirez, N. C., Rathmell, W. K., Roach, J., Robertson, A. G., Sadeghi, S., Saksena, G., Salvesen, H. B., Schein, J. E., Schumacher, S. E., Sheth, M., Shi, Y., Shih, J., Simons, J. V., Sipahimalani, P., Skelly, T., Sofia, H. J., Soloway, M. G., Sougnez, C., Sun, C., Tam, A., Tan, D., Tarnuzzer, R., Thiessen, N., Thorne, L. B., Tse, K., Tseng, J., Van Den Berg, D. J., Veluvolu, U., Verhaak, R. G. W., Voet, D., von Bismarck, A., Wan, Y., Wang, Z., Wang, C., Weinstein, J. N., Weisenberger, D. J., Wilkerson, M. D., Winterhoff, B., Wise, L., Wong, T., Wu, Y., Yang, L., Zenklusen, J. C., Zhang, J. J., Zhang, H., Zhang, W., Zhu, J. C., Zmuda, E. & Zhang, J., Mar 13 2017, In : Cancer Cell. 31, 3, p. 411-423 13 p.

Research output: Contribution to journal › Article

Carcinosarcoma
Epithelial-Mesenchymal Transition
Epigenomics
Proteomics
Mutation
125 Citations (Scopus)

Integrative Analysis Identifies Four Molecular and Clinical Subsets in Uveal Melanoma

Robertson, A. G., Shih, J., Yau, C., Gibb, E. A., Oba, J., Mungall, K. L., Hess, J. M., Uzunangelov, V., Walter, V., Danilova, L., Lichtenberg, T. M., Kucherlapati, M., Kimes, P. K., Tang, M., Penson, A., Babur, O., Akbani, R., Bristow, C. A., Hoadley, K. A., Iype, L. & 150 others, Chang, M. T., Abdel-Rahman, M. H., Ally, A., Auman, J. T., Balasundaram, M., Balu, S., Benz, C., Beroukhim, R., Birol, I., Bodenheimer, T., Bowen, J., Bowlby, R., Brooks, D., Carlsen, R., Cebulla, C. M., Cherniack, A. D., Chin, L., Cho, J., Chuah, E., Chudamani, S., Cibulskis, C., Cibulskis, K., Cope, L., Coupland, S. E., Defreitas, T., Demchok, J. A., Desjardins, L., Dhalla, N., Esmaeli, B., Felau, I., Ferguson, M. L., Frazer, S., Gabriel, S. B., Gastier-Foster, J. M., Gehlenborg, N., Gerken, M., Gershenwald, J. E., Getz, G., Griewank, K. G., Grimm, E. A., Hayes, D. N., Hegde, A. M., Heiman, D. I., Helsel, C., Hobensack, S., Holt, R. A., Hoyle, A. P., Hu, X., Hutter, C. M., Jager, M. J., Jefferys, S. R., Jones, C. D., Jones, S. J. M., Kandoth, C., Kasaian, K., Kim, J., Kucherlapati, R., Lander, E., Lawrence, M. S., Lazar, A. J., Lee, S., Leraas, K. M., Lin, P., Liu, J., Liu, W., Lolla, L., Lu, Y., Ma, Y., Mahadeshwar, H. S., Mariani, O., Marra, M. A., Mayo, M., Meier, S., Meng, S., Meyerson, M., Mieczkowski, P. A., Mills, G. B., Moore, R. A., Mose, L. E., Mungall, A. J., Murray, B. A., Naresh, R., Noble, M. S., Pantazi, A., Parfenov, M., Park, P. J., Parker, J. S., Perou, C. M., Pihl, T., Pilarski, R., Protopopov, A., Radenbaugh, A., Rai, K., Ramirez, N. C., Ren, X., Reynolds, S. M., Roach, J., Roman-Roman, S., Roszik, J., Sadeghi, S., Saksena, G., Sastre, X., Schadendorf, D., Schein, J. E., Schoenfield, L., Schumacher, S. E., Seidman, J., Seth, S., Sethi, G., Sheth, M., Shi, Y., Shields, C., Shmulevich, I., Simons, J. V., Singh, A. D., Sipahimalani, P., Skelly, T., Sofia, H., Soloway, M. G., Song, X., Stern, M. H., Stuart, J., Sun, Q., Sun, H., Tam, A., Tan, D., Tang, J., Tarnuzzer, R., Taylor, B. S., Thiessen, N., Thorsson, V., Tse, K., Veluvolu, U., Verhaak, R. G. W., Voet, D., Wan, Y., Wang, Z., Weinstein, J. N., Wilkerson, M. D., Williams, M. D., Wise, L., Woodman, S. E., Wong, T., Wu, Y., Yang, L., Yang, L., Zenklusen, J. C., Zhang, J., Zhang, H. & Zmuda, E., Aug 14 2017, In : Cancer Cell. 32, 2, p. 204-220.e15

