Checking file: http://genome.ucsc.edu/goldenPath/pubs.html ---------------------------------- Link = Biased clustered substitutions in the human genome: the footprints of male-driven biased gene conversion URL = http://www.genome.org/cgi/content/abstract/gr.6395807v1 Response Code = 0 ---------------------------------- ---------------------------------- Link = Evolution of genes and genomes on the Drosophila phylogeny URL = http://www.nature.com/nature/journal/v450/n7167/full/nature06341.html Response Code = 0 ---------------------------------- ---------------------------------- Link = Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project URL = http://www.nature.com/nature/journal/v447/n7146/full/nature05874.html Response Code = 0 ---------------------------------- ---------------------------------- Link = PhenCode: connecting ENCODE data with mutations and phenotype URL = http://www3.interscience.wiley.com/cgi-bin/abstract/114129848/ABSTRACT Response Code = 0 ---------------------------------- ---------------------------------- Link = A second generation human haplotype map of over 3.1 million SNPs URL = http://www.nature.com/nature/journal/v449/n7164/full/nature06258.html Response Code = 0 ---------------------------------- ---------------------------------- Link = Human genome ultraconserved elements are ultraselected URL = http://www.sciencemag.org/cgi/content/abstract/317/5840/915?ijkey=fKd1P5nCfP5fo&keytype=ref&siteid=sci Response Code = 0 ---------------------------------- ---------------------------------- Link = reprints URL = http://www.sciencemag.org/cgi/reprint/317/5840/915?ijkey=fKd1P5nCfP5fo&keytype=ref&siteid=sci Response Code = 0 ---------------------------------- ---------------------------------- Link = supporting online materials] URL = http://www.sciencemag.org/cgi/content/full/317/5840/915/DC1?ijkey=%2FvY8%2Fa6EB7Vyk&keytype=ref&siteid=sci Response Code = 0 ---------------------------------- ---------------------------------- Link = A heuristic algorithm for reconstructing ancestral gene orders with duplications URL = http://www.springerlink.com/content/u531m71r72464p45/?p=b7bf5c849a504388a9c79d4e11291df4%3F%3D9 Response Code = 0 ---------------------------------- ---------------------------------- Link = Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome URL = http://www.genome.org/cgi/content/full/17/6/760 Response Code = 0 ---------------------------------- ---------------------------------- Link = 28-Way vertebrate alignment and conservation track in the UCSC Genome Browser URL = http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=retrieve&db=pubmed&list_uids=17984227&dopt=AbstractPlus Response Code = 0 ---------------------------------- ---------------------------------- Link = Ultraconserved elements are associated with homeostatic control of splicing regulators by alternative splicing and nonsense-mediated decay URL = http://www.genesdev.org/cgi/content/full/21/6/708 Response Code = 0 ---------------------------------- ---------------------------------- Link = Editing modifies the GABAA receptor subunit a3 URL = http://www.rnajournal.org/cgi/doi/10.1261/rna.349107 Response Code = 0 ---------------------------------- ---------------------------------- Link = Evolutionary and biomedical insights from the rhesus macaque genome URL = http://www.sciencemag.org/cgi/content/full/316/5822/222 Response Code = 0 ---------------------------------- ---------------------------------- Link = Targeted discovery of novel human exons by comparative genomics URL = http://www.genome.org/cgi/content/abstract/gr.7128207v1 Response Code = 0 ---------------------------------- ---------------------------------- Link = Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures URL = http://www.nature.com/nature/journal/v450/n7167/full/nature06340.html Response Code = 0 ---------------------------------- ---------------------------------- Link = Structured RNAs in the ENCODE selected regions of the human genome URL = http://www.genome.org/cgi/content/full/17/6/852 Response Code = 0 ---------------------------------- ---------------------------------- Link = Detecting coevolution in and among protein domains URL = http://compbiol.plosjournals.org/perlserv/?request=get-document&doi=10.1371%2Fjournal.pcbi.0030211 Response Code = 0 ---------------------------------- ---------------------------------- Link = Pseudogenes in the ENCODE regions: Consensus annotation, analysis of transcription and evolution URL = http://www.genome.org/cgi/content/full/17/6/839 Response Code = 0 ---------------------------------- ---------------------------------- Link = Comparative