Publications

IDBA-UD: a <i>de novo</i> assembler for single-cell and metagenomic sequencing data with highly uneven depth

Abstract Motivation: Next-generation sequencing allows us to sequence reads from a microbial environment using single-cell sequencing or metagenomic sequencing technologies. How...

Molden: a pre- and post-processing program for molecular and electronic structures*

De novo assembly of human genomes with massively parallel short read sequencing

Next-generation massively parallel DNA sequencing technologies provide ultrahigh throughput at a substantially lower unit data cost; however, the data are very short read length...

De novo mutations in schizophrenia implicate synaptic networks

GeneMark.hmm: new solutions for gene finding

The number of completely sequenced bacterial genomes has been growing fast. There are computer methods available for finding genes but yet there is a need for more accurate algo...

Markov Chains

Markov chains are central to the understanding of random processes. This is not only because they pervade the applications of random processes, but also because one can calculat...

A framework for the interpretation of de novo mutation in human disease

De Novo Hair Follicle Morphogenesis and Hair Tumors in Mice Expressing a Truncated β-Catenin in Skin

Swarm: robust and fast clustering method for amplicon-based studies

Popular de novo amplicon clustering methods suffer from two fundamental flaws: arbitrary global clustering thresholds, and input-order dependency induced by centroid selection. ...

GAGE: A critical evaluation of genome assemblies and assembly algorithms

New sequencing technology has dramatically altered the landscape of whole-genome sequencing, allowing scientists to initiate numerous projects to decode the genomes of previousl...

De novo assembly and genotyping of variants using colored de Bruijn graphs

Measurement of Separate Cosmic-Ray Electron and Positron Spectra with the Fermi Large Area Telescope

We measured separate cosmic-ray electron and positron spectra with the Fermi Large Area Telescope. Because the instrument does not have an onboard magnet, we distinguish the two...