• 500 University Drive

    17033 Hershey

    United States

Research Output 1975 2019

2015
1152 Citations (Scopus)

Comprehensive genomic characterization of head and neck squamous cell carcinomas

The Cancer Genome Atlas Network, Jan 29 2015, In : Nature. 517, 7536, p. 576-582 7 p.

Research output: Contribution to journalArticle

Mutation
Neoplasms
TNF Receptor-Associated Factor 3
cdc Genes
Atlases

Consistent testing for recurrent genomic aberrations

Walter, V., Wright, F. A. & Nobel, A. B., Dec 1 2015, In : Biometrika. 102, 4, p. 783-796 14 p.

Research output: Contribution to journalArticle

Markov Chains
Genome-Wide Association Study
Fourier Analysis
DNA Methylation
Aberrations
84 Citations (Scopus)

Epigenetic priming of enhancers predicts developmental competence of hESC-derived endodermal lineage intermediates

Wang, A., Yue, F., Li, Y., Xie, R., Harper, T., Patel, N. A., Muth, K., Palmer, J., Qiu, Y., Wang, J., Lam, D. K., Raum, J. C., Stoffers, D. A., Ren, B. & Sander, M., Apr 2 2015, In : Cell Stem Cell. 16, 4, p. 386-399 14 p.

Research output: Contribution to journalArticle

Epigenomics
Mental Competency
Chromatin
Transcription Factors
Stem Cells
862 Citations (Scopus)

Genomic Classification of Cutaneous Melanoma

The Cancer Genome Atlas Network, Jun 20 2015, In : Cell. 161, 7, p. 1681-1696 16 p.

Research output: Contribution to journalArticle

Melanoma
Skin
T-cells
Lymphocytes
Pathology
5 Citations (Scopus)

Global deletion of BCATm increases expression of skeletal muscle genes associated with protein turnover

Lynch, C. J., Kimball, S., Xu, Y., Salzberg, A. C. & Imamura, Y., Nov 1 2015, In : Physiological genomics. 47, 11, p. 569-580 12 p.

Research output: Contribution to journalArticle

Skeletal Muscle
Knockout Mice
Genes
Proteins
RNA Sequence Analysis
32 Citations (Scopus)
Abdominal Obesity
Sleep
Carbohydrates
Intra-Abdominal Fat
Fats
25 Citations (Scopus)

Habitual sleep variability, not sleep duration, is associated with caloric intake in adolescents

He, F., Bixler, E., Berg, A., Imamura, Y., Vgontzas, A., Fernandez-Mendoza, J., Yanosky, J. & Liao, D., Jul 1 2015, In : Sleep Medicine. 16, 7, p. 856-861 6 p.

Research output: Contribution to journalArticle

Energy Intake
Sleep
Snacks
Fats
Carbohydrates
98 Citations (Scopus)

Integrative analysis of haplotype-resolved epigenomes across human tissues

Leung, D., Jung, I., Rajagopal, N., Schmitt, A., Selvaraj, S., Lee, A. Y., Yen, C. A., Lin, S., Lin, Y., Qiu, Y., Xie, W., Yue, F., Hariharan, M., Ray, P., Kuan, S., Edsall, L., Yang, H., Chi, N. C., Zhang, M. Q., Ecker, J. R. & 1 others, Ren, B., Feb 19 2015, In : Nature. 518, 7539, p. 350-354 5 p.

Research output: Contribution to journalArticle

Haplotypes
Chromatin
Histone Code
Chromosomes
Human Genome
33 Citations (Scopus)

Loss of FOXA1 drives sexually dimorphic changes in urothelial differentiation and is an independent predictor of poor prognosis in bladder cancer

Reddy, O. L., Cates, J. M., Gellert, L. L., Crist, H., Yang, Z., Yamashita, H., Taylor, J. A., Smith, J. A., Chang, S. S., Cookson, M. S., You, C., Barocas, D. A., Grabowska, M. M., Ye, F., Wu, X. R., Yi, Y., Matusik, R. J., Kaestner, K. H., Clark, P. E. & Degraff, D., May 1 2015, In : American Journal of Pathology. 185, 5, p. 1385-1395 11 p., 1980.