genomics search for losses of long-established genes on the human lineage URL = http://compbiol.plosjournals.org/perlserv/?request=get-document&doi=10.1371%2Fjournal.pcbi.0030247.eor Response Code = 0 ---------------------------------- ---------------------------------- Link = A distal enhancer and an ultraconserved exon are derived from a novel retroposon URL = http://www.nature.com/nature/journal/v441/n7089/abs/nature04696.html Response Code = 0 ---------------------------------- ---------------------------------- Link = Piloting the zebrafish genome browser URL = http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16372332&query_hl=1&itool=pubmed_docsum Response Code = 0 ---------------------------------- ---------------------------------- Link = Conserved noncoding sequences are selectively constrained and not mutation cold spots URL = http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16380714&itool=iconabstr&query_hl=20&itool=pubmed_docsum Response Code = 0 ---------------------------------- ---------------------------------- Link = Intronic Alternative Splicing Regulators Identified by Comparative Genomics in Nematodes URL = http://compbiol.plosjournals.org/perlserv/?request=get-document&doi=10.1371%2Fjournal.pcbi.0020086 Response Code = 0 ---------------------------------- ---------------------------------- Link = XML, SQL, and C URL = http://www.ddj.com/dept/database/193402895;jsessionid=31G1HTV04PNE2QSNDLRCKH0CJUNN2JVN Response Code = 0 ---------------------------------- ---------------------------------- Link = Reconstructing contiguous regions of an ancestral genome URL = http://www.genome.org/cgi/content/abstract/16/12/1557 Response Code = 0 ---------------------------------- ---------------------------------- Link = Identification and Classification of Conserved RNA Secondary Structures in the Human Genome URL = http://dx.doi.org/10.1371/journal.pcbi.0020033 Response Code = 0 ---------------------------------- ---------------------------------- Link = Forces shaping the fastest evolving regions in the human genome URL = http://genetics.plosjournals.org/perlserv/?request=get-document&doi=10.1371%2Fjournal.pgen.0020168 Response Code = 0 ---------------------------------- ---------------------------------- Link = An RNA gene expressed during cortical development evolved rapidly in humans URL = http://www.nature.com/nature/journal/v443/n7108/abs/nature05113.html;jsessionid=9795AD73E07CCA3325794A9BEBA344D5 Response Code = 0 ---------------------------------- ---------------------------------- Link = Common fragile sites, extremely large genes, neural development and cancer URL = http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16221525&itool=iconabstr&query_hl=8&itool=pubmed_docsum Response Code = 0 ---------------------------------- ---------------------------------- Link = Human chromosome 11 DNA sequence and analysis including novel gene identification URL = http://www.nature.com/nature/journal/v440/n7083/full/nature04632.html Response Code = 0 ---------------------------------- ---------------------------------- Link = RORA, a large common fragile site gene, is involved in cellular stress response URL = http://www.nature.com/onc/journal/v25/n20/abs/1209314a.html Response Code = 0 ---------------------------------- ---------------------------------- Link = Computational screening of conserved genomic DNA in search of functional noncoding elements URL = http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16170870&query_hl=4&itool=pubmed_docsum Response Code = 0 ---------------------------------- ---------------------------------- Link = Genomic regions exhibiting positive selection identified from dense genotype data URL = http://www.genome.org/cgi/content/abstract/15/11/1553 Response Code = 0 ---------------------------------- ---------------------------------- Link = Initial sequence of the chimpanzee genome and comparison with the human genome URL = http://www.nature.com/nature/journal/v437/n7055/full/nature04072.html Response Code = 0 ---------------------------------- ---------------------------------- Link = Ultraconserved elements in insect genomes: a highly conserved intronic sequence implicated in the control of homothorax mRNA splicing URL = http://www.genome.org/cgi/content/abstract/15/6/800 Response Code = 0 ---------------------------------- ---------------------------------- Link = A haplotype map of the human genome URL = http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16255080&query_hl=15&itool=pubmed_docsum Response Code = 0 ---------------------------------- ---------------------------------- Link = Exploring relationships