Research output: Contribution to journal › Article

Monosomy
DNA Methylation
Mutation
Uveal melanoma
Neoplasms
6 Citations (Scopus)

Mediator binds to boundaries of chromosomal interaction domains and to proteins involved in DNA looping, RNA metabolism, chromatin remodeling, and actin assembly

Chereji, R. V., Bharatula, V., Elfving, N., Blomberg, J., Larsson, M., Morozov, A. V., Broach, J. R. & Björklund, S., Sep 1 2017, In : Nucleic acids research. 45, 15, p. 8806-8821 16 p.

Research output: Contribution to journal › Article

Protein Interaction Domains and Motifs
Chromatin Assembly and Disassembly
Chromatin
Actins
RNA
45 Citations (Scopus)

Molecular and cellular reorganization of neural circuits in the human lineage

Sousa, A. M. M., Zhu, Y., Raghanti, M. A., Kitchen, R. R., Onorati, M., Tebbenkamp, A. T. N., Stutz, B., Meyer, K. A., Li, M., Kawasawa, Y. I., Liu, F., Perez, R. G., Mele, M., Carvalho, T., Skarica, M., Gulden, F. O., Pletikos, M., Shibata, A., Stephenson, A. R., Edler, M. K. & 18 others, Ely, J. J., Elsworth, J. D., Horvath, T. L., Hof, P. R., Hyde, T. M., Kleinman, J. E., Weinberger, D. R., Reimers, M., Lifton, R. P., Mane, S. M., Noonan, J. P., State, M. W., Lein, E. S., Knowles, J. A., Marques-Bonet, T., Sherwood, C. C., Gerstein, M. B. & Sestan, N., Nov 24 2017, In : Science. 358, 6366, p. 1027-1032 6 p.

Research output: Contribution to journal › Article

Brain
Genes
Pan troglodytes
Neocortex
Hominidae
2 Citations (Scopus)

Multi-variant genetic panel for genetic risk of opioid addiction

Donaldson, K., Demers, L., Taylor, K., Lopez, J. & Chang, S., Jul 1 2017, In : Annals of Clinical and Laboratory Science. 47, 4, p. 452-456 5 p.

Research output: Contribution to journal › Article

Opioid Analgesics
Prescriptions
Statistics
Heroin Dependence
Heroin
14 Citations (Scopus)

MYC activation cooperates with Vhl and Ink4a/Arf loss to induce clear cell renal cell carcinoma

Bailey, S. T., Smith, A. M., Kardos, J., Wobker, S. E., Wilson, H. L., Krishnan, B., Saito, R., Lee, H. J., Zhang, J., Eaton, S. C., Williams, L. A., Manocha, U., Peters, D. J., Pan, X., Carroll, T. J., Felsher, D. W., Walter, V., Zhang, Q., Parker, J. S., Yeh, J. J. & 3 others, Moffitt, R. A., Leung, J. Y. & Kim, W. Y., Jun 8 2017, In : Nature communications. 8, 15770.

Research output: Contribution to journal › Article

Renal Cell Carcinoma
Tumors
tumors
cancer
Chemical activation

NOD2 genetic variants predispose one of two familial adenomatous polyposis siblings to pouchitis through microbiome dysbiosis

Schieffer, K. M., Wright, J. R., Harris, L. R., Deiling, S., Yang, Z., Lamendellab, R., Yochum, G. S. & Koltun, W. A., Nov 1 2017, In : Journal of Crohn's and Colitis. 11, 11, p. 1393-1397 5 p.

Research output: Contribution to journal › Article

Dysbiosis
Pouchitis
Adenomatous Polyposis Coli
Microbiota
Siblings
3 Citations (Scopus)

Phosphorylation and nuclear transit modulate the balance between normal function and terminal aggregation of the yeast RNA-binding protein Ssd1

Kurischko, C. & Broach, J. R., Nov 1 2017, In : Molecular biology of the cell. 28, 22, p. 3057-3069 13 p.

