NBIS staff

The current NBIS staff is listed below, with locations and expertise. For more information about individual staff members, follow the links in the table.

Please note that many of the NBIS experts are active in several sub disciplines of bioinformatics.


Management

Bengt Persson (UU/KI)SciLifeLabNBIS director
Mikael Borg (SU)SciLifeLabcoordination, infrastructure
Björn Nystedt (UU)SciLifeLabde novo genome assembly, evolution
Pär Engström (SU)SciLifeLabtranscriptomics, functional and comparative genomics, genetic variation
Thomas Svensson (CTH)SciLifeLabfunctional genomics, metabolism, fysiology, systems biology, sequence analysis, Head of Facility
Marcus Holm (UU)Uppsala Universityuppmax, compute, storage, high-performance computing
Jessica Lindberg (UU)Scilifelabadministration, economy

Genomics

Adnan Niazi (SLU)ScilifelabRNAseq, Genome assembly
Agata Smialowska (SU)Scilifelabexperimental design, transcriptomics, epigenomics, chromatin, RNA biology, RNA-seq, sRNA-seq, ChIP-seq
Allison Churcher (UmU)Scilifelabgenomics
Anna Johansson (UU)ScilifelabNGS variant analysis
Åsa Björklund (UU)ScilifelabRNAseq, scRNAseq
Bengt Sennblad (SU)SciLifeLabomics integration, reproducible research, probabilistic modeling, algorithmics, genetic interactions, genetic associations studies, genome evolution
Dag Ahrén (LU)Lund UniversityGenomics, Transcriptomics, Genomic Ecology, Microbial Genomics, Reduced representation sequencing, RADSeq, NGS coordinator
Diana Ekman (SU)ScilifelabNGS variant analysis
Estelle Proux-Wera (SU)ScilifelabRNA-seq, de novo RNA-seq assembly
Jakub Orzechowski Westholm (SU)ScilifelabRNA-seq, non-coding RNA, ChIP-seq, gene regulation
Jeanette Tångrot (UmU)Umeå Universitygenomics
Jessica Lindvall (SU)ScilifeLabhigh throughput analyses
Johan Reimegård (UU)SciLifeLabde novo RNA assembly, RNAseq, RNA structure analysis, Allele specific expression, non-coding RNA, miRNA, sRNA, education
John Sundh (SU)SciLifeLabmetagenomics, bacterial genomics, cyanobacteria
Katarina Truvé (GU)University of Gothenburgclinical NGS data
Magnus Alm Rosenblad (GU)University of Gothenburgsequence analysis, transcriptomics, NGS coordinator
Malin Larsson (LiU)Linköping Universitygenetic variation, somatic variation
Marcel Martin (SU)Scilifelabhigh-throughput sequencing
Marcin Kierczak (UU)SciLifeLabgenmics, GWAS, GxG and GxE interactions, machine learning, linear mixed models, R programming, data visualisation, population genomics, eDNA
Markus Mayrhofer (UU)Scilifelabcancer genomics, copy number analysis, mutational profiling
Markus Ringnér (LU)SciLifeLabCancer genomics
Mihaela Martis (LiU)Linköping Universitytranscriptomics, comparative genomics
Nikolay Oskolkov (LU)Scilifelabgenomics, transcriptomics, statistical analysis
Nina Norgren (UmU)Umeå Universitygenomics
Olga Dethlefsen (SU)SciLifeLabRNA-seq, scRNA-seq, experimental design, biostatistics, genomics, transcriptomics, metabolomics
Paulo Czarnewski (SU)SciLifeLabRNA-seq, scRNAseq, transcriptomics, Proximity Extension Assay (PEA), microbiome profiling, Flow cytometry (FACS)
Per Unneberg (UU)SciLifeLabevolution, reproducible research, statistics, RNAseq, scRNAseq, genomics, variation analysis, population genetics
Roy Francis (UU)Scilifelabexperimental design, transcriptomics, RNA-seq, sRNA-seq, scRNA-seq, SNPs, GATK variant-calling, R programming, data visualisation
Sebastian DiLorenzo (UU)SciLifeLabCancer data analysis, NGS, epigenetics, Pipelines
Verena Kutschera (SU)SciLifeLabpopulation genetics, phylogenetics, comparative genomics, molecular evolution

