Life, the universe, and everything: an interview with David Haussler. Interviewed by Jane Gitschier.
Published in PLoS Genetics
The Cancer Genomics Hub (CGHub): overcoming cancer through the power of torrential data.
Published in Database
The Cancer Genomics Hub (CGHub) is the online repository of the sequencing programs of the National Cancer Institute (NCI), including The Cancer Genomics Atlas (TCGA), the Cancer Cell Line Encyclopedia (CCLE) and the Therapeutically Applicable Research to Generate Effective Treatments (TARGET) projects, with data from 25 different types of cancer. ...
The ENCODE Project at UC Santa Cruz.
Published in Nucleic Acids Research
The goal of the Encyclopedia Of DNA Elements (ENCODE) Project is to identify all functional elements in the human genome. The pilot phase is for comparison of existing methods and for the development of new methods to rigorously analyze a defined 1% of the human genome sequence. Experimental datasets are focused on the origin of replication, DNase ...
A high-resolution map of human evolutionary constraint using 29 mammals.
Published in Nature
The comparison of related genomes has emerged as a powerful lens for genome interpretation. Here we report the sequencing and comparative analysis of 29 eutherian genomes. We confirm that at least 5.5% of the human genome has undergone purifying selection, and locate constrained elements covering ∼4.2% of the genome. We use evolutionary signatures ...
Building a pan-genome reference for a population.
Published in Journal of Computational Biology
A reference genome is a high quality individual genome that is used as a coordinate system for the genomes of a population, or genomes of closely related subspecies. Given a set of genomes partitioned by homology into alignment blocks we formalize the problem of ordering and orienting the blocks such that the resulting ordering maximally agrees wit...
Species-specific endogenous retroviruses shape the transcriptional network of the human tumor suppressor protein p53.
Published in Proceedings of the National Academy of Sciences
The evolutionary forces that establish and hone target gene networks of transcription factors are largely unknown. Transposition of retroelements may play a role, but its global importance, beyond a few well described examples for isolated genes, is not clear. We report that LTR class I endogenous retrovirus (ERV) retroelements impact considerably ...
Support vector machine classification and validation of cancer tissue samples using microarray expression data.
Published in Bioinformatics
Sequence comparisons using multiple sequences detect three times as many remote homologues as pairwise methods.
Published in Journal of Molecular Biology
The sequences of related proteins can diverge beyond the point where their relationship can be recognised by pairwise sequence comparisons. In attempts to overcome this limitation, methods have been developed that use as a query, not a single sequence, but sets of related sequences or a representation of the characteristics shared by related sequen...
Canonical, stable, general mapping using context schemes.
Published in Bioinformatics
Thousands of human mobile element fragments undergo strong purifying selection near developmental genes.
Published in Proceedings of the National Academy of Sciences
At least 5% of the human genome predating the mammalian radiation is thought to have evolved under purifying selection, yet protein-coding and related untranslated exons occupy at most 2% of the genome. Thus, the majority of conserved and, by extension, functional sequence in the human genome seems to be nonexonic. Recent work has highlighted a han...
The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genom...
Published in Genome Research
Effective use of the human and mouse genomes requires reliable identification of genes and their products. Although multiple public resources provide annotation, different methods are used that can result in similar but not identical representation of genes, transcripts, and proteins. The collaborative consensus coding sequence (CCDS) project track...
Using the Fisher kernel method to detect remote protein homologies.
Published in International Conference on Intelligent Systems for Molecular Biology
A new method, called the Fisher kernel method, for detecting remote protein homologies is introduced and shown to perform well in classifying protein domains by SCOP superfamily. The method is a variant of support vector machines using a new kernel function. The kernel function is derived from a hidden Markov model. The general approach of combinin...
The UCSC Genome Browser Database: update 2006.
Published in Nucleic Acids Research
The University of California Santa Cruz Genome Browser Database (GBD) contains sequence and annotation data for the genomes of about a dozen vertebrate species and several major model organisms. Genome annotations typically include assembly data, sequence composition, genes and gene predictions, mRNA and expressed sequence tag evidence, comparative...
Sequence landscapes.
Published in Nucleic Acids Research
We describe a method for representing the structure of repeating sequences in nucleic-acids, proteins and other texts. A portion of the sequence is presented at the bottom of a CRT screen. Above the sequence is its landscape, which looks like a mountain range. Each mountain corresponds to a subsequence of the sequence. At the peak of every mountain...
Bounds for predictive errors in the statistical mechanics of supervised learning.
Published in Physical Review Letters
LS-SNP: large-scale annotation of coding non-synonymous SNPs based on multiple information sources.
Published in Bioinformatics
Optimally parsing a sequence into different classes based on multiple types of evidence.
Published in International Conference on Intelligent Systems for Molecular Biology
We consider the problem of parsing a sequence into different classes of subsequences. Two common examples are finding the exons and introns in genomic sequences and identifying the secondary structure domains of protein sequences. In each case there are various types of evidence that are relevant to the classification, but none are completely relia...
Computational screening of conserved genomic DNA in search of functional noncoding elements.
Published in Nature Methods
Integrative analysis of 111 reference human epigenomes.
Published in Nature
The reference human genome sequence set the stage for studies of genetic variation and its association with human disease, but epigenomic studies lack a similar reference. To address this need, the NIH Roadmap Epigenomics Consortium generated the largest collection so far of human epigenomes for primary cells and tissues. Here we describe the integ...
The UCSC Known Genes.
Published in Bioinformatics
The University of California Santa Cruz (UCSC) Known Genes dataset is constructed by a fully automated process, based on protein data from Swiss-Prot/TrEMBL (UniProt) and the associated mRNA data from Genbank. The detailed steps of this process are described. Extensive cross-references from this dataset to other genomic and proteomic data were cons...
