Research Paper

Gastroenterology: Integrative Genomic Identification of Genes on 8p Associated With Hepatocellular Carcinoma Progression and Patient Survival

December 3, 2011

Background & Aims Hepatocellular carcinoma (HCC) is an aggressive malignancy; its mechanisms of development and progression are poorly understood. We used an integrative approach to identify HCC driver genes, defined as genes whose copy numbers associate with gene expression and cancer progression.

Stand Genomic Sciences: Minimum Information about a Genotyping Experiment (MIGEN)

November 30, 2011

Jie Huang, Daniel Mirel, Elizabeth Pugh, Chao Xing, Peter N Robinson, Alexander Pertsemlidis, Lianghao Ding, Julia Kozlitina, Joseph Maher, Jonathan Rios, Michael Story, Nishanth Marthandan, Richard H Scheuermann Abstract Genotyping experiments are widely used in clinical and basic research laboratories to identify associations between genetic variations and normal/abnormal phenotypes. Genotyping assay techniques vary from single genomic regions that are interrogated using PCR reactions to high throughput assays […]

Breast Cancer Research: Common breast cancer susceptibility alleles are associated with tumour subtypes in BRCA1 and BRCA2 mutation carriers: results from the Consortium of Investigators of Modifiers of BRCA1/2

November 12, 2011

Anna Marie Mulligan 1, Fergus J Couch, Daniel Barrowdale, Susan M Domchek, Diana Eccles, Heli Nevanlinna, Susan J Ramus, Mark Robson, Mark Sherman, Amanda B Spurdle, Barbara Wappenschmidt, Andrew Lee, Lesley McGuffog, Sue Healey, Olga M Sinilnikova, Ramunas Janavicius, Thomas vO Hansen, Finn C Nielsen, Bent Ejlertsen, Ana Osorio, Iván Muñoz-Repeto, Mercedes Durán, Javier Godino, Maroulio Pertesi, Javier Benítez, Paolo Peterlongo, Siranoush Manoukian, Bernard Peissel, Daniela Zaffaroni, Elisa Cattaneo, Bernardo Bonanni, Alessandra Viel, Barbara Pasini, Laura Papi, Laura Ottini, Antonella Savarese, Loris Bernard, Paolo Radice, Ute Hamann, Martijn Verheus, Hanne E J Meijers-Heijboer, Juul Wijnen, Encarna B Gómez […]

Biotechniques: Isolation of Sertoli, Leydig, and spermatogenic cells from the mouse testis

November 5, 2011

Yao-Fu Chang 1, Jennifer S Lee-Chang, Subbarayalu Panneerdoss, James A MacLean 2nd, Manjeet K Rao Abstract A thorough understanding of the events during mammalian spermatogenesis requires studying specific molecular signatures of individual testicular cell populations as well as their interaction in co-cultures. However, most purification techniques to isolate specific testicular cell populations are time-consuming, require large numbers of animals, and/or […]

Journal of Biological Chemistry: Mutant p53 Disrupts Role of ShcA Protein in Balancing Smad Protein-dependent and -independent Signaling Activity of Transforming Growth Factor-β (TGF-β)*

October 26, 2011

Shu Lin‡, Lan Yu‡, Junhua Yang‡, Zhao Liu‡, Bijal Karia‡§, Alexander J. R. Bishop‡§¶, James Jackson‖, Guillermina Lozano‖, John A. Copland**, Xiaoxin Mu‡‡‡, Beicheng Sun‡‡ and Lu-Zhe Sun‡¶,1 Abstract Biomarkers are lacking for identifying the switch of transforming growth factor-β (TGF-β) from tumor-suppressing to tumor-promoting. Mutated p53 (mp53) has been suggested to switch TGF-β to a tumor promoter. However, we found that mp53 does not always promote […]

IEEE: Stochastic Modeling of the Relationship between Copy Number and Gene Expression Based on Transcriptional Logic

October 24, 2011

Fang-Han Hsu; Erchin Serpedin; Yidong Chen; Edward R. Dougherty Abstract: DNA copy number alterations (CNAs) can cause genetic diseases, and studies have revealed a relationship between CNAs and gene expression; however, the manner in which CNAs relate to gene expression and what regulatory mechanisms underlying the relationship remain unclear. In many instances, real data have revealed a nonlinear […]

Molecular Profiling: Genome-Wide Methylation Profiling in Archival Formalin-Fixed Paraffin-Embedded Tissue Samples

October 21, 2011

J. Keith Killian, Robert L. Walker, Sven Bilke, Yidong Chen, Sean Davis, Robert Cornelison, William I. Smith, Paul S. Meltzer Abstract New technologies allow for the genome-scale measurement of DNA methylation. In an effort to increase the clinical utility of DNA methylation as a biomarker, we have adapted a commercial bisulfite epigenotype assay for genome-wide methylation profiling in archival formalin-fixed paraffin-embedded pathology specimens. This […]

Proteome Science: Bayesian non-negative factor analysis for reconstructing transcription factor mediated regulatory networks

October 14, 2011

Jia Meng, Jianqiu (Michelle) Zhang, Yidong Chen & Yufei Huang Abstract Background Transcriptional regulation by a transcription factor (TF) controls the time and abundance of mRNA transcription. Due to the limitation of current proteomics technologies, large scale measurements of protein level activities of TFs is usually infeasible, making computational reconstruction of the transcriptional regulatory network a difficult task. Results […]

BMC Research Notes: A model-based circular binary segmentation algorithm for the analysis of array CGH data

October 10, 2011

Fang-Han Hsu, Hung-I H Chen, Mong-Hsun Tsai, Liang-Chuan Lai, Chi-Cheng Huang, Shih-Hsin Tu, Eric Y Chuang & Yidong Chen Abstract Background Circular Binary Segmentation (CBS) is a permutation-based algorithm for array Comparative Genomic Hybridization (aCGH) data analysis. CBS accurately segments data by detecting change-points using a maximal-t test, but an extensive computational burden is involved for evaluating the significance of change-points using permutations. […]

BMC Cancer: Activating mutation in MET oncogene in familial colorectal cancer

October 4, 2011

Deborah W Neklason 1, Michelle W Done, Nykole R Sargent, Ann G Schwartz, Hoda Anton-Culver, Constance A Griffin, Dennis J Ahnen, Joellen M Schildkraut, Gail E Tomlinson, Louise C Strong, Alexander R Miller, Jill E Stopfer, Randall W Burt Abstract Background: In developed countries, the lifetime risk of developing colorectal cancer (CRC) is 5%, and it is the second leading cause of death from cancer. The presence of family […]