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Research Output

2014

Prior robust empirical Bayes inference for large-scale data by conditioning on rank with application to microarray data

Liao, J. G., Mcmurry, T. & Berg, A., Jan 1 2014, In : Biostatistics. 15, 1, p. 63-73 11 p.

Research output: Contribution to journalArticle

4 Scopus citations
66 Scopus citations

Single nucleotide polymorphisms in osteogenic genes in atrophic delayed fracture-healing: A preliminary investigation

Sathyendra, V., Donahue, H. J., Vrana, K., Berg, A., Fryzel, D., Gandhi, J. & Reid, J., Aug 6 2014, In : Journal of Bone and Joint Surgery - American Volume. 96, 15, p. 1242-1248 7 p.

Research output: Contribution to journalArticle

7 Scopus citations

Single nucleotide polymorphisms of the tcdC gene and presence of the binary toxin gene predict recurrent episodes of Clostridium difficile infection

Stewart, D. B., Berg, A. S. & Hegarty, J. P., Aug 2014, In : Annals of surgery. 260, 2, p. 299-304 6 p.

Research output: Contribution to journalArticle

8 Scopus citations
2 Scopus citations

Social disadvantage, genetic sensitivity, and children's telomere length

Mitchell, C., Hobcraft, J., McLanahan, S. S., Siegeld, S. R., Berg, A., Brooks-Gunn, J., Garfinkel, I. & Notterman, D., Apr 22 2014, In : Proceedings of the National Academy of Sciences of the United States of America. 111, 16, p. 5944-5949 6 p.

Research output: Contribution to journalArticle

Open Access
145 Scopus citations

T-cell activation Rho GTPase-activating protein expression varies with inflammation location and severity in Crohn's disease

Connelly, T. M., Berg, A. S., Harris, L. R., Hegarty, J. P., Ruggiero, F. M., Deiling, S. M., Brinton, D. L. & Koltun, W. A., Aug 2014, In : Journal of Surgical Research. 190, 2, p. 457-464 8 p.

Research output: Contribution to journalArticle

12 Scopus citations

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

15 Scopus citations

The NFκB inhibitor, SN50, induces differentiation of glioma stem cells and suppresses their oncogenic phenotype

Zhang, L., Ren, X., Cheng, Y., Liu, X., Allen, J. E., Zhang, Y., Yuan, Y., Huang, S. Y., Yang, W., Berg, A., Webb, B. S., Connor, J., Liu, C. G., Lu, Z., El-Deiry, W. S. & Yang, J. M., May 2014, In : Cancer Biology and Therapy. 15, 5, p. 602-611 10 p.

Research output: Contribution to journalArticle

10 Scopus citations

The TNFSF15 gene single nucleotide polymorphism rs7848647 is associated with surgical diverticulitis

Connelly, T. M., Berg, A., Hegarty, J. P., Deiling, S., Brinton, D., Poritz, L. & Koltun, W., Jan 1 2014, In : Annals of surgery. 259, 6, p. 1132-1137 6 p.

Research output: Contribution to journalArticle

40 Scopus citations

Ulcerative colitis neoplasia is not associated with common inflammatory bowel disease single-nucleotide polymorphisms

Connelly, T. M., Berg, A. S., Harris, L. R., Brinton, D. L., Hegarty, J. P., Deiling, S. M., Stewart, D. B. & Koltun, W. A., Aug 2014, In : Surgery (United States). 156, 2, p. 253-262 10 p.

Research output: Contribution to journalArticle

9 Scopus citations
2013

A single nucleotide polymorphism in the STAT5 gene favors colonic as opposed to small-bowel inflammation in crohn's disease

Connelly, T. M., Koltun, W., Berg, A., Hegarty, J. P., Brinton, D., Deiling, S., Poritz, L. & Stewart, D., Sep 1 2013, In : Diseases of the Colon and Rectum. 56, 9, p. 1068-1074 7 p.

Research output: Contribution to journalArticle

8 Scopus citations

Assessing the impact of the NIH ctsa program on institutionally sponsored clinical trials

Liu, G., Chen, G., Sinoway, L. & Berg, A., Jun 1 2013, In : Clinical and Translational Science. 6, 3, p. 196-200 5 p.

