Publications by authors named "Atif Shahab"

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Coherence analysis discriminates between retroviral integration patterns in CD34(+) cells transduced under differing clinical trial conditions.
Claus V Hallwirth, Gagan Garg, Timothy J Peters, Belinda A Kramer, Nirav V Malani, Atif Shahab

Mol Ther Methods Clin Dev· June 2015

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Long span DNA paired-end-tag (DNA-PET) sequencing strategy for the interrogation of genomic structural mutations and fusion-point-guided reconstruction of amplicons.
Fei Yao, Pramila N Ariyaratne, Axel M Hillmer, Wah Heng Lee, Guoliang Li, Atif Shahab

PLoS One· February 2013

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Whole-genome reconstruction and mutational signatures in gastric cancer.
Niranjan Nagarajan, Denis Bertrand, Axel M Hillmer, Zhi Jiang Zang, Fei Yao, Atif Shahab

Genome Biol· December 2012

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Landscape of transcription in human cells.
Sarah Djebali, Carrie A Davis, Angelika Merkel, Alex Dobin, Timo Lassmann, Atif Shahab

Nature· September 2012

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A common BIM deletion polymorphism mediates intrinsic resistance and inferior responses to tyrosine kinase inhibitors in cancer.
King Pan Ng, Axel M Hillmer, Charles T H Chuah, Wen Chun Juan, Tun Kiat Ko, Atif Shahab

Nat Med· March 2012

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CTCF-mediated functional chromatin interactome in pluripotent cells.
Lusy Handoko, Han Xu, Guoliang Li, Chew Yee Ngan, Elaine Chew, Atif Shahab

Nat Genet· June 2011

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Transcriptional consequences of genomic structural aberrations in breast cancer.
Koichiro Inaki, Axel M Hillmer, Leena Ukil, Fei Yao, Xing Yi Woo, Atif Shahab

Genome Res· May 2011

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Comprehensive long-span paired-end-tag mapping reveals characteristic patterns of structural variations in epithelial cancer genomes.
Axel M Hillmer, Fei Yao, Koichiro Inaki, Wah Heng Lee, Pramila N Ariyaratne, Atif Shahab

Genome Res· May 2011

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Deconvolution of chromatin immunoprecipitation-microarray (ChIP-chip) analysis of MBF occupancies reveals the temporal recruitment of Rep2 at the MBF target genes.
Majid Eshaghi, Lei Zhu, Zhaoqing Chu, Juntao Li, Chee Seng Chan, Atif Shahab

Eukaryot Cell· January 2011

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Genome-wide analysis reveals methyl-CpG-binding protein 2-dependent regulation of microRNAs in a mouse model of Rett syndrome.
Hao Wu, Jifang Tao, Pauline J Chen, Atif Shahab, Weihong Ge

Proc Natl Acad Sci U S A· October 2010

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webMGR: an online tool for the multiple genome rearrangement problem.
Chi Ho Lin, Hao Zhao, Sean Harry Lowcay, Atif Shahab, Guillaume Bourque

Bioinformatics· February 2010

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Integration of external signaling pathways with the core transcriptional network in embryonic stem cells.
Xi Chen, Han Xu, Ping Yuan, Fang Fang, Mikael Huss, Atif Shahab

Cell· June 2008

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Quality assessment of the Affymetrix U133A&B probesets by target sequence mapping and expression data analysis.
Yuriy L Orlov, Jiangtao Zhou, Leonard Lipovich, Atif Shahab, Vladimir A Kuznetsov

In Silico Biol· May 2008

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Whole-genome mapping of histone H3 Lys4 and 27 trimethylations reveals distinct genomic compartments in human embryonic stem cells.
Xiao Dong Zhao, Xu Han, Joon Lin Chew, Jun Liu, Kuo Ping Chiu, Atif Shahab

Cell Stem Cell· September 2007

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Genome-wide mapping of RELA(p65) binding identifies E2F1 as a transcriptional activator recruited by NF-kappaB upon TLR4 activation.
Ching-Aeng Lim, Fei Yao, Joyce Jing-Yi Wong, Joshy George, Han Xu, Atif Shahab

Mol Cell· August 2007

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Fusion transcripts and transcribed retrotransposed loci discovered through comprehensive transcriptome analysis using Paired-End diTags (PETs).
Yijun Ruan, Hong Sain Ooi, Siew Woh Choo, Kuo Ping Chiu, Xiao Dong Zhao, Atif Shahab

Genome Res· June 2007

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Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.

Nature· June 2007

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Global mapping of c-Myc binding sites and target gene networks in human B cells.
Karen I Zeller, XiaoDong Zhao, Charlie W H Lee, Kuo Ping Chiu, Fei Yao, Atif Shahab

Proc Natl Acad Sci U S A· November 2006

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A global map of p53 transcription-factor binding sites in the human genome.
Chia-Lin Wei, Qiang Wu, Vinsensius B Vega, Kuo Ping Chiu, Patrick Ng, Atif Shahab

Cell· January 2006

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Gene identification signature (GIS) analysis for transcriptome characterization and genome annotation.
Patrick Ng, Chia-Lin Wei, Wing-Kin Sung, Kuo Ping Chiu, Leonard Lipovich, Atif Shahab

Nat Methods· February 2005

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