Research output: Contribution to journalArticle

Keratin-14
Urinary Bladder Neoplasms
Urothelium
Knockout Mice
Urinary Bladder
51 Citations (Scopus)

Lymphoid neoplasia: A genome-wide association study of susceptibility to acute lymphoblastic leukemia in adolescents and young adults

Perez-Andreu, V., Roberts, K. G., Xu, H., Smith, C., Zhang, H., Yang, W., Harvey, R. C., Payne-Turner, D., Devidas, M., Cheng, I. M., Carroll, W. L., Heerema, N. A., Carroll, A. J., Raetz, E. A., Gastier-Foster, J. M., Marcucci, G., Bloomfield, C. D., Mrózek, K., Kohlschmidt, J., Stock, W. & 21 others, Kornblau, S. M., Konopleva, M., Paietta, E., Rowe, J. M., Luger, S. M., Tallman, M. S., Dean, M., Burchard, E. G., Torgerson, D. G., Yue, F., Wang, Y., Pui, C. H., Jeha, S., Relling, M. V., Evans, W. E., Gerhard, D. S., Loh, M. L., Willman, C. L., Hunger, S. P., Mullighan, C. G. & Yang, J. J., Jan 22 2015, In : Blood. 125, 4, p. 680-686 7 p.

Research output: Contribution to journalArticle

Genome-Wide Association Study
Precursor Cell Lymphoblastic Leukemia-Lymphoma
Young Adult
Genes
Polymorphism
7 Citations (Scopus)

Mapping the osteocytic cell response to fluid flow using RNA-Seq

Govey, P. M., Imamura, Y. & Donahue, H. J., Dec 16 2015, In : Journal of Biomechanics. 48, 16, p. 4327-4332 6 p.

Research output: Contribution to journalArticle

RNA
Flow of fluids
Osteocytes
Microarrays
Gene expression
34 Citations (Scopus)
Neuroendocrine Tumors
Mitosis
Pancreas
Staining and Labeling
Coloring Agents
9 Citations (Scopus)

Regorafenib with a fluoropyrimidine for metastatic colorectal cancer after progression on multiple 5-FU-containing combination therapies and regorafenib monotherapy

Marks, E. I., Tan, C., Zhang, J., Zhou, L., Yang, Z., Scicchitano, A. & El-Deiry, W. S., Dec 2 2015, In : Cancer Biology and Therapy. 16, 12, p. 1710-1719 10 p.

Research output: Contribution to journalArticle

Fluorouracil
Colorectal Neoplasms
Therapeutics
Mutation
regorafenib
1 Citation (Scopus)

Replicating sequencing-based association studies of rare variants

Liu, D. & Leal, S. M., Jan 1 2015, Assessing Rare Variation in Complex Traits: Design and Analysis of Genetic Studies. Springer New York, p. 201-213 13 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Exome
Genes
Chromosome Mapping
Genetic Models
Population Genetics
6 Citations (Scopus)

RNA sequencing reveals a slow to fast muscle fiber type transition after olanzapine infusion in rats

Lynch, C. J., Xu, Y., Hajnal, A., Salzberg, A. C. & Imamura, Y., Apr 20 2015, In : PloS one. 10, 4, e0123966.

Research output: Contribution to journalArticle

olanzapine
RNA Sequence Analysis
muscle fibers
Muscle
Rats
13 Citations (Scopus)

SEQMINER: An R-Package to Facilitate the Functional Interpretation of Sequence-Based Associations

Zhan, X. & Liu, D., Dec 1 2015, In : Genetic Epidemiology. 39, 8, p. 619-623 5 p.

Research output: Contribution to journalArticle

Databases
Computational Biology
Linkage Disequilibrium
Genetic Association Studies
Documentation
180 Citations (Scopus)

The high-grade (WHO G3) pancreatic neuroendocrine tumor category is morphologically and biologically heterogenous and includes both well differentiated and poorly differentiated neoplasms

Basturk, O., Yang, Z., Tang, L. H., Hruban, R. H., Adsay, V., McCall, C. M., Krasinskas, A. M., Jang, K. T., Frankel, W. L., Balci, S., Sigel, C. & Klimstra, D. S., Apr 28 2015, In : American Journal of Surgical Pathology. 39, 5, p. 683-690 8 p.

Research output: Contribution to journalArticle

Neuroendocrine Tumors
Neoplasms
Neuroendocrine Carcinoma
Survival
3 Citations (Scopus)
Cholangiocarcinoma
Carcinoma, Ductal, Breast
Differential Diagnosis
Estrogen Receptors
Breast Neoplasms
29 Citations (Scopus)

The yeast genome undergoes significant topological reorganization in quiescence

Rutledge, M. T., Russo, M., Belton, J. M., Dekker, J. & Broach, J. R., Sep 30 2015, In : Nucleic Acids Research. 43, 17, p. 8299-8313 15 p.