Research output: Contribution to journalArticle

4 Scopus citations

Association of dietary and supplemental folate intake and polymorphisms in three FOCM pathway genes with colorectal cancer in a population-based case-control study

Ashmore, J. H., Lesko, S. M., Muscat, J. E., Gallagher, C. J., Berg, A. S., Miller, P. E., Hartman, T. J. & Lazarus, P., Oct 1 2013, In : Genes Chromosomes and Cancer. 52, 10, p. 945-953 9 p.

Research output: Contribution to journalArticle

9 Scopus citations

Chronic Use of PPI and H2 Antagonists Decreases the Risk of Pouchitis After IPAA for Ulcerative Colitis

Poritz, L., Sehgal, R., Berg, A., Laufenberg Puopolo, L. J., Choi, C. & Williams, E., Mar 1 2013, In : Journal of Gastrointestinal Surgery. 17, 6, p. 1027-1031 5 p.

Research output: Contribution to journalArticle

10 Scopus citations

Effect of varenicline on individual nicotine withdrawal symptoms: A combined analysis of eight randomized, placebo-controlled trials

Foulds, J., Russ, C., Yu, C. R., Zou, K. H., Galaznik, A., Franzon, M., Berg, A. & Hughes, J. R., Nov 1 2013, In : Nicotine and Tobacco Research. 15, 11, p. 1849-1857 9 p.

Research output: Contribution to journalArticle

29 Scopus citations

Focused, high accuracy 5-methylcytosine quantitation with base resolution by benchtop next-generation sequencing

Masser, D. R., Berg, A. & Freeman, W. M., Oct 16 2013, In : Epigenetics and Chromatin. 6, 1, 33.

Research output: Contribution to journalArticle

61 Scopus citations

Identification of Aurora Kinase B and Wee1-Like Protein Kinase as Downstream Targets of V600EB-RAF in Melanoma

Sharma, A., Madhunapantula, S. V., Gowda, R., Berg, A., Neves, R. I. & Robertson, G. P., Apr 1 2013, In : American Journal of Pathology. 182, 4, p. 1151-1162 12 p.

Research output: Contribution to journalArticle

26 Scopus citations
2 Scopus citations

Molecular phylogeography of a human autosomal skin color locus under natural selection

Canfield, V. A., Berg, A., Peckins, S., Wentzel, S. M., Ang, K. C., Oppenheimer, S. & Cheng, K. C., Nov 2013, In : G3: Genes, Genomes, Genetics. 3, 11, p. 2059-2067 9 p.

Research output: Contribution to journalArticle

10 Scopus citations

NOD2 mutations affect muramyl dipeptide stimulation of human B lymphocytes and interact with other IBD-associated genes

Lin, Z., Hegarty, J. P., John, G., Berg, A., Wang, Z., Sehgal, R., Pastor, D. M., Wang, Y., Harris, L. R., Poritz, L. S., Schreiber, S. & Koltun, W. A., Sep 1 2013, In : Digestive Diseases and Sciences. 58, 9, p. 2599-2607 9 p.

Research output: Contribution to journalArticle

8 Scopus citations

Predicting Recurrence of C. difficile Colitis Using Bacterial Virulence Factors: Binary Toxin Is the Key

Stewart, D., Berg, A. & Hegarty, J., Jan 1 2013, In : Journal of Gastrointestinal Surgery. 17, 1, p. 118-125 8 p.

Research output: Contribution to journalArticle

64 Scopus citations

Talactoferrin alfa versus placebo in patients with refractory advanced non-small-cell lung cancer (FORTIS-M trial)

