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Items: 1 to 50 of 59

1.

Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type.

Boldog E, Bakken TE, Hodge RD, Novotny M, Aevermann BD, Baka J, Bordé S, Close JL, Diez-Fuertes F, Ding SL, Faragó N, Kocsis ÁK, Kovács B, Maltzer Z, McCorrison JM, Miller JA, Molnár G, Oláh G, Ozsvár A, Rózsa M, Shehata SI, Smith KA, Sunkin SM, Tran DN, Venepally P, Wall A, Puskás LG, Barzó P, Steemers FJ, Schork NJ, Scheuermann RH, Lasken RS, Lein ES, Tamás G.

Nat Neurosci. 2018 Sep;21(9):1185-1195. doi: 10.1038/s41593-018-0205-2. Epub 2018 Aug 27.

PMID:
30150662
2.

Author Correction: L1-associated genomic regions are deleted in somatic cells of the healthy human brain.

Erwin JA, Paquola ACM, Singer T, Gallina I, Novotny M, Quayle C, Bedrosian TA, Alves FIA, Butcher CR, Herdy JR, Sarkar A, Lasken RS, Muotri AR, Gage FH.

Nat Neurosci. 2018 Jul;21(7):1016. doi: 10.1038/s41593-018-0131-3.

PMID:
29703932
3.

Cell type discovery using single-cell transcriptomics: implications for ontological representation.

Aevermann BD, Novotny M, Bakken T, Miller JA, Diehl AD, Osumi-Sutherland D, Lasken RS, Lein ES, Scheuermann RH.

Hum Mol Genet. 2018 May 1;27(R1):R40-R47. doi: 10.1093/hmg/ddy100.

4.

Cell type discovery and representation in the era of high-content single cell phenotyping.

Bakken T, Cowell L, Aevermann BD, Novotny M, Hodge R, Miller JA, Lee A, Chang I, McCorrison J, Pulendran B, Qian Y, Schork NJ, Lasken RS, Lein ES, Scheuermann RH.

BMC Bioinformatics. 2017 Dec 21;18(Suppl 17):559. doi: 10.1186/s12859-017-1977-1.

5.

Corrigendum: L1-associated genomic regions are deleted in somatic cells of the healthy human brain.

Erwin JA, Paquola ACM, Singer T, Gallina I, Novotny M, Quayle C, Bedrosian TA, Alves FIA, Butcher CR, Herdy JR, Sarkar A, Lasken RS, Muotri AR, Gage FH.

Nat Neurosci. 2017 Sep 28;20(10):1427. doi: 10.1038/nn1017-1427a. No abstract available.

PMID:
28949329
6.

A Whole Blood Molecular Signature for Acute Myocardial Infarction.

Muse ED, Kramer ER, Wang H, Barrett P, Parviz F, Novotny MA, Lasken RS, Jatkoe TA, Oliveira G, Peng H, Lu J, Connelly MC, Schilling K, Rao C, Torkamani A, Topol EJ.

Sci Rep. 2017 Sep 25;7(1):12268. doi: 10.1038/s41598-017-12166-0.

7.

Pan-cancer analysis reveals technical artifacts in TCGA germline variant calls.

Buckley AR, Standish KA, Bhutani K, Ideker T, Lasken RS, Carter H, Harismendy O, Schork NJ.

BMC Genomics. 2017 Jun 12;18(1):458. doi: 10.1186/s12864-017-3770-y.

8.

The metabolic potential of the single cell genomes obtained from the Challenger Deep, Mariana Trench within the candidate superphylum Parcubacteria (OD1).

León-Zayas R, Peoples L, Biddle JF, Podell S, Novotny M, Cameron J, Lasken RS, Bartlett DH.

Environ Microbiol. 2017 Jul;19(7):2769-2784. doi: 10.1111/1462-2920.13789. Epub 2017 Jun 22.

9.

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.

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 RS, Lein ED, Schork N, Scheuermann RH.

Pac Symp Biocomput. 2017;22:564-575. doi: 10.1142/9789813207813_0052.

10.

L1-associated genomic regions are deleted in somatic cells of the healthy human brain.