Research output: Contribution to journalArticle

Chromosomes
Yeasts
Genome
Centromere
Spindle Pole Bodies
2014
554 Citations (Scopus)

A comparative encyclopedia of DNA elements in the mouse genome

Yue, F., Cheng, Y., Breschi, A., Vierstra, J., Wu, W., Ryba, T., Sandstrom, R., Ma, Z., Davis, C., Pope, B. D., Shen, Y., Pervouchine, D. D., Djebali, S., Thurman, R. E., Kaul, R., Rynes, E., Kirilusha, A., Marinov, G. K., Williams, B. A., Trout, D. & 117 others, Amrhein, H., Fisher-Aylor, K., Antoshechkin, I., DeSalvo, G., See, L. H., Fastuca, M., Drenkow, J., Zaleski, C., Dobin, A., Prieto, P., Lagarde, J., Bussotti, G., Tanzer, A., Denas, O., Li, K., Bender, M. A., Zhang, M., Byron, R., Groudine, M. T., McCleary, D., Pham, L., Ye, Z., Kuan, S., Edsall, L., Wu, Y. C., Rasmussen, M. D., Bansal, M. S., Kellis, M., Keller Capone, C. A., Morrissey, C. S., Mishra, T., Jain, D., Dogan, N., Harris, R. S., Cayting, P., Kawli, T., Boyle, A. P., Euskirchen, G., Kundaje, A., Lin, S., Lin, Y., Jansen, C., Malladi, V. S., Cline, M. S., Erickson, D. T., Kirkup, V. M., Learned, K., Sloan, C. A., Rosenbloom, K. R., De Sousa, B. L., Beal, K., Pignatelli, M., Flicek, P., Lian, J., Kahveci, T., Lee, D., Kent, W. J., Santos, M. R., Herrero, J., Notredame, C., Johnson, A., Vong, S., Lee, K., Bates, D., Neri, F., Diegel, M., Canfield, T., Sabo, P. J., Wilken, M. S., Reh, T. A., Giste, E., Shafer, A., Kutyavin, T., Haugen, E., Dunn, D., Reynolds, A. P., Neph, S., Humbert, R., Hansen, R. S., De Bruijn, M., Selleri, L., Rudensky, A., Josefowicz, S., Samstein, R., Eichler, E. E., Orkin, S. H., Levasseur, D., Papayannopoulou, T., Chang, K. H., Skoultchi, A., Gosh, S., Disteche, C., Treuting, P., Wang, Y., Weiss, M. J., Blobel, G. A., Cao, X., Zhong, S., Wang, T., Good, P. J., Lowdon, R. F., Adams, L. B., Zhou, X. Q., Pazin, M. J., Feingold, E. A., Wold, B., Taylor, J., Mortazavi, A., Weissman, S. M., Stamatoyannopoulos, J. A., Snyder, M. P., Guigo, R., Gingeras, T. R., Gilbert, D. M., Hardison, R. C., Beer, M. A. & Ren, B., Nov 20 2014, In : Nature. 515, 7527, p. 355-364 10 p.

Research output: Contribution to journalArticle

Encyclopedias
Genome
Chromatin
DNA
Nucleic Acid Regulatory Sequences
27 Citations (Scopus)

A dynamic interplay of nucleosome and Msn2 binding regulates kinetics of gene activation and repression following stress

Elfving, N., Chereji, R. V., Bharatula, V., Björklund, S., Morozov, A. V. & Broach, J., Jan 1 2014, In : Nucleic acids research. 42, 9, p. 5468-5482 15 p.

Research output: Contribution to journalArticle

Nucleosomes
Transcriptional Activation
Gene Expression
Chromatin Immunoprecipitation
Transcription Factors
42 Citations (Scopus)

A splice variant of the human ion channel TRPM2 modulates neuroblastoma tumor growth through hypoxia-inducible factor (HIF)-1/2α

Chen, S., Hoffman, N. E., Shanmughapriy, S., Bao, L., Keefer, K., Conrad, K., Merali, S., Takahashi, Y., Abraham, T., Hirschler-Laszkiewicz, I., Wang, J. F., Zhang, X. Q., Song, J., Barrero, C., Shi, Y., Imamura, Y., Bayerl, M., Sun, T., Barbour, M., Wang, H-G. & 3 others, Madesh, M., Cheung, J. Y. & Miller, B., Jan 1 2014, In : Journal of Biological Chemistry. 289, 52, p. 36284-36302 19 p.

