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List of works by Erik Sonnhammer

A Novel ACKR2-Dependent Role of Fibroblast-Derived CXCL14 in Epithelial-to-Mesenchymal Transition and Metastasis of Breast Cancer

scientific article published on 08 March 2019

A Workbench for large-scale sequence homology analysis

article

A combined transmembrane topology and signal peptide prediction method

scientific article (publication date: 14 May 2004)

A comparison of sequence and structure protein domain families as a basis for structural genomics.

scientific article published in June 1999

A comprehensive structural, biochemical and biological profiling of the human NUDIX hydrolase family

scientific article published on 16 November 2017

A dot-matrix program with dynamic threshold control suited for genomic DNA and protein sequence analysis

scientific article published in December 1995

A general model of G protein-coupled receptor sequences and its application to detect remote homologs

scientific article published in February 2006

A genome-wide IR-induced RAD51 foci RNAi screen identifies CDC73 involved in chromatin remodeling for DNA repair.

scientific article

A large-scale benchmark of gene prioritization methods

scientific article published on 21 April 2017

A novel method for crosstalk analysis of biological networks: improving accuracy of pathway annotation

scientific article published on 22 September 2016

A novel transmembrane topology of presenilin based on reconciling experimental and computational evidence

article

Advances and Applications in the Quest for Orthologs

scientific article published on 01 October 2019

Advantages of combined transmembrane topology and signal peptide prediction--the Phobius web server

scientific article

An HMM posterior decoder for sequence feature prediction that includes homology information

scientific article published in June 2005

Analysis of Protein Domain Families in Caenorhabditis elegans ⬇️

scientific article published on December 1, 1997

Assessment of protein distance measures and tree-building methods for phylogenetic tree reconstruction

scientific article published on 27 July 2005

Automated ortholog inference from phylogenetic trees and calculation of orthology reliability

scientific article

Automatic assessment of alignment quality

scientific article

Automatic clustering of orthologs and in-paralogs from pairwise species comparisons

scientific article (publication date: 14 December 2001)

Automatic clustering of orthologs and inparalogs shared by multiple proteomes

scientific article published in July 2006

Automatic extraction of reliable regions from multiple sequence alignments.

scientific article

Avoiding pitfalls in L1-regularised inference of gene networks.

scientific article published on 7 November 2014

Avoiding pitfalls in gene (co)expression meta-analysis

scientific article

Benchmarking homology detection procedures with low complexity filters

scientific article published on 20 July 2009

Benchmarking the next generation of homology inference tools

scientific article published on June 2016

Big data and other challenges in the quest for orthologs

scientific article

ChromoWheel: a new spin on eukaryotic chromosome visualization

scholarly article by S. Ekdahl & Erik Sonnhammer published 22 January 2004 in Bioinformatics

Chromosomal clustering of nuclear genes encoding mitochondrial and chloroplast proteins in Arabidopsis

article

Classification of transmembrane protein families in the Caenorhabditis elegans genome and identification of human orthologs

scientific article published on November 2000

Comparative analysis and unification of domain-domain interaction networks

scientific article

Comparative interactomics with Funcoup 2.0.

scientific article

Comparison of the human germline and rearranged VH repertoire reveals complementarity between germline variability and somatic mutation

article

Comprehensive analysis of orthologous protein domains using the HOPS database

scientific article

Comprehensive sequence analysis of the 182 predicted open reading frames of yeast chromosome III.

scientific article published on December 1992

Computational antisense oligo prediction with a neural network model

scientific article published in December 2002

Conspicuous accumulation of transcription elongation repressor hrp130/CA150 on the intron-rich Balbiani ring 3 gene

article

DASher: a stand-alone protein sequence client for DAS, the Distributed Annotation System

scientific article

Discovering viral genomes in human metagenomic data by predicting unknown protein families

scientific article published on 8 January 2018

Domain architecture conservation in orthologs

scientific article

Domain tree-based analysis of protein architecture evolution

scientific article published on 19 November 2007

Dynamic contact maps of protein structures

scientific article

Dynamic zebrafish interactome reveals transcriptional mechanisms of dioxin toxicity

scientific article

Employing conservation of co-expression to improve functional inference

scientific article

Evolution of protein domain architectures

scientific article published on January 2012

Experimental validation of predicted cancer genes using FRET.