Ramalingam, S., Crawford, J., Chang, A., Manegold, C., Perez-Soler, R., Douillard, J. Y., Thatcher, N., Barlesi, F., Owonikoko, T., Wang, Y., Pultar, P., Zhu, J., Malik, R., Malik Giaccone, R., Della-Fiorentina, S., Begbie, S., Jennens, R., Dass, J., Pittman, K., Ivanova, N. & 173 others, Koynova, T., Petrov, P., Tomova, A., Tzekova, V., Couture, F., Hirsh, V., Burkes, R., Sangha, R., Ambrus, M., Janaskova, T., Musil, J., Novotny, J., Zatloukal, P., Jakesova, J., Klenha, K., Roubec, J., Vanasek, J., Fayette, J., Barlesi, F., Bennouna-Louridi, J., Chouaid, C., Mazières, J., Vallerand, H., Robinet, G., Souquet, P. J., Spaeth, D., Schott, R., Lena, H., Martinet, Y., Kouri, C. E., Baize, N., Scherpereel, A., Molinier, O., Fuchs, F., Josten, K. M., Manegold, C., Marschner, N., Schneller, F., Overbeck, T., Thomas, M., von Pawel, J., Reck Schuette, M., Hagen, V., Schneider, C. P., Georgoulias, V., Varthalitis, I., Zarogoulidis, K., Syrigos, K., Papandreou, C., Bocskei, C., Csanky, E., Juhasz, E., Losonczy, G., Mark, Z., Molnar, I., Papai-Szekely, Z., Tehenes, S., Vinkler, I., Almel, S., Bakshi, A., Bondarde, S., Maru, A., Pathak, A., Pedapenki, R. M., Prasad, K., Prasad, S. V. S. S., Kilara, N., Gorijavolu, D., Deshmukh, C. D., John, S., Sharma, L. M., Amoroso, D., Bajetta, E., Bidoli, P., Bonetti, A., De Marinis, F., Maio, M., Passalacqua, R., Cascinu, S., Bearz, A., Bitina, M., Brize, A., Purkalne, G., Skrodele, M., Baba, A. A., Ratnavelu, K., Saw, M. H., Samson-Fernando, M. C., Ladrera, G. E., Jassem, J., Koralewski, P., Sikorska, L., Serwatowski, P., Krzakowski, M., Cebotaru, C., Filip, D., Ganea-Motan, D. E., Ianuli, C. H., Manolescu, I. G., Udrea, A., Burdaeva, O., Byakhov, M., Filippov, A., Lazarev, S., Mosin, I., Orlov, S., Udovitsa, D., Khorinko, A., Protsenko, S., Chang, A., Lim, H. L., Tan, Y. O., Tan, E. H., Bastus Piulats, R., Garcia-Foncillas, J., Valdivia, J., de Castro, J., Domine Gomez, M., Kim, S. W., Lee, J. S., Kim, H. K., Lee, J. S., Shin, S. W., Kim, D. W., Kim, Y. C., Park, K. C., Chang, C. S., Chang, G. C., Goan, Y. G., Su, W. C., Tsai, C. M., Kuo, H. P., Benekli, M., Demir, G., Gokmen, E., Sevinc, A., Crawford, J., Giaccone, G., Haigentz, M., Owonikoko, T., Agarwal, M., Pandit, S., Araujo, R., Vrindavanam, N., Bonomi, P., Berg, A., Wade, J., Bloom, R., Amin, B., Camidge, R., Hill, D., Rarick, M., Flynn, P., Klein, L., Lo Russo, K., Neubauer, M., Richards, P., Ruxer, R., Savin, M., Weckstein, D., Rosenberg, R., Whittaker, T., Richards Berry, D., Ottensmeier, C., Dangoor, A., Steele, N., Summers, Y., Rankin, E., Rowley, K., Giridharan, S., Kristeleit, H., Humber, C. & Taylor, P., Nov 1 2013, In : Annals of Oncology. 24, 11, p. 2875-2880 6 p., mdt371.

Research output: Contribution to journalArticle

33 Scopus citations

The effect of copy number variation in the phase II detoxification genes UGT2B17 and UGT2B28 on colorectal cancer risk

Angstadt, A. Y., Berg, A., Zhu, J., Miller, P., Hartman, T. J., Lesko, S. M., Muscat, J. E., Lazarus, P. & Gallagher, C. J., Jul 1 2013, In : Cancer. 119, 13, p. 2477-2485 9 p.

Research output: Contribution to journalArticle

34 Scopus citations
2012

Circulating tumor cells in melanoma patients

Clawson, G. A., Kimchi, E., Patrick, S. D., Xin, P., Harouaka, R., Zheng, S., Berg, A., Schell, T., Staveley-O'Carroll, K. F., Neves, R. I., Mosca, P. J. & Thiboutot, D., Jul 19 2012, In : PloS one. 7, 7, e41052.

Research output: Contribution to journalArticle

46 Scopus citations

Comparison and evaluation of network clustering algorithms applied to genetic interaction networks

Hou, L., Wang, L., Berg, A., Qian, M., Zhu, Y., Li, F. & Deng, M., Jan 1 2012, In : Frontiers in Bioscience - Elite. 4 E, 6, p. 2150-2161 12 p.

Research output: Contribution to journalArticle

1 Scopus citations

Electronic cigarettes: A response to Leelavathi and das

Foulds, J., Veldheer, S. & Berg, A., Apr 1 2012, In : International Journal of Clinical Practice. 66, 4, p. 417-418 2 p.

