Below are a selection of scientific publications, along with what I consider the reasons for their significance.
For a complete list, see my curriculum vitae.
Methods and algorithm development
Malde 2013a uses a database of intermediate sequences to construct pairwise alignments that
are roughly twice as accurate as direct BLAST alignments.
Skern 2013 uses sealouse data to examine the effect of inbreeding the host organism
on genome assembly.
Balzer 2013 develops a new method for duplicate filtering for 454 sequence data.
Balzer 2010 and Balzer 2011 investigate the characteristics of 454 sequencing data, and we develop
a sequencing simulator, FlowSim.
In Malde 2008, I develop a natural extension of the family of standard local and global
alignment algorithms to generate more accurate scores by taking Phred qualities into
Malde 2006a and Schneeberger 2005 introduce
a novel method for library-less masking of repeats (i.e. without a priori knowledge of them).
Introduction of new methods
Malde 2013b applies Software Transactional Memory to sequence assembly, which
makes it possible to parallelize the entire process of the traditional overlap-layout-consensus assembly strategy.
Malde 2009 is to my knowledge the first application of Bloom filters to bioinformatics.
Malde 2006b demonstrates a very simple, efficient and succinct way to translate PSSM
scores into p-values using lazy evaluation.
Malde 2011 implements a free utility for extracting information from binary 454 sequence data
(SFF files) and generating statistics.
Malde 2005 is an early implementation of the now ubiquitous de Bruijn graph assembly, applied to EST sequences.
Malde 2003 applies suffix arrays to sequence clustering.
In Malde 2010 I discovered that variation in background radiation was not accounted
for properly, leading to incorrect analysis. In response, Copenhagen University Hospital (Rigshospitalet) has modified their analysis to incorporate this.
I also participate with analysis and data management in many biologically oriented
papers, some recently published examples are Kleppe 2012, Star 2011, and Edvardsen 2011.