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    Roger Lasken

    TitleAdjunct Professor
    SchoolUniversity of California, San Diego
    DepartmentSchool of Pharmacy and Pharmaceutical Science
    Address9500 Gilman Drive #0719
    CA La Jolla 92093
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      Collapse Research 
      Collapse Research Activities and Funding
      Transcriptomics from Single Circulating Tumor Cells
      NIH/NHGRI RC1HG005471Sep 26, 2009 - Jul 31, 2011
      Role: Principal Investigator
      Single Cell Genomics of Human Microbial Flora
      NIH/NHGRI R01HG003647May 12, 2005 - Apr 30, 2014
      Role: Principal Investigator
      Isothermal cDNA/mRNA Amplification Technology
      NIH/NIGMS R43GM069068Jul 1, 2003 - Oct 12, 2004
      Role: Principal Investigator
      Affordable large population genomic DNA collections
      NIH/NIDDK R43DK063837Apr 1, 2003 - Sep 30, 2004
      Role: Principal Investigator

      Collapse Bibliographic 
      Collapse Publications
      Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
      List All   |   Timeline
      1. Buckley AR, Standish KA, Bhutani K, Ideker T, Lasken R, Carter H, Harismendy O, Schork NJ. Pan-cancer analysis reveals technical artifacts in TCGA germline variant calls. BMC Genomics. 2017 Jun 12; 18(1):458. PMID: 28606096.
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      2. Lacar B, Linker SB, Jaeger BN, Krishnaswami SR, Barron JJ, Kelder MJ, Parylak SL, Paquola AC, Venepally P, Novotny M, O'Connor C, Fitzpatrick C, Erwin JA, Hsu JY, Husband D, McConnell MJ, Lasken R, Gage FH. Corrigendum: Nuclear RNA-seq of single neurons reveals molecular signatures of activation. Nat Commun. 2017 Mar 17; 8:15047. PMID: 28303884.
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      3. Bardy C, van den Hurk M, Kakaradov B, Erwin JA, Jaeger BN, Hernandez RV, Eames T, Paucar AA, Gorris M, Marchand C, Jappelli R, Barron J, Bryant AK, Kellogg M, Lasken R, Rutten BP, Steinbusch HW, Yeo GW, Gage FH. Predicting the functional states of human iPSC-derived neurons with single-cell RNA-seq and electrophysiology. Mol Psychiatry. 2016 Oct 04. PMID: 27698428.
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      4. Erwin JA, Paquola AC, Singer T, Gallina I, Novotny M, Quayle C, Bedrosian TA, Alves FI, Butcher CR, Herdy JR, Sarkar A, Lasken R, Muotri AR, Gage FH. L1-associated genomic regions are deleted in somatic cells of the healthy human brain. Nat Neurosci. 2016 Sep 12. PMID: 27618310.
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      5. Lacar B, Linker SB, Jaeger BN, Krishnaswami SR, Barron JJ, Kelder MJ, Parylak SL, Paquola AC, Venepally P, Novotny M, O'Connor C, Fitzpatrick C, Erwin JA, Hsu JY, Husband D, McConnell MJ, Lasken R, Gage FH. Corrigendum: Nuclear RNA-seq of single neurons reveals molecular signatures of activation. Nat Commun. 2016; 7:12020. PMID: 27295945.
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      6. Lacar B, Linker SB, Jaeger BN, Krishnaswami S, Barron J, Kelder M, Parylak S, Paquola A, Venepally P, Novotny M, O'Connor C, Fitzpatrick C, Erwin J, Hsu JY, Husband D, McConnell MJ, Lasken R, Gage FH. Nuclear RNA-seq of single neurons reveals molecular signatures of activation. Nat Commun. 2016; 7:11022. PMID: 27090946.
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      7. Krishnaswami SR, Grindberg RV, Novotny M, Venepally P, Lacar B, Bhutani K, Linker SB, Pham S, Erwin JA, Miller JA, Hodge R, McCarthy JK, Kelder M, McCorrison J, Aevermann BD, Fuertes FD, Scheuermann RH, Lee J, Lein ES, Schork N, McConnell MJ, Gage FH, Lasken R. Using single nuclei for RNA-seq to capture the transcriptome of postmortem neurons. Nat Protoc. 2016 Mar; 11(3):499-524. PMID: 26890679.
