Issue Special Issue 6/2012
Beyond the Genome 2012
Content (84 Articles)
Abstract not submitted for online publication
Abstract not submitted for online publication
Abstract not submitted for online publication
Hypothesis-generating clinical genomics research and predictive medicine
Leslie Biesecker
De novo diagnostics of patients with intellectual disability
Joris A Veltman
Abstract not submitted for online publication
Clinical diagnostic whole genome sequencing in a paediatric population: experience from our WGS genetics clinic
Elizabeth Worthey, David Bick, David Dimmock, Mary Shimoyama, Regan Veith, George Kowalski, Bradley Taylor, Brandon Wilk, Sharon Tsaih, Jeremy Harris, Michael Tschannen, Jaime Wendt-Andrae, Ken Brodie, Howard Jacob
Characterizing epistatic hotspots of human disease
Tallulah Andrews, Caleb Webber
How to avoid one thousand opportunities to do harm in genomic medicine
Isaac Kohane
Abstract not submitted for online publication
Interrogating of cancer genomes: towards more profile-based therapeutics
John David Carpten
Abstract not submitted for online publication
Abstract not submitted for online publication
Abstract not submitted for online publication
Abstract not submitted for online publication
Abstract not submitted for online publication
MutaScope: a high-sensitivity variant caller dedicated to high-throughput PCR amplicons sequencing
Shawn Yost, Hakan Alakus, Hiroko Matsui, Kristen Jepsen, Richard Schwab, Kelly Frazer, Olivier Harismendy
Analysis of somatic retrotransposition in human cancers
Eunjung Lee, Rebecca Iskow, Lixing Yang, Omer Gokcumen, Psalm Haseley, Lovelace J Luquette III, Jens G Lohr, Christopher C Harris, Li Ding, Richard K Wilson, David A Wheeler, Richard A Gibbs, Raju Kucherlapati, Charles Lee, Peter V Kharchenko, Peter J Park
Exploring the cancer methylome
Benjamin P Berman, Daniel J Weisenberger, Toshinori Hinoue, Houtan Noushmehr, Yaping Liu, Joseph F Aman, Toshinori Hinoue, Hui Shen, Simeen Malik, Swapna Mahurkar, Timothy Triche Jr, Zachary Ramjan, Charles M Nicolet, David Van Den Berg, Leslie Cope, James G Herman, Stephen B Baylin, Peter W Laird
Ultra-high resolution mapping of protein-genome interactions using ChIP-exo
B Franklin Pugh
Epigenetic reprogramming in the epithelial-to-mesenchymal transition
Stephen Hoang, Marcin Cieślik, Sanjay Chodaparambil, Natalya Baranova, Manish Kumar, David Allison, Jake Wamsley, Lisa Gray, Marty Mayo, Stefan Bekiranov
Development of a computational strategy to compare repetitive element enrichment between experimental conditions from high-throughput sequencing datasets
Steven Criscione, Nicola Neretti
Life stage and tissue speciation of cathepsin B (AGAP004533) derives different functional properties in the G3 strain of the mosquito Anopheles gambiae
Daniel Achinko, Dan Masiga, Paul Mireji, Flaminia Catteruccia
Abstract not submitted for online publication
Targeted next-generation sequencing of colorectal cancer identified metastatic specific genetic alterations
A Rose Brannon, Efsevia Vakiani, Sasinya Scott, Brooke Sylvester, Krishan Kania, Agnes Viale, David Solit, Michael Berger
Moving beyond gene expression: identification of lung-disease-associated novel transcripts and alternative splicing by RNA sequencing
John Brothers II, Rebecca Kusko, Gang Liu, Lingqi Luo, Brenda Juan Guardela, John Tedrow, Yuriy Alekesyev, Ivana V Yang, Mick Correll, Mark Geraci, John Quackenbush, Frank Sciurba, Paola Sebastiani, Marc Lenburg, Naftali Kaminski, David A Schwartz, Avrum Spira, Jennifer Beane
Integration of a standardized pharmacogenomic platform for clinical decision support at Boston Children's Hospital
Catherine Brownstein, Vincent A Fusaro, Sarah Savage, Catherine Clinton, Kenneth Mandl, David Margulies, Wendy Wolf, Shannon Manzi
Characterizing the small RNA transcriptome associated with COPD and ILD using next-generation sequencing
Joshua D Campbell, Lingqi Luo, Gang Liu, Ji Xiao, Joseph Gerrein, Brenda J Guardela, John Tedrow, Yuriy O Aleksyev, Ivana V Yang, Mick Correll, Mark Geraci, John Quackenbush, Frank Sciurba, David A Schwartz, Naftali Kaminski, Marc E Lenburg, Jennifer Beane, Avrum Spira
Major differences in microRNA quantification are platform and sequence dependent
Ester Feldmesser, Dena Leshkowitz, Yisrael Parmet, Shirley Horn-Saban
