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Genomes

van Bakel et al., 2011, Genome Biology
"The draft genome and transcriptome of Cannabis sativa."



Cannabis genome browser

ChIP-seq

Schmitges et al., 2016, Genome Research
"Multiparameter functional diversity of human C2H2 zinc finger proteins."



Supplementary Data
Najafabadi et al., 2015, Nature Biotech
"C2H2 zinc finger proteins greatly expand the human regulatory lexicon."



Supplementary Data

PBM experiments

Narasimhan et al., 2015, eLife
"Mapping and analysis of Caenorhabditis elegans transcription factor sequence specificities."



Supplementary Data
Weirauch et al., 2014, Cell
"Determination and inference of eukaryotic transcription factor sequence specificity."



Supplementary Data
Weirauch et al., 2013, Nature Biotechnology
"Evaluation of methods for modeling transcription factor sequence specificity."



Supplementary Data
Lam et al., 2011, Nucleic Acids Research
"Sequence specificity is obtained from the majority of modular C2H2 zinc-finger arrays."



Supplementary Data
Badis et al., 2008, Molecular Cell
"A new library of yeast transcription factor motifs reveals a widespread function for Rsc3 in targeting nucleosome exclusion at promoters"



Supplementary Data
Alleyne et al., 2008, Bioinformatics
"Predicting the Binding Preference of Transcription Factors to Individual DNA k-mers"



Supplementary Data
Berger, Badis et al., 2008, Cell
"Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences"



Supplementary Data

RNA-binding protein motifs

Ray et al., 2013, Nature
"A compendium of RNA-binding motifs for decoding gene regulation."



Supplementary Data
Ray et al., 2009, Nature Biotechnology
"RNAcompete: a method for rapid and systematic analysis of the RNA recognition specificities of RNA-binding proteins"

Supplementary Data

Databases

Database of TF sequence specificities across Eukarya
Created to accompany Weirauch et al., 2014, Cell



CisBP
Database of RNA-binding protein sequence specificities across Eukarya
Created to accompany Ray et al., 2013, Nature



CisBP-RNA
de Boer et al., 2011, NAR
"YeTFaSCo: a database of evaluated yeast transcription factor sequence specificities."



YeTFasCo
Cook et al., 2010, NAR
"RBPDB: a database of RNA-binding specificities."



RBP-DB

Models of transcription

de Boer et al., 2013, Genome Research
"A Unified Model for yeast transcript definition"



TranscriptionModel

Yeast mRNA expression data

Chua et al., 2006, PNAS
"Identifying transcription factor functions and targets by phenotypic activation"

Microarray expression analysis of overexpressors and knockouts for 55 yeast transcription factors

Supplementary Data
Mnaimneh et al., 2004, Cell
"Exploration of essential gene functions via titratable promoter alleles"

Microarray expression analysis of tet-promoter alleles of 200 essential yeast genes

Supplementary Data
Grigull et al., 2004, Molecular and Cellular Biology
"Genome-wide analysis of mRNA decay using transcription inhibitors and microarrays reveals post-transcriptional control of ribosome biogenesis factors"

Microarray analysis of yeast mRNA decay profiles

Supplementary Data
Archives: pre-2001 Rosetta Inpharmatics data
Holds supplementary data previously hosted at http://www.rii.com/

Supplementary Data

Mouse mRNA expression data

Lovegrove, Peņa-Castillo et al., 2006 BMC Genomics
"Simultaneous host and parasite expression profiling identifies tissue-specific transcriptional programs associated with susceptibility or resistance to experimental cerebral malaria"

Expression analysis of both Plasmodium berghei and mouse over the course of a malaria infection

Supplementary Data
Zhang et al., 2006 Nucleic Acids Research
"Zfp206 regulates ES cell gene expression and differentiation"

Expression analysis of overexpression and knockdown of Zfp206 in mouse Embryonic Stem cells

Supplementary Data
Frey et al., 2005, Nature Genetics
"Genome-wide analysis of mouse transcription using exon-resolution microarrays and factor graphs"

Expression analysis of over one million known and predicted mouse exons over 12 pools of mRNA from mouse tissues

Supplementary Data
Zhang, Morris et al., 2004, Journal of Biology
"The functional landscape of mouse gene expression"

Expression analysis of ~40,000 known and predicted mouse genes in 55 organs and tissues

Supplementary Data Viewer (MGPD)

Yeast noncoding RNA data

Leeds et al., 2006, Molecular and Cellular Biology
"The Splicing Factor Prp43, a DEAH box ATPase, Functions in Ribosome Biogenesis"

Supplementary Data
Hoang et al., 2005, Molecular and Cellular Biology
"Esf2p, a U3-associated factor required for small-subunit processome assembly and compaction"

Supplementary Data
Hiley et al., 2005, Nucleic Acids Research
"Global analysis of yeast RNA processing by microarray identifies new targets of Rnase III and uncovers a link between tRNA 5'-end processing and tRNA splicing"

Supplementary Data
Xing et al., 2004, Journal of Biological Chemistry
"The specificities of four yeast dihydrouridine synthetases for cytoplasmic tRNAs"

Supplementary Data
Peng et al., 2003, Cell
"A panoramic view of yeast non-coding RNA processing"

Supplementary Data

Mouse noncoding RNA data

Babak et al., 2005, BMC Genomics
"A systematic search for new mammalian noncoding RNAs indicates little conserved intergenic transcription"

Supplementary Data
Babak et al., 2004, RNA
"Probing microRNAs with microarrays: tissue specificity and functional inference"

Supplementary Data

Reagents

Mnaimneh et al., 2004, Cell
"Exploration of essential gene functions via titratable promoter alleles"

Yeast tet-promoter strains

Supplementary Data

Other data types, tools, etc.

Tillo and Hughes, 2009, BMC Bioinformatics
"G+C content dominates intrinsic nucleosome occupancy"

Supplementary Data
Chan et al., 2009, Journal of Biology
"Conservation of core gene expression in vertebrate tissues"

Supplementary Data
Peņa-Castillo, 2008, Genome Biology
"A critical assessment of Mus musculus gene function prediction using integrated genomic evidence"

Supplementary Data
Lee et al., 2007, Nature Genetics
"A high-resolution atlas of nucleosome occupancy in yeast"

Supplementary Data
Hughes and Peņa-Castillo, 2007, Genetics
"Why are there still over 1,000 uncharacterized yeast genes?"

Yeast gene functions

Supplementary Data
Davierwala et al., 2005, Nature Genetics
"The synthetic genetic interaction spectrum of essential genes"

Yeast genetic interactions involving essential genes

Supplementary Data
Mnaimneh et al., 2004, Cell
"Exploration of essential gene functions via titratable promoter alleles"

Cell size profiles, morphology, drug sensitivity

Supplementary Data
Hughes et al., 2004, Current Opinion in Microbiology
"The promise of functional genomics: completing the encyclopedia of a cell"

Predicted gene functions

Supplementary Data
Krogan et al., 2004, Molecular Cell
"High-definition macromolecular composition of yeast RNA processing complexes"

Protein complexes - data generated by the Greenblatt and Emili labs

Supplementary Data
Robinson et al., 2002, BMC Bioinformatics
"FUNSPEC: A Web-Based Cluster Interpreter for Yeast"

P-value calculator for yeast gene lists vs. annotation categories

Web site
Wu, Hughes et al., 2002, Nature Genetics
"Large-scale prediction of Saccharomyces cerevisiae gene function using overlapping transcriptional clusters"

Predicted yeast gene functions

Supplementary Data

r26 - 01 Feb 2017 - 04:09:43 - Main.mihai
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