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      8. Aevermann B, McCorrison J, Venepally P, Hodge R, Bakken T, Miller J, Novotny M, Tran DN, Diezfuertes F, Christiansen L, Zhang F, Steemers F, Lasken R, Lein ED, Schork N, Scheuermann RH. PRODUCTION OF A PRELIMINARY QUALITY CONTROL PIPELINE FOR SINGLE NUCLEI RNA-SEQ AND ITS APPLICATION IN THE ANALYSIS OF CELL TYPE DIVERSITY OF POST-MORTEM HUMAN BRAIN NEOCORTEX. Pac Symp Biocomput. 2016; 22:564-575. PMID: 27897007.
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      9. León-Zayas R, Novotny M, Podell S, Shepard CM, Berkenpas E, Nikolenko S, Pevzner P, Lasken R, Bartlett DH. Single Cells within the Puerto Rico Trench Suggest Hadal Adaptation of Microbial Lineages. Appl Environ Microbiol. 2015 Dec 15; 81(24):8265-76. PMID: 26386059.
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      10. Kang J, Lienhard M, Pastor WA, Chawla A, Novotny M, Tsagaratou A, Lasken R, Thompson EC, Surani MA, Koralov SB, Kalantry S, Chavez L, Rao A. Simultaneous deletion of the methylcytosine oxidases Tet1 and Tet3 increases transcriptome variability in early embryogenesis. Proc Natl Acad Sci U S A. 2015 Aug 4; 112(31):E4236-45. PMID: 26199412.
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      11. McLean JS, Lasken R. Single cell genomics of bacterial pathogens: outlook for infectious disease research. Genome Med. 2014; 6(11):108. PMID: 25621014.
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      12. McCorrison JM, Venepally P, Singh I, Fouts DE, Lasken R, Methé BA. NeatFreq: reference-free data reduction and coverage normalization for De Novo sequence assembly. BMC Bioinformatics. 2014; 15(1):357. PMID: 25407910.
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      13. Lasken R, McLean JS. Recent advances in genomic DNA sequencing of microbial species from single cells. Nat Rev Genet. 2014 Sep; 15(9):577-84. PMID: 25091868.
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      14. Grindberg RV, Yee-Greenbaum JL, McConnell MJ, Novotny M, O'Shaughnessy AL, Lambert GM, Araúzo-Bravo MJ, Lee J, Fishman M, Robbins GE, Lin X, Venepally P, Badger JH, Galbraith DW, Gage FH, Lasken R. RNA-sequencing from single nuclei. Proc Natl Acad Sci U S A. 2013 Dec 3; 110(49):19802-7. PMID: 24248345.
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      15. McConnell MJ, Lindberg MR, Brennand KJ, Piper JC, Voet T, Cowing-Zitron C, Shumilina S, Lasken R, Vermeesch JR, Hall IM, Gage FH. Mosaic copy number variation in human neurons. Science. 2013 Nov 1; 342(6158):632-7. PMID: 24179226.
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      16. Nurk S, Bankevich A, Antipov D, Gurevich AA, Korobeynikov A, Lapidus A, Prjibelski AD, Pyshkin A, Sirotkin A, Sirotkin Y, Stepanauskas R, Clingenpeel SR, Woyke T, McLean JS, Lasken R, Tesler G, Alekseyev MA, Pevzner PA. Assembling single-cell genomes and mini-metagenomes from chimeric MDA products. J Comput Biol. 2013 Oct; 20(10):714-37. PMID: 24093227.
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      17. McLean JS, Lombardo MJ, Badger JH, Edlund A, Novotny M, Yee-Greenbaum J, Vyahhi N, Hall AP, Yang Y, Dupont CL, Ziegler MG, Chitsaz H, Allen AE, Yooseph S, Tesler G, Pevzner PA, Friedman RM, Nealson KH, Venter JC, Lasken R. Candidate phylum TM6 genome recovered from a hospital sink biofilm provides genomic insights into this uncultivated phylum. Proc Natl Acad Sci U S A. 2013 Jun 25; 110(26):E2390-9. PMID: 23754396.
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      18. Zeigler Allen L, Ishoey T, Novotny MA, McLean JS, Lasken R, Williamson SJ. Isolation and genome analysis of single virions using 'single virus genomics'. J Vis Exp. 2013; (75):e3899. PMID: 23728084.
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      19. McLean JS, Lombardo MJ, Ziegler MG, Novotny M, Yee-Greenbaum J, Badger JH, Tesler G, Nurk S, Lesin V, Brami D, Hall AP, Edlund A, Allen LZ, Durkin S, Reed S, Torriani F, Nealson KH, Pevzner PA, Friedman R, Venter JC, Lasken R. Genome of the pathogen Porphyromonas gingivalis recovered from a biofilm in a hospital sink using a high-throughput single-cell genomics platform. Genome Res. 2013 May; 23(5):867-77. PMID: 23564253.