Erwin JA, Paquola AC, Singer T, Gallina I, Novotny M, Quayle C, Bedrosian TA, Alves FI, Butcher CR, Herdy JR, Sarkar A, Lasken RS, Muotri AR, Gage FH.

Nat Neurosci. 2016 Dec;19(12):1583-1591. doi: 10.1038/nn.4388. Epub 2016 Sep 12. Erratum in: Nat Neurosci. 2017 Sep 28;20(10 ):1427. Nat Neurosci. 2018 Apr 27;:.

11.

Predicting the functional states of human iPSC-derived neurons with single-cell RNA-seq and electrophysiology.

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 RS, Rutten BP, Steinbusch HW, Yeo GW, Gage FH.

Mol Psychiatry. 2016 Nov;21(11):1573-1588. doi: 10.1038/mp.2016.158. Epub 2016 Oct 4.

12.

Using single nuclei for RNA-seq to capture the transcriptome of postmortem neurons.

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 RS.

Nat Protoc. 2016 Mar;11(3):499-524. doi: 10.1038/nprot.2016.015. Epub 2016 Feb 18.

13.

Single cells within the Puerto Rico trench suggest hadal adaptation of microbial lineages.

León-Zayas R, Novotny M, Podell S, Shepard CM, Berkenpas E, Nikolenko S, Pevzner P, Lasken RS, Bartlett DH.

Appl Environ Microbiol. 2015 Dec;81(24):8265-76. doi: 10.1128/AEM.01659-15. Epub 2015 Sep 18.

14.

Simultaneous deletion of the methylcytosine oxidases Tet1 and Tet3 increases transcriptome variability in early embryogenesis.

Kang J, Lienhard M, Pastor WA, Chawla A, Novotny M, Tsagaratou A, Lasken RS, Thompson EC, Surani MA, Koralov SB, Kalantry S, Chavez L, Rao A.

Proc Natl Acad Sci U S A. 2015 Aug 4;112(31):E4236-45. doi: 10.1073/pnas.1510510112. Epub 2015 Jul 21.

15.

Single cell genomics of bacterial pathogens: outlook for infectious disease research.

McLean JS, Lasken RS.

Genome Med. 2014 Nov 20;6(11):108. doi: 10.1186/s13073-014-0108-0. eCollection 2014.

16.

NeatFreq: reference-free data reduction and coverage normalization for De Novo sequence assembly.

McCorrison JM, Venepally P, Singh I, Fouts DE, Lasken RS, Methé BA.

BMC Bioinformatics. 2014 Nov 19;15:357. doi: 10.1186/s12859-014-0357-3.

17.

Recent advances in genomic DNA sequencing of microbial species from single cells.

Lasken RS, McLean JS.

Nat Rev Genet. 2014 Sep;15(9):577-84. doi: 10.1038/nrg3785. Epub 2014 Aug 5. Review.

18.

RNA-sequencing from single nuclei.

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 RS.

Proc Natl Acad Sci U S A. 2013 Dec 3;110(49):19802-7. doi: 10.1073/pnas.1319700110. Epub 2013 Nov 18.

19.

Mosaic copy number variation in human neurons.

McConnell MJ, Lindberg MR, Brennand KJ, Piper JC, Voet T, Cowing-Zitron C, Shumilina S, Lasken RS, Vermeesch JR, Hall IM, Gage FH.

Science. 2013 Nov 1;342(6158):632-7. doi: 10.1126/science.1243472.

20.

Candidate phylum TM6 genome recovered from a hospital sink biofilm provides genomic insights into this uncultivated phylum.

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 RS.

Proc Natl Acad Sci U S A. 2013 Jun 25;110(26):E2390-9. doi: 10.1073/pnas.1219809110. Epub 2013 Jun 10.

21.

Isolation and genome analysis of single virions using 'single virus genomics'.

Zeigler Allen L, Ishoey T, Novotny MA, McLean JS, Lasken RS, Williamson SJ.

J Vis Exp. 2013 May 26;(75):e3899. doi: 10.3791/3899.

22.

Genome of the pathogen Porphyromonas gingivalis recovered from a biofilm in a hospital sink using a high-throughput single-cell genomics platform.

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 RS.

