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#	Item
501	Maximum likelihood estimation of optimal scaling factors for expression array normalization Alexander J. Harteminka , David K. Gifforda,b , Tommi S. Jaakkolab , and Richard A. Youngc a MIT Laboratory for Computer Scienc Add to Reading List Source URL: www.psrg.lcs.mit.edu Language: English - Date: 2013-07-14 14:56:24 Estimation theory DNA DNA microarray Microtechnology Maximum likelihood Standard deviation Normal distribution Normalization Statistics Microarrays Gene expression
502	a r t ic l e s Synergistic binding of transcription factors to cell-specific enhancers programs motor neuron identity npg Add to Reading List Source URL: www.psrg.lcs.mit.edu Language: English - Date: 2013-12-12 12:02:17 Transcription factors Cellular processes Neurulation Sonic hedgehog Induced pluripotent stem cell Cellular differentiation Neuron Neural tube Spinal cord Biology Nervous system Developmental biology
503	MARIS: Method for Analyzing RNA following Intracellular Sorting Sinisˇa Hrvatin1, Francis Deng1, Charles W. O’Donnell1,2, David K. Gifford2, Douglas A. Melton1,3* 1 The Harvard Department of Stem Cell and Regenerative Add to Reading List Source URL: www.psrg.lcs.mit.edu Language: English - Date: 2014-05-21 15:11:47 Chemistry RNA Gene expression Laboratory techniques Transcriptome RNA-Seq Reverse transcription polymerase chain reaction Cell biology Chromatin immunoprecipitation Biology Biochemistry Molecular biology
504	A n a ly s i s Discovery of directional and nondirectional pioneer transcription factors by modeling DNase profile magnitude and shape Add to Reading List Source URL: www.psrg.lcs.mit.edu Language: English - Date: 2014-05-21 15:52:05 Molecular genetics DNA Protein methods Chip-sequencing DNA binding site Chromatin immunoprecipitation Hypersensitive site DNase-Seq Chromatin Biology Transcription factors Gene expression
505	COMBINING LOCATION AND EXPRESSION DATA FOR PRINCIPLED DISCOVERY OF GENETIC REGULATORY NETWORK MODELS ALEXANDER J. HARTEMINK Duke University Department of Computer Science Box 90129, Durham, NC[removed] Add to Reading List Source URL: www.psrg.lcs.mit.edu Language: English - Date: 2003-05-27 14:50:51 Mycology Bayesian statistics Statistical models Gene regulatory network Systems biology Bayesian network Mating type Saccharomyces cerevisiae Algorithm Biology Microbiology Networks
506	Control of Transcription by Cell Size Chia-Yung Wu1,2, P. Alexander Rolfe3, David K. Gifford2,3,4, Gerald R. Fink1,2* 1 Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United State Add to Reading List Source URL: www.psrg.lcs.mit.edu Language: English - Date: 2011-01-04 15:46:51 Cellular processes Genetics RNA Ridge Transcriptome Gene Polyploid Cell cycle Ploidy Biology Gene expression Molecular biology
507	a r t ic l e s Saltatory remodeling of Hox chromatin in response to rostrocaudal patterning signals npg Add to Reading List Source URL: www.psrg.lcs.mit.edu Language: English - Date: 2013-12-12 11:20:25 Genes Proteins Gene expression Hox gene GDF11 Neural development Homeobox CDX2 Retinoic acid Biology Developmental biology Transcription factors
508	RESEARCH ARTICLES transport[removed]The model was also used for tracer forecasts during the MINOS campaign. 40. E. Roeckner et al. “The atmospheric general circulation model ECHAM-4: Model description and simulation of p Add to Reading List Source URL: www.psrg.lcs.mit.edu Language: English - Date: 2004-11-22 16:43:14 Genetics Networks Genomics Ridge Promoter Gene regulatory network Cell cycle Gene Ultrasensitivity Biology Gene expression Molecular biology
509	Discovering Regulatory Overlapping RNA Transcripts Timothy Danford1 , Robin Dowell1? , Sudeep Agarwala2 , Paula Grisafi2 , Gerald Fink2 , David Gifford1 1 Massachusetts Institute of Technology Add to Reading List Source URL: www.psrg.lcs.mit.edu Language: English - Date: 2012-03-04 09:49:22 Gene expression RNA Molecular biology DNA Tiling array Regulation of gene expression Gene RNA polymerase Transcription Biology Genetics Biochemistry
510	USING GRAPHICAL MODELS AND GENOMIC EXPRESSION DATA TO STATISTICALLY VALIDATE MODELS OF GENETIC REGULATORY NETWORKS ALEXANDER J. HARTEMINK MIT Laboratory for Computer Science 545 Technology Square, Cambridge, MA 02139 Add to Reading List Source URL: www.psrg.lcs.mit.edu Language: English - Date: 2013-07-14 14:56:24 Bayesian statistics Graphical models Estimation theory Latent variable Mutual information Maximum likelihood Variable-order Bayesian network Statistics Statistical models Bayesian networks

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