Joining forces in the quest for orthologs (2009)
Gabaldón, Toni, Dessimoz, Christophe, Huxley-Jones, Julie, Vilella, Albert J, Sonnhammer, Erik LL, Lewis, Suzanna
Abstract Better orthology-prediction resources would be beneficial for the whole biological community. A recent meeting discussed how to coordinate and leverage current efforts.
MetaTM - a consensus method for transmembrane protein topology prediction (2009)
Klammer, Martin, Messina, David N, Schmitt, Thomas, Sonnhammer, Erik LL
Abstract Background Transmembrane (TM) proteins are proteins that span a biological membrane one or more times. As their 3-D structures are hard to determine, experiments focus on identifying their...
Benchmarking homology detection procedures with low complexity filters (2009)
Forslund, Kristoffer, Sonnhammer, Erik LL
Background: Low-complexity sequence regions present a common problem in finding true homologs to a protein query sequence. Several solutions to this have been suggested, but a detailed comparison...
Employing conservation of co-expression to improve functional inference (2008)
Daub, Carsten O, Sonnhammer, Erik LL
Abstract Background Observing co-expression between genes suggests that they are functionally coupled. Co-expression of orthologous gene pairs across species may improve function prediction beyond...
Automatic extraction of reliable regions from multiple sequence alignments (2007)
Lassmann, Timo, Sonnhammer, Erik LL
Abstract Background High quality multiple alignments are crucial in the transfer of annotation from one genome to another. Multiple alignment methods strive to achieve ever increasing levels of...
NovelFam3000 – Uncharacterized human protein domains conserved across model organisms (2006)
Kemmer, Danielle, Podowski, Raf M, Arenillas, David, Lim, Jonathan, Hodges, Emily, Roth, Peggy, ...
Abstract Background Despite significant efforts from the research community, an extensive portion of the proteins encoded by human genes lack an assigned cellular function. Most metazoan proteins are...
Kalign – an accurate and fast multiple sequence alignment algorithm (2005)
Lassmann, Timo, Sonnhammer, Erik LL
Abstract Background The alignment of multiple protein sequences is a fundamental step in the analysis of biological data. It has traditionally been applied to analyzing protein families for conserved...
Scoredist: A simple and robust protein sequence distance estimator (2005)
Sonnhammer, Erik LL, Hollich, Volker
Abstract Background Distance-based methods are popular for reconstructing evolutionary trees thanks to their speed and generality. A number of methods exist for estimating distances from sequence...
Wistrand, Markus, Sonnhammer, Erik LL
Abstract Background Profile hidden Markov model (HMM) techniques are among the most powerful methods for protein homology detection. Yet, the critical features for successful modelling are not fully...
Genome informatics: taming the avalanche of genomic data (2004)
A report on the fourth Cold Spring Harbor Laboratory/Wellcome Trust Conference on Genome Informatics, Hinxton, UK, 22-26 September 2004.
Functional characterization in Caenorhabditis elegansof transmembrane worm-human orthologs (2004)
Henricson, Anna, Sonnhammer, Erik LL, Baillie, David L, Gomes, Ana
Abstract Background The complete genome sequences for human and the nematode Caenorhabditis elegans offer an opportunity to learn more about human gene function through functional characterization of...
Profiled support vector machines for antisense oligonucleotide efficacy prediction (2004)
Camps-Valls, Gustavo, Chalk, Alistair M, Serrano-López, Antonio J, Martín-Guerrero, José D, Sonnhammer, Erik LL
Abstract Background This paper presents the use of Support Vector Machines (SVMs) for prediction and analysis of antisense oligonucleotide (AO) efficacy. The collected database comprises 315 AO...
Profiled support vector machines for antisense oligonucleotide efficacy prediction (2004)
Camps-Valls, Gustavo, Chalk, Alistair Morgan, Serrano-López, Antonio J., Martín-Guerrero, José D., Sonnhammer, Erik LL
Background This paper presents the use of Support Vector Machines (SVMs) for prediction and analysis of antisense oligonucleotide (AO) efficacy. The collected database comprises 315 AO molecules...
Profiled support vector machines for antisense oligonucleotide efficacy prediction (2004)
Camps-Valls, Gustavo, Chalk, Alistair Morgan, Serrano-López, Antonio J., Martín-Guerrero, José D., Sonnhammer, Erik LL
Background This paper presents the use of Support Vector Machines (SVMs) for prediction and analysis of antisense oligonucleotide (AO) efficacy. The collected database comprises 315 AO molecules...
Erik Ll Sonnhammer, Volker Hollich
Background: Distance-based methods are popular for reconstructing evolutionary trees thanks to their speed and generality. A number of methods exist for estimating distances from sequence alignments,...
Profiled support vector machines for antisense oligonucleotide efficacy prediction (2004)
Camps-Valls, Gustavo, Chalk, Alistair Morgan, Serrano-López, Antonio J., Martín-Guerrero, José D., Sonnhammer, Erik LL
Background This paper presents the use of Support Vector Machines (SVMs) for prediction and analysis of antisense oligonucleotide (AO) efficacy. The collected database comprises 315 AO molecules...
Bmc Genomics, Anna Henricson, Erik Ll Sonnhammer, David L Baillie, Ana Vaz Gomes
Research article Functional characterization in Caenorhabditis elegans of transmembrane worm-human orthologs
Profiled support vector machines for antisense oligonucleotide efficacy prediction
Camps-Valls, Gustavo, Chalk, Alistair M, Serrano-López, Antonio J, Martín-Guerrero, José D, Sonnhammer, Erik LL
Functional characterization in Caenorhabditis elegans of transmembrane worm-human orthologs
Henricson, Anna, Sonnhammer, Erik LL, Baillie, David L, Gomes, Ana Vaz
Genome informatics: taming the avalanche of genomic data
A report on the fourth Cold Spring Harbor Laboratory/Wellcome Trust Conference on Genome Informatics, Hinxton, UK, 22-26 September 2004.
NovelFam3000 – Uncharacterized human protein domains conserved across model organisms
Kemmer, Danielle, Podowski, Raf M, Arenillas, David, Lim, Jonathan, Hodges, Emily, Roth, Peggy, ...
Profiled support vector machines for antisense oligonucleotide efficacy prediction
Camps-Valls, Gustavo, Chalk, Alistair M, Serrano-López, Antonio J, Martín-Guerrero, José D, Sonnhammer, Erik LL
Functional characterization in Caenorhabditis elegans of transmembrane worm-human orthologs
Henricson, Anna, Sonnhammer, Erik LL, Baillie, David L, Gomes, Ana Vaz
Genome informatics: taming the avalanche of genomic data
A report on the fourth Cold Spring Harbor Laboratory/Wellcome Trust Conference on Genome Informatics, Hinxton, UK, 22-26 September 2004.
NovelFam3000 – Uncharacterized human protein domains conserved across model organisms
Kemmer, Danielle, Podowski, Raf M, Arenillas, David, Lim, Jonathan, Hodges, Emily, Roth, Peggy, ...
MetaTM - a consensus method for transmembrane protein topology prediction
Klammer, Martin, Messina, David N, Schmitt, Thomas, Sonnhammer, Erik LL
Joining forces in the quest for orthologs
Gabaldón, Toni, Dessimoz, Christophe, Huxley-Jones, Julie, Vilella, Albert J, Sonnhammer, Erik LL, Lewis, Suzanna
Building momentum to coordinate and leverage community orthology prediction resources.