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      20. Fitzsimons MS, Novotny M, Lo CC, Dichosa AE, Yee-Greenbaum JL, Snook JP, Gu W, Chertkov O, Davenport KW, McMurry K, Reitenga KG, Daughton AR, He J, Johnson SL, Gleasner CD, Wills PL, Parson-Quintana B, Chain PS, Detter JC, Lasken R, Han CS. Nearly finished genomes produced using gel microdroplet culturing reveal substantial intraspecies genomic diversity within the human microbiome. Genome Res. 2013 May; 23(5):878-88. PMID: 23493677.
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      21. Lasken R. Single-cell sequencing in its prime. Nat Biotechnol. 2013 Mar; 31(3):211-2. PMID: 23471069.
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      22. Romano C, D'Imperio S, Woyke T, Mavromatis K, Lasken R, Shock EL, McDermott TR. Comparative genomic analysis of phylogenetically closely related Hydrogenobaculum sp. isolates from Yellowstone National Park. Appl Environ Microbiol. 2013 May; 79(9):2932-43. PMID: 23435891.
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      23. Rusch DB, Lombardo MJ, Yee-Greenbaum J, Novotny M, Brinkac LM, Lasken R, Dupont CL. Draft Genome Sequence of a Single Cell of SAR86 Clade Subgroup IIIa. Genome Announc. 2013 Jan; 1(1). PMID: 23405308; PMCID: PMC3569297.
      24. Kirkness EF, Grindberg RV, Yee-Greenbaum J, Marshall CR, Scherer SW, Lasken R, Venter JC. Sequencing of isolated sperm cells for direct haplotyping of a human genome. Genome Res. 2013 May; 23(5):826-32. PMID: 23282328.
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      25. Suzuki Y, Stam J, Novotny M, Yachie N, Lasken R, Roth FP. The green monster process for the generation of yeast strains carrying multiple gene deletions. J Vis Exp. 2012; (70):e4072. PMID: 23271437.
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      26. Lasken R. Genomic sequencing of uncultured microorganisms from single cells. Nat Rev Microbiol. 2012 Sep; 10(9):631-40. PMID: 22890147.
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      27. Dupont CL, Rusch DB, Yooseph S, Lombardo MJ, Richter RA, Valas R, Novotny M, Yee-Greenbaum J, Selengut JD, Haft DH, Halpern AL, Lasken R, Nealson K, Friedman R, Venter JC. Genomic insights to SAR86, an abundant and uncultivated marine bacterial lineage. ISME J. 2012 Jun; 6(6):1186-99. PMID: 22170421.
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      28. Chitsaz H, Yee-Greenbaum JL, Tesler G, Lombardo MJ, Dupont CL, Badger JH, Novotny M, Rusch DB, Fraser LJ, Gormley NA, Schulz-Trieglaff O, Smith GP, Evers DJ, Pevzner PA, Lasken R. Efficient de novo assembly of single-cell bacterial genomes from short-read data sets. Nat Biotechnol. 2011 Oct; 29(10):915-21. PMID: 21926975.
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      29. Eloe EA, Fadrosh DW, Novotny M, Zeigler Allen L, Kim M, Lombardo MJ, Yee-Greenbaum J, Yooseph S, Allen EE, Lasken R, Williamson SJ, Bartlett DH. Going deeper: metagenome of a hadopelagic microbial community. PLoS One. 2011; 6(5):e20388. PMID: 21629664.
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      30. Jones AC, Monroe EA, Podell S, Hess WR, Klages S, Esquenazi E, Niessen S, Hoover H, Rothmann M, Lasken R, Yates JR, Reinhardt R, Kube M, Burkart MD, Allen EE, Dorrestein PC, Gerwick WH, Gerwick L. Genomic insights into the physiology and ecology of the marine filamentous cyanobacterium Lyngbya majuscula. Proc Natl Acad Sci U S A. 2011 May 24; 108(21):8815-20. PMID: 21555588.
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      31. Grindberg RV, Ishoey T, Brinza D, Esquenazi E, Coates RC, Liu WT, Gerwick L, Dorrestein PC, Pevzner P, Lasken R, Gerwick WH. Single cell genome amplification accelerates identification of the apratoxin biosynthetic pathway from a complex microbial assemblage. PLoS One. 2011; 6(4):e18565. PMID: 21533272.
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      32. Allen LZ, Ishoey T, Novotny MA, McLean JS, Lasken R, Williamson SJ. Single virus genomics: a new tool for virus discovery. PLoS One. 2011; 6(3):e17722. PMID: 21436882.
