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Genome Medicine

ISSN Print: 1756-994X

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Website: http://genomemedicine.com

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Visualizing multidimensional cancer genomics data

Michael P Schroeder, Abel Gonzalez-Perez, Nuria Lopez-Bigas

Genetics is a major determinant of expression of the human hepatic uptake transporter OATP1B1, but not of OATP1B3 and OATP2B1

Anne T Nies, Mikko Niemi, Oliver Burk, Stefan Winter, Ulrich M Zanger, Bruno Stieger, Matthias Schwab, Elke Schaeffeler

Incidental genetic findings in randomized clinical trials: recommendations from the Genomics and Randomized Trials Network (GARNET)

Ebony B Bookman, Corina Din-Lovinescu, Bradford B Worrall, Teri A Manolio, Siiri N Bennett, Cathy Laurie, Daniel B Mirel, Kimberly F Doheny, Garnet L Anderson, Kate Wehr, Richard Weinshilboum, Donna T Chen, for GARNET

2012 highlights in translational 'omics

Charles Auffray, Timothy Caulfield, Muin J Khoury, James R Lupski, Matthias Schwab, Timothy Veenstra

Characterizing biobank organizations in the U.S.: results from a national survey

Gail E Henderson, R Jean Cadigan, Teresa P Edwards, Ian Conlon, Anders G Nelson, James P Evans, Arlene M Davis, Catherine Zimmer, Bryan J Weiner

De novo truncating mutations in ASXL3 are associated with a novel clinical phenotype with similarities to Bohring-Opitz syndrome

Matthew N Bainbridge, Hao Hu, Donna M Muzny, Luciana Musante, James R Lupski, Brett H Graham, Wei Chen, Karen W Gripp, Kim Jenny, Thomas F Wienker, Yaping Yang, V REID Sutton, Richard A Gibbs, H HILGER Ropers

Identification and MS assisted interpretation of genetically influenced NMR signals in human plasma

Johannes Raffler, Werner Romisch-Margl, Ann-Kristin Petersen, Philipp Pagel, Florian Blochl, Christian Hengstenberg, Thomas Illig, Christa Meisinger, Klaus Stark, H-Erich Wichmann, Jerzy Adamski, Christian Gieger, Gabi Kastenmuller, Karsten Suhre

MicroRNA paraffin-based studies in osteosarcoma reveal reproducible independent prognostic profiles at 14q32

Andrew D Kelly, Benjamin Haibe-Kains, Katherine A Janeway, Katherine E Hill, Eleanor Howe, Jeffrey Goldsmith, Kyle Kurek, Antonio R Perez-Atayde, Nancy Francoeur, Jian-Bing Fan, Craig April, Hal Schneider, Mark C Gebhardt, Aedin Culhane, John Quackenbush, Dimitrios Spentzos

Improving bioinformatic pipelines for exome variant calling

Hanlee P Ji

An epigenomic mechanism in retinoblastoma: the end of the story?

A Linn Murphree, Timothy J Triche

Mobile elements in the human genome: implications for disease

Szilvia Solyom, Haig H Kazazian

Open science versus commercialization: a modern research conflict?

Timothy Caulfield, Shawn HE Harmon, Yann Joly

PTPN22 splice forms: a new role in rheumatoid arthritis

Lina-Marcela Diaz-Gallo, Javier Martin

Sample-level enrichment analysis unravels shared stress phenotypes among multiple cancer types

Gunes Gundem, Nuria Lopez-Bigas

A yeast phenomic model for the gene interaction network modulating F508del-CFTR protein biogenesis

Raymond J Louie, Jingyu Guo, John W Rodgers, Rick White, Najaf Shah, Silvere Pagant, Peter Kim, Michael Livstone, Kara Dolinski, Brett A McKinney, Jeong Hong, Eric J Sorscher, Jennifer Bryan, Elizabeth A Miller, John L Hartman

Genomic vulnerability to LINE-1 hypomethylation is a potential determinant of the clinicogenetic features of multiple myeloma