Research output: Contribution to journalArticle

Hypoxia-Inducible Factor 1
Neuroblastoma
Ion Channels
Tumors
Growth
1 Citation (Scopus)

BRAF mutation testing in solid tumors: A methodological comparison

Weyant, G. W., Wisotzkey, J. D., Benko, F. A. & Donaldson, K., Jan 1 2014, In : Journal of Molecular Diagnostics. 16, 5, p. 481-485 5 p.

Research output: Contribution to journalArticle

Alleles
Mutation
Neoplasms
Proto-Oncogenes
Multiplex Polymerase Chain Reaction
47 Citations (Scopus)

BRG1/SMARCA4 inactivation promotes non-small cell lung cancer aggressiveness by altering chromatin organization

Orvis, T., Hepperla, A., Walter, V., Song, S., Simon, J., Parker, J., Wilkerson, M. D., Desai, N., Major, M. B., Hayes, D. N., Davis, I. J. & Weissman, B., Nov 15 2014, In : Cancer Research. 74, 22, p. 6486-6498 13 p.

Research output: Contribution to journalArticle

Non-Small Cell Lung Carcinoma
Chromatin
Chromatin Assembly and Disassembly
Nucleosomes
Gene Expression
58 Citations (Scopus)

Cancer-derived mutations in KEAP1 impair NRF2 degradation but not ubiquitination

Hast, B. E., Cloer, E. W., Goldfarb, D., Li, H., Siesser, P. F., Yan, F., Walter, V., Zheng, N., Hayes, D. N. & Major, M. B., Feb 1 2014, In : Cancer Research. 74, 3, p. 808-817 10 p.

Research output: Contribution to journalArticle

Ubiquitination
Mutation
Neoplasms
Ubiquitin-Protein Ligases
Proteasome Endopeptidase Complex

Erratum: Molecular subtypes in head and neck cancer exhibit distinct patterns of chromosomal gain and loss of canonical cancer genes (PLoS ONE (2014) 9:1 DOI: 10.1371/annotation/e9ad5950-a048-4a44-8e26-d8b07a9d4bb8)

Walter, V., Yin, X., Wilkerson, M. D., Cabanski, C. R., Zhao, N., Du, Y., Ang, M. K., Hayward, M. C., Salazar, A. H., Hoadley, K. A., Fritchie, K., Sailey, C. G., Weissler, M. C., Shockley, W. W., Zanation, A. M., Hackman, T., Thorne, L. B., Funkhouser, W. D., Muldrew, K. L., Olshan, A. F. & 4 others, Randell, S. H., Wright, F. A., Shores, C. G. & Hayes, D. N., Jan 16 2014, In : PloS one. 9, 1, 1315.

Research output: Contribution to journalComment/debate

Neoplasm Genes
Head and Neck Neoplasms
neoplasms
genes
head and neck neoplasms

First North American case of Hemoglobin Shepherds Bush (β 74[E18] Gly → Asp) in a central Pennsylvania family

Paradise, S. L., Estep, L., Olson, J. & Donaldson, K., Jan 15 2014, In : BMC Clinical Pathology. 14, 1, 4.

Research output: Contribution to journalArticle

Viperidae
Hemoglobins
Gallbladder Diseases
Hemoglobinopathies
Hemolytic Anemia
12 Citations (Scopus)

Gene silencing associated with SWI/SNF complex loss during NSCLC development

Song, S., Walter, V., Karaca, M., Li, Y., Bartlett, C. S., Smiraglia, D. J., Serber, D., Sproul, C. D., Plass, C., Zhang, J., Hayes, D. N., Zheng, Y. & Weissman, B. E., Jan 1 2014, In : Molecular Cancer Research. 12, 4, p. 560-570 11 p.

Research output: Contribution to journalArticle

Gene Silencing
Non-Small Cell Lung Carcinoma
Methyltransferases
Epigenomics
Histone Deacetylase Inhibitors
50 Citations (Scopus)

Genetic heterogeneity of amyotrophic lateral sclerosis: Implications for clinical practice and research

Su, X. W., Broach, J., Connor, J., Gerhard, G. S. & Simmons, Z., Jan 1 2014, In : Muscle and Nerve. 49, 6, p. 786-803 18 p.