and mining data with the UCSC Gene Sorter URL = http://www.genome.org/cgi/content/abstract/15/5/737 Response Code = 0 ---------------------------------- ---------------------------------- Link = Counterexample to a Claim About the Reconstruction of Ancestral Character States URL = http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16126665&query_hl=1 Response Code = 0 ---------------------------------- ---------------------------------- Link = DNA sequence and analysis of human chromosome 18 URL = http://www.nature.com/nature/journal/v437/n7058/abs/nature03983.html Response Code = 0 ---------------------------------- ---------------------------------- Link = The structure of a rigorously conserved RNA element within the SARS virus genome URL = http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371%2Fjournal.pbio.0030005 Response Code = 0 ---------------------------------- ---------------------------------- Link = The DNA sequence of the human X chromosome URL = http://www.nature.com/nature/journal/v434/n7031/abs/nature03440.html;jsessionid=AF942C085166B02D7215034DAFC14A2A Response Code = 0 ---------------------------------- ---------------------------------- Link = Identifying genetic networks underlying myometrial transition to labor URL = http://genomebiology.com/2005/6/2/R12 Response Code = 0 ---------------------------------- ---------------------------------- Link = The finished DNA sequence of human chromosome 12 URL = http://www.nature.com/nature/journal/v440/n7082/full/nature04569.html Response Code = 0 ---------------------------------- ---------------------------------- Link = Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes URL = http://www.genome.org/cgi/doi/10.1101/gr.3715005 Response Code = 0 ---------------------------------- ---------------------------------- Link = Sequence features in regions of weak and strong linkage disequilibrium URL = http://www.genome.org/cgi/content/abstract/15/11/1519 Response Code = 0 ---------------------------------- ---------------------------------- Link = Hotspots of mammalian chromosomal evolution URL = http://genomebiology.com/2004/5/4/R23 Response Code = 0 ---------------------------------- ---------------------------------- Link = Ultraconserved elements in the human genome URL = http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15131266&query_hl=1 Response Code = 0 ---------------------------------- ---------------------------------- Link = Reconstructing large regions of an ancestral mammalian genome in silico URL = http://www.genome.org/cgi/content/abstract/14/12/2412 Response Code = 0 ---------------------------------- ---------------------------------- Link = Aligning multiple genomic sequences with the threaded blockset aligner URL = http://www.genome.org/cgi/content/abstract/14/4/708 Response Code = 0 ---------------------------------- ---------------------------------- Link = The ENCODE (ENCyclopedia Of DNA Elements) Project URL = http://www.sciencemag.org/cgi/content/full/306/5696/636 Response Code = 0 ---------------------------------- ---------------------------------- Link = Analysis of human mRNAs with the reference genome sequence reveals potential errors, polymorphisms, and RNA editing URL = http://www.genome.org/cgi/content/abstract/14/10b/2034 Response Code = 0 ---------------------------------- ---------------------------------- Link = The DNA sequence and biology of human chromosome 19 URL = http://www.nature.com/nature/journal/v428/n6982/full/nature02399.html Response Code = 0 ---------------------------------- ---------------------------------- Link = Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution URL = http://www.nature.com/nature/journal/v432/n7018/full/nature03154.html Response Code = 0 ---------------------------------- ---------------------------------- Link = Finishing the euchromatic sequence of the human genome URL = http://www.nature.com/nature/journal/v431/n7011/full/nature03001.html Response Code = 0 ---------------------------------- ---------------------------------- Link = Comparative recombination rates in the rat, mouse, and human genomes URL = http://www.genome.org/cgi/content/abstract/14/4/528 Response Code = 0 ---------------------------------- ---------------------------------- Link = The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC) URL = http://www.genome.org/cgi/content/abstract/14/10b/2121 Response Code = 0 ---------------------------------- ---------------------------------- Link = Genome sequence of the brown Norway rat yields insights into mammalian evolution URL = http://www.nature.com/nature/journal/v428/n6982/full/nature02426.html