Yuka Aoki, Masanori Nojima, Hiromu Suzuki, Hiroshi Yasui, Reo Maruyama, Eiichiro Yamamoto, Masami Ashida, Mitsuhiro Itagaki, Hideki Asaoku, Hiroshi Ikeda, Toshiaki Hayashi, Kohzoh Imai, Mitsuru Mori, Takashi Tokino, Tadao Ishida, Minoru Toyota, Yasuhisa Shinomura

Recycling side-effects into clinical markers for drug repositioning

Miquel Duran-Frigola, Patrick Aloy

Differential effects of dietary supplements on metabolomic profile of smokers versus non-smokers

Robert C Spitale, Michelle Y Cheng, Kimberly A Chun, Emily S Gorell, Claudia A Munoz, Dale G Kern, Steve M Wood, Helen E Knaggs, Jacob Wulff, Kirk D Beebe, Anne Lynn S Chang

Systems-level analysis of age-related macular degeneration reveals global biomarkers and phenotype-specific functional networks

Aaron M Newman, Natasha B Gallo, Lisa S Hancox, Norma J Miller, Carolyn M Radeke, Michelle A Maloney, James B Cooper, Gregory S Hageman, Don H Anderson, Lincoln V Johnson, Monte J Radeke

FMR1 CGG allele size and prevalence ascertained through newborn screening in the United States

Flora Tassone, Ka Pou Long, Tzu-Han Tong, Joyce Lo, Louise W Gane, Elizabeth Berry-Kravis, Danh Nguyen, Lisa Y Mu, Jennifer Laffin, Don B Bailey, Randi J Hagerman

Drug transporter regulation in tumors by DNA methylation

Oliver Zolk, Martin F Fromm

Emerging patterns of genetic overlap across autoimmune disorders

Corinne Richard-Miceli, Lindsey A Criswell

Rule-based induction method for haplotype comparison and identification of candidate disease loci

Sirkku Karinen, Silva Saarinen, Rainer Lehtonen, Pasi Rastas, Pia Vahteristo, Lauri A Aaltonen, Sampsa Hautaniemi

Epigenetic variability in cells of normal cytology is associated with the risk of future morphological transformation

Andrew E Teschendorff, Allison Jones, Heidi Fiegl, Alexandra Sargent, Joanna J Zhuang, Henry C Kitchener, Martin Widschwendter

Multi-platform characterization of the human cerebrospinal fluid metabolome: a comprehensive and quantitative update

Rupasri Mandal, An Chi Guo, Kruti K Chaudhary, Philip Liu, Faizath S Yallou, Edison Dong, Farid Aziat, David S Wishart

Generalizing complexity: a fruitful partnership of functional genomics and systems biology

Diego Villar, Duncan T Odom

The long journey of stem cell therapeutics

Sarah Crawford

Shifts in human skin and nares microbiota of healthy children and adults

Julia Oh, Sean Conlan, Eric C Polley, Julia A Segre, Heidi H Kong

Comprehensive analysis of the genome transcriptome and proteome landscapes of three tumor cell lines

Pelin Akan, Andrey Alexeyenko, Paul Costea, Lilia Hedberg, Beata Solnestam, Sverker Lundin, Jimmie H？llman, Emma Lundberg, Mathias Uhlén, Joakim Lundeberg

The balance of expression of PTPN22 splice forms is significantly different in rheumatoid arthritis patients compared with controls

Marcus Ronninger, Yongjing Guo, Klementy Shchetynsky, Andrew Hill, Mohsen Khademi, Tomas Olsson, Padmalatha S Reddy, Maria Seddighzadeh, James D Clark, Lih-Ling Lin, Margot O'Toole, Leonid Padyukov

Serum metabolomic profile as a means to distinguish stage of colorectal cancer

Farshad Farshidfar, Aalim M Weljie, Karen Kopciuk, W Don Buie, Anthony MacLean, Elijah Dixon, Francis R Sutherland, Andrea Molckovsky, Hans J Vogel, Oliver F Bathe

Gene regulatory network inference: evaluation and application to ovarian cancer allows the prioritization of drug targets

Piyush B Madhamshettiwar, Stefan R Maetschke, Melissa J Davis, Antonio Reverter, Mark A Ragan

Digital transcriptome profiling of normal and glioblastoma-derived neural stem cells identifies genes associated with patient survival

