About me
I live in Stockholm (Solna), Sweden, and my professional
interests include all things Linux, programming, open source,
data analysis and visualization.
I'm a former researcher in bioinformatics .
p.oscar.franzen@gmail.com (GPG key)
Active certifications
Projects, Software, misc. open source contributions
that I have developed:
Education
- Doctor of Philosophy (med. doktor), 2008-2012, Karolinska Institutet. Link to thesis .
- Master of Science (Magisterexamen), 2004-2008, Karolinska Institutet
Scientific papers
- Franzén O, Björkegren J. alona: a web server for single cell RNA-seq
analysis. Bioinformatics (2020)
doi:10.1093/bioinformatics/btaa269
- Glicksberg B, Amadori L, Akers N, Sukhavasi K, Franzén O, Li L, Belbin G,
Akers K, Shameer K, Badgeley M, Johnson K, Readhead B, Darrow B, Kenny
E, Betsholtz C, Ermel R, Skogsberg J, Ruusalepp A, Schadt E, Dudley J, Ren
H, Kovacic J, Giannarelli C, Li S, Björkegren J, Chen R. Integrative analysis
of loss-of-function variants in clinical and genomic data reveals novel
genes associated with cardiovascular traits. BMC Medical Genomics (2019)
doi:10.1186/s12920-019-0542-3
- Franzén O, Li-Ming Gan, Björkegren J. PanglaoDB: A Web Server for Exploration of Mouse and Human Single Cell RNA Sequencing Data.
Database (2019)
doi:10.1093/database/baz046
- Ochaya S, Franzén O, Buhwa DA, Foyn H, Butler CE, Stove SI, Tyler KM, Arnesen T, Matovu E, Åslund L, Andersson B. Characterization of Evolutionarily Conserved Trypanosoma cruzi NatC and NatA-N-Terminal
Acetyltransferase Complexes. Journal of Parasitology Research (2019)
doi:10.1155/2019/6594212
- Zhang Z, Cheng H, Hong X, Di Narzo AF, Franzén O, Peng S, Ruusalepp A,
Kovacic JC, Björkegren J, Wang X, Hao K. EnsembleCNV: an ensemble
machine learning algorithm to identify and genotype copy number
variation using SNP array data. Nucleic Acids Research (2019)
doi:10.1093/nar/gkz068
- Nanda V, Wang T, Pjanic M, Liu B, Nguyen T, Matic L, Hedin U, Koplev S,
M Lijiang, Franzén O, Ruusalepp A, Schadt E, Björkegren J, Montgomery S,
Snyder M, Quertermous T, Leeper N, Miller C. Functional regulatory mechanism of smooth muscle cell-restricted LMOD1 coronary artery disease
locus. PLOS Genetics (2018)
doi:10.1371/journal.pgen.1007755
- 158 authors. GWAS and co-localization analyses implicate carotid intimamedia thickness and carotid plaque loci in cardiovascular outcomes.
Nature Communications (2018)
doi:10.1038/s41467-018-07340-5
- Michelis K, Nomura-Kitabayashi A, Lecce L, Franzén O, Koplev S, Xu Y, Paola
Santini M, D’Escamard V, Lee J, Fuster V, Hajjar R, Reddy R, Chikwe J, Stelzer
P, Filsoufi F, Stewart A, Anyanwu A, Björkegren J, Kovacic J. CD90 Identifies
Adventitial Mesenchymal Progenitor Cells in Adult Human Medium and Large-Sized Arteries. Stem Cell Reports (2018)
doi:10.1016/j.stemcr.2018.06.001
- Franzén O, Ermel R, Sukhavasi K, Jain R, Jain A, Betsholtz C, Giannarelli C,
Kovacic JC, Ruusalepp A, Skogsberg J, Hao K, Schadt ES, Björkegren JLM.