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      33. Kathju S, Lasken R, Satish L, Johnson S, Stoodley P, Post JC, Ehrlich GD. Multiple displacement amplification as an adjunct to PCR-based detection of Staphylococcus aureus in synovial fluid. BMC Res Notes. 2010; 3:259. PMID: 20942932.
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      34. Cuvelier ML, Allen AE, Monier A, McCrow JP, Messié M, Tringe SG, Woyke T, Welsh RM, Ishoey T, Lee JH, Binder BJ, DuPont CL, Latasa M, Guigand C, Buck KR, Hilton J, Thiagarajan M, Caler E, Read B, Lasken R, Chavez FP, Worden AZ. Targeted metagenomics and ecology of globally important uncultured eukaryotic phytoplankton. Proc Natl Acad Sci U S A. 2010 Aug 17; 107(33):14679-84. PMID: 20668244.
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      35. Lasken R. Genomic DNA amplification by the multiple displacement amplification (MDA) method. Biochem Soc Trans. 2009 Apr; 37(Pt 2):450-3. PMID: 19290880.
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      36. Ishoey T, Woyke T, Stepanauskas R, Novotny M, Lasken R. Genomic sequencing of single microbial cells from environmental samples. Curr Opin Microbiol. 2008 Jun; 11(3):198-204. PMID: 18550420.
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      37. Binga EK, Lasken R, Neufeld JD. Something from (almost) nothing: the impact of multiple displacement amplification on microbial ecology. ISME J. 2008 Mar; 2(3):233-41. PMID: 18256705.
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      38. Lasken R. Single-cell genomic sequencing using Multiple Displacement Amplification. Curr Opin Microbiol. 2007 Oct; 10(5):510-6. PMID: 17923430.
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      39. Kiesling T, Cox K, Davidson EA, Dretchen K, Grater G, Hibbard S, Lasken R, Leshin J, Skowronski E, Danielsen M. Sequence specific detection of DNA using nicking endonuclease signal amplification (NESA). Nucleic Acids Res. 2007; 35(18):e117. PMID: 17827214.
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      40. Mussmann M, Hu FZ, Richter M, de Beer D, Preisler A, Jørgensen BB, Huntemann M, Glöckner FO, Amann R, Koopman WJ, Lasken R, Janto B, Hogg J, Stoodley P, Boissy R, Ehrlich GD. Insights into the genome of large sulfur bacteria revealed by analysis of single filaments. PLoS Biol. 2007 Sep; 5(9):e230. PMID: 17760503.
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      41. Marcy Y, Ishoey T, Lasken R, Stockwell TB, Walenz BP, Halpern AL, Beeson KY, Goldberg SM, Quake SR. Nanoliter reactors improve multiple displacement amplification of genomes from single cells. PLoS Genet. 2007 Sep; 3(9):1702-8. PMID: 17892324.
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      42. Lasken R, Stockwell TB. Mechanism of chimera formation during the Multiple Displacement Amplification reaction. BMC Biotechnol. 2007; 7:19. PMID: 17430586.
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      43. Kvist T, Ahring BK, Lasken R, Westermann P. Specific single-cell isolation and genomic amplification of uncultured microorganisms. Appl Microbiol Biotechnol. 2007 Mar; 74(4):926-35. PMID: 17109170.
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      44. Raghunathan A, Ferguson HR, Bornarth CJ, Song W, Driscoll M, Lasken R. Genomic DNA amplification from a single bacterium. Appl Environ Microbiol. 2005 Jun; 71(6):3342-7. PMID: 15933038.
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      45. Barker DL, Hansen MS, Faruqi AF, Giannola D, Irsula OR, Lasken R, Latterich M, Makarov V, Oliphant A, Pinter JH, Shen R, Sleptsova I, Ziehler W, Lai E. Two methods of whole-genome amplification enable accurate genotyping across a 2320-SNP linkage panel. Genome Res. 2004 May; 14(5):901-7. PMID: 15123587.
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      46. Lasken R, Egholm M. Whole genome amplification: abundant supplies of DNA from precious samples or clinical specimens. Trends Biotechnol. 2003 Dec; 21(12):531-5. PMID: 14624861.
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      47. Alsmadi OA, Bornarth CJ, Song W, Wisniewski M, Du J, Brockman JP, Faruqi AF, Hosono S, Sun Z, Du Y, Wu X, Egholm M, Abarzúa P, Lasken R, Driscoll MD. High accuracy genotyping directly from genomic DNA using a rolling circle amplification based assay. BMC Genomics. 2003 May 30; 4(1):21. PMID: 12777185.
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      48. Hosono S, Faruqi AF, Dean FB, Du Y, Sun Z, Wu X, Du J, Kingsmore SF, Egholm M, Lasken R. Unbiased whole-genome amplification directly from clinical samples. Genome Res. 2003 May; 13(5):954-64. PMID: 12695328.
