List of works - Iddo Friedberg

A large scale prediction of bacteriocin gene blocks suggests a wide functional spectrum for bacteriocins

scientific article

A large-scale evaluation of computational protein function prediction

scientific article

A metagenomic study of diet-dependent interaction between gut microbiota and host in infants reveals differences in immune response.

scientific article published on 30 April 2012

A primer on metagenomics

scientific article

An event-driven approach for studying gene block evolution in bacteria

scientific article published on 25 February 2015

An expanded evaluation of protein function prediction methods shows an improvement in accuracy ⬇️

scientific article

Assessing computational predictions of the phenotypic effect of cystathionine-beta-synthase variants

scientific article published on 03 September 2019

Automated protein function prediction--the genomic challenge

scientific article published on 23 May 2006

Biases in the experimental annotations of protein function and their effect on our understanding of protein function space

scientific article

Biological database of images and genomes: tools for community annotations linking image and genomic information

scientific article published on 02 April 2013

Biopython: freely available Python tools for computational molecular biology and bioinformatics

scientific article

Characterizing domain-specific open educational resources by linking ISCB Communities of Special Interest to Wikipedia

scientific article published on 27 June 2022

Chikungunya Virus in Febrile Humans and Aedes aegypti Mosquitoes, Yucatan, Mexico

scientific article (publication date: October 2016)

Community-Wide Evaluation of Computational Function Prediction

scientific article published on January 2017

Comparative analysis of error-prone replication mononucleotide repeats across baculovirus genomes

scientific article published on 17 October 2013

Computational protein function prediction: are we making progress?

scientific article published on October 2007

Connecting the protein structure universe by using sparse recurring fragments.

scientific article

Correction: Ten Simple Rules for Selecting a Postdoctoral Position

scientific article (publication date: 2006)

Crowdsourcing Image Analysis for Plant Phenomics to Generate Ground Truth Data for Machine Learning

article

Crowdsourcing biocuration: The Community Assessment of Community Annotation with Ontologies (CACAO)

scientific article published on 28 October 2021

Crowdsourcing image analysis for plant phenomics to generate ground truth data for machine learning

article

Evaluation of PSI-BLAST alignment accuracy in comparison to structural alignments.

scientific article published on November 2000

Fragnostic: walking through protein structure space

scientific article

Functional differentiation of proteins: implications for structural genomics.

scientific article

Glimmers in the midnight zone: characterization of aligned identical residues in sequence-dissimilar proteins sharing a common fold.

scientific article

Host-microbe interactions in the neonatal intestine: role of human milk oligosaccharides.

scientific article published on May 2012

IPRStats: visualization of the functional potential of an InterProScan run.

scientific article

Identification and characterization of DUSP27, a novel dual-specific protein phosphatase

scientific article

Identifying Antimicrobial Peptides using Word Embedding with Deep Recurrent Neural Networks

scholarly article published 29 January 2018

Identifying antimicrobial peptides using word embedding with deep recurrent neural networks

scientific article published on 01 June 2019

JAFA: a protein function annotation meta-server

scientific article published on July 2006

MaizeDIG: Maize Database of Images and Genomes

scientific article published on 28 August 2019

Meeting Report: "Metagenomics, Metadata and Meta-analysis" (M3) Special Interest Group at ISMB 2009

scientific article (publication date: 29 December 2009)

Meeting Report: BioSharing at ISMB 2010

scientific article (publication date: 4 December 2010)

Meeting Report: Metagenomics, Metadata and MetaAnalysis (M3) at ISMB 2010

scientific article (publication date: 4 December 2010)

MetaMiner: A Scalable Peptidogenomics Approach for Discovery of Ribosomal Peptide Natural Products with Blind Modifications from Microbial Communities

scientific article published on 16 October 2019

New Drosophila long-term memory genes revealed by assessing computational function prediction methods

article

New Long-Term Memory Genes Revealed by Assessing Computational Function Prediction Methods

article

New avenues in protein function prediction

scientific article published in June 2006

Novel antimicrobial peptide discovery using machine learning and biophysical selection of minimal bacteriocin domains

scientific article published on 04 September 2019

PeCoP: automatic determination of persistently conserved positions in protein families

scientific article

Persistently conserved positions in structurally similar, sequence dissimilar proteins: roles in preserving protein fold and function.

scientific article

Protein tyrosine phosphatases in the human genome

scientific article

Protist diversity in a permanently ice-covered Antarctic lake during the polar night transition

scientific article

Submitochondrial distribution of three key steroidogenic proteins (steroidogenic acute regulatory protein and cytochrome p450scc and 3beta-hydroxysteroid dehydrogenase isomerase enzymes) upon stimulation by intracellular calcium in adrenal [...]

scientific journal article

SwiftOrtho: A fast, memory-efficient, multiple genome orthology classifier

scientific article published on 01 October 2019

Ten simple rules for a community computational challenge

scientific article (publication date: April 2015)

Ten simple rules for selecting a postdoctoral position

scientific article

The 2006 Automated Function Prediction Meeting

scientific article

The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

scientific article published on 19 November 2019

The COMBREX project: design, methodology, and initial results

scientific article

The automated function prediction SIG looks back at 2013 and prepares for 2014.