Research output: Contribution to journalArticle

Genetic Heterogeneity
Amyotrophic Lateral Sclerosis
Research
Clinical Trials
Exome
60 Citations (Scopus)

Hedgehog-GLI signaling inhibition suppresses tumor growth in squamous lung cancer

Huang, L., Walter, V., Hayes, D. N. & Onaitis, M., Jan 1 2014, In : Clinical Cancer Research. 20, 6, p. 1566-1575 10 p.

Research output: Contribution to journalArticle

Hedgehogs
Squamous Cell Carcinoma
Lung Neoplasms
Lung
Growth
909 Citations (Scopus)

Integrated Genomic Characterization of Papillary Thyroid Carcinoma

Agrawal, N., Akbani, R., Aksoy, B. A., Ally, A., Arachchi, H., Asa, S. L., Auman, J. T., Balasundaram, M., Balu, S., Baylin, S. B., Behera, M., Bernard, B., Beroukhim, R., Bishop, J. A., Black, A. D., Bodenheimer, T., Boice, L., Bootwalla, M. S., Bowen, J., Bowlby, R. & 223 others, Bristow, C. A., Brookens, R., Brooks, D., Bryant, R., Buda, E., Butterfield, Y. S. N., Carling, T., Carlsen, R., Carter, S. L., Carty, S. E., Chan, T. A., Chen, A. Y., Cherniack, A. D., Cheung, D., Chin, L., Cho, J., Chu, A., Chuah, E., Cibulskis, K., Ciriello, G., Clarke, A., Clayman, G. L., Cope, L., Copland, J. A., Covington, K., Danilova, L., Davidsen, T., Demchok, J. A., DiCara, D., Dhalla, N., Dhir, R., Dookran, S. S., Dresdner, G., Eldridge, J., Eley, G., El-Naggar, A. K., Eng, S., Fagin, J. A., Fennell, T., Ferris, R. L., Fisher, S., Frazer, S., Frick, J., Gabriel, S. B., Ganly, I., Gao, J., Garraway, L. A., Gastier-Foster, J. M., Getz, G., Gehlenborg, N., Ghossein, R., Gibbs, R. A., Giordano, T. J., Gomez-Hernandez, K., Grimsby, J., Gross, B., Guin, R., Hadjipanayis, A., Harper, H. A., Hayes, D. N., Heiman, D. I., Herman, J. G., Hoadley, K. A., Hofree, M., Holt, R. A., Hoyle, A. P., Huang, F. W., Huang, M., Hutter, C. M., Ideker, T., Iype, L., Jacobsen, A., Jefferys, S. R., Jones, C. D., Jones, S. J. M., Kasaian, K., Kebebew, E., Khuri, F. R., Kim, J., Kramer, R., Kreisberg, R., Kucherlapati, R., Kwiatkowski, D. J., Ladanyi, M., Lai, P. H., Laird, P. W., Lander, E., Lawrence, M. S., Lee, D., Lee, E., Lee, S., Lee, W., Leraas, K. M., Lichtenberg, T. M., Lichtenstein, L., Lin, P., Ling, S., Liu, J., Liu, W., Liu, Y., LiVolsi, V. A., Lu, Y., Ma, Y., Mahadeshwar, H. S., Marra, M. A., Mayo, M., McFadden, D. G., Meng, S., Meyerson, M., Mieczkowski, P. A., Miller, M., Mills, G., Moore, R. A., Mose, L. E., Mungall, A. J., Murray, B. A., Nikiforov, Y. E., Noble, M. S., Ojesina, A. I., Owonikoko, T. K., Ozenberger, B. A., Pantazi, A., Parfenov, M., Park, P. J., Parker, J. S., Paull, E. O., Pedamallu, C. S., Perou, C. M., Prins, J. F., Protopopov, A., Ramalingam, S. S., Ramirez, N. C., Ramirez, R., Raphael, B. J., Rathmell, W. K., Ren, X., Reynolds, S. M., Rheinbay, E., Ringel, M. D., Rivera, M., Roach, J., Robertson, A. G., Rosenberg, M. W., Rosenthal, M., Sadeghi, S., Saksena, G., Sander, C., Santoso, N., Schein, J. E., Schultz, N., Schumacher, S. E., Seethala, R. R., Seidman, J., Senbabaoglu, Y., Seth, S., Sharpe, S., Shaw, K. R. M., Shen, J. P., Shen, R., Sherman, S., Sheth, M., Shi, Y., Shmulevich, I., Sica, G. L., Simons, J. V., Sinha, R., Sipahimalani, P., Smallridge, R. C., Sofia, H. J., Soloway, M. G., Song, X., Sougnez, C., Stewart, C., Stojanov, P., Stuart, J. M., Sumer, S. O., Sun, Y., Tabak, B., Tam, A., Tan, D., Tang, J., Tarnuzzer, R., Taylor, B. S., Thiessen, N., Thorne, L., Thorsson, V., Tuttle, R. M., Umbricht, C. B., Van Den Berg, D. J., Vandin, F., Veluvolu, U., Verhaak, R. G. W., Vinco, M., Voet, D., Walter, V., Wang, Z., Waring, S., Weinberger, P. M., Weinhold, N., Weinstein, J. N., Weisenberger, D. J., Wheeler, D., Wilkerson, M. D., Wilson, J., Williams, M., Winer, D. A., Wise, L., Wu, J., Xi, L., Xu, A. W., Yang, L., Yang, L., Zack, T. I., Zeiger, M. A., Zeng, D., Zenklusen, J. C., Zhao, N., Zhang, H., Zhang, J., Zhang, J., Zhang, W., Zmuda, E. & Zou, L., Oct 23 2014, In : Cell. 159, 3, p. 676-690 15 p.

