Publications by authors named "Joseph D Szustakowski"

22Publications

The use of haplotype-specific transcripts improves sample annotation consistency.

Biomark Res 2014 30;2:17. Epub 2014 Sep 30.

Novartis Institutes for BioMedical Research (NIBR), Biomarker Development, Fabrikstrasse 10.13, CH-4002 Basel, Switzerland.

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http://dx.doi.org/10.1186/2050-7771-2-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4184161PMC
October 2014

DeconRNASeq: a statistical framework for deconvolution of heterogeneous tissue samples based on mRNA-Seq data.

Bioinformatics 2013 Apr 21;29(8):1083-5. Epub 2013 Feb 21.

Biomarker Development, Translational Medicine, Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/btt090DOI Listing
April 2013

RAMP: a bioinformatics framework for researching imaging agents through molecular pathways.

Mol Imaging 2013 Jan-Feb;12(1):2-7

Novartis Institutes for Biomedical Research, Biomarker Development, Cambridge, MA 02139, USA.

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July 2013

Uncovering mechanisms of transcriptional regulations by systematic mining of cis regulatory elements with gene expression profiles.

BioData Min 2008 Jul 17;1(1). Epub 2008 Jul 17.

Developmental and Molecular Pathways, Novartis Institutes For Biomedical Research Inc, 250 Massachusetts Avenue, Cambridge, MA 02139, USA.

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http://dx.doi.org/10.1186/1756-0381-1-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2553773PMC
July 2008

Dynamic resolution of functionally related gene sets in response to acute heat stress.

BMC Mol Biol 2007 Jun 5;8:46. Epub 2007 Jun 5.

Developmental and Molecular Pathways, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts, USA.

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http://dx.doi.org/10.1186/1471-2199-8-46DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1904231PMC
June 2007

Extending the pathway analysis framework with a test for transcriptional variance implicates novel pathway modulation during myogenic differentiation.

Bioinformatics 2007 Jun 28;23(11):1356-62. Epub 2007 Mar 28.

Diabetes and Metabolism Disease Area, Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA.

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http://dx.doi.org/10.1093/bioinformatics/btm116DOI Listing
June 2007

Pyruvate induces mitochondrial biogenesis by a PGC-1 alpha-independent mechanism.

Am J Physiol Cell Physiol 2007 May 20;292(5):C1599-605. Epub 2006 Dec 20.

Novartis Institutes for BioMedical Research, 100 Technology Square, Cambridge, MA 02139, USA.

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http://dx.doi.org/10.1152/ajpcell.00428.2006DOI Listing
May 2007

Identification of novel pathway regulation during myogenic differentiation.

Genomics 2006 Jan 21;87(1):129-38. Epub 2005 Nov 21.

Life Science Informatics, Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA.

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http://dx.doi.org/10.1016/j.ygeno.2005.08.009DOI Listing
January 2006

Less is more: towards an optimal universal description of protein folds.

Bioinformatics 2005 Sep;21 Suppl 2:ii66-71

Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA.

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http://bioinformatics.oxfordjournals.org/content/21/suppl_2/
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http://bioinformatics.oxfordjournals.org/cgi/doi/10.1093/bio
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http://dx.doi.org/10.1093/bioinformatics/bti1111DOI Listing
September 2005

Clustering protein sequences with a novel metric transformed from sequence similarity scores and sequence alignments with neural networks.

BMC Bioinformatics 2005 Oct 3;6:242. Epub 2005 Oct 3.

Biomedical Computing, Genome and Proteome Sciences, Novartis Institutes for BioMedical Research, Inc., Cambridge, MA 02139, USA.

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http://dx.doi.org/10.1186/1471-2105-6-242DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1261163PMC
October 2005

Computational identification of operons in microbial genomes.

Genome Res 2002 Aug;12(8):1221-30

Bioinformatics Graduate Program, Boston University, Boston, Massachusetts 02215, USA.

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http://dx.doi.org/10.1101/gr.200602DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC186635PMC
August 2002

Gene discovery in the auditory system: characterization of additional cochlear-expressed sequences.

J Assoc Res Otolaryngol 2002 Mar;3(1):45-53

Department of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women's Hospital, Boston, MA 02115, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3202364PMC
http://dx.doi.org/10.1007/s101620020005DOI Listing
March 2002