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Items: 22

1.

A Genome-wide Analysis of Human Pluripotent Stem Cell-Derived Endothelial Cells in 2D or 3D Culture.

Zhang J, Schwartz MP, Hou Z, Bai Y, Ardalani H, Swanson S, Steill J, Ruotti V, Elwell A, Nguyen BK, Bolin J, Stewart R, Thomson JA, Murphy WL.

Stem Cell Reports. 2017 Apr 11;8(4):907-918. doi: 10.1016/j.stemcr.2017.02.014. Epub 2017 Mar 23.

2.

Saturation analysis for whole-genome bisulfite sequencing data.

Libertini E, Heath SC, Hamoudi RA, Gut M, Ziller MJ, Herrero J, Czyz A, Ruotti V, Stunnenberg HG, Frontini M, Ouwehand WH, Meissner A, Gut IG, Beck S.

Nat Biotechnol. 2016 Jul;34(7):691-693. doi: 10.1038/nbt.3524. Epub 2016 Jun 27. No abstract available.

PMID:
27347755
3.

Information recovery from low coverage whole-genome bisulfite sequencing.

Libertini E, Heath SC, Hamoudi RA, Gut M, Ziller MJ, Czyz A, Ruotti V, Stunnenberg HG, Frontini M, Ouwehand WH, Meissner A, Gut IG, Beck S.

Nat Commun. 2016 Jun 27;7:11306. doi: 10.1038/ncomms11306.

4.

EBSeq: an empirical Bayes hierarchical model for inference in RNA-seq experiments.

Leng N, Dawson JA, Thomson JA, Ruotti V, Rissman AI, Smits BM, Haag JD, Gould MN, Stewart RM, Kendziorski C.

Bioinformatics. 2013 Apr 15;29(8):1035-43. doi: 10.1093/bioinformatics/btt087. Epub 2013 Feb 21. Erratum in: Bioinformatics. 2013 Aug 15;29(16):2073.

5.

Single read and paired end mRNA-Seq Illumina libraries from 10 nanograms total RNA.

Sengupta S, Bolin JM, Ruotti V, Nguyen BK, Thomson JA, Elwell AL, Stewart R.

J Vis Exp. 2011 Oct 27;(56):e3340. doi: 10.3791/3340.

6.

Proteomic and phosphoproteomic comparison of human ES and iPS cells.

Phanstiel DH, Brumbaugh J, Wenger CD, Tian S, Probasco MD, Bailey DJ, Swaney DL, Tervo MA, Bolin JM, Ruotti V, Stewart R, Thomson JA, Coon JJ.

Nat Methods. 2011 Sep 11;8(10):821-7. doi: 10.1038/nmeth.1699.

7.

Chemically defined conditions for human iPSC derivation and culture.

Chen G, Gulbranson DR, Hou Z, Bolin JM, Ruotti V, Probasco MD, Smuga-Otto K, Howden SE, Diol NR, Propson NE, Wagner R, Lee GO, Antosiewicz-Bourget J, Teng JM, Thomson JA.

Nat Methods. 2011 May;8(5):424-9. doi: 10.1038/nmeth.1593. Epub 2011 Apr 10.

8.

Highly consistent, fully representative mRNA-Seq libraries from ten nanograms of total RNA.

Sengupta S, Ruotti V, Bolin J, Elwell A, Hernandez A, Thomson J, Stewart R.

Biotechniques. 2010 Dec;49(6):898-904. doi: 10.2144/000113556.

9.

Distinct epigenomic landscapes of pluripotent and lineage-committed human cells.

Hawkins RD, Hon GC, Lee LK, Ngo Q, Lister R, Pelizzola M, Edsall LE, Kuan S, Luu Y, Klugman S, Antosiewicz-Bourget J, Ye Z, Espinoza C, Agarwahl S, Shen L, Ruotti V, Wang W, Stewart R, Thomson JA, Ecker JR, Ren B.

Cell Stem Cell. 2010 May 7;6(5):479-91. doi: 10.1016/j.stem.2010.03.018.

10.

RNA-Seq gene expression estimation with read mapping uncertainty.

