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Research Output 1975 2019

2012
274 Citations (Scopus)

Nutritional control of growth and development in yeast

Broach, J., Sep 1 2012, In : Genetics. 192, 1, p. 73-105 33 p.

Research output: Contribution to journalReview article

Growth and Development
Yeasts
Nitrogen Compounds
Sugar Acids
ras Proteins
41 Citations (Scopus)

Regulation of Yeast Pyruvate Kinase by Ultrasensitive Allostery Independent of Phosphorylation

Xu, Y. F., Zhao, X., Glass, D. S., Absalan, F., Perlman, D. H., Broach, J. R. & Rabinowitz, J. D., Oct 12 2012, In : Molecular cell. 48, 1, p. 52-62 11 p.

Research output: Contribution to journalArticle

Pyruvate Kinase
Yeasts
Phosphorylation
Glucose
Phosphoenolpyruvate
2338 Citations (Scopus)

Topological domains in mammalian genomes identified by analysis of chromatin interactions

Dixon, J. R., Selvaraj, S., Yue, F., Kim, A., Li, Y., Shen, Y., Hu, M., Liu, J. S. & Ren, B., May 17 2012, In : Nature. 485, 7398, p. 376-380 5 p.

Research output: Contribution to journalArticle

Chromatin
Genome
Chromosomes
Retroelements
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
230 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

Genes
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
35 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
130 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
132 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
36 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. R., 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
32 Citations (Scopus)

Nucleotide degradation and ribose salvage in yeast

Xu, Y. F., Létisse, F., Absalan, F., Lu, W., Kuznetsova, E., Brown, G., Caudy, A. A., Yakunin, A. F., Broach, J. R. & Rabinowitz, J. D., Jan 1 2013, In : Molecular Systems Biology. 9, 1, 665.

Research output: Contribution to journalArticle

Salvaging
Ribose
ribose
Nucleotides
Phosphate
26 Citations (Scopus)

Off-label use of cetuximab plus sorafenib and panitumumab plus regorafenib to personalize therapy for a patient with V600E BRAF-mutant metastatic colon cancer

Al-Marrawi, M. Y., Saroya, B. S., Brennan, M. C., Yang, Z., Dykes, T. & El-Deiry, W. S., Aug 1 2013, In : Cancer Biology and Therapy. 14, 8, p. 703-710 8 p.

Research output: Contribution to journalArticle

Off-Label Use
Colonic Neoplasms
Colorectal Neoplasms
Therapeutics
Clinical Trials
13 Citations (Scopus)

Predicting brain activity using a Bayesian spatial model

Derado, G., Bowman, F. D. & Zhang, L., Aug 1 2013, In : Statistical Methods in Medical Research. 22, 4, p. 382-397 16 p.

Research output: Contribution to journalArticle

Functional Neuroimaging
Spatial Model
Bayesian Model
Neuroimaging
Positron-Emission Tomography
14 Citations (Scopus)

Predicting therapy response in live tumor cells isolated with the flexible micro spring array device

Gallant, J. N., Matthew, E. M., Cheng, H., Harouaka, R., Lamparella, N. E., Kunkel, M., Yang, Z., Harvey, H. A., Cream, L. V., Kumar, S. M., Robertson, G. P., Zheng, S., Drabick, J. J., Truica, C. I. & El-Deiry, W. S., Jul 1 2013, In : Cell Cycle. 12, 13, p. 2132-2143 12 p.

Research output: Contribution to journalArticle

Circulating Neoplastic Cells
Equipment and Supplies
Neoplasms
Lab-On-A-Chip Devices
Therapeutics
43 Citations (Scopus)

The Yeast Environmental Stress Response Regulates Mutagenesis Induced by Proteotoxic Stress

Shor, E., Fox, C. A. & Broach, J., Aug 1 2013, In : PLoS genetics. 9, 8, e1003680.

Research output: Contribution to journalArticle

environmental stress
mutagenesis
Mutagenesis
yeast
stress response
2014
575 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, 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. R., May 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
49 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
59 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

Genes

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., Apr 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
51 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
61 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
934 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., 2014, In : Nucleic acids research. 42, 13, p. e107

Research output: Contribution to journalArticle

RNA Sequence Analysis
Exome
DNA Sequence Analysis
Mutation
DNA
33 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
105 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
99 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
99 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
14 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
336 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
2015
27 Citations (Scopus)

Abdominal obesity and metabolic syndrome burden in adolescents-penn state children cohort study

He, F., Rodriguez-Colon, S., Fernandez-Mendoza, J., Vgontzas, A. N., Bixler, E. O., Berg, A., Imamura Kawasawa, Y., Sawyer, M. D. & Liao, D., Jan 1 2015, In : Journal of Clinical Densitometry. 18, 1, p. 30-36 7 p.

Research output: Contribution to journalArticle

Abdominal Obesity
Cohort Studies
Insulin Resistance
Subcutaneous Fat
X-Rays
15 Citations (Scopus)

Aberrant over-expression of TRPM7 ion channels in pancreatic cancer: Required for cancer cell invasion and implicated in tumor growth and metastasis

Yee, N. S., Kazi, A. A., Li, Q., Yang, Z., Berg, A. & Yee, R. K., Jan 1 2015, In : Biology Open. 4, 4, p. 507-514 8 p.