The association between LRP1 and chylomicron uptake after the ingestion of a high-fat meal
AC Frazier-Wood, EK Kabagambe, MK Wojczynski, IB Borecki, HK Tiwari, CE Smith, JM Ordovas, DK Arnett
Genome-wide analysis of primate and rodent protein-coding and associated non-coding nucleotide sequences
Sudhindra R Gadagkar, Luke A Rond
Exome sequencing combined with semantic discovery identifies strong disease-associated candidates in a single case of relapsing remitting multiple sclerosis
Mahjoubeh Jalali Sefid Dashti, Maritha Kotze, Susan Janse van Rensburg, Alan Christoffels, Junaid Gamieldien
The consequences of denoising marker-based metagenomic data
John M Gaspar, W Kelley Thomas
Abstract not submitted for online publication
Discovering epigenetic changes in response to tungsten-alloy treatment using next-generation sequencing technologies
Ranjana Verma, Deepak Grover, Zygmunt Galdzicki
An integrative genomics approach for mapping the emerging genetic susceptibility landscape of triple-negative breast cancer
Chindo Hicks, Antonio Pannuti, Kandis Backus, Lucio Miele
Bernoulli mixture models in application to the evaluation of algorithms estimating functionality of missense mutations
Stephanie Hicks, Sharon E Plon, Marek Kimmel
In silico drug screening and potential target identification for hepatocellular carcinoma using support vector machine
Wu-Lung R Yang, Yu-En Lee, Ming-Huang Chen, Yu-Wen Liu, Pei-Ying Lee, Kun-Mao Chao, Chi-Ying F Huang
Mining cancer genomes in COSMIC
Mingming Jia, Simon A Forbes, David Beare, Nidhi Bindal, Prasad Gunasekaran, Kenric Leung, Chai Yin Kok, Sally Bamford, Charlotte Cole, Sari Ward, Jon Teague, Michael R Stratton, Peter Campbell, Andrew Futreal
Deploying next-generation sequencing in a hospital setting
Lars GT Jorgensen, Katherine Siminovitch
Investigation of rare variation in one thousand cancer genes and its association with risk of breast and prostate cancer
Daniel Klevebring, Johan Lindberg, Simon Sundling, Mårten Neiman, Julia Sandberg, Fredrik Wiklund, Per Hall, Henrik Grönberg, Kamila Czene
Abstract not submitted for online publication
Comprehensive genomic profiling of the lung transcriptome in emphysema and idiopathic pulmonary fibrosis using RNA-Seq
Rebecca L Kusko, John Brothers II, Gang Liu, Lingqi Luo, Brenda Juan Guardela, John Tedrow, Yuriy Aleksyev, Ivana V Yang, Mick Correll, Mark Geraci, John Quackenbush, Frank Sciurba, Marc Lenburg, David A Schwartz, Jennifer Beane, Naftali Kaminski, Avrum Spira
Investigation of retroviral integration preference via high-throughput sequencing
Matthew C LaFave, Gaurav K Varshney, Shawn M Burgess
Reflex™: a novel method to sequence barcoded long-range PCR products in a pooled population of hundreds of DNA samples
James Casbon, Andrew Slatter, Esther Musgrave-Brown, Robert Osborne, Conrad Lichtenstein, Sydney Brenner
Extended homozygous haplotypes at genes involved in brain development associated with autism
Ping-I Lin
Multiple de novo copy number variations in two subjects with developmental problems and multiple congenital anomalies
Pengfei Liu, Klaudia Walter, Karin Writzl, Violet Gelowani, Sarah Lindsay, Claudia MB Carvalho, Marjorie Withers, Joanna Wiszniewska, Ankita Patel, Bernd Rautenstrauss, Matthew E Hurles, James R Lupski
A fast solution to NGS library preparation with low nanogram DNA input
Pingfang Liu, Gregory JS Lohman, Eric Cantor, Bradley W Langhorst, Erbay Yigit, Lynne M Apone, Daniela B Munafo, Christine Sumner, Fiona J Stewart, Thomas C Evans Jr, Nicole M Nichols, Eileen T Dimalanta, Theodore B Davis
A functional role of the SNP -592 of human IL10 gene regulatory region is associated with an increased IL-10 expression and risk for human papillomavirus cervical lesion and cervical cancer development
K Torres-Poveda, A Burguete-García, M Bahena-Román, E Ortíz-Flores, K Delgado-Romero, D Cantú, A García-Carrancá, V Madrid-Marina
Enhancer network revealed by correlated DNAse HS states of enhancers
Justin Malin, Radhouane Aniba, Sridhar Hannenhalli
siRNAs targeting the ERK2 signaling pathway and AML1/MTG8 fusion gene attenuate the differentiation, proliferation and growth arrest in t(8;21) leukemia
Salem Bashanfer, Faisal Mutee Al-Hassan, Rosline Hassan, Olaf Heidenreich, Mohamed Saifulaman Mohamed Said, Narazah Mohd Yusoff