Research output: Contribution to journal › Article

Fungal Proteins
RNA-Binding Proteins
Prions
Cytoplasm
Phosphorylation
1 Citation (Scopus)

PIGN gene expression aberration is associated with genomic instability and leukemic progression in acute myeloid leukemia with myelodysplastic features

Teye, E. K., Sido, A., Xin, P., Finnberg, N. K., Gokare, P., Kawasawa, Y. I., Salzberg, A. C., Shimko, S., Bayerl, M., Ehmann, W. C., Claxton, D. F., Rybka, W. B., Drabick, J. J., Wang, H. G., Abraham, T., El-Deiry, W. S., Brodsky, R. A., J.Hohl, R. & Pu, J. J., Jan 1 2017, In : Oncotarget. 8, 18, p. 29887-29905 19 p.

Research output: Contribution to journal › Article

Genomic Instability
Acute Myeloid Leukemia
Gene Expression
Protein Deficiency
M Phase Cell Cycle Checkpoints
5 Citations (Scopus)

Pitfalls of exome sequencing: A case study of the attribution of HABP2 rs7080536 in familial non-medullary thyroid cancer

Gerhard, G. S., Bann, D. V., Broach, J. & Goldenberg, D., Dec 1 2017, In : npj Genomic Medicine. 2, 1, 8.

Research output: Contribution to journal › Review article

Exome
Neoplasm Genes
Gene Frequency
Population
Guidelines
2 Citations (Scopus)

Population-specific associations of deleterious rare variants in coding region of P2RY1–P2RY12 purinergic receptor genes in large-vessel ischemic stroke patients

Janicki, P. K., Eyileten, C., Ruiz-Velasco, V., Sedeek, K. A., Pordzik, J., Czlonkowska, A., Kurkowska-Jastrzebska, I., Sugino, S., Imamura-Kawasawa, Y., Mirowska-Guzel, D. & Postula, M., Dec 11 2017, In : International journal of molecular sciences. 18, 12, 2678.

Research output: Contribution to journal › Article

Purinergic Receptors
strokes
genes
vessels
coding

Predicting the multi-domain progression of Parkinson's disease: A Bayesian multivariate generalized linear mixed-effect model

Wang, M., Li, Z., Lee, E. Y., Lewis, M. M., Zhang, L., Sterling, N. W., Wagner, D., Eslinger, P., Du, G. & Huang, X., Sep 25 2017, In : BMC Medical Research Methodology. 17, 1, 147.

Research output: Contribution to journal › Article

Parkinson Disease
National Institute of Neurological Disorders and Stroke
Organized Financing
Statistical Models
ROC Curve
179 Citations (Scopus)

Rare and low-frequency coding variants alter human adult height

MAGIC Investigators, The EPIC-InterAct Consortium, EPIC-CVD Consortium, CHD Exome+ Consortium, ExomeBP Consortium, T2D-Genes Consortium, GoT2D Genes Consortium, Global Lipids Genetics Consortium & ReproGen Consortium, Feb 9 2017, In : Nature. 542, 7640, p. 186-190 5 p.

Research output: Contribution to journal › Article

Alleles
Insulin-Like Growth Factor Binding Protein 4
Pregnancy-Associated Plasma Protein-A
Growth Disorders
Multifactorial Inheritance
10 Citations (Scopus)

RNA-seq implicates deregulation of the immune system in the pathogenesis of diverticulitis

Schieffer, K. M., Choi, C. S., Emrich, S., Harris, L., Deiling, S., Karamchandani, D. M., Salzberg, A., Kawasawa, Y. I., Yochum, G. S. & Koltun, W. A., Sep 2017, In : American Journal of Physiology - Gastrointestinal and Liver Physiology. 313, 3, p. G277-G284

Research output: Contribution to journal › Article

Diverticulitis
Immune System
RNA
Diverticulum
Sigmoid Colon
1 Citation (Scopus)

Spatial-temporal analysis of prostate cancer incidence from the Pennsylvania cancer registry, 2000-2011

Wang, M., Matthews, S. A., Iskandarani, K., Li, Y., Li, Z., Chinchilli, V. M. & Zhang, L., Jan 1 2017, In : Geospatial Health. 12, 2, p. 369-375 7 p., 611.

Research output: Contribution to journal › Article

Spatio-Temporal Analysis
temporal analysis
Registries
cancer
Prostatic Neoplasms
6 Citations (Scopus)

"Stealth dissemination" of macrophage-tumor cell fusions cultured from blood of patients with pancreatic ductal adenocarcinoma

Clawson, G. A., Matters, G. L., Xin, P., McGovern, C., Wafula, E., DePamphilis, C., Meckley, M., Wong, J., Stewart, L., D’Jamoos, C., Altman, N., Kawasawa, Y. I., Du, Z., Honaas, L. & Abraham, T., Sep 2017, In : PloS one. 12, 9, e0184451.

