User:Jarle Pahr

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Contact Info

Jarle Pahr
  • Jarle Pahr
  • Norwegian University of Science and Technology


2007-2013: Msc., Chemical engineering & Biotechnology, Norwegian University of Science & Technology


See Notes


ppGpp MSc. project


See Organisms

Interesting articles

Engineering microbes to sense and eradicate Pseudomonas aeruginosa, a human pathogen

Environmentally controlled invasion of cancer cells by engineered bacteria

Dual role of lldR in regulation of the lldPRD operon, involved in L-lactate metabolism in E. coli

A Whole-Cell Computational Model Predicts Phenotype from Genotype

Genetic programs constructed from layered logic gates in single cells

Research centres/labs

Wyss institute:

Laboratory for Molecular Infection Medicine Sweden - Umeå:

Cold Spring Harbor Laboratory:

Wellcome Trust Sanger Institute:

Insititute for Systems Biology:

Virginia Bioinformatics Institute:

European Bioinformatics Institute:


European Molecular Biology Laboratory (EMBL):

Research programs/projects


Online learning

See Online learning


Synthetic Biology

See Synthetic Biology

Biological part collections (

DIY Bio/Citizen science

See DIY Bio

Art and Strategy


Personal genomics

uBiome - sequencing your microbiome:


Evolutionary Solutions:


DNA electronics:

Genome Compiler:



DNA 2.0:

Integrated DNA Technologies (IDT):


Desktop Genetics:

Ginkgo Bioworks:


Cambrian Genomics:





DongSheng Biotech:

Macrogen Inc.:

Carolina Biological:

Epoch Life Sciences:

United Nuclear:

New England Biolabs:

Elemental Scientific:

Jena BioScience:

Thermo scientific:

See also

Open Biotechnology:

Used equipment vendors:

Useful links

Conferences and meetings

See Conferences

Scientific challenges and competitions

CAGI - Critical Assesment of Genome Information:




Sequence squeeze:

Resources for researchers

Educational resources

ROSALIND Bioinformatics challenges:

Project Euler:

AddGene molecular biology reference:

Wiki sites

Discussion and communities



Persons/Research groups

Mark Pallen:

Chris Anderson lab:

Magni Paolo:

Heng Li. "Alignment God".

Dworkin lab:

Titus Brown:

Erlich lab:

Cristopher mason:

Markus Gershater

Heng Li

Michael Cashel:

Jim Collins:

Jason Kelly:

Tom Ellis:

George Church:

Jay Keasling:

Chris Voigt

Bernahrd Ø Pallsson:

Tom Knight

Joe Felsenstein:

  • Professor of Genome Sciences and Biology, University of Washington.

Drew Endy:

Densmore lab:

Ron Weiss:

Jean Peccoud

Jonathan Eisen

Martin Fusenegger

Pamela Silver

Rob Carlson

Ethan Perlstein:

Anthony Evans

Nick Loman:

Titus Brown:

Lex Nedebragt:

Manual Corpas:

Barry L Wanner:

  • Made many E. coli strains.

Andrew Hessel:

Societies and associations

Society for applied microbiology:

American Association for Clinical Chemistry :

Royal Society of Chemistry:

Society for general microbiology:

American society for microbiology:

Norsk Kjemisk selskap:

International Society for Systems Biology:

Genetics Society of America:

British Society for Gene and Cell Therapy:

American Society of Human Genetics (ASHG):

Society for Molecular Biology and Evolution (SMBE):


