Oscar FranzenOscar Franzén, PhD

About me

I reside in Stockholm (Solna), Sweden, and my professional interests include Linux systems, programming, open source, data analysis and visualization, and science. I used to work in bioinformatics , and I have authored/co-authored more than 30 scientific papers in this research field.

p.oscar.franzen@gmail.com (GPG key)

+46(0)763128049

Skills

Linux (and its open source ecosystem), Python programming, R programming, statistics, machine learning.

Active certifications

Projects / Software

that I have developed:
  • PanglaoDB - www.panglaodb.se . A scientific database for analysis of single cell RNA-seq data.
  • alona . A web-based analysis tool for single cell RNA-seq data.
  • adobo / docs. A Python package to analyze single cell RNA-seq data.

Education

  1. Doctor of Philosophy (med. doktor), 2008-2012, Karolinska Institutet. Link to thesis .
  2. Master of Science (Magisterexamen), 2004-2008, Karolinska Institutet

Scientific papers

  1. Franzén O, Björkegren J. alona: a web server for single cell RNA-seq analysis. Bioinformatics (2020) doi:10.1093/bioinformatics/btaa269
  2. 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
  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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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
  11. 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
  12. 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
  13. 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
  14. 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
  15. (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
  16. 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
  17. 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
  18. 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
  19. 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
  20. 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
  21. 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
  22. 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
  23. 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
  24. 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
  25. 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
  26. 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
  27. 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
  28. 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
  29. 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
  30. 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
  31. 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
  32. 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
  33. 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
  34. 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
  35. 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