Difference between pages "Research Interests" and "Publications"

Revision as of 17:20, 26 April 2011

Identification of miR-21 targets in breast cancer cells using a quantitative proteomic approach. Yang Y, Chaerkady R, Beer MA, Mendell JT, Pandey A. Proteomics. 2009 Mar;9(5):1374-84

Lin-28B transactivation is necessary for Myc-mediated let-7 repression and proliferation. Chang TC, Zeitels LR, Hwang HW, Chivukula RR, Wentzel EA, Dews M, Jung J, Gao P, Dang CV, Beer MA, Thomas-Tikhonenko A, Mendell JT. Proc Natl Acad Sci U S A. 2009 Mar 3;106(9):3384-9. Epub 2009 Feb 11.

Metrics of sequence constraint overlook regulatory sequences in an exhaustive analysis at phox2b. McGaughey DM, Vinton RM, Huynh J, Al-Saif A, Beer MA, McCallion AS. Genome Res. 2008 Feb;18(2):252-60. Epub 2007 Dec 10

Transactivation of miR-34a by p53 broadly influences gene expression and promotes apoptosis. Chang TC, Wentzel EA, Kent OA, Ramachandran K, Mullendore M, Lee KH, Feldmann G, Yamakuchi M, Ferlito M, Lowenstein CJ, Arking DE, Beer MA, Maitra A, Mendell JT. Mol Cell. 2007 Jun 8;26(5):745-52. Epub 2007 May 31

Functional characterization of a novel Ku70/80 pause site at the H19/Igf2 imprinting control region. D. J. Katz, M. A. Beer, J. M. Levorse and S. M. Tilghman, Mol Cell Biol 25, p3855-3863 (2005).

Whole-genome discovery of transcription factor finding sites by network-level conservation. M. Pritsker, Y. C. Liu, M. A. Beer, and S. Tavazoie, Genome Res. 2004 Jan;14(1):99-108. Epub 2003 Dec 12.

Predicting Gene Expression from Sequence. M. A. Beer and S. Tavazoie, Cell 117, p185-198 (2004)

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-The ultimate goal of our research is to understand how genomic DNA sequence specifies gene regulation. We are currently focused on 1) developing computational tools to identify functional regulatory elements in non-coding DNA, and 2) experimentally testing and characterizing how these elements function.
+* [http://www.ncbi.nlm.nih.gov/pubmed/19253296 Identification of miR-21 targets in breast cancer cells using a quantitative proteomic approach. Yang Y, Chaerkady R, Beer MA, Mendell JT, Pandey A. Proteomics. 2009 Mar;9(5):1374-84]
-In our computational work, we are using microarray gene expression data, genome-wide location analysis, and whole-genome DNA sequence to systematically identify DNA functional elements and infer combinatorial regulatory logic. We use pattern recognition algorithms to identify over-represented and phylogenetically conserved DNA sequence elements (or putative transcription factor binding sites). We then use a probabilistic Bayesian network to find the most likely functional constraints on the position, spacing, orientation, and combinations of these DNA sequence elements. This methodology has generated a large set of high confidence predictions for regulatory interactions, and is in principle applicable to any organism with microarray and genome sequence data.
+* [http://www.ncbi.nlm.nih.gov/pubmed/19211792 Lin-28B transactivation is necessary for Myc-mediated let-7 repression and proliferation. Chang TC, Zeitels LR, Hwang HW, Chivukula RR, Wentzel EA, Dews M, Jung J, Gao P, Dang CV, Beer MA, Thomas-Tikhonenko A, Mendell JT. Proc Natl Acad Sci U S A. 2009 Mar 3;106(9):3384-9. Epub 2009 Feb 11.]
-In our experimental work, we are testing these computational predictions by rapid generation of transgenic GFP reporter strains in C. elegans via microparticle bombardment. C. elegans is an attractive model system for several reasons:
+* [http://www.ncbi.nlm.nih.gov/pubmed/18071029 Metrics of sequence constraint overlook regulatory sequences in an exhaustive analysis at phox2b. McGaughey DM, Vinton RM, Huynh J, Al-Saif A, Beer MA, McCallion AS. Genome Res. 2008 Feb;18(2):252-60. Epub 2007 Dec 10]
-* Relevance to human disease: About 60% of C. elegans genes have a human homologue (Harris et al., NAR 2004); and 80% of genes implicated in human cancer have a worm homologue (Futreal et al., Nat Rev Cancer 2004; Poulin et al, Oncogene 2004).
+* [http://www.ncbi.nlm.nih.gov/pubmed/17540599 Transactivation of miR-34a by p53 broadly influences gene expression and promotes apoptosis. Chang TC, Wentzel EA, Kent OA, Ramachandran K, Mullendore M, Lee KH, Feldmann G, Yamakuchi M, Ferlito M, Lowenstein CJ, Arking DE, Beer MA, Maitra A, Mendell JT. Mol Cell. 2007 Jun 8;26(5):745-52. Epub 2007 May 31]
-* The high quality of the genome sequence data and microarray tools.
-* Rapid and effective transformation techniques and GFP reporter assays.
+* [http://www.ncbi.nlm.nih.gov/pubmed/15870260 Functional characterization of a novel Ku70/80 pause site at the H19/Igf2 imprinting control region. D. J. Katz, M. A. Beer, J. M. Levorse and S. M. Tilghman, Mol Cell Biol 25, p3855-3863 (2005).]
-* Availablity of bacterial feeding library for genome wide RNAi screens to further characterize regulatory interactions.
-* Relative ease and cost of strain maintenance.
+* [http://www.ncbi.nlm.nih.gov/pubmed/14672978 Whole-genome discovery of transcription factor finding sites by network-level conservation. M. Pritsker, Y. C. Liu, M. A. Beer, and S. Tavazoie, Genome Res. 2004 Jan;14(1):99-108. Epub 2003 Dec 12.]
+* [http://www.ncbi.nlm.nih.gov/pubmed/15084257 Predicting Gene Expression from Sequence. M. A. Beer and S. Tavazoie, Cell 117, p185-198 (2004)]

Difference between pages "Research Interests" and "Publications"

Revision as of 17:20, 26 April 2011

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