scientific article published on 23 March 2018

Exploring the foundation of genomics: a northern blot reference set for the comparative analysis of transcript profiling technologies

scientific article published on January 2004

FAT: a novel domain in PIK-related kinases

scientific article published on 01 May 2000

Focusing on RISC assembly in mammalian cells

scientific article published on 4 February 2008

FunCoup 3.0: database of genome-wide functional coupling networks

scientific article published on 31 October 2013

FunCoup 4: new species, data, and visualization

scientific article

FunShift: a database of function shift analysis on protein subfamilies

scientific article

Functional association networks as priors for gene regulatory network inference

scientific article published on June 2014

Functional characterization in Caenorhabditis elegans of transmembrane worm-human orthologs

scientific article

GRNbenchmark - a web server for benchmarking directed gene regulatory network inference methods

scientific article published on 25 May 2022

Gearing up to handle the mosaic nature of life in the quest for orthologs

scientific article published on 30 August 2017

GeneSPIDER - gene regulatory network inference benchmarking with controlled network and data properties.

scientific article

Genome informatics: taming the avalanche of genomic data

scientific article

Genomic gene clustering analysis of pathways in eukaryotes

scientific article

Global networks of functional coupling in eukaryotes from comprehensive data integration

scientific article

HieranoiDB: a database of orthologs inferred by Hieranoid

scientific article (publication date: 4 January 2017)

Hieranoid: hierarchical orthology inference

scientific article

Improved and automated prediction of effective siRNA.

scientific article published in June 2004

Improved orthology inference with Hieranoid 2.

scientific article published on 17 January 2017

Improved profile HMM performance by assessment of critical algorithmic features in SAM and HMMER

scientific article

Improving profile HMM discrimination by adapting transition probabilities

scientific article published in May 2004

InParanoid 6: eukaryotic ortholog clusters with inparalogs

scientific article

InParanoid 7: new algorithms and tools for eukaryotic orthology analysis

scientific article

InParanoid 8: orthology analysis between 273 proteomes, mostly eukaryotic

scientific article published on 27 November 2014

Inparanoid: a comprehensive database of eukaryotic orthologs

scientific article

Kalign, Kalignvu and Mumsa: web servers for multiple sequence alignment

scientific article published on July 2006

Kalign--an accurate and fast multiple sequence alignment algorithm

scientific article

Kalign2: high-performance multiple alignment of protein and nucleotide sequences allowing external features

scientific article

Large-scale prediction of function shift in protein families with a focus on enzymatic function

scholarly article by Saraswathi Abhiman published in July 2005

Letter to the editor: SeqXML and OrthoXML: standards for sequence and orthology information

scientific article published on 11 June 2011

MGclus: network clustering employing shared neighbors

scientific article

MaxLink: network-based prioritization of genes tightly linked to a disease seed set.

scientific article published on 20 May 2014

Membrane topology of the Drosophila OR83b odorant receptor

scientific article published on 20 November 2007

MetaTM - a consensus method for transmembrane protein topology prediction

scientific article

Modular arrangement of proteins as inferred from analysis of homology.

scientific article

Network analysis of functional genomics data: application to avian sex-biased gene expression

scientific article published on 23 December 2012

Network-based Identification of novel cancer genes

scientific article

NovelFam3000--uncharacterized human protein domains conserved across model organisms

scientific article published on 13 March 2006

Optimal sparsity criteria for network inference.