scientific article published on 3 March 2014

The impact of incomplete knowledge on the evaluation of protein function prediction: a structured-output learning perspective

scientific article

The interplay of fold recognition and experimental structure determination in structural genomics

scientific article published on June 2004

The status of structural genomics defined through the analysis of current targets and structures

scientific article published on January 2004

Tracing the ancestry of operons in bacteria

scientific article published on 01 September 2019

Unraveling a Tangled Skein: Evolutionary Analysis of the Bacterial Gibberellin Biosynthetic Operon

scientific article published on 03 June 2020

Using an alignment of fragment strings for comparing protein structures.

scientific article

List of works by Iddo Friedberg

A large scale prediction of bacteriocin gene blocks suggests a wide functional spectrum for bacteriocins

A large-scale evaluation of computational protein function prediction

A metagenomic study of diet-dependent interaction between gut microbiota and host in infants reveals differences in immune response.

A primer on metagenomics

An event-driven approach for studying gene block evolution in bacteria

An expanded evaluation of protein function prediction methods shows an improvement in accuracy ⬇️

Assessing computational predictions of the phenotypic effect of cystathionine-beta-synthase variants

Automated protein function prediction--the genomic challenge

Biases in the experimental annotations of protein function and their effect on our understanding of protein function space

Biological database of images and genomes: tools for community annotations linking image and genomic information

Biopython: freely available Python tools for computational molecular biology and bioinformatics

Characterizing domain-specific open educational resources by linking ISCB Communities of Special Interest to Wikipedia

Chikungunya Virus in Febrile Humans and Aedes aegypti Mosquitoes, Yucatan, Mexico

Community-Wide Evaluation of Computational Function Prediction

Comparative analysis of error-prone replication mononucleotide repeats across baculovirus genomes

Computational protein function prediction: are we making progress?

Connecting the protein structure universe by using sparse recurring fragments.

Correction: Ten Simple Rules for Selecting a Postdoctoral Position

Crowdsourcing Image Analysis for Plant Phenomics to Generate Ground Truth Data for Machine Learning

Crowdsourcing biocuration: The Community Assessment of Community Annotation with Ontologies (CACAO)

Crowdsourcing image analysis for plant phenomics to generate ground truth data for machine learning

Evaluation of PSI-BLAST alignment accuracy in comparison to structural alignments.

Fragnostic: walking through protein structure space

Functional differentiation of proteins: implications for structural genomics.

Glimmers in the midnight zone: characterization of aligned identical residues in sequence-dissimilar proteins sharing a common fold.

Host-microbe interactions in the neonatal intestine: role of human milk oligosaccharides.

IPRStats: visualization of the functional potential of an InterProScan run.

Identification and characterization of DUSP27, a novel dual-specific protein phosphatase

Identifying Antimicrobial Peptides using Word Embedding with Deep Recurrent Neural Networks

Identifying antimicrobial peptides using word embedding with deep recurrent neural networks

JAFA: a protein function annotation meta-server

MaizeDIG: Maize Database of Images and Genomes

Meeting Report: "Metagenomics, Metadata and Meta-analysis" (M3) Special Interest Group at ISMB 2009

Meeting Report: BioSharing at ISMB 2010

Meeting Report: Metagenomics, Metadata and MetaAnalysis (M3) at ISMB 2010

MetaMiner: A Scalable Peptidogenomics Approach for Discovery of Ribosomal Peptide Natural Products with Blind Modifications from Microbial Communities

New Drosophila long-term memory genes revealed by assessing computational function prediction methods

New Long-Term Memory Genes Revealed by Assessing Computational Function Prediction Methods

New avenues in protein function prediction

Novel antimicrobial peptide discovery using machine learning and biophysical selection of minimal bacteriocin domains

PeCoP: automatic determination of persistently conserved positions in protein families

Persistently conserved positions in structurally similar, sequence dissimilar proteins: roles in preserving protein fold and function.

Protein tyrosine phosphatases in the human genome

Protist diversity in a permanently ice-covered Antarctic lake during the polar night transition

Submitochondrial distribution of three key steroidogenic proteins (steroidogenic acute regulatory protein and cytochrome p450scc and 3beta-hydroxysteroid dehydrogenase isomerase enzymes) upon stimulation by intracellular calcium in adrenal [...]

SwiftOrtho: A fast, memory-efficient, multiple genome orthology classifier

Ten simple rules for a community computational challenge

Ten simple rules for selecting a postdoctoral position

The 2006 Automated Function Prediction Meeting

The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

The COMBREX project: design, methodology, and initial results

The automated function prediction SIG looks back at 2013 and prepares for 2014.

The impact of incomplete knowledge on the evaluation of protein function prediction: a structured-output learning perspective

The interplay of fold recognition and experimental structure determination in structural genomics

The status of structural genomics defined through the analysis of current targets and structures

Tracing the ancestry of operons in bacteria

Unraveling a Tangled Skein: Evolutionary Analysis of the Bacterial Gibberellin Biosynthetic Operon

Using an alignment of fragment strings for comparing protein structures.