Research output: Contribution to journal › Article

cell fusion
Cell Fusion
Macrophages
adenocarcinoma
Tumors
13 Citations (Scopus)

Targeting a non-oncogene addiction to the ATR/CHK1 axis for the treatment of small cell lung cancer

Doerr, F., George, J., Schmitt, A., Beleggia, F., Rehkämper, T., Hermann, S., Walter, V., Weber, J. P., Thomas, R. K., Wittersheim, M., Büttner, R., Persigehl, T. & Christian Reinhardt, H., Dec 1 2017, In : Scientific reports. 7, 1, 15511.

Research output: Contribution to journal › Article

Small Cell Lung Carcinoma
Therapeutics
Cell Cycle Checkpoints
Lung Neoplasms
Drug Therapy
1 Citation (Scopus)

The accuracy of the sysmex uf-1000i in urine bacterial detection compared with the standard urine analysis and culture

Erdman, P., Anderson, B., Zacko, J. C., Taylor, K. & Donaldson, K., Nov 1 2017, In : Archives of Pathology and Laboratory Medicine. 141, 11, p. 1540-1543 4 p.

Research output: Contribution to journal › Article

Urine
Agar
Bacteria
Sensitivity and Specificity
Urinalysis
4 Citations (Scopus)

Variations in brain defects result from cellular mosaicism in the activation of heat shock signalling

Ishii, S., Torii, M., Son, A. I., Rajendraprasad, M., Morozov, Y. M., Kawasawa, Y. I., Salzberg, A. C., Fujimoto, M., Brennand, K., Nakai, A., Mezger, V., Gage, F. H., Rakic, P. & Hashimoto-Torii, K., Jan 1 2017, In : Nature communications. 8, 15157.

Research output: Contribution to journal › Article

Mosaicism
brain
Shock
Brain
Hot Temperature
2018
4 Citations (Scopus)

Activity-Induced Regulation of Synaptic Strength through the Chromatin Reader L3mbtl1

Mao, W., Salzberg, A. C., Uchigashima, M., Hasegawa, Y., Hock, H., Watanabe, M., Akbarian, S., Kawasawa, Y. I. & Futai, K., Jun 12 2018, In : Cell Reports. 23, 11, p. 3209-3222 14 p.

Research output: Contribution to journal › Article

Brain Neoplasms
Chromatin
Tumors
Brain
Histone Code
3 Citations (Scopus)

Adaptive-weight burden test for associations between quantitative traits and genotype data with complex correlations

Wu, X., Guan, T., Liu, D., Novelo, L. G. L. & Bandyopadhyay, D., Sep 1 2018, In : Annals of Applied Statistics. 12, 3, p. 1558-1582 25 p.

Research output: Contribution to journal › Article

Genotype
Genes
Glucose
Throughput
Statistics
4 Citations (Scopus)

A malaria protein factor induces IL-4 production by dendritic cells via PI3K–Akt–NF-B signaling independent of MyD88/ TRIF and promotes Th2 response

Wu, X., Gowda, N. M., Imamura, Y. & Gowda, C., Jan 1 2018, In : Journal of Biological Chemistry. 293, 27, p. 10425-10434 10 p.

Research output: Contribution to journal › Article

Interleukin-4
Dendritic Cells
Malaria
Interleukin-12
Proteins
1 Citation (Scopus)

A possible role for platelet-activating factor receptor in amyotrophic lateral sclerosis treatment

Briones, M. R. S., Snyder, A., Ferreira, R. C., Neely, E. B., Connor, J. & Broach, J., Feb 6 2018, In : Frontiers in Neurology. 9, FEB, 39.

Research output: Contribution to journal › Article

Amyotrophic Lateral Sclerosis
Platelet Activating Factor
ginkgolide B
Interleukin-18
WEB 2086
6 Citations (Scopus)

B-Cell-Intrinsic Type 1 Interferon Signaling Is Crucial for Loss of Tolerance and the Development of Autoreactive B Cells

Domeier, P. P., Chodisetti, S. B., Schell, S. L., Imamura, Y., Fasnacht, M. J., Soni, C. & Rahman, Z., Jul 10 2018, In : Cell Reports. 24, 2, p. 406-418 13 p.