scientific article published in May 2013

OrthoDisease: a database of human disease orthologs

scientific article published in August 2004

OrthoDisease: tracking disease gene orthologs across 100 species

scientific article published on 12 May 2011

OrthoGUI: graphical presentation of Orthostrapper results

scientific article published in September 2002

Orthology confers intron position conservation

scientific article

Orthology, paralogy and proposed classification for paralog subtypes

scientific article published on 01 December 2002

Overview and comparison of ortholog databases

scientific article published on January 2006

PathwAX: a web server for network crosstalk based pathway annotation

scientific article published on 5 May 2016

Pfam: clans, web tools and services

scientific article

Pfam: multiple sequence alignments and HMM-profiles of protein domains

scientific article published in January 1998

Pfam: the protein families database

scientific article (publication date: 2014)

PfamAlyzer: domain-centric homology search

scientific article

Predicting protein function from domain content

scientific article published on 30 June 2008

Predicting protein function from domain content

scientific article published in 2009

Predicting protein function from domain content

scientific article published in 2008

Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes

scientific article (publication date: 19 January 2001)

Prediction of function divergence in protein families using the substitution rate variation parameter alpha

scientific article published on 3 May 2006

Profiled support vector machines for antisense oligonucleotide efficacy prediction

scientific article

Prognostic significance in breast cancer of a gene signature capturing stromal PDGF signaling

scientific article published on 10 April 2013

Quality assessment of multiple alignment programs

scientific article published in October 2002

Quality criteria for finding genes with high mRNA-protein expression correlation and coexpression correlation

scientific article published on 4 February 2012

Reliability of transmembrane predictions in whole-genome data

scientific article

Scoredist: a simple and robust protein sequence distance estimator

scientific article

Sequence of the human immunoglobulin diversity (D) segment locus: a systematic analysis provides no evidence for the use of DIR segments, inverted D segments, “minor” D segments or D-D recombination 1 1Edited By J. Karn ⬇️

scientific article published on July 25, 1997

Sfixem--graphical sequence feature display in Java

scientific article published on 15 April 2004

Spatial maps of prostate cancer transcriptomes reveal an unexplored landscape of heterogeneity.

scientific article published on 20 June 2018

Standardized benchmarking in the quest for orthologs

scientific article (publication date: 4 April 2016)

Statistical assessment of crosstalk enrichment between gene groups in biological networks ⬇️

scientific article

Sub-grouping and sub-functionalization of the RIFIN multi-copy protein family

scientific article

The C. elegans expression pattern database: a beginning

scientific article

The Chironomus tentans genome sequence and the organization of the Balbiani ring genes

scientific article

The Imprint of Somatic Hypermutation on the Repertoire of Human Germline V Genes

article

The Pfam protein families database

scientific article (publication date: 2004)

The Pfam protein families database

scientific article (publication date: 2012)

The Pfam protein families database

scientific article (published 2010-01-01)

The Pfam protein families database ⬇️

scientific article

The Pfam protein families database

scientific article (publication date: 2002)

The Pfam protein families database in 2019

scholarly article by Sara El-Gebali et al published 24 October 2018 in Nucleic Acids Research

The Quest for Orthologs benchmark service and consensus calls in 2020

scientific article published on 06 May 2020

Toward community standards in the quest for orthologs ⬇️

scientific article (publication date: 15 March 2012)

TreeDom: a graphical web tool for analysing domain architecture evolution

scientific article published on 12 March 2016

Uncovering cancer gene regulation by accurate regulatory network inference from uninformative data

scientific article published on 09 November 2020

Volume changes in protein evolution

scientific article published in March 1994

What's in a genome?

scientific article published in Nature

jSquid: a Java applet for graphical on-line network exploration

scientific article

siRNA specificity searching incorporating mismatch tolerance data

scientific article

siRNAdb: a database of siRNA sequences

scientific article (publication date: 2005)

siRNAdb: a database of siRNA sequences

scientific article

transition priors for protein hidden Markov models: an empirical study towards maximum discrimination

scientific article

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