Global analysis of A-to-I RNA editing reveals association with common disease variants. PeerJ (2018)
doi:10.7717/peerj.4466
- Ankarklev J, Lebbad M, Einarsson E, Franzén O, Ahola H, Troell K, Svärd SG. A
novel high-resolution multilocus sequence typing of Giardia intestinalis
Assemblage A isolates reveals zoonotic transmission, clonal outbreaks
and recombination. Infection, Genetics and Evolution (2018)
doi:10.1016/j.meegid.2018.02.012
- Lempiäinen H, Brænne I, Michoel T, Tragante V, Vilne B, Webb T, Kyriakou
T, Eichner J, Zeng L, Willenborg C, Franzén O, Ruusalepp A, Goel A, van
der Laan S, Biegert C, Hamby S, Talukdar H, Foroughi Asl H, Pasterkamp G,
Watkins H, Samani N, Wittenberger T, Erdmann J, Schunkert H, Asselbergs F,
Bjö rkegren J. Network analysis of coronary artery disease risk genes
elucidates disease mechanisms and druggable targets. Scientific Reports
(2018)
doi:10.1038/s41598-018-20721-6
- Hauberg ME, Zhang W, Giambartolomei C, Franzén O, Morris DL, Vyse TJ,
Ruusalepp A, Sklar P, Schadt E, Bjorkegren J, Roussos P. Large-Scale Identification of Common Trait and Disease Variants Affecting Gene Ex-
pression. The American Journal of Human Genetics (2017)
doi:10.1016/j.ajhg.2017.04.016
- Chan S, Frasch A, Mandava C, Chang JH, Quintana MP, Vesterlund M, Ghor-
bal M, Joannin N, Franzén O, Lopez-Rubio JJ, Barbieri S, Lanzavecchia A,
Sanyal S, Wahlgren M. Regulation of PfEMP1-VAR2CSA Translation by
a Plasmodium Translation-Enhancing Factor. Nature Microbiology (2017)
doi:10.1038/nmicrobiol.2017.68
- Rossignoli A, Shang M, Gladh H, Moessinger C, Foroughi Asl H, Talukdar H,
Franzén O, Mueller S, Björkegren J, Folestad E, Skogsberg J. Poliovirus Receptor-
A Cholesterol Responsive Gene Affecting Atherosclerosis Development by Modulating Leukocyte Migration. Arteriosclerosis,
Thrombosis, and Vascular Biology (2016)
doi:10.1161/ATVBAHA.116.308715
- (118 authors). Meta-Analysis of Genome-Wide Association Studies for
Abdominal Aortic Aneurysm Identifies Four New Disease-Specific Risk
Loci. Circulation Research (2016)
doi:10.1161/CIRCRESAHA.116.308765
- Myocardial Infarction Genetics and CARDIoGRAM Exome Consortia Investigators
(134 authors). Systematic evaluation of pleiotropy identifies six further
loci associated with coronary artery disease. Journal of the American
College of Cardiology (2016)
doi:10.1016/j.jacc.2016.11.056
- Codoni V, Blum Y, Civelek M, Proust C, Franzén O, Björkegren JLM, Goff LW,
Cambien F, Lusis AJ, Trégouët DA. Preservation Analysis of Macrophage
Gene Co-expression Between Human and Mouse Identifies PARK2 as
a Genetically controlled Master Regulator of Oxydative Phosphorylation in Humans. G3 (2016)
doi:10.1534/g3.116.033894
- Franzén O, Ermel R, Cohain A, Akers NK, Narzo AD, Talukdar HA, Foroughi-
Asl H, Giambartolomei C, Fullard JF, Sukhavasi K, Köks S, Gan LM, Giannarelli
C, Kovacic JC, Betsholtz C, Losic B, Michoel T, Hao K, Roussos P, Skogsberg J,
Ruusalepp A, Schadt EE and Björkegren JLM. Cardiometabolic Risk Loci
Share Downstream Cis- and Trans-Gene Regulation Across Tissues
and Diseases. Science (2016)
doi:10.1126/science.aad6970
- Miller C, Pjanic M, Wang T, Nguyen T, Cohain A, Lee J, Perisic L, Hedin U, Kundu
RK, Majmudar D, Kim J, Wang O, Betsholtz C, Ruusalepp A, Franzén O,
Assimes T, Montgomery S, Schadt E, Björkegren J, Quertermous T. Integrative functional genomics identifies regulatory mechanisms at coronary
artery disease loci. Nature Communications (2016)
doi:10.1038/ncomms12092
- Talukdar H, Foroughi Asl H, Jain R, Ermel R, Ruusalepp A, Franzén O, Kidd
B, Readhead B, Giannarelli C, Kovacic J, Ivert T, Dudley J, Civelek M, Lusis
A, Schadt E, Skogsberg J, Michoel T, Björkegren J. Cross-Tissue Regulatory
Gene Networks in Coronary Artery Disease. Cell Systems (2016)
doi:10.1016/j.cels.2016.02.002
- Ankarklev J, Franzén O, Peirasmaki D, Jerlström-Hultqvist J, Lebbad M, Ander-
sson J, Andersson B, Svärd SG. Comparative genomic analyses of freshly
isolated Giardia intestinalis assemblage A isolates. BMC Genomics (2015)
doi:10.1186/s12864-015-1893-6
- Franzén O, Hu J, Bao X, Itzkowitz SH, Peter I, Bashir A. Improved OTU-
picking using long-read 16S amplicon sequencing and generic hierarchical clustering. Microbiome (2015)
doi:10.1186/s40168-015-0105-6
- Pendleton M, Sebra R, Pang AW, Ummat A, Franzén O, Rausch T, Stütz S, Sted-
man W, Anantharaman T, Hastie A, Dai H, Fritz MH, Cao H, Cohain A, Deikus
G, Durrett RE, Blanchard SC, Altman R, Chin CS, Guo Y, Paxinos EE, Korbel
JO, Darnell RB, McCombie WR, Kwok PY, Mason CE, Schadt EE, Bashir A.