Genome Assembly and Annotation

Henrik Lantz (UU)SciLifeLabgenomics, transcriptomics, NGS coordinator
Jacques Dainat (UU)SciLifeLabgenome annotation, transcriptome annotation, transcriptome assembly, phylogenetics, phylogenomics, comparative genomics, evolutionary sequence analysis
Lucile Soler (UU)SciLifeLabgenome annotation, whole genome alignment, comparative genomic
Mahesh Binzer-Panchal (UU)SciLifeLabgenomic assembly

Proteomics

Fredrik Levander (LU)University of Lundproteomics, coordinator, mass spectrometry, data standards

Systems biology

Andrey Alexeyenko (KI)SciLifeLabsystems biology
Leif Väremo (Chalmers)ChalmersRNAseq, scRNAseq, metabolic modeling, systems biology
Rasmus Ågren (Chalmers)Chalmersomics integration, reproducible research, metabolism, systems biology
Sergiu Netotea (Chalmers)Chalmerssystems biology, network analysis, machine learning, cloud computing
Viktor Jonsson (Chalmers)Chalmersmetageonmics, biostatistics, statistical modelling, RNAseq, scRNAseq

Metabolomics

Daniel Malmodin (GU)University of Gothenburgmetabolomics

Sequence analysis

Johan Nylander (NRM)Swedish Museum of Natural History / SciLifeLabevolutionary sequence analysis, phylogenetics, phylogenomics
Sara Light (SU)SciLifeLabbioinformatics, training coordinator
Yvonne Kallberg (SU)SciLifeLabprotein bioinformatics

Development

Anders Larsson (UU)SciLifeLabSystems development, Java, Ferns, Cloud computing
Andreas Kähäri (UU)SciLifeLabUNIX, C, Perl, MySQL, shell scripting, systems development
Joakim Bygdell (UmU)Umeå Universitysystems development, cloud computing
Johan Viklund (UU)SciLifeLabSystem development, perl, python, groovy, git, R, containers
Jonas Hagberg (SU)SciLifeLab/telecommutingDevelopment Team Manager, systems development
Jorrit Boekel (KI)SciLifeLabmass spectrometry proteomics support
Malin Ahlberg (UU)SciLifeLabsystems development, python
Martin Norling (UU)SciLifeLabgenome assembly
Nanjiang Shu (SU)SciLifeLabProtein bioinformatics, Protein structure prediction, Machine learning, Web-server development, Cloud computing

Software and Systems

Jonas Söderberg (UU)SciLifeLabUPPMAX, SciLifeLab
Martin Dahlö (UU)SciLifeLabsystems development, uppmax
Pontus Freyhult (UU)UPPMAXdata management, software development
Stefan Fleischmann (SU)SciLifeLabsystem administration, GNU/Linux, virtualization, LXC/LXD, MAAS, Ansible, Salt
Valentin Georgiev (UU)SciLifeLabscientific computing, uppmax, bioinformatics support

Statistics

Eva Freyhult (UU)Uppsala Universitystatistics, multivariate analysis, network analysis

Data services

Niclas Jareborg (SU)SciLifeLabdata management, agile project management, lean, informatics, programming

The NBIS staff is distributed over all major Swedish universities. They all have a national responsibility, which means that they will provide their expertise to all Swedish scientists, regardless of affiliation.

Stockholm (Stockholm University, KI, KTH)