Research output: Contribution to journalArticle

Thyroid Neoplasms
Factor IX
Methylation
Pathology
Gene expression
46 Citations (Scopus)

Integrated RNA and DNA sequencing improves mutation detection in low purity tumors

Wilkerson, M. D., Cabanski, C. R., Sun, W., Hoadley, K. A., Walter, V., Mose, L. E., Troester, M. A., Hammerman, P. S., Parker, J. S., Perou, C. M. & Hayes, D. N., Jan 1 2014, In : Nucleic acids research. 42, 13

Research output: Contribution to journalArticle

RNA Sequence Analysis
Exome
DNA Sequence Analysis
Mutation
DNA
31 Citations (Scopus)

Laminar and temporal expression dynamics of coding and noncoding RNAs in the mouse neocortex

Fertuzinhos, S., Li, M., Imamura, Y., Ivic, V., Franjic, D., Singh, D., Crair, M. & Šestan, N., Jan 1 2014, In : Cell Reports. 6, 5, p. 938-950 13 p.

Research output: Contribution to journalArticle

Untranslated RNA
Neocortex
Messenger RNA
MicroRNAs
Biological Phenomena
103 Citations (Scopus)

Meta-analysis of gene-level tests for rare variant association

Liu, D., Peloso, G. M., Zhan, X., Holmen, O. L., Zawistowski, M., Feng, S., Nikpay, M., Auer, P. L., Goel, A., Zhang, H., Peters, U., Farrall, M., Orho-Melander, M., Kooperberg, C., Mcpherson, R., Watkins, H., Willer, C. J., Hveem, K., Melander, O., Kathiresan, S. & 1 others, Abecasis, G. R., Jan 1 2014, In : Nature Genetics. 46, 2, p. 200-204 5 p.

Research output: Contribution to journalArticle

Meta-Analysis
Genes
Exome
Genetic Association Studies
Sample Size
97 Citations (Scopus)

Poorly differentiated neuroendocrine carcinomas of the pancreas: A clinicopathologic analysis of 44 cases

Basturk, O., Tang, L., Hruban, R. H., Adsay, V., Yang, Z., Krasinskas, A. M., Vakiani, E., La Rosa, S., Jang, K. T., Frankel, W. L., Liu, X., Zhang, L., Giordano, T. J., Bellizzi, A. M., Chen, J. H., Shi, C., Allen, P., Reidy, D. L., Wolfgang, C. L., Saka, B. & 3 others, Rezaee, N., Deshpande, V. & Klimstra, D. S., Jan 1 2014, In : American Journal of Surgical Pathology. 38, 4, p. 437-447 11 p.

Research output: Contribution to journalArticle

Neuroendocrine Carcinoma
Pancreas
Large Cell Carcinoma
Neuroendocrine Tumors
Acinar Cell Carcinoma
97 Citations (Scopus)

Temporal specification and bilaterality of human neocortical topographic gene expression

Pletikos, M., Sousa, A. M. M., Sedmak, G., Meyer, K. A., Zhu, Y., Cheng, F., Li, M., Imamura, Y. & Šestan, N., Jan 22 2014, In : Neuron. 81, 2, p. 321-332 12 p.

Research output: Contribution to journalArticle

Neocortex
Macaca
Human Development
Gene Expression
Transcriptome
13 Citations (Scopus)

The circadian pattern of cardiac autonomic modulation and obesity in adolescents

Rodríguez-Colón, S., He, F., Bixler, E., Fernandez-Mendoza, J., Vgontzas, A., Berg, A., Imamura, Y. & Liao, D., Dec 5 2014, In : Clinical Autonomic Research. 24, 6, p. 265-273 9 p.