Research output: Contribution to journal › Article

Interferon Type I
B-Lymphocytes
Cells
Germinal Center
Antibodies
2 Citations (Scopus)

CD4 T cells control development and maintenance of brain-resident CD8 T cells during polyomavirus infection

Mockus, T. E., Shwetank, Lauver, M. D., Ren, H. M., Netherby, C. S., Salameh, T., Imamura, Y., Yue, F., Broach, J. & Lukacher, A., Oct 1 2018, In : PLoS Pathogens. 14, 10, e1007365.

Research output: Contribution to journal › Article

Polyomavirus Infections
Maintenance
T-Lymphocytes
Brain
JC Virus

Dynamic chromatin accessibility unveils a regulatory landscape in early embryogenesis in human

Liu, T. & Yue, F., Dec 1 2018, In : Biology of reproduction. 99, 6, p. 1116-1118 3 p.

Research output: Contribution to journal › Comment/debate

Chromatin
Embryonic Development
10 Citations (Scopus)

Effectiveness of Practices to Support Appropriate Laboratory Test Utilization

Rubinstein, M., Hirsch, R., Bandyopadhyay, K., Madison, B., Taylor, T., Ranne, A., Linville, M., Donaldson, K., Lacbawan, F. & Cornish, N., Feb 17 2018, In : American journal of clinical pathology. 149, 3, p. 197-221 25 p.

Research output: Contribution to journal › Review article

Medical Order Entry Systems
Reflex
Length of Stay
Clinical Decision Support Systems
Education
21 Citations (Scopus)

Enhancing Hi-C data resolution with deep convolutional neural network HiCPlus

Zhang, Y., An, L., Xu, J., Zhang, B., Zheng, W. J., Hu, M., Tang, J. & Yue, F., Dec 1 2018, In : Nature communications. 9, 1, 750.

Research output: Contribution to journal › Article

sequencing
Genes
Neural networks
Chromatin
chromatin
9 Citations (Scopus)

Erratum: Integrative Analysis Identifies Four Molecular and Clinical Subsets in Uveal Melanoma (Cancer Cell (2017) 32(2) (204–220.e15)(S1535610817302957)(10.1016/j.ccell.2017.07.003))

TCGA Research Network, Jan 8 2018, In : Cancer Cell. 33, 1, 1 p.

Research output: Contribution to journal › Comment/debate

Manuscripts
Neoplasms
Chromosomes
Uveal melanoma
2 Citations (Scopus)

Evidence of a positive association between malpractice climate and thyroid cancer incidence in the United States

Labarge, B., Walter, V., Lengerich, E. J., Crist, H., Karamchandani, D., Williams, N., Goldenberg, D., Bann, D. V. & Warrick, J. I., Jul 2018, In : PloS one. 13, 7, e0199862.

Research output: Contribution to journal › Article

Malpractice
Climate
Thyroid Neoplasms
climate
incidence
5 Citations (Scopus)

Exosomes impact survival to radiation exposure in cell line models of nervous system cancer

Mrowczynski, O. D., Madhankumar, A., Sundstrom, J., Zhao, Y., Imamura, Y., Slagle-Webb, B., Mau, C., Payne, R. A., Rizk, E., Zacharia, B. & Connor, J., Nov 1 2018, In : Oncotarget. 9, 90, p. 36083-36101 19 p.

Research output: Contribution to journal › Article

Exosomes
Nervous System
Cell Line
Survival
Neoplasms
5 Citations (Scopus)

Frequent HPV-independent p16/INK4A overexpression in head and neck cancer

Lechner, M., Chakravarthy, A. R., Walter, V., Masterson, L., Feber, A., Jay, A., Weinberger, P. M., McIndoe, R. A., Forde, C. T., Chester, K., Kalavrezos, N., O'Flynn, P., Forster, M., Jones, T. M., Vaz, F. M., Hayes, D. N. & Fenton, T. R., Aug 2018, In : Oral Oncology. 83, p. 32-37 6 p.

Research output: Contribution to journal › Article

Head and Neck Neoplasms
Squamous Cell Neoplasms
Protein Array Analysis
Head
Mutation

Genetically modified labeling policies: Moving forward or backward?

Borges, B. J. P., Arantes, O. M. N., Fernandes, A. A. R., Broach, J. & Fernandes, P. M. B., Nov 27 2018, In : Frontiers in Bioengineering and Biotechnology. 6, NOV, 181.

