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Publications

The Genomics core has processed a lot of samples, generating data for many of the publications coming out of the Cambridge Institute, we've really enjoyed being part of this work and seeing the final results in such high-impact journals. If you use data from the Genomics Core is your publication and we're not coauthors, please don't forget to acknowledge us.

Acknowledging our contribution:

Please do remember us when writing your own manuscript, as authorship and acknowledgment are metrics that our success is measured by; so if we've contributed to the experimental design, produced experimental data, and/or helped with analysis or interpretation or writing the manuscript then please don't forget us. If the work carried out has been exceptional or the person doing it has done significantly more than would normally be expected you might consider naming that person in the acknowledgment or adding that individual as an author on the paper. It's up to you to decide authorship and/or acknowledgment.

Suggested acknowledgment text: We thank the Cambridge Institute Genomics Core for their support with this work or We thank the Cambridge Institute Genomics Core for their support with this work, especially James Hadfield for his work on the RNA-seq library preparation (if someone in particular played a role not quite enough for authorship).

Please send us a copy of your paper, or e-mail us a PubMed link and we'll add it to the work below. Who know's we might even blog or Tweet about it!

Papers co-authored by Genomics core staff:

Hadfield & Eldridge. Multi-genome alignment for quality control and contamination screening of next-generation sequencing data. Frontiers in Genetics 2013.

Azizan et al. Somatic mutations in ATP1A1 and CACNA1D underlie a common subtype of adrenal hypertension. Nat Genet. 2013

Murtaza et al. Non-invasive analysis of acquired resistance to cancer therapy by sequencing of plasma DNA. Nature 2013

Idris et al. The role of high-throughput technologies in clinical cancer genomics. Expert Rev Mol Diagn 2013

Forshew et al. Noninvasive identification and monitoring of cancer mutations by targeted deep sequencing of plasma DNA. Sci Transl Med. 2012

Curtis et al. The genomic and transcriptomic architecture of 2000 breast tumours reveals novel subgroups. Nature 2012.

Holmes et al. Transducin-like enhancer protein 1 mediates estrogen receptor binding and transcriptional activity in breast cancer cells. PNAS, May 2012

Aldridge and Hadfield. Introduction to miRNA profiling technologies and cross-platform comparison. Methods Mol Biol 2012.

Massie et al. The androgen receptor fuels prostate cancer by regulating central metabolism and biosynthesis. EMBO J. 2011

Katsnelson et al. Genomes by the thousand. Nature 2010

Lynch et al. The cost of reducing starting RNA quantity for Illumina BeadArrays: A bead-level dilution experiment. Bioinformatics BMC Genomics 2010

Git et al. Systematic comparison of microarray profiling, real-time PCR, and next-generation sequencing technologies for measuring differential microRNA expression. RNA 2010

Curtis et al. The pitfalls of platform comparison: DNA copy number array technologies assessed. BMC Genomics 2009

Schmidt et al. ChIP-seq: using high-throughput sequencing to discover protein-DNA interactions. Methods 2009

Das et al. Piwi and piRNAs act upstream of an endogenous siRNA pathway to suppress Tc3 transposon mobility in the Caenorhabditis elegans germline. Molecular Cell 2008

Other publications with data from the Genomics Core:

more coming soon...

Schwalie et al. Co-binding by YY1 identifies the transcriptionally active, highly conserved set of CTCF-bound regions in primate genomes. Genome Biology, Dec 2013.

Stefflova et al. Cooperativity and rapid evolution of cobound transcription factors in closely related mammals. Cell, Aug 2013.

Hussain et al. NSun2-mediated cytosine-5 methylation of vault noncoding RNA determines its processing into regulatory small RNAs. Cell Reports, Jul 2013.

Marshall et al. Global gene expression profiling reveals SPINK1 as a potential hepatocellular carcinoma marker. PLoS One, Mar 2013.

Ward et al. Latent Regulatory Potential of Human-Specific Repetitive Elements. Molecular Cell, Jan 2013.

Barbosa-Morais et al. The evolutionary landscape of alternative splicing in vertebrate species. Science, Dec 2012

Goncalves et al. Extensive compensatory cis-trans regulation in the evolution of mouse gene expression. Genome Research, Aug 2012.

Faure et al. Cohesin regulates tissue-specific expression by stabilizing highly occupied cis-regulatory modules. Genome Research, Jul 2012.

Chandra et al. Independence of repressive histone marks and chromatin compaction during senescent heterochromatic layer formation. Molecular Cell, Jul 2012.

Kutter et al. Rapid turnover of long noncoding RNAs and the evolution of gene expression. PLoS Genetics, Jul 2012.

Schmidt et al. Waves of retrotransposon expansion remodel genome organization and CTCF binding in multiple mammalian lineages. Cell, Jan 2012.

Nascimento et al. The opposing transcriptional functions of Sin3a and c-Myc are required to maintain tissue homeostasis. Nature Cell Biology, Nov 2011.

Kutter et al. Pol III binding in six mammals shows conservation among amino acid isotypes despite divergence among tRNA genes. Nature Genetics, Aug 2011.

Ip et al. Global impact of RNA polymerase II elongation inhibition on alternative splicing regulation. Genome Research, Mar 2011.

Schmidt et al. Five-vertebrate ChIP-seq reveals the evolutionary dynamics of transcription factor binding. Science, May 2010.

Schmidt et al. A CTCF-independent role for cohesin in tissue-specific transcription. Genome Research, May 2010.

Molnar et al. Small Silencing RNAs in Plants Are Mobile and Direct Epigenetic Modification in Recipient Cells. Science, May 2010.

Wilson et al. Species-specific transcription in mice carrying human chromosome 21. Science, Jul 2008.

Schmidt et al. Genome-scale validation of deep-sequencing libraries. PLoS One, Oct 2008.