Genome Res. 2013 May;23(5):867-77. doi: 10.1101/gr.150433.112. Epub 2013 Apr 5.

23.

Nearly finished genomes produced using gel microdroplet culturing reveal substantial intraspecies genomic diversity within the human microbiome.

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 RS, Han CS.

Genome Res. 2013 May;23(5):878-88. doi: 10.1101/gr.142208.112. Epub 2013 Mar 14.

24.

Single-cell sequencing in its prime.

Lasken RS.

Nat Biotechnol. 2013 Mar;31(3):211-2. doi: 10.1038/nbt.2523. No abstract available.

PMID:
23471069
25.

Draft Genome Sequence of a Single Cell of SAR86 Clade Subgroup IIIa.

Rusch DB, Lombardo MJ, Yee-Greenbaum J, Novotny M, Brinkac LM, Lasken RS, Dupont CL.

Genome Announc. 2013 Jan;1(1). pii: e00030-12. doi: 10.1128/genomeA.00030-12. Epub 2013 Jan 15.

26.

Sequencing of isolated sperm cells for direct haplotyping of a human genome.

Kirkness EF, Grindberg RV, Yee-Greenbaum J, Marshall CR, Scherer SW, Lasken RS, Venter JC.

Genome Res. 2013 May;23(5):826-32. doi: 10.1101/gr.144600.112. Epub 2013 Jan 2.

27.

The green monster process for the generation of yeast strains carrying multiple gene deletions.

Suzuki Y, Stam J, Novotny M, Yachie N, Lasken RS, Roth FP.

J Vis Exp. 2012 Dec 15;(70):e4072. doi: 10.3791/4072.

28.

Genomic sequencing of uncultured microorganisms from single cells.

Lasken RS.

Nat Rev Microbiol. 2012 Sep;10(9):631-40. doi: 10.1038/nrmicro2857. Review.

PMID:
22890147
29.

Genomic insights to SAR86, an abundant and uncultivated marine bacterial lineage.

Dupont CL, Rusch DB, Yooseph S, Lombardo MJ, Richter RA, Valas R, Novotny M, Yee-Greenbaum J, Selengut JD, Haft DH, Halpern AL, Lasken RS, Nealson K, Friedman R, Venter JC.

ISME J. 2012 Jun;6(6):1186-99. doi: 10.1038/ismej.2011.189. Epub 2011 Dec 15.

30.

Efficient de novo assembly of single-cell bacterial genomes from short-read data sets.

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 RS.

Nat Biotechnol. 2011 Sep 18;29(10):915-21. doi: 10.1038/nbt.1966.

31.

Genomic insights into the physiology and ecology of the marine filamentous cyanobacterium Lyngbya majuscula.

Jones AC, Monroe EA, Podell S, Hess WR, Klages S, Esquenazi E, Niessen S, Hoover H, Rothmann M, Lasken RS, Yates JR 3rd, Reinhardt R, Kube M, Burkart MD, Allen EE, Dorrestein PC, Gerwick WH, Gerwick L.

Proc Natl Acad Sci U S A. 2011 May 24;108(21):8815-20. doi: 10.1073/pnas.1101137108. Epub 2011 May 9.

32.

Single virus genomics: a new tool for virus discovery.

Allen LZ, Ishoey T, Novotny MA, McLean JS, Lasken RS, Williamson SJ.

PLoS One. 2011 Mar 23;6(3):e17722. doi: 10.1371/journal.pone.0017722.

33.

Multiple displacement amplification as an adjunct to PCR-based detection of Staphylococcus aureus in synovial fluid.

Kathju S, Lasken RS, Satish L, Johnson S, Stoodley P, Post JC, Ehrlich GD.

BMC Res Notes. 2010 Oct 13;3:259. doi: 10.1186/1756-0500-3-259.

34.

Targeted metagenomics and ecology of globally important uncultured eukaryotic phytoplankton.

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 RS, Chavez FP, Worden AZ.

Proc Natl Acad Sci U S A. 2010 Aug 17;107(33):14679-84. doi: 10.1073/pnas.1001665107. Epub 2010 Jul 28.

35.

Genomic DNA amplification by the multiple displacement amplification (MDA) method.

Lasken RS.