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      49. Buckley PG, Mantripragada KK, Benetkiewicz M, Tapia-Páez I, Diaz De Ståhl T, Rosenquist M, Ali H, Jarbo C, De Bustos C, Hirvelä C, Sinder Wilén B, Fransson I, Thyr C, Johnsson BI, Bruder CE, Menzel U, Hergersberg M, Mandahl N, Blennow E, Wedell A, Beare DM, Collins JE, Dunham I, Albertson D, Pinkel D, Bastian BC, Faruqi AF, Lasken R, Ichimura K, Collins VP, Dumanski JP. A full-coverage, high-resolution human chromosome 22 genomic microarray for clinical and research applications. Hum Mol Genet. 2002 Dec 1; 11(25):3221-9. PMID: 12444106.
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      50. Dean FB, Hosono S, Fang L, Wu X, Faruqi AF, Bray-Ward P, Sun Z, Zong Q, Du Y, Du J, Driscoll M, Song W, Kingsmore SF, Egholm M, Lasken R. Comprehensive human genome amplification using multiple displacement amplification. Proc Natl Acad Sci U S A. 2002 Apr 16; 99(8):5261-6. PMID: 11959976.
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      51. Nallur G, Luo C, Fang L, Cooley S, Dave V, Lambert J, Kukanskis K, Kingsmore S, Lasken R, Schweitzer B. Signal amplification by rolling circle amplification on DNA microarrays. Nucleic Acids Res. 2001 Dec 1; 29(23):E118. PMID: 11726701.
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      52. Faruqi AF, Hosono S, Driscoll MD, Dean FB, Alsmadi O, Bandaru R, Kumar G, Grimwade B, Zong Q, Sun Z, Du Y, Kingsmore S, Knott T, Lasken R. High-throughput genotyping of single nucleotide polymorphisms with rolling circle amplification. BMC Genomics. 2001; 2:4. PMID: 11511324.
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      53. Dean FB, Nelson JR, Giesler TL, Lasken R. Rapid amplification of plasmid and phage DNA using Phi 29 DNA polymerase and multiply-primed rolling circle amplification. Genome Res. 2001 Jun; 11(6):1095-9. PMID: 11381035.
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      54. Zhao Y, Jeruzalmi D, Moarefi I, Leighton L, Lasken R, Kuriyan J. Crystal structure of an archaebacterial DNA polymerase. Structure. 1999 Oct 15; 7(10):1189-99. PMID: 10545321.
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      55. Lasken R, Schuster DM, Rashtchian A. Archaebacterial DNA polymerases tightly bind uracil-containing DNA. J Biol Chem. 1996 Jul 26; 271(30):17692-6. PMID: 8663453.
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      56. Wahle E, Lasken R, Kornberg A. The dnaB-dnaC replication protein complex of Escherichia coli. I. Formation and properties. J Biol Chem. 1989 Feb 15; 264(5):2463-8. PMID: 2536712.
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      57. Wahle E, Lasken R, Kornberg A. The dnaB-dnaC replication protein complex of Escherichia coli. II. Role of the complex in mobilizing dnaB functions. J Biol Chem. 1989 Feb 15; 264(5):2469-75. PMID: 2536713.
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      58. Lasken R, Kornberg A. The primosomal protein n' of Escherichia coli is a DNA helicase. J Biol Chem. 1988 Apr 25; 263(12):5512-8. PMID: 2833507.
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      59. Lasken R, Kornberg A. The beta subunit dissociates readily from the Escherichia coli DNA polymerase III holoenzyme. J Biol Chem. 1987 Feb 5; 262(4):1720-4. PMID: 3543011.
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      60. Lasken R, Goodman MF. A fidelity assay using "dideoxy" DNA sequencing: a measurement of sequence dependence and frequency of forming 5-bromouracil X guanine base mispairs. Proc Natl Acad Sci U S A. 1985 Mar; 82(5):1301-5. PMID: 3856263.
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      61. Goodman MF, Hopkins RL, Lasken R, Mhaskar DN. The biochemical basis of 5-bromouracil- and 2-aminopurine-induced mutagenesis. Basic Life Sci. 1985; 31:409-23. PMID: 3994630.
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      62. Lasken R, Goodman MF. The biochemical basis of 5-bromouracil-induced mutagenesis. Heteroduplex base mispairs involving bromouracil in G x C----A x T and A x T----G x C mutational pathways. J Biol Chem. 1984 Sep 25; 259(18):11491-5. PMID: 6088545.
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