Assembly and Diploid Architecture of an Individual Human Genome
via Single Molecule Technologies. Nature Methods (2015)
doi:10.1038/nmeth.3454
- Veiga MI, Osorio SN, Ferreira EP, Franzén O, Dahlstrom S, Lum KJ, Nosten F,
Gil PJ. Complex polymorphisms in the Plasmodium falciparum Mul-
tidrug Resistance Protein 2 gene and its contribution to antimalarial
response. Antimicrob. Agents Chemother. (2014)
doi:10.1128/AAC.03337-14
- Garcia-Silva MR, Sanguinetti J, Cabrera-Cabrera F, Franzén O, Cayota A. A
particular set of small non-coding RNAs is bound to the distinctive Argonaute protein of Trypanosoma cruzi : Insights from RNA-
interference deficient organisms. Gene (2014)
doi:10.1016/j.gene.2014.01.023
- Browall S, Norman M, Tångrot J, Galanis I, Sjöström K, Dagerhamn J, Hellberg
C, Pathak A, Spadafina T, Sandgren A, Battig P, Franzén O, Andersson B, Ortqvist A, Normark S, Henriques-Normark B. Intra-clonal variations among
Streptococcus pneumoniae isolates influence likelihood of invasive disease in children. Journal of Infectious Diseases (2013)
doi:10.1093/infdis/jit481
- Brolund A, Franzén O, Melefors Ö, Tegmark-Wisell K, Sandegren L. Plasmidome-
analysis of ESBL-producing Escherichia coli Using Conventional Typing and High-throughput Sequencing. PLOS One (2013)
doi:10.1371/journal.pone.0065793
- Franzén O, Jerlström-Hultqvist J, Einarsson E, Ankarklev J, Ferella M, Ander-
sson B, Svärd SG. Transcriptome Profiling of Giardia intestinalis Using
Strand-specific RNA-Seq. PLOS Computational Biology (2013)
doi:10.1371/journal.pcbi.1003000
- Franzén O, Talavera-López C, Ochaya S, Butler CE, Messenger LA, Lewis MD,
Llewellyn MS, Marinkelle CJ, Tyler KM, Miles MA, Andersson B. Comparative genomic analysis of human infective Trypanosoma cruzi lineages with the bat-restricted subspecies T. cruzi marinkellei. BMC Genomics
(2012)
doi:10.1186/1471-2164-13-531
- Messenger LA, Llewellyn MS, Bhattacharyya T, Franzén O, Lewis MD, Ramirez
JD, Carrasco HJ, Andersson B, Miles MA. Multiple Mitochondrial Introgression Events and Heteroplasmy in Trypanosoma cruzi Revealed
by Maxicircle MLST and Next Generation Sequencing. PLoS Neglected
Tropical Diseases (2012)
doi:10.1371/journal.pntd.0001584
- Franzén O, Arner E, Ferella M, Nilsson D, Respuela P, Carninci P, Hayashizaki
Y, Åslund L, Andersson B, Daub CO. The Short Non-Coding Transcriptome of the Protozoan Parasite Trypanosoma cruzi. PLoS Neglected
Tropical Diseases (2011)
doi:10.1371/journal.pntd.0001283
- Jerlström-Hultqvist J, Franzén O, Ankarklev J, Xu F, Nohýnková E, Andersson
JO, Svärd SG, Andersson B. Genome analysis and comparative genomics
of a Giardia intestinalis assemblage E isolate. BMC Genomics (2010)
doi:10.1186/1471-2164-11-543
- Franzén O, Ochaya O, Sherwood E, Lewis MD, Llewellyn MS, Miles MA, Ander-
sson B. Shotgun Sequencing Analysis of Trypanosoma cruzi I Sylvio
X10/1 and Comparison with T. cruzi VI CL Brener. PLoS Neglected
Tropical Diseases (2010)
doi:10.1371/journal.pntd.0000984
- Jiao W, Masich S, Franzén O, Shupliakov O. Two pools of vesicles associated
with the presynaptic cytosolic projection in Drosophila neuromuscular
junctions. Journal of Structural Biology (2010)
doi:10.1016/j.jsb.2010.07.007
- Franzén O, Jerlström-Hultqvist J, Castro E, Sherwood E, Ankarklev J, Reiner DS,
Palm D, Andersson JO, Andersson B, Svärd SG. Draft Genome Sequencing
of Giardia intestinalis Assemblage B Isolate GS: Is Human Giardiasis
Caused by Two Different Species?. PLoS Pathogens (2009)
doi:10.1371/journal.ppat.1000560