Agata Smialowska (SU)Scilifelabexperimental design, transcriptomics, epigenomics, chromatin, RNA biology, RNA-seq, sRNA-seq, ChIP-seq
Andrey Alexeyenko (KI)SciLifeLabsystems biology
Bengt Persson (UU/KI)SciLifeLabNBIS director
Bengt Sennblad (SU)SciLifeLabomics integration, reproducible research, probabilistic modeling, algorithmics, genetic interactions, genetic associations studies, genome evolution
Diana Ekman (SU)ScilifelabNGS variant analysis
Estelle Proux-Wera (SU)ScilifelabRNA-seq, de novo RNA-seq assembly
Jakub Orzechowski Westholm (SU)ScilifelabRNA-seq, non-coding RNA, ChIP-seq, gene regulation
Jessica Lindvall (SU)ScilifeLabhigh throughput analyses
Johan Nylander (NRM)Swedish Museum of Natural History / SciLifeLabevolutionary sequence analysis, phylogenetics, phylogenomics
John Sundh (SU)SciLifeLabmetagenomics, bacterial genomics, cyanobacteria
Jonas Hagberg (SU)SciLifeLab/telecommutingDevelopment Team Manager, systems development
Jorrit Boekel (KI)SciLifeLabmass spectrometry proteomics support
Marcel Martin (SU)Scilifelabhigh-throughput sequencing
Mikael Borg (SU)SciLifeLabcoordination, infrastructure
Nanjiang Shu (SU)SciLifeLabProtein bioinformatics, Protein structure prediction, Machine learning, Web-server development, Cloud computing
Niclas Jareborg (SU)SciLifeLabdata management, agile project management, lean, informatics, programming
Olga Dethlefsen (SU)SciLifeLabRNA-seq, scRNA-seq, experimental design, biostatistics, genomics, transcriptomics, metabolomics
Pär Engström (SU)SciLifeLabtranscriptomics, functional and comparative genomics, genetic variation
Paulo Czarnewski (SU)SciLifeLabRNA-seq, scRNAseq, transcriptomics, Proximity Extension Assay (PEA), microbiome profiling, Flow cytometry (FACS)
Sara Light (SU)SciLifeLabbioinformatics, training coordinator
Stefan Fleischmann (SU)SciLifeLabsystem administration, GNU/Linux, virtualization, LXC/LXD, MAAS, Ansible, Salt
Verena Kutschera (SU)SciLifeLabpopulation genetics, phylogenetics, comparative genomics, molecular evolution
Yvonne Kallberg (SU)SciLifeLabprotein bioinformatics

Uppsala (Uppsala University, SLU)

Adnan Niazi (SLU)ScilifelabRNAseq, Genome assembly
Anders Larsson (UU)SciLifeLabSystems development, Java, Ferns, Cloud computing
Andreas Kähäri (UU)SciLifeLabUNIX, C, Perl, MySQL, shell scripting, systems development
Anna Johansson (UU)ScilifelabNGS variant analysis
Åsa Björklund (UU)ScilifelabRNAseq, scRNAseq
Björn Nystedt (UU)SciLifeLabde novo genome assembly, evolution
Eva Freyhult (UU)Uppsala Universitystatistics, multivariate analysis, network analysis
Henrik Lantz (UU)SciLifeLabgenomics, transcriptomics, NGS coordinator
Jacques Dainat (UU)SciLifeLabgenome annotation, transcriptome annotation, transcriptome assembly, phylogenetics, phylogenomics, comparative genomics, evolutionary sequence analysis
Jessica Lindberg (UU)Scilifelabadministration, economy
Johan Reimegård (UU)SciLifeLabde novo RNA assembly, RNAseq, RNA structure analysis, Allele specific expression, non-coding RNA, miRNA, sRNA, education
Johan Viklund (UU)SciLifeLabSystem development, perl, python, groovy, git, R, containers
Jonas Söderberg (UU)SciLifeLabUPPMAX, SciLifeLab
Lucile Soler (UU)SciLifeLabgenome annotation, whole genome alignment, comparative genomic
Mahesh Binzer-Panchal (UU)SciLifeLabgenomic assembly
Malin Ahlberg (UU)SciLifeLabsystems development, python
Marcin Kierczak (UU)SciLifeLabgenmics, GWAS, GxG and GxE interactions, machine learning, linear mixed models, R programming, data visualisation, population genomics, eDNA
Marcus Holm (UU)Uppsala Universityuppmax, compute, storage, high-performance computing
Markus Mayrhofer (UU)Scilifelabcancer genomics, copy number analysis, mutational profiling
Martin Dahlö (UU)SciLifeLabsystems development, uppmax
Martin Norling (UU)SciLifeLabgenome assembly
Per Unneberg (UU)SciLifeLabevolution, reproducible research, statistics, RNAseq, scRNAseq, genomics, variation analysis, population genetics
Pontus Freyhult (UU)UPPMAXdata management, software development
Roy Francis (UU)Scilifelabexperimental design, transcriptomics, RNA-seq, sRNA-seq, scRNA-seq, SNPs, GATK variant-calling, R programming, data visualisation
Sebastian DiLorenzo (UU)SciLifeLabCancer data analysis, NGS, epigenetics, Pipelines
Valentin Georgiev (UU)SciLifeLabscientific computing, uppmax, bioinformatics support

Umeå (Umeå University)

Allison Churcher (UmU)Scilifelabgenomics
Jeanette Tångrot (UmU)Umeå Universitygenomics
Joakim Bygdell (UmU)Umeå Universitysystems development, cloud computing
Nina Norgren (UmU)Umeå Universitygenomics

Göteborg (University of Gothenburg, Chalmers)

