Author details

Full Name

Petri T??r??nen

Affiliation

Institute of Biotechnology, University of Helsinki

ORCID

Career Start Year

1999

Papers

H Index

Expertise

CM4AI Collaborator

PMID	Paper Title	Journal Title	Published Year
36419248	DALI shines a light on remote homologs: One hundred discoveries.	Protein Sci	2023
37699397	Global analysis of aging-related protein structural changes uncovers enzyme-polymerization-based control of longevity.	Mol Cell	2023
36890232	The giant diploid faba genome unlocks variation in a global protein crop.	Nature	2023
34562305	PANNZER-A practical tool for protein function prediction.	Protein Sci	2022
35679225	Correction: Novel comparison of evaluation metrics for gene ontology classifiers reveals drastic performance differences.	PLoS Comput Biol	2022
32583859	Epigenome-450K-wide methylation signatures of active cigarette smoking: The Young Finns Study.	Biosci Rep	2020
33053343	Molecular Fingerprint and Developmental Regulation of the Tegmental GABAergic and Glutamatergic Neurons Derived from the Anterior Hindbrain.	Cell Rep	2020
31682632	Novel comparison of evaluation metrics for gene ontology classifiers reveals drastic performance differences.	PLoS Comput Biol	2019
31744546	The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens.	Genome Biol	2019
29762724	AAI-profiler: fast proteome-wide exploratory analysis reveals taxonomic identity, misclassification and contamination.	Nucleic Acids Res	2018
29701748	Mlh1 deficiency in normal mouse colon mucosa associates with chromosomally unstable colon cancer.	Carcinogenesis	2018
29741643	PANNZER2: a rapid functional annotation web server.	Nucleic Acids Res	2018
27604469	An expanded evaluation of protein function prediction methods shows an improvement in accuracy.	Genome Biol	2016
27938331	Robust multi-group gene set analysis with few replicates.	BMC Bioinformatics	2016
25653249	PANNZER: high-throughput functional annotation of uncharacterized proteins in an error-prone environment.	Bioinformatics	2015
24903419	Gene set analysis: limitations in popular existing methods and proposed improvements.	Bioinformatics	2014
23353650	A large-scale evaluation of computational protein function prediction.	Nat Methods	2013
23815736	Defense-related transcription factors WRKY70 and WRKY54 modulate osmotic stress tolerance by regulating stomatal aperture in Arabidopsis.	New Phytol	2013
23927037	GOParGenPy: a high throughput method to generate gene ontology data matrices.	BMC Bioinformatics	2013
23133391	Revised phylogeny and novel horizontally acquired virulence determinants of the model soft rot phytopathogen Pectobacterium wasabiae SCC3193.	PLoS Pathog	2012
20150667	Heuristic Bayesian segmentation for discovery of coexpressed genes within genomic regions.	IEEE/ACM Trans Comput Biol Bioinform	2010
19041732	Interspliced transcription chimeras: neglected pathological mechanism infiltrating gene accession queries?	J Biomed Inform	2009
19811632	Generation of Gene Ontology benchmark datasets with various types of positive signal.	BMC Bioinformatics	2009
19775443	Robust extraction of functional signals from gene set analysis using a generalized threshold free scoring function.	BMC Bioinformatics	2009
16870932	Bayesian search of functionally divergent protein subgroups and their function specific residues.	Bioinformatics	2006
17003050	Identifying functional gene sets from hierarchically clustered expression data: map of abiotic stress regulated genes in Arabidopsis thaliana.	Nucleic Acids Res	2006
16845065	POXO: a web-enabled tool series to discover transcription factor binding sites.	Nucleic Acids Res	2006
15987504	Theme discovery from gene lists for identification and viewing of multiple functional groups.	BMC Bioinformatics	2005
15043761	Selection of informative clusters from hierarchical cluster tree with gene classes.	BMC Bioinformatics	2004
15217381	Brain-derived neurotrophic factor signaling modifies hippocampal gene expression during epileptogenesis in transgenic mice.	Eur J Neurosci	2004
15176480	Effects of antidepressant drug imipramine on gene expression in rat prefrontal cortex.	Neurochem Res	2004
14552657	Trustworthiness and metrics in visualizing similarity of gene expression.	BMC Bioinformatics	2003
12437575	Antipsychotic drug treatment induces differential gene expression in the rat cortex.	J Neurochem	2002
12208467	Changes in gene expression in atherosclerotic plaques analyzed using DNA array.	Atherosclerosis	2002
12225872	Synexpression analysis of ESTs in the rat brain reveals distinct patterns and potential drug targets.	Brain Res Mol Brain Res	2002
12462419	Expression profiling to understand actions of NMDA/glutamate receptor antagonists in rat brain.	Neurochem Res	2002
12416686	Analysis and visualization of gene expression data using self-organizing maps.	Neural Netw	2002
10371154	Analysis of gene expression data using self-organizing maps.	FEBS Lett	1999

1 - 38 of 38

Jan Baumbach

University of Hamburg

Career Start Year 2006

Number of shared co-authors 2

Andy D Perkins

Mississippi State University

Career Start Year 2006

Number of shared co-authors 1

F??tima Al-Shahrour

Spanish National Cancer Research Centre (CNIO)