Journal name Publisher Open access status Link
ACS Synthetic Biology American Chemical Society No
Bioengineered (Previously: Bioengineered bugs) Landes Bioscience Partial
Bioinformatics Oxford Journals
Biology Open Company of Biologists Yes
BMC Medical Genomics BMC Yes
BMC Proceedings BMC Yes
PLOS One Public Library of Science Yes
Nucleic Acids Research Oxford Journals Yes
BMC Systems Biology BioMedCentral Yes
BMC Microbiology BioMedCentral Yes
Cell Cell Press
Cell Reports Cell Press Yes
The EMBO Journal Nature Publishing Group No
Frontiers in Synthetic Biology Nature Publishing Group
Genetics Genetics Society of America
G3: Genes, Genomes, Genetics Mission Genetics Society of America
Genome Research Cold Spring Harbor Press Partial (6 month embargo)
Genome Biology BMC Yes
Genome Medicine BioMedCentral Yes
Journal of Experimental Biology Company of Biologists
Journal of molecular biology Elsevier Partial
Journal of biological chemistry American Society for Biochemistry and Molecular Biology. No
Journal of bacteriology American Society for Microbiology No
Journal of Bioscience and Engineering
Journal of clinical microbiology American Society for Microbiology No
mBio ASM Yes
Methods Elsevier No
Microbiology SGM/HighWire Press No
Microbiology and Molecular Biology Reviews (MMBR). Formerly Bacteriology Reviews ASM
Metabolic Engineering Elsevier Partial
Molecular Systems Biology EMBO/Nature Publishing Group Yes
PLOS Computational Biology Public Library of Science Yes
PLOS Pathogens PLOS Yes
Proceedings of the National Academy of Sciences National Academy of Sciences No
Protein expression and purification Elsevier No
Genome Announcements ASM Yes
Futures Elsevier ?
Microbial Cell Factories BioMedCentral Yes
Engineering Studies Taylor & Francis  ?
FEMS Microbiology Reviews
Nature Biotechnology Nature Publishing Group No
Nature Genetics Nature Publishing group No
Plasmid Elsevier No
Journal of Computational Biology Liebert Publishing No
Trends in Biochemical Sciences Elsevier
Trends in Microbiology Elsevier/Cell Press
Molecular Genetics & Genomic Medicine Wiley Yes
Molecular genetics and genomics Springer Verlag
Biochemistry and Molecular Biology Education Wiley No
Current opinion in chemical biology Elsevier
New England Journal of Medicine NEJM Group
Systems and Synthetic Biology Springer
Scientific Reports Nature Publishing Group Yes

Cold Spring Harbor Perspectives:

Computational and Structural Biotechnology Journal


Current protocols in molecular biology:


Faculty of 1000:

Social Science Research Network:

Open access:

Publication tools:

Reference management / Social bookmarking:

JabRef reference manager:




CRC Press

Horizon Press


PlasmID database:

Addgene plasmid repository:

DNASU plasid repository:

The Open Construct Database:

Bionumbers - The database of useful biological numbers

EcoCyc - E. coli K-12 MG1655 database:


JWS Online model database:

Genome-Scale metabolic network database:

Array express:

Rebase restriction enzyme database:

1000 genomes project:

BRENDA Enzymes:



Codon usage

Codon usage analyzer:

Other informational resources

National Centre for Biotechnology Education:


The DDBJ/EMBL/GenBank Feature Table Definition: - Contains many protocols

Bite Size Bio:

BenchFly: - Genomics and bioinformatics resources.



CodEval - programming challenges:

Law and ethics

American journal of Bioethics:

IASB Code of Conduct for best practices in gene synthesis:

IASB - About Biosafety & Security:

Andrew W Torrance on DNA copyright:


SLIC, Gibson, CPEC and SLiCE assembly methods:

RF cloning:

PCR Primer design:


OpenWetWare - designing primers:

PCR Guide:

PCR troubleshooting:

DNA Tm estimation methods:

DNA stability:

E. coli cloning checklist:

Guide to Gibson assembly:

Primer design guidelines:


Design of sequencing primers:

Conserved primer sequences for PCR amplification and sequencing from nuclear ribosomal RNA in fungi:

GenScript DNA Sequencing Primers Design Tool:

Software tools

Molecular Biology Freeware for Windows:

Molecular Biology & Bioinformatics Resources:

Bioinformatics Tools and Resources for Biomedical Scientists and Students -

DNA copy number calculator:

Graphics software:

Systems Biology


CAIN stochastic simulations for chemical kinetics:

COBRA Constraints-based modelling toolbox:




Systems Biology Markup Language:

SBML to LaTex report generator:

Systems Biology Toolbox 2 for MATLAB:

Handbook of Systems Biology:

Reflexive Systems Biology:

Bioinformatics & Annotation

Neural Network Promoter Prediction:

Artemis genome browser:

BASYS Bacterial Annotation software:



GLIMMER microbial gene-finding system:

Promoter & termination site search tools:

Phyre 2 - protein fold recognition:

FITBAR DNA binding protein binding site predictor:

Simple Consensus Maker:

Model SEED - blog:

Model SEED - Viewer:

Plasmid map drawer:

EMBOSS ((European Molecular Biology Open Software Suite):

BioBrick -> GenBank converter:


Jcat Codon Adaption Tool:

Cloning & Construction

The Constructor:


J5 automated DNA assembly:

Genome Compiler:


Transcription and Translation:


GENtle 2:

DNA oligomer design tools:


QuickChange primer design script:

IDT SciTools - oligo design and analysis:



Primer3 plus:

InvitroGen OligoPerfect designer:


JCVI Primer designer:

Primer Design Assistant:


Primo PCR Primer Design:

Eurofins PCR primer design:

Eurofins Sequencing primer design:

DNA/oligomer property calculators:

In silico PCR tools:


OpenWetWare protocols - main page:

Springer Protocols:

Complementary annealing of oligonucleotides:

Knight lab - annealing protocol:

Knight lab -restriction digest protocol:

Endy: Colony PCR:

Addgene Moleular cloning guide:

Addgene restriction digest protocol:

Current Protocols:

Science Advisory Board - protocols:

Protocol online:


Misc. molecular biology freeware:

J Craig Venter Institute - software:

DNA sequence transformation tools:

The Oligator:

Nucleic Acid sequence massager:

String functional protein interaction networks:

ProtLifePred protein lifetime calculator:

See also: and

US National Human Genome Research Institute:

Codon table:

LaTeX lab book:

Los Alamos Technical Reports collection:

The reproducibility project:

NCBI Coffee Break:

Addgene - Genome engineering Guide:

Science News & Discussion


The SynBioLogist:

SciTech Daily:

The Scientist:

GEN Magazine:

Synthetic biology - Biohacking:

Super awesome Sylvia:


The hardest science - a psychology blog:

Michael Eisen - It's Not Junk:

Open Helix:

See also


The Daily Plasmid: Norwegian:

Social & personalized media:

Discussion sites:

In the news/Commentaries

George Church - Reading and writing omes:

Synthetic Biology comes down to Earth:

Predictability - the brass ring for synthetic biology:

Press Release - Bootstrapping Biotechnology: Engineers Cooperate to Realize Precision Grammar for Programming Cells

HeLa genome sequenced:

Tools for the synthetic biology revolution:;jsessionid=3TGCRFyZ9XnN15qs8j88ln1pDTfthtMjVl182LxzvNVG84tp0M1g!-943464721!1767787818?_nfpb=true&_windowLabel=awardSummary_1&_urlType=action&awardSummary_1_action=selectAwardDetail&awardSummary_1_id=%2FresearchGov%2FAwardHighlight%2FPublicAffairs%2F23670_ToolsfortheSyntheticBiologyRevolution.html




Search professional/business search sites for companies in fields of interest. Company webpages may not be updated to show vacant positions. To avoid missing vacancies, save pages on job portals showing vacancies on a company basis.


BioHack: (publication:

Just for Fun

Origin of the Species in Dub:


The PCR song:

Biorad GTCA song:

iGEM style!

English Tea Time Gene:

Trust me, I'm an engineer:

I'm an Engineering failure:

DNA text codec:

Funny bioinformatic tool names:

Enclothed cognition:

robotniknin: .

Arxiv vs Snarxiv:


Success in Science in 16 minutes:


Favorite things of all kinds:

Bioinformatics blogs:

To read

Composability of regulatory sequences controlling transcription and translation in E. coli.