P？r G Engstr？m, Diva Tommei, Stefan H Stricker, Christine Ender, Steven M Pollard, Paul Bertone

Consensus: a framework for evaluation of uncertain gene variants in laboratory test reporting

David K Crockett, Perry G Ridge, Andrew R Wilson, Elaine Lyon, Marc S Williams, Scott P Narus, Julio C Facelli, Joyce A Mitchell

Concentration of endogenous estrogens and estrogen metabolites in the NCI-60 human tumor cell lines

Xia Xu, Timothy D Veenstra

Cancer detection and biopsy classification using concurrent histopathological and metabolomic analysis of core biopsies

Meredith V Brown, Jonathan E McDunn, Philip R Gunst, Elizabeth M Smith, Michael V Milburn, Dean A Troyer, Kay A Lawton

H3K4me3 inversely correlates with DNA methylation at a large class of non-CpG-island-containing start sites

Dheepa Balasubramanian, Batool Akhtar-Zaidi, Lingyun Song, Cynthia F Bartels, Martina Veigl, Lydia Beard, Lois Myeroff, Kishore Guda, James Lutterbaugh, Joseph Willis, Gregory E Crawford, Sanford D Markowitz, Peter C Scacheri

Metabolomic analysis of rat serum in streptozotocin-induced diabetes and after treatment with oral triethylenetetramine (TETA)

Marta Ugarte, Marie Brown, Katherine A Hollywood, Garth J Cooper, Paul N Bishop, Warwick B Dunn

Annotate-it: a Swiss-knife approach to annotation, analysis and interpretation of single nucleotide variation in human disease

Alejandro Sifrim, Jeroen KJ Van Houdt, Leon-Charles Tranchevent, Beata Nowakowska, Ryo Sakai, Georgios A Pavlopoulos, Koen Devriendt, Joris R Vermeesch, Yves Moreau, Jan Aerts

Cancer of the ampulla of Vater: analysis of the whole genome sequence exposes a potential therapeutic vulnerability

Michael J Demeure, David W Craig, Shripad Sinari, Tracy M Moses, Alexis Christoforides, Jennifer Dinh, Tyler Izatt, Jessica Aldrich, Ardis Decker, Angela Baker, Irene Cherni, April Watanabe, Lawrence Koep, Douglas Lake, Galen Hostetter, Jeffrey M Trent, Daniel D Von Hoff, John D Carpten

In silico analysis of HLA associations with drug-induced liver injury: use of a HLA-genotyped DNA archive from healthy volunteers

Ana Alfirevic, Faviel Gonzalez-Galarza, Catherine Bell, Klara Martinsson, Vivien Platt, Giovanna Bretland, Jane Evely, Maike Lichtenfels, Karin Cederbrant, Neil French, Dean Naisbitt, B Kevin Park, Andrew R Jones, Munir Pirmohamed

Exploring the interaction between SNP genotype and postmenopausal hormone therapy effects on stroke risk

Ying Huang, Dennis G Ballinger, Renee Stokowski, Erica Beilharz, Jennifer G Robinson, Simin Liu, Randal D Robinson, Victor W Henderson, Jacques E Rossouw, Ross L Prentice

Ethical, legal and social issues: out in the open

Rebecca F Furlong

HLA typing from RNA-Seq sequence reads

Sebastian Boegel, Martin Lower, Michael Schafer, Thomas Bukur, Jos de Graaf, Valesca Boisguerin, Ozlem Tureci, Mustafa Diken, John C Castle, Ugur Sahin

Improving the prediction of the functional impact of cancer mutations by baseline tolerance transformation

Abel Gonzalez-Perez, Jordi Deu-Pons, Nuria Lopez-Bigas

Correction: Gene expression and network-based analysis reveals a novel role for hsa-miR-9 and drug control over the p38 network in glioblastoma multiforme progression

Rotem Ben-Hamo, Sol Efroni

Pharmacogenomics: a key component of personalized therapy

Matthias Schwab, Elke Schaeffeler

Looking back at genomic medicine in 2011

Charles Auffray, Timothy Caulfield, Muin J Khoury, James R Lupski, Matthias Schwab, Timothy Veenstra

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