Career Start Year 2003

Number of shared co-authors 3

Chunlei Wu

The Scripps Research Institute

Career Start Year 2002

Number of shared co-authors 2

Xijin Ge

South Dakota State University

Career Start Year 2002

Number of shared co-authors 0

Alberto Pascual-Montano

National Center for Biotechnology-CSIC

Career Start Year 2001

Number of shared co-authors 5

Johan Rung

Uppsala University

Career Start Year 2001

Number of shared co-authors 3

Olga G Troyanskaya

Lewis-Sigler Institute for Integrative Genomics, Princeton University

Career Start Year 2001

Number of shared co-authors 7

Carlos Prieto

Hospital Rey Juan Carlos

Career Start Year 2000

Number of shared co-authors 0

Ana Conesa

Institute for Integrative Systems Biology, Spanish National Research Council (CSIC)

Career Start Year 2000

Number of shared co-authors 8

Hedi Peterson

Institute of Computer Science, University of Tartu

Career Start Year 2000

Number of shared co-authors 9

Vladimir B Bajic

King Abdullah University of Science and Technology (KAUST)

Career Start Year 2000

Number of shared co-authors 10

Ralf Herwig

Max Planck Institute for Molecular Genetics

Career Start Year 1998

Number of shared co-authors 1

Lars Juhl Jensen

Novo Nordisk Foundation Center for Protein Research, University of Copenhagen

Career Start Year 1998

Number of shared co-authors 13

Benno Schwikowski

Center for Bioinformatics, Institut Pasteur CNRS

Career Start Year 1997

Number of shared co-authors 1

Jaak Vilo

Institute of Computer Science, University of Tartu

Career Start Year 1996

Number of shared co-authors 6

Alvis Brazma

European Bioinformatics Institute

Career Start Year 1996

Number of shared co-authors 6

Ralf Zimmer

Ludwig-Maximilians-Universitat Munchen

Career Start Year 1995

Number of shared co-authors 0

Christopher T Workman

Technical University of Denmark

Career Start Year 1995

Number of shared co-authors 3

Ron Shamir

Tel Aviv University

Career Start Year 1995

Number of shared co-authors 1

Finn Drabl??s

NTNU - Norwegian University of Science and Technology

Career Start Year 1994

Number of shared co-authors 5

Ioannis Xenarios

University of Lausanne

Career Start Year 1994

Number of shared co-authors 26

Simon Kasif

Boston University

Career Start Year 1993

Number of shared co-authors 4

Jill P Mesirov

University of California San Diego

Career Start Year 1992

Number of shared co-authors 5

Andreas Beyer

University of Cologne

Career Start Year 1991

Number of shared co-authors 2

Miguel A Andrade-Navarro

Institute of Organismic and Molecular Evolution, Johannes Gutenberg University

Career Start Year 1991

Number of shared co-authors 8

Winston Hide

Harvard Medical School

Career Start Year 1991

Number of shared co-authors 11

John Quackenbush

Harvard T. H. Chan School of Public Health

Career Start Year 1989

Number of shared co-authors 8

Michael F Ochs

The College of New Jersey

Career Start Year 1988

Number of shared co-authors 1

Joaqu??n Dopazo

Andalusian Public Foundation Progress and Health-FPS

Career Start Year 1977

Number of shared co-authors 7

row(s) 1 - 30 of 30

Liisa Holm

Institute of Biotechnology, University of Helsinki

Co-authored papers 24

Pekka Koskinen

University of Helsinki and Helsinki University Hospital

Co-authored papers 4

Alan Medlar

Institute of Biotechnology, University of Helsinki

Co-authored papers 4

Prajwal Bhat

Royal Holloway University of London

Co-authored papers 3

Slobodan Vucetic

Temple University

Co-authored papers 3

Mark N Wass

University of Kent

Co-authored papers 3

Alberto Paccanaro

University of London

Co-authored papers 3

Julian Gough

Medical Research Council Laboratory of Molecular Biology

Co-authored papers 3

Christine Orengo

University College London, Institute of Structural and Molecular Biology

Co-authored papers 3

Jianlin Cheng

University of Missouri

Co-authored papers 3

Marco Falda

University of Padova

Co-authored papers 3

Alfonso E Romero

University of Miami

Co-authored papers 3

Enrico Lavezzo

University of Padova

Co-authored papers 3

Paolo Fontana

San Pio Hospital

Co-authored papers 3

Predrag Radivojac

Indiana University

Co-authored papers 3

Fran Supek

Catalan Institution for Research and Advanced Studies (ICREA)

Co-authored papers 3

Haixuan Yang

University of Galway

Co-authored papers 3

Sean D Mooney

University of Washington

Co-authored papers 3

Hai Fang

University of Bristol

Co-authored papers 3

Stefano Toppo

University of Padova

Co-authored papers 3

Patricia C Babbitt

University of California san francisco

Co-authored papers 3

Asa Ben-Hur

Colorado State University

Co-authored papers 3

Michal Linial

Institute of Life Sciences, The Hebrew University of Jerusalem

Co-authored papers 3

Daisuke Kihara

Purdue University

Co-authored papers 3

Iddo Friedberg

Iowa State University

Co-authored papers 3

David T Jones

University College London

Co-authored papers 3

Steven E Brenner

University of California berkeley

Co-authored papers 3

Rita Casadio

Department of Pharmacy and Biotechnology, University of Bologna

Co-authored papers 3

Burkhard Rost

Technical University of Munich (TUM)

Co-authored papers 3

Domenico Cozzetto

Imperial College London

Co-authored papers 3

1 - 30

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