Daniel Malmodin (GU)University of Gothenburgmetabolomics
Katarina Truvé (GU)University of Gothenburgclinical NGS data
Leif Väremo (Chalmers)ChalmersRNAseq, scRNAseq, metabolic modeling, systems biology
Magnus Alm Rosenblad (GU)University of Gothenburgsequence analysis, transcriptomics, NGS coordinator
Rasmus Ågren (Chalmers)Chalmersomics integration, reproducible research, metabolism, systems biology
Sergiu Netotea (Chalmers)Chalmerssystems biology, network analysis, machine learning, cloud computing
Thomas Svensson (CTH)SciLifeLabfunctional genomics, metabolism, fysiology, systems biology, sequence analysis, Head of Facility
Viktor Jonsson (Chalmers)Chalmersmetageonmics, biostatistics, statistical modelling, RNAseq, scRNAseq

Lund (Lund University, SLU)

Dag Ahrén (LU)Lund UniversityGenomics, Transcriptomics, Genomic Ecology, Microbial Genomics, Reduced representation sequencing, RADSeq, NGS coordinator
Fredrik Levander (LU)University of Lundproteomics, coordinator, mass spectrometry, data standards
Markus Ringnér (LU)SciLifeLabCancer genomics
Nikolay Oskolkov (LU)Scilifelabgenomics, transcriptomics, statistical analysis

Linköping (Linköping University)

Malin Larsson (LiU)Linköping Universitygenetic variation, somatic variation
Mihaela Martis (LiU)Linköping Universitytranscriptomics, comparative genomics

NBIS staff organized by Scilifelab facility.

Support and Infrastructure

Adnan Niazi (SLU)ScilifelabRNAseq, Genome assembly
Agata Smialowska (SU)Scilifelabexperimental design, transcriptomics, epigenomics, chromatin, RNA biology, RNA-seq, sRNA-seq, ChIP-seq
Andreas Kähäri (UU)SciLifeLabUNIX, C, Perl, MySQL, shell scripting, systems development
Andrey Alexeyenko (KI)SciLifeLabsystems biology
Bengt Persson (UU/KI)SciLifeLabNBIS director
Dag Ahrén (LU)Lund UniversityGenomics, Transcriptomics, Genomic Ecology, Microbial Genomics, Reduced representation sequencing, RADSeq, NGS coordinator
Daniel Malmodin (GU)University of Gothenburgmetabolomics
Eva Freyhult (UU)Uppsala Universitystatistics, multivariate analysis, network analysis
Fredrik Levander (LU)University of Lundproteomics, coordinator, mass spectrometry, data standards
Henrik Lantz (UU)SciLifeLabgenomics, transcriptomics, NGS coordinator
Jacques Dainat (UU)SciLifeLabgenome annotation, transcriptome annotation, transcriptome assembly, phylogenetics, phylogenomics, comparative genomics, evolutionary sequence analysis
Jeanette Tångrot (UmU)Umeå Universitygenomics
Jessica Lindvall (SU)ScilifeLabhigh throughput analyses
Joakim Bygdell (UmU)Umeå Universitysystems development, cloud computing
Johan Nylander (NRM)Swedish Museum of Natural History / SciLifeLabevolutionary sequence analysis, phylogenetics, phylogenomics
Johan Viklund (UU)SciLifeLabSystem development, perl, python, groovy, git, R, containers
Jonas Hagberg (SU)SciLifeLab/telecommutingDevelopment Team Manager, systems development
Jorrit Boekel (KI)SciLifeLabmass spectrometry proteomics support
Katarina Truvé (GU)University of Gothenburgclinical NGS data
Lucile Soler (UU)SciLifeLabgenome annotation, whole genome alignment, comparative genomic
Magnus Alm Rosenblad (GU)University of Gothenburgsequence analysis, transcriptomics, NGS coordinator
Mahesh Binzer-Panchal (UU)SciLifeLabgenomic assembly
Malin Ahlberg (UU)SciLifeLabsystems development, python
Martin Norling (UU)SciLifeLabgenome assembly
Mihaela Martis (LiU)Linköping Universitytranscriptomics, comparative genomics
Mikael Borg (SU)SciLifeLabcoordination, infrastructure
Nanjiang Shu (SU)SciLifeLabProtein bioinformatics, Protein structure prediction, Machine learning, Web-server development, Cloud computing
Niclas Jareborg (SU)SciLifeLabdata management, agile project management, lean, informatics, programming
Olga Dethlefsen (SU)SciLifeLabRNA-seq, scRNA-seq, experimental design, biostatistics, genomics, transcriptomics, metabolomics
Pontus Freyhult (UU)UPPMAXdata management, software development
Roy Francis (UU)Scilifelabexperimental design, transcriptomics, RNA-seq, sRNA-seq, scRNA-seq, SNPs, GATK variant-calling, R programming, data visualisation
Sara Light (SU)SciLifeLabbioinformatics, training coordinator
Sebastian DiLorenzo (UU)SciLifeLabCancer data analysis, NGS, epigenetics, Pipelines
Stefan Fleischmann (SU)SciLifeLabsystem administration, GNU/Linux, virtualization, LXC/LXD, MAAS, Ansible, Salt
Yvonne Kallberg (SU)SciLifeLabprotein bioinformatics