Response Code = 0 ---------------------------------- ---------------------------------- Link = The structure and evolution of centromeric transition regions within the human genome URL = http://www.nature.com/nature/journal/v430/n7002/abs/nature02806.html Response Code = 0 ---------------------------------- ---------------------------------- Link = Combining phylogenetic and hidden Markov models in biosequence analysis URL = http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15285899 Response Code = 0 ---------------------------------- ---------------------------------- Link = Patterns of insertions and their covariation with substitutions in the rat, mouse and human genomes URL = http://www.genome.org/cgi/content/abstract/14/4/517 Response Code = 0 ---------------------------------- ---------------------------------- Link = Covariation in frequencies of substitution, deletion, transposition and recombination during eutherian evolution URL = http://www.genome.org/cgi/content/abstract/13/1/13 Response Code = 0 ---------------------------------- ---------------------------------- Link = The DNA sequence of human chromosome 7 URL = http://www.nature.com/nature/journal/v424/n6945/full/nature01782.html Response Code = 0 ---------------------------------- ---------------------------------- Link = Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes URL = http://www.pnas.org/cgi/content/abstract/1932072100v1 Response Code = 0 ---------------------------------- ---------------------------------- Link = Identification and characterization of multi-species conserved sequences URL = http://www.genome.org/cgi/content/abstract/13/12/2507?etoc Response Code = 0 ---------------------------------- ---------------------------------- Link = Human-mouse alignments with BLASTZ URL = http://www.genome.org/cgi/content/abstract/13/1/103 Response Code = 0 ---------------------------------- ---------------------------------- Link = Comparative analyses of multi-species sequences from targeted genomic regions URL = http://www.nature.com/nature/journal/v424/n6950/abs/nature01858.html Response Code = 0 ---------------------------------- ---------------------------------- Link = Highly accurate classification of Watson-Crick basepairs on termini of single DNA molecules URL = http://www.biophysj.org/cgi/content/abstract/84/2/967 Response Code = 0 ---------------------------------- ---------------------------------- Link = Genomewide analysis of mRNA processing in yeast using splicing-specific microarrays URL = http://www.sciencemag.org/cgi/content/abstract/296/5569/907 Response Code = 0 ---------------------------------- ---------------------------------- Link = Information theoretic dissection of pairwise contact potentials URL = http://www3.interscience.wiley.com/cgi-bin/abstract/97517898/START Response Code = 0 ---------------------------------- ---------------------------------- Link = BLAT - the BLAST-like alignment tool URL = http://www.genome.org/cgi/content/abstract/12/4/656 Response Code = 0 ---------------------------------- ---------------------------------- Link = autoSQL and autoXml: code generators from the Genome Project URL = http://www.linuxjournal.com/article.php?sid=5949 Response Code = 0 ---------------------------------- ---------------------------------- Link = The human genome browser at UCSC URL = http://www.genome.org/cgi/content/abstract/12/6/996 Response Code = 0 ---------------------------------- ---------------------------------- Link = Integration of cytogenetic landmarks into the draft sequence of the human genome URL = http://www.nature.com/nature/journal/v409/n6822/abs/409953a0.html Response Code = 0 ---------------------------------- ---------------------------------- Link = Initial sequencing and analysis of the human genome URL = http://www.nature.com/nature/journal/v409/n6822/abs/409860a0.html Response Code = 0 ---------------------------------- ---------------------------------- Link = A physical map of the human genome URL = http://www.nature.com/nature/journal/v409/n6822/full/409934a0.html Response Code = 0 ---------------------------------- ---------------------------------- Link = Assembly of the working draft of the human genome with gigAssembler URL = http://www.genome.org/cgi/content/abstract/GR-1832Rv1 Response Code = 0 ---------------------------------- ---------------------------------- Link = Knowledge-based analysis of microarray gene expression data using support vector machines URL = http://www.pnas.org/cgi/content/abstract/97/1/262 Response Code = 0 ---------------------------------- Count of links checked = 137 Count of error links = 78