Research output: Contribution to journalArticle

Pediatric Obesity
Heart Rate
Obesity
Population
Electrocardiography
327 Citations (Scopus)

Topologically associating domains are stable units of replication-timing regulation

Pope, B. D., Ryba, T., Dileep, V., Yue, F., Wu, W., Denas, O., Vera, D. L., Wang, Y., Hansen, R. S., Canfield, T. K., Thurman, R. E., Cheng, Y., Gülsoy, G., Dennis, J. H., Snyder, M. P., Stamatoyannopoulos, J. A., Taylor, J., Hardison, R. C., Kahveci, T., Ren, B. & 1 others, Gilbert, D. M., Nov 20 2014, In : Nature. 515, 7527, p. 402-405 4 p.

Research output: Contribution to journalArticle

Replicon
Chromatin
Chromosome Structures
Chromosomes, Human, Pair 7
Heterochromatin
2013
11 Citations (Scopus)

Circulating tumor cells are associated with diffuse spread in stage IV colorectal cancer patients

Kaifi, J. T., Kunkel, M., Zhu, J., Dicker, D. T., Gusani, N. J., Yang, Z., Sarwani, N. E., Li, G., Kimchi, E. T., Staveley-O'Carroll, K. F. & El-Deiry, W. S., Dec 1 2013, In : Cancer Biology and Therapy. 14, 12, p. 1174-1181 8 p.

Research output: Contribution to journalArticle

Circulating Neoplastic Cells
Colorectal Neoplasms
Neoplasm Metastasis
Cell Count
Lung
5 Citations (Scopus)

Contradictory KRAS mutation test results in a patient with metastatic colon cancer: A clinical dilemma in the era of personalized medicine

Lamparella, N. E., Saroya, B. S., Yang, Z., Sarwani, N. & El-Deiry, W. S., Aug 1 2013, In : Cancer Biology and Therapy. 14, 8, p. 699-702 4 p.

Research output: Contribution to journalArticle

Precision Medicine
Colonic Neoplasms
Mutation
irinotecan
Oncogenes
229 Citations (Scopus)

Epigenetic memory at embryonic enhancers identified in DNA methylation maps from adult mouse tissues

Hon, G. C., Rajagopal, N., Shen, Y., McCleary, D. F., Yue, F., Dang, M. D. & Ren, B., Oct 1 2013, In : Nature Genetics. 45, 10, p. 1198-1206 9 p.

Research output: Contribution to journalArticle

DNA Methylation
Epigenomics
Embryonic Development
Histone Code
Gene Expression
3 Citations (Scopus)

Erratum: Molecular subtypes in head and neck cancer exhibit distinct patterns of chromosomal gain and loss of canonical cancer genes (PLoS ONE (2013) 8:7 DOI:10.1371/annotation/b42f61c5-cb7e-49ca-8cd6-6e1f7903ad08)

Walter, V., Yin, X., Wilkerson, M. D., Cabanski, C. R., Zhao, N., Du, Y., Ang, M. K., Hayward, M. C., Salazar, A. H., Hoadley, K. A., Fritchie, K., Sailey, C. J., Weissler, M. C., Shockley, W. W., Zanation, A. M., Hackman, T., Thorne, L. B., Funkhouser, W. D., Muldrew, K. L., Olshan, A. F. & 4 others, Randell, S. H., Wright, F. A., Shores, C. G. & Hayes, D. N., Jul 16 2013, In : PloS one. 8, 7, A2275.

Research output: Contribution to journalComment/debate

Neoplasm Genes
Head and Neck Neoplasms
neoplasms
genes
head and neck neoplasms
6 Citations (Scopus)

FOLFIRI plus dulanermin (rhApo2L/TRAIL) in a patient with BRAF-mutant metastatic colon cancer

Lim, B., Scicchitano, A., Beachler, C., Gusani, N. J., Sarwani, N., Yang, Z., Staveley-O'Carroll, K., Ashkenazi, A., Portera, C. & El-Deiry, W. S., Aug 1 2013, In : Cancer Biology and Therapy. 14, 8, p. 711-719 9 p.