Research output: Contribution to journal › Review article

Genetically Modified Food
Food Labeling
Genetically Modified Organisms
Labeling
Food Supply
30 Citations (Scopus)

Genetics of blood lipids among ~300,000 multi-ethnic participants of the Million Veteran Program

The Geisinger-Regeneron DiscovEHR Collaboration, The VA Million Veteran Program, Global Lipids Genetics Consortium & Myocardial Infarction Genetics (MIGen) Consortium, Nov 1 2018, In : Nature Genetics. 50, 11, p. 1514-1523 10 p.

Research output: Contribution to journal › Article

Veterans
Lipids
Electronic Health Records
Abdominal Aortic Aneurysm
Hispanic Americans
67 Citations (Scopus)

Genome-wide Analyses Identify KIF5A as a Novel ALS Gene

ITALSGEN Consortium, Genomic Translation for ALS Care (GTAC) Consortium, ALS Sequencing Consortium, NYGC ALS Consortium, Answer ALS Foundation, Clinical Research in ALS and Related Disorders for Therapeutic Development (CReATe) Consortium, SLAGEN Consortium, French ALS Consortium & Project MinE ALS Sequencing Consortium, Mar 21 2018, In : Neuron. 97, 6, p. 1268-1283.e6

Research output: Contribution to journal › Article

Kinesin
Genome
Mutation
Genes
Genome-Wide Association Study
34 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 journal › Article

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

GM-CSF overexpression after influenza a virus infection prevents mortality and moderates M1-like airway monocyte/macrophage polarization

Halstead, E. S., Umstead, T. M., Davies, M. L., Kawasawa, Y. I., Silveyra, P., Howyrlak, J., Yang, L., Guo, W., Hu, S., Hewage, E. K. & Chroneos, Z. C., Jan 5 2018, In : Respiratory research. 19, 1, 1 p.

Research output: Contribution to journal › Article

Virus Diseases
Granulocyte-Macrophage Colony-Stimulating Factor
Orthomyxoviridae
Monocytes
Macrophages

Hepatitis C virus (HCV) RNA level in plasma and kidney tissue in HCV antibody-positive donors: Quantitative comparison

Shike, H., Kadry, Z., Imamura, Y., Greene, W., Riley III, T., Nathan, H. M., Hasz, R. D. & Jain, A., Sep 1 2018, In : Clinical Transplantation. 32, 9, e13358.

Research output: Contribution to journal › Article

Hepatitis C Antibodies
Hepacivirus
Tissue Donors
RNA
Kidney
1 Citation (Scopus)

Homozygosity for the SCN10A polymorphism rs6795970 is associated with hypoalgesic inflammatory bowel disease phenotype

Gonzalez-Lopez, E., Imamura, Y., Walter, V., Zhang, L., Koltun, W., Huang, X., Vrana, K. & Coates, M., Jan 1 2018, In : Frontiers in Medicine. 5, NOV, 324.

Research output: Contribution to journal › Article

Open Access
Inflammatory Bowel Diseases
Phenotype
Voltage-Gated Sodium Channels
Abdominal Pain
Single Nucleotide Polymorphism
25 Citations (Scopus)

Integrative detection and analysis of structural variation in cancer genomes

Dixon, J. R., Xu, J., Dileep, V., Zhan, Y., Song, F., Le, V. T., Yardımcı, G. G., Chakraborty, A., Bann, D. V., Wang, Y., Clark, R., Zhang, L., Yang, H., Liu, T., Iyyanki, S., An, L., Pool, C., Sasaki, T., Rivera-Mulia, J. C., Ozadam, H. & 17 others, Lajoie, B. R., Kaul, R., Buckley, M., Lee, K., Diegel, M., Pezic, D., Ernst, C., Hadjur, S., Odom, D. T., Stamatoyannopoulos, J. A., Broach, J. R., Hardison, R. C., Ay, F., Noble, W. S., Dekker, J., Gilbert, D. M. & Yue, F., Oct 1 2018, In : Nature Genetics. 50, 10, p. 1388-1398 11 p.

Research output: Contribution to journal › Article

Genome
Genomic Structural Variation
DNA Replication Timing
Neoplasms
Sequence Deletion
37 Citations (Scopus)

Integrative functional genomic analysis of human brain development and neuropsychiatric risks

BrainSpan Consortium, PsychENCODE Consortium & PsychENCODE Developmental Subgroup, Dec 14 2018, In : Science. 362, 6420, 1264.

Research output: Contribution to journal › Article

Open Access
Human Development
Epigenomics
Brain
Gene Regulatory Networks
Genes