Comparative analysis of strand-specific RNA sequencing approaches
Daniela Munafo, Ping Liu, Christine Sumner, Erbay Yigit, Landon Merrill, Lynne Apone, Brad Langhorst, Fiona Stewart, Eileen T Dimalanta, Theodore Davis
A study on genetic aspects of male infertility in North-east Indian population, India
Purnali Nath Barbhuiya, Anannya Gogoi, Giasuddin Ahmed, Rita Mahanta
Transcriptomics analysis revealed an indirect effect of aqueous cigarette smoke extract in promoting the adhesion of monocytic cells to endothelial cells
Carine Poussin, Inka Gallitz, Walter Schlage, Yvonne Steffen, Katrin Stolle, Stephan Lebrun, Julia Hoeng, Michael Lietz
Targeted genome reconstruction strategy for endosymbionts in eukaryotic genomes
Surya Saha, Wayne B Hunter, Magdalen Lindeberg
Dissecting the genetic architecture of coronary artery disease by genome engineering
David J Segal, Mital S Bhakta, Kumitaa Theva Das, Chongxiu Sun, Natalie M Grace, Jan A Nolta, Anne A Knowlton, David M Rocke, Scott I Simon
Exome sequencing identifies somatic point mutations associated with acquired endocrine resistance in breast cancer cell lines
Natasja S Ehlers, Zhu Shi Da, Daniel Elias, Xue Lin, Jian Li, Christina Bjerre, Nils Brunner, Lars Bolund, Wang Jun, Ramneek Gupta, Henrik J Ditzel
AVIA: an interactive web-server for annotation, visualization and impact analysis of genomic variations
Hue Vuong, Robert M Stephens, Natalia Volfovsky
Deep sequencing of the microRNA transcriptome in current, former, and never smokers with lung adenocarcinoma
Teresa W Wang, Josh D Campbell, Lingqi Luo, Gang Liu, Ji Xiao, Marc E Lenburg, Steven A Belinsky, Avrum Spira
Metastatic outgrowth encompasses COL-I, FN1 and POSTN upregulation and assembly to fibrillar networks regulating cell adhesion, migration and growth
J Soikkeli, M Yin, E Hölttä
Massively parallel sequencing of formalin-fixed paraffin-embedded tissues
Rachel L Erlich, Emanuele Palescandolo, Robert T Jones, Ashwini Sunkavalli, Alina Raza, Matthew Ducar, Charles Hatton, Christina Go, Christine Roden, Megan Hanna, Adri Mills, Ravali Adusumilli, Prateek Kumar, Priscilla K Brastianos, Matthew L Meyerson, William C Hahn, Laura E MacConaill, Paul Van Hummelen
Metabolomic and exome sequence analysis reveal novel molecular signatures associated with colorectal cancer relapse
Robinder Gauba, Thanemozhi G Natarajan, Lei Song, Krithika Bhuvaneshwar, Subha Madhavan, Yuriy Gusev
Optimizing genotype quality metrics for individual exomes and cohort analysis
Paul MK Gordon, Leo Dimnik, Ryan Lamont, Micheil Innes, Francois Bernier, Jillian Parboosingh
ICGC PedBrain - dissecting the genomic complexity underlying medulloblastoma using whole-genome sequencing
Natalie Jäger, David TW Jones, Marcel Kool, Thomas Zichner, Barbara Hutter, Marc Sultan, Yoon-Jae Cho, Trevor J Pugh, Volker Hovestadt, Adrian M Stütz, Tobias Rausch, Hans-Jörg Warnatz, Benedikt Brors, Paul A Northcott, Michael D Taylor, Matthew Meyerson, Scott L Pomeroy, Marie-Laure Yaspo, Jan O Korbel, Andrey Korshunov, Roland Eils, Stefan M Pfister, Peter Lichter
Apoptotic gene expression in melanoma cells treated with kaurenic acid
María B Rivero, Hernán J Mendoza, Miguel AChiurillo, Miriam C Sosa-Seguera
Abstract not submitted for online publication
Abstract not submitted for online publication
Verification of systems biology research in the age of collaborative competition
Carine Poussin
Dirichlet process model for joint haplotype inference and GWAS
Avinash Das Sahu, Sridhar Hannenhalli
Structural effect of P278A mutation conferring breast cancer susceptibility in the p53 DNA-binding core domain
Y Suneetha, C Kumaraswamy Naidu
Simple and precise targeted editing of the human genome using rAAV-mediated homologous recombination
Christopher J Torrance
Mutational spectrum of WTX, WT1, CTNNB1, APC and PLCG2 genes in Wilms tumor defined by massive parallel resequencing
Bruna D Barros, Giovana T Torrezan, Elisa N Ferreira, Mariana Maschietto, Ana CV Krepíschi, Dirce M Carraro
RNA-Seq analysis of two brain regions vulnerable to Alzheimer's disease
Xinkun Wang
CLIA-certified next-generation sequencing analysis in the cloud
Ying Zhang, Jesse Erdmann, John Chilton, Getiria Onsongo, Matthew Bower, Kenny Beckman, Bharat Thyagarajan, Kevin Silverstein, Anne-Francoise Lamblin