Research output: Contribution to journalArticle

pancreatic neoplasms
cell invasion
ion channels
Pancreatic Neoplasms
Ion Channels
2 Citations (Scopus)

A case of heterogeneous sensitivity to panitumumab in cetuximab-refractory colorectal adenocarcinoma metastases

Marks, E., Rizvi, S. M., Sarwani, N., Yang, Z. & El-Deiry, W. S., Mar 1 2015, In : Cancer Biology and Therapy. 16, 3, p. 377-382 6 p.

Research output: Contribution to journalArticle

Adenocarcinoma
Neoplasm Metastasis
Liver
Disease Progression
Anti-Idiotypic Antibodies
12 Citations (Scopus)
Gastric Bypass
Intravenous Infusions
Anemia
Iron
Blood Cell Count
3 Citations (Scopus)

Autoimmune Pancreatitis: A Diagnostic Challenge for the Clinician

Chintanaboina, J., Yang, Z. & Mathew, A., Sep 5 2015, In : Southern Medical Journal. 108, 9, p. 579-589 11 p.

Research output: Contribution to journalArticle

Pancreatitis
Pancreatic Neoplasms
Remission Induction
Obstructive Jaundice
Azathioprine
26 Citations (Scopus)

Circulating tumor cell isolation during resection of colorectal cancer lung and liver metastases: A prospective trial with different detection techniques

Kaifi, J. T., Kunkel, M., Das, A., Harouaka, R. A., Dicker, D. T., Li, G., Zhu, J., Clawson, G., Yang, Z., Reed, M. F., Gusani, N. J., Kimchi, E. T., Staveley-O’Carroll, K. F., Zheng, S. & El-Deiry, W. S., Jan 1 2015, In : Cancer Biology and Therapy. 16, 5, p. 699-708 10 p.

Research output: Contribution to journalArticle

Circulating Neoplastic Cells
Cell Separation
Liver Neoplasms
Colorectal Neoplasms
Lung Neoplasms
10 Citations (Scopus)

Circulating tumor cell levels are elevated in colorectal cancer patients with high tumor burden in the liver

Kaifi, J. T., Kunkel, M., Dicker, D. T., Joude, J., Allen, J. E., Das, A., Zhu, J., Yang, Z., Sarwani, N., Li, G., Staveley-O’Carroll, K. F. & El-Deiry, W. S., Jan 1 2015, In : Cancer Biology and Therapy. 16, 5, p. 690-698 9 p.

Research output: Contribution to journalArticle

Circulating Neoplastic Cells
Tumor Burden
Colorectal Neoplasms
Liver
Neoplasms
23 Citations (Scopus)

Clinical significance of high c-MYC and low MYCBP2 expression and their association with Ikaros dysfunction in adult acute lymphoblastic leukemia

Ge, Z., Guo, X., Li, J., Hartman, M., Kawasawa, Y. I., Dovat, S. & Song, C., Jan 1 2015, In : Oncotarget. 6, 39, p. 42300-42311 12 p.

Research output: Contribution to journalArticle

Precursor Cell Lymphoblastic Leukemia-Lymphoma
Carrier Proteins
Precursor T-Cell Lymphoblastic Leukemia-Lymphoma
Messenger RNA
Ubiquitin-Protein Ligases
14 Citations (Scopus)

Clinico-pathological correlation of serial measurement of circulating tumor cells in 24 metastatic colorectal cancer patients receiving chemotherapy reveals interpatient heterogeneity correlated with CEA levels but independent of KRAS and BRAF mutation

Das, A., Kunkel, M., Joudeh, J., Dicker, D. T., Scicchitano, A., Allen, J. E., Sarwani, N., Yang, Z., Kaifi, J., Zhu, J., Liao, J. & El-Deiry, W. S., Jan 1 2015, In : Cancer Biology and Therapy. 16, 5, p. 709-713 5 p.

Research output: Contribution to journalArticle

Circulating Neoplastic Cells
Colorectal Neoplasms
Antigens
Drug Therapy
Mutation
22 Citations (Scopus)

Combined targeted DNA sequencing in Non-Small Cell Lung Cancer (NSCLC) using UNCseq and NGScopy, and RNA sequencing using UNCqeR for the detection of genetic aberrations in NSCLC

Zhao, X., Wang, A., Walter, V., Patel, N. M., Eberhard, D. A., Hayward, M. C., Salazar, A. H., Jo, H., Soloway, M. G., Wilkerson, M. D., Parker, J. S., Yin, X., Zhang, G., Siegel, M. B., Rosson, G. B., Earp, H. S., Sharpless, N. E., Gulley, M. L., Weck, K. E., Hayes, D. N. & 1 others, Moschos, S. J., Jun 15 2015, In : PloS one. 10, 6, e0129280.

Research output: Contribution to journalArticle

RNA Sequence Analysis
lung neoplasms
Aberrations
DNA Sequence Analysis
Non-Small Cell Lung Carcinoma
1239 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