Research output: Contribution to journalArticle

Colonic Neoplasms
Colorectal Neoplasms
Survival
Neoplasms
human TNFSF10 protein
34 Citations (Scopus)

Gastroenteropancreatic neuroendocrine neoplasms: Historical context and current issues

Yang, Z., Tang, L. H. & Klimstra, D. S., Aug 1 2013, In : Seminars in Diagnostic Pathology. 30, 3, p. 186-196 11 p.

Research output: Contribution to journalArticle

Neuroendocrine Tumors
Neoplasms
Neuroendocrine Cells
Neurosecretory Systems
Gastro-enteropancreatic neuroendocrine tumor
8 Citations (Scopus)

High hydrostatic pressure activates gene expression that leads to ethanol production enhancement in a Saccharomyces cerevisiae distillery strain

Bravim, F., Lippman, S. I., Da Silva, L. F., Souza, D. T., Fernandes, A. A. R., Masuda, C. A., Broach, J. & Fernandes, P. M. B., Mar 1 2013, In : Applied Microbiology and Biotechnology. 97, 5, p. 2093-2107 15 p.

Research output: Contribution to journalArticle

Hydrostatic Pressure
Fermentation
Saccharomyces cerevisiae
Ethanol
Gene Expression

Identification of Recurrent DNA Copy Number Aberrations in Tumors

Walter, V., Nobel, A. B., Hayes, D. N. & Wright, F. A., Apr 8 2013, Statistical Diagnostics for Cancer: Analyzing High-Dimensional Data. Wiley-VCH, Vol. 3. p. 239-260 22 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Aberrations
Tumors
DNA
Neoplasms
Genes
20 Citations (Scopus)

Identifying rare variants associated with complex traits via sequencing

Li, B., Liu, D. & Leal, S. M., Jan 1 2013, In : Current protocols in human genetics. SUPPL.78, 1.26.

Research output: Contribution to journalArticle

Genome
Genome-Wide Association Study
Technology
Genes
Surveys and Questionnaires
122 Citations (Scopus)

Inherited GATA3 variants are associated with Ph-like childhood acute lymphoblastic leukemia and risk of relapse

Perez-Andreu, V., Roberts, K. G., Harvey, R. C., Yang, W., Cheng, C., Pei, D., Xu, H., Gastier-Foster, J., Shuyu, E., Lim, J. Y. S., Chen, I. M., Fan, Y., Devidas, M., Borowitz, M. J., Smith, C., Neale, G., Burchard, E. G., Torgerson, D. G., Klussmann, F. A., Villagran, C. R. N. & 18 others, Winick, N. J., Camitta, B. M., Raetz, E., Wood, B., Yue, F., Carroll, W. L., Larsen, E., Bowman, W. P., Loh, M. L., Dean, M., Bhojwani, D., Pui, C. H., Evans, W. E., Relling, M. V., Hunger, S. P., Willman, C. L., Mullighan, C. G. & Yang, J. J., Dec 1 2013, In : Nature Genetics. 45, 12, p. 1494-1498 5 p.

Research output: Contribution to journalArticle

Precursor Cell Lymphoblastic Leukemia-Lymphoma
Recurrence
Odds Ratio
Philadelphia Chromosome
Gene Rearrangement
131 Citations (Scopus)

Molecular Subtypes in Head and Neck Cancer Exhibit Distinct Patterns of Chromosomal Gain and Loss of Canonical Cancer Genes

Walter, V., Yin, X., Wilkerson, M. D., Cabanski, C. R., Zhao, N., Du, Y., Ang, M. K., Hayward, M. C., Salazar, A. H., Hoadley, K. A., Fritchie, K., Sailey, C. G., Weissler, M. C., Shockley, W. W., Zanation, A. M., Hackman, T., Thorne, L. B., Funkhouser, W. D., Muldrew, K. L., Olshan, A. F. & 4 others, Randell, S. H., Wright, F. A., Shores, C. G. & Hayes, D. N., Feb 22 2013, In : PloS one. 8, 2, e56823.

Research output: Contribution to journalArticle

Papillomaviridae
papilloma
Neoplasm Genes
squamous cell carcinoma
Head and Neck Neoplasms
34 Citations (Scopus)

Noise and interlocking signaling pathways promote distinct transcription factor dynamics in response to different stresses

Petrenko, N., Chereji, R. V., McClean, M. N., Morozov, A. V. & Broach, J., Jun 15 2013, In : Molecular biology of the cell. 24, 12, p. 2045-2057 13 p.

Research output: Contribution to journalArticle

Noise
Transcription Factors
Mitogen-Activated Protein Kinase Phosphatases
Protein Phosphatase 1
ras Proteins