Biochem Soc Trans. 2009 Apr;37(Pt 2):450-3. doi: 10.1042/BST0370450. Review.

PMID:
19290880
36.

Genomic sequencing of single microbial cells from environmental samples.

Ishoey T, Woyke T, Stepanauskas R, Novotny M, Lasken RS.

Curr Opin Microbiol. 2008 Jun;11(3):198-204. doi: 10.1016/j.mib.2008.05.006. Epub 2008 Jun 10. Review.

37.

Something from (almost) nothing: the impact of multiple displacement amplification on microbial ecology.

Binga EK, Lasken RS, Neufeld JD.

ISME J. 2008 Mar;2(3):233-41. doi: 10.1038/ismej.2008.10. Epub 2008 Feb 7. Review.

PMID:
18256705
38.

Single-cell genomic sequencing using Multiple Displacement Amplification.

Lasken RS.

Curr Opin Microbiol. 2007 Oct;10(5):510-6. Epub 2007 Oct 17. Review.

PMID:
17923430
39.

Nanoliter reactors improve multiple displacement amplification of genomes from single cells.

Marcy Y, Ishoey T, Lasken RS, Stockwell TB, Walenz BP, Halpern AL, Beeson KY, Goldberg SM, Quake SR.

PLoS Genet. 2007 Sep;3(9):1702-8.

40.

Sequence specific detection of DNA using nicking endonuclease signal amplification (NESA).

Kiesling T, Cox K, Davidson EA, Dretchen K, Grater G, Hibbard S, Lasken RS, Leshin J, Skowronski E, Danielsen M.

Nucleic Acids Res. 2007;35(18):e117. Epub 2007 Sep 7.

41.

Insights into the genome of large sulfur bacteria revealed by analysis of single filaments.

Mussmann M, Hu FZ, Richter M, de Beer D, Preisler A, Jørgensen BB, Huntemann M, Glöckner FO, Amann R, Koopman WJ, Lasken RS, Janto B, Hogg J, Stoodley P, Boissy R, Ehrlich GD.

PLoS Biol. 2007 Sep;5(9):e230.

42.
43.

Specific single-cell isolation and genomic amplification of uncultured microorganisms.

Kvist T, Ahring BK, Lasken RS, Westermann P.

Appl Microbiol Biotechnol. 2007 Mar;74(4):926-35. Epub 2006 Nov 16.

PMID:
17109170
44.

Genomic DNA amplification from a single bacterium.

Raghunathan A, Ferguson HR Jr, Bornarth CJ, Song W, Driscoll M, Lasken RS.

Appl Environ Microbiol. 2005 Jun;71(6):3342-7.

45.

Two methods of whole-genome amplification enable accurate genotyping across a 2320-SNP linkage panel.

Barker DL, Hansen MS, Faruqi AF, Giannola D, Irsula OR, Lasken RS, Latterich M, Makarov V, Oliphant A, Pinter JH, Shen R, Sleptsova I, Ziehler W, Lai E.

Genome Res. 2004 May;14(5):901-7.

46.

Whole genome amplification: abundant supplies of DNA from precious samples or clinical specimens.

Lasken RS, Egholm M.

Trends Biotechnol. 2003 Dec;21(12):531-5. Review. No abstract available.

PMID:
14624861
47.

High accuracy genotyping directly from genomic DNA using a rolling circle amplification based assay.

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 RS, Driscoll MD.

BMC Genomics. 2003 May 30;4(1):21. Epub 2003 May 30.

48.

Unbiased whole-genome amplification directly from clinical samples.

Hosono S, Faruqi AF, Dean FB, Du Y, Sun Z, Wu X, Du J, Kingsmore SF, Egholm M, Lasken RS.

Genome Res. 2003 May;13(5):954-64. Epub 2003 Apr 14.

49.

A full-coverage, high-resolution human chromosome 22 genomic microarray for clinical and research applications.

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 RS, Ichimura K, Collins VP, Dumanski JP.

Hum Mol Genet. 2002 Dec 1;11(25):3221-9.

PMID:
12444106
50.

Comprehensive human genome amplification using multiple displacement amplification.

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 RS.

Proc Natl Acad Sci U S A. 2002 Apr 16;99(8):5261-6.

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