Research output: Contribution to journalLetter

Functional Assessment of Human Coding Mutations Affecting Skin Pigmentation Using Zebrafish

Tsetskhladze, Z. R., Canfield, V. A., Ang, K. C., Wentzel, S. M., Reid, K. P., Berg, A. S., Johnson, S. L., Kawakami, K. & Cheng, K. C., Oct 10 2012, In : PloS one. 7, 10, e47398.

Research output: Contribution to journalArticle

30 Scopus citations

Genetic risk profiling and gene signature modeling to predict risk of complications after IPAA

Sehgal, R., Berg, A., Polinski, J. I., Hegarty, J. P., Lin, Z., McKenna, K., Stewart, D., Poritz, L. & Koltun, W., Mar 1 2012, In : Diseases of the Colon and Rectum. 55, 3, p. 239-248 10 p.

Research output: Contribution to journalArticle

25 Scopus citations
5 Scopus citations

Mutation in TAGAP is protective of anal sepsis in ileocolic crohn's disease

Connelly, T. M., Sehgal, R., Berg, A., Hegarty, J. P., Deiling, S., Stewart, D., Poritz, L. & Koltun, W., Nov 1 2012, In : Diseases of the Colon and Rectum. 55, 11, p. 1145-1152 8 p.

Research output: Contribution to journalArticle

8 Scopus citations

Mutations in IRGM are associated with more frequent need for surgery in patients with ileocolonic crohn's disease

Sehgal, R., Berg, A., Polinski, J. I., Hegarty, J. P., Lin, Z., McKenna, K. J., Stewart, D. B., Poritz, L. S. & Koltun, W. A., Feb 1 2012, In : Diseases of the colon and rectum. 55, 2, p. 115-121 7 p.

Research output: Contribution to journalArticle

33 Scopus citations

PPI Therapy and Albumin are Better Predictors of Recurrent Clostridium difficile Colitis than Choice of Antibiotics

Rotramel, A., Poritz, L., Messaris, E., Berg, A. & Stewart, D., Dec 1 2012, In : Journal of Gastrointestinal Surgery. 16, 12, p. 2267-2273 7 p.

Research output: Contribution to journalArticle

21 Scopus citations

PTPN2 is associated with Crohn's disease and its expression is regulated by NKX2-3

Yu, W., Hegarty, J. P., Berg, A., Kelly, A. A., Wang, Y., Poritz, L., Franke, A., Schreiber, S., Koltun, W. & Lin, Z., Jan 1 2012, In : Disease Markers. 32, 2, p. 83-91 9 p.

Research output: Contribution to journalArticle

14 Scopus citations

Regression of established hepatocellular carcinoma is induced by chemoimmunotherapy in an orthotopic murine model

Avella, D. M., Li, G., Schell, T. D., Liu, D., Zhang, S. S. M., Lou, X., Berg, A., Kimchi, E. T., Tagaram, H. R. S., Yang, Q., Shereef, S., Garcia, L. S., Kester, M., Isom, H. C., Rountree, C. B. & Staveley-O'Carroll, K. F., Jan 1 2012, In : Hepatology. 55, 1, p. 141-152 12 p.

Research output: Contribution to journalArticle

24 Scopus citations

Skin color variation in Orang Asli tribes of Peninsular Malaysia

Ang, K. C., Ngu, M. S., Reid, K. P., Teh, M. S., Aida, Z. S., Koh, D. X. R., Berg, A., Oppenheimer, S., Salleh, H., Clyde, M. M., Md-Zain, B. M., Canfield, V. A. & Cheng, K. C., Aug 13 2012, In : PloS one. 7, 8, e42752.

Research output: Contribution to journalArticle

20 Scopus citations

Stage and Gene Specific Signatures Defined by Histones H3K4me2 and H3K27me3 Accompany Mammalian Retina Maturation In Vivo

Popova, E. Y., Xu, X., DeWan, A. T., Salzberg, A. C., Berg, A., Hoh, J., Zhang, S. S. & Barnstable, C. J., Oct 9 2012, In : PloS one. 7, 10, e46867.

Research output: Contribution to journalArticle

35 Scopus citations

Testing Time Series Linearity. Traditional and Bootstrap Methods

Berg, A., McMurry, T. & Politis, D. N., 2012, Handbook of Statistics. Elsevier B.V., p. 27-42 16 p. (Handbook of Statistics; vol. 30).

