Publications

UPARSE: highly accurate OTU sequences from microbial amplicon reads

Cluster analysis and display of genome-wide expression patterns

A system of cluster analysis for genome-wide expression data from DNA microarray hybridization is described that uses standard statistical algorithms to arrange genes according ...

A new mixing of Hartree–Fock and local density-functional theories

Previous attempts to combine Hartree–Fock theory with local density-functional theory have been unsuccessful in applications to molecular bonding. We derive a new coupling of th...

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

Molecular portraits of human breast tumours

Embryonic Stem Cell Lines Derived from Human Blastocysts

Human blastocyst-derived, pluripotent cell lines are described that have normal karyotypes, express high levels of telomerase activity, and express cell surface markers that cha...

RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models

Abstract Summary: RAxML-VI-HPC (randomized axelerated maximum likelihood for high performance computing) is a sequential and parallel program for inference of large phylogenies ...

The influence of polarization functions on molecular orbital hydrogenation energies

Integrative Analysis of Complex Cancer Genomics and Clinical Profiles Using the cBioPortal

The cBioPortal enables integration, visualization, and analysis of multidimensional cancer genomic and clinical data.

Self—Consistent Molecular Orbital Methods. XII. Further Extensions of Gaussian—Type Basis Sets for Use in Molecular Orbital Studies of Organic Molecules

Two extended basis sets (termed 5–31G and 6–31G) consisting of atomic orbitals expressed as fixed linear combinations of Gaussian functions are presented for the first row atoms...

UCHIME improves sensitivity and speed of chimera detection

Abstract Motivation: Chimeric DNA sequences often form during polymerase chain reaction amplification, especially when sequencing single regions (e.g. 16S rRNA or fungal Interna...

Tissue-based map of the human proteome

Protein expression across human tissues Sequencing the human genome gave new insights into human biology and disease. However, the ultimate goal is to understand the dynamic exp...