Long-term Support

Allison Churcher (UmU)Scilifelabgenomics
Anna Johansson (UU)ScilifelabNGS variant analysis
Åsa Björklund (UU)ScilifelabRNAseq, scRNAseq
Bengt Sennblad (SU)SciLifeLabomics integration, reproducible research, probabilistic modeling, algorithmics, genetic interactions, genetic associations studies, genome evolution
Björn Nystedt (UU)SciLifeLabde novo genome assembly, evolution
Diana Ekman (SU)ScilifelabNGS variant analysis
Estelle Proux-Wera (SU)ScilifelabRNA-seq, de novo RNA-seq assembly
Jakub Orzechowski Westholm (SU)ScilifelabRNA-seq, non-coding RNA, ChIP-seq, gene regulation
Johan Reimegård (UU)SciLifeLabde novo RNA assembly, RNAseq, RNA structure analysis, Allele specific expression, non-coding RNA, miRNA, sRNA, education
John Sundh (SU)SciLifeLabmetagenomics, bacterial genomics, cyanobacteria
Jonas Söderberg (UU)SciLifeLabUPPMAX, SciLifeLab
Leif Väremo (Chalmers)ChalmersRNAseq, scRNAseq, metabolic modeling, systems biology
Malin Larsson (LiU)Linköping Universitygenetic variation, somatic variation
Marcel Martin (SU)Scilifelabhigh-throughput sequencing
Marcin Kierczak (UU)SciLifeLabgenmics, GWAS, GxG and GxE interactions, machine learning, linear mixed models, R programming, data visualisation, population genomics, eDNA
Markus Mayrhofer (UU)Scilifelabcancer genomics, copy number analysis, mutational profiling
Markus Ringnér (LU)SciLifeLabCancer genomics
Nikolay Oskolkov (LU)Scilifelabgenomics, transcriptomics, statistical analysis
Nina Norgren (UmU)Umeå Universitygenomics
Pär Engström (SU)SciLifeLabtranscriptomics, functional and comparative genomics, genetic variation
Paulo Czarnewski (SU)SciLifeLabRNA-seq, scRNAseq, transcriptomics, Proximity Extension Assay (PEA), microbiome profiling, Flow cytometry (FACS)
Per Unneberg (UU)SciLifeLabevolution, reproducible research, statistics, RNAseq, scRNAseq, genomics, variation analysis, population genetics
Sergiu Netotea (Chalmers)Chalmerssystems biology, network analysis, machine learning, cloud computing
Verena Kutschera (SU)SciLifeLabpopulation genetics, phylogenetics, comparative genomics, molecular evolution
Viktor Jonsson (Chalmers)Chalmersmetageonmics, biostatistics, statistical modelling, RNAseq, scRNAseq

Systems Biology

Rasmus Ågren (Chalmers)Chalmersomics integration, reproducible research, metabolism, systems biology
Thomas Svensson (CTH)SciLifeLabfunctional genomics, metabolism, fysiology, systems biology, sequence analysis, Head of Facility

Compute and Storage

Marcus Holm (UU)Uppsala Universityuppmax, compute, storage, high-performance computing
Martin Dahlö (UU)SciLifeLabsystems development, uppmax
Valentin Georgiev (UU)SciLifeLabscientific computing, uppmax, bioinformatics support

NBIS affiliates are bioinformaticians who collaborate with NBIS.

Daniel Lundin (KTH)SciLifeLabmetagenomics
David Gomez-Cabrero (KI)Karolinska InstitutetRNA analysis
Henric Zazzi (KTH)PDC/SciLifeLabbioinformatics software development
Petter Ranefall (UU)Centre for Image Analysisimage analysis