Research output: Chapter in Book/Report/Conference proceedingChapter

3 Scopus citations
2011

A dynamic model for functional mapping of biological rhythms

Fu, G., Luo, J., Berg, A., Wang, Z., Li, J., Das, K., Li, R. & Wu, R., Jan 1 2011, In : Journal of Biological Dynamics. 5, 1, p. 84-101 18 p.

Research output: Contribution to journalArticle

7 Scopus citations

Association studies of excision repair cross-complementation group 1 (ERCC1) haplotypes with lung and head and neck cancer risk in a Caucasian population

Jones, N. R., Spratt, T. E., Berg, A. S., Muscat, J. E., Lazarus, P. & Gallagher, C. J., Apr 1 2011, In : Cancer Epidemiology. 35, 2, p. 175-181 7 p.

Research output: Contribution to journalArticle

13 Scopus citations

DLG5 P1371Q is associated with inflammatory bowel disease and complementary to R30Q in disease susceptibility

Lin, Z., Hegarty, J. P., Berg, A., Wang, Z., Kelly, A. A., Wang, Y., Poritz, L. S., Wu, R. & Koltun, W. A., Nov 1 2011, In : Swiss Medical Weekly. 141, NOVEMBER

Research output: Contribution to journalArticle

6 Scopus citations
127 Scopus citations

Functional mapping of expression quantitative trait loci that regulate oscillatory gene expression.

Berg, A., Li, N., Tong, C., Wang, Z., Berceli, S. A. & Wu, R., Jul 14 2011, In : Methods in molecular biology (Clifton, N.J.). 734, p. 241-255 15 p.

Research output: Contribution to journalArticle

4 Scopus citations

Genetic Variants and Monoallelic Expression of Surfactant Protein-D in Inflammatory Bowel Disease

Lin, Z., John, G., Hegarty, J. P., Berg, A., Yu, W., Wang, Y., Kelly, A. A., Peterson, B. Z., Poritz, L. S., Floros, J. & Koltun, W. A., Sep 1 2011, In : Annals of Human Genetics. 75, 5, p. 559-568 10 p.

Research output: Contribution to journalArticle

9 Scopus citations

NKX2-3 transcriptional regulation of endothelin-1 and VEGF signaling in human intestinal microvascular endothelial cells

Yu, W., Hegarty, J. P., Berg, A., Chen, X., West, G., Kelly, A. A., Wang, Y., Poritz, L. S., Koltun, W. A. & Lin, Z., May 31 2011, In : PloS one. 6, 5, e20454.

Research output: Contribution to journalArticle

15 Scopus citations

NKX2-3 variant rs11190140 is associated with IBD and alters binding of NFAT

John, G., Hegarty, J. P., Yu, W., Berg, A., Pastor, D. M., Kelly, A. A., Wang, Y., Poritz, L., Schreiber, S., Koltun, W. & Lin, Z., Sep 1 2011, In : Molecular Genetics and Metabolism. 104, 1-2, p. 174-179 6 p.

Research output: Contribution to journalArticle

15 Scopus citations

Plasma netrin-1 is a diagnostic biomarker of human cancers

Ramesh, G., Berg, A. & Jayakumar, C., Mar 1 2011, In : Biomarkers. 16, 2, p. 172-180 9 p.

Research output: Contribution to journalArticle

34 Scopus citations

Psychological health in patients with ALS is maintained as physical function declines

Cupp, J., Simmons, Z., Berg, A., Felgoise, S. H., Walsh, S. M. & Stephens, H. E., Jul 1 2011, In : Amyotrophic Lateral Sclerosis. 12, 4, p. 290-296 7 p.

Research output: Contribution to journalArticle

25 Scopus citations

Risk factors for surgical site infections after colorectal resection in diabetic patients

Sehgal, R., Berg, A., Figueroa, R., Poritz, L., McKenna, K., Stewart, D. & Koltun, W., Jan 1 2011, In : Journal of the American College of Surgeons. 212, 1, p. 29-34 6 p.

Research output: Contribution to journalArticle

51 Scopus citations

Risk factors for surgical site infections after colorectal resection in diabetic patients

Sehgal, R. S., Berg, A. & Figueroa, R., Nov 1 2011, In : Diseases of the colon and rectum. 54, 11

Research output: Contribution to journalComment/debate