Li B, Ruotti V, Stewart RM, Thomson JA, Dewey CN.

Bioinformatics. 2010 Feb 15;26(4):493-500. doi: 10.1093/bioinformatics/btp692. Epub 2009 Dec 18.

11.

Human DNA methylomes at base resolution show widespread epigenomic differences.

Lister R, Pelizzola M, Dowen RH, Hawkins RD, Hon G, Tonti-Filippini J, Nery JR, Lee L, Ye Z, Ngo QM, Edsall L, Antosiewicz-Bourget J, Stewart R, Ruotti V, Millar AH, Thomson JA, Ren B, Ecker JR.

Nature. 2009 Nov 19;462(7271):315-22. doi: 10.1038/nature08514. Epub 2009 Oct 14.

12.

ProbeMatch: rapid alignment of oligonucleotides to genome allowing both gaps and mismatches.

Kim YJ, Teletia N, Ruotti V, Maher CA, Chinnaiyan AM, Stewart R, Thomson JA, Patel JM.

Bioinformatics. 2009 Jun 1;25(11):1424-5. doi: 10.1093/bioinformatics/btp178. Epub 2009 Apr 7.

13.

Molecular profiling reveals similarities and differences between primitive subsets of hematopoietic cells generated in vitro from human embryonic stem cells and in vivo during embryogenesis.

Salvagiotto G, Zhao Y, Vodyanik M, Ruotti V, Stewart R, Marra M, Thomson J, Eaves C, Slukvin I.

Exp Hematol. 2008 Oct;36(10):1377-89. doi: 10.1016/j.exphem.2008.06.015.

14.

A study of the relationships between oligonucleotide properties and hybridization signal intensities from NimbleGen microarray datasets.

Wei H, Kuan PF, Tian S, Yang C, Nie J, Sengupta S, Ruotti V, Jonsdottir GA, Keles S, Thomson JA, Stewart R.

Nucleic Acids Res. 2008 May;36(9):2926-38. doi: 10.1093/nar/gkn133. Epub 2008 Apr 1.

15.

Whole-genome analysis of histone H3 lysine 4 and lysine 27 methylation in human embryonic stem cells.

Pan G, Tian S, Nie J, Yang C, Ruotti V, Wei H, Jonsdottir GA, Stewart R, Thomson JA.

Cell Stem Cell. 2007 Sep 13;1(3):299-312. doi: 10.1016/j.stem.2007.08.003.

16.

Induced pluripotent stem cell lines derived from human somatic cells.

Yu J, Vodyanik MA, Smuga-Otto K, Antosiewicz-Bourget J, Frane JL, Tian S, Nie J, Jonsdottir GA, Ruotti V, Stewart R, Slukvin II, Thomson JA.

Science. 2007 Dec 21;318(5858):1917-20. Epub 2007 Nov 20.

17.

Tools and strategies for physiological genomics: the Rat Genome Database.

Twigger SN, Pasko D, Nie J, Shimoyama M, Bromberg S, Campbell D, Chen J, dela Cruz N, Fan C, Foote C, Harris G, Hickmann B, Ji Y, Jin W, Li D, Mathis J, Nenasheva N, Nigam R, Petri V, Reilly D, Ruotti V, Schauberger E, Seiler K, Slyper R, Smith J, Wang W, Wu W, Zhao L, Zuniga-Meyer A, Tonellato PJ, Kwitek AE, Jacob HJ.

Physiol Genomics. 2005 Oct 17;23(2):246-56. Epub 2005 Aug 16.

18.

DeNovoID: a web-based tool for identifying peptides from sequence and mass tags deduced from de novo peptide sequencing by mass spectroscopy.

Halligan BD, Ruotti V, Twigger SN, Greene AS.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W376-81.

19.

Automated analysis of conserved syntenies for the zebrafish genome.

Postlethwait J, Ruotti V, Carvan MJ, Tonellato PJ.

Methods Cell Biol. 2004;77:255-71. No abstract available.

PMID:
15602916
20.

ProMoST (Protein Modification Screening Tool): a web-based tool for mapping protein modifications on two-dimensional gels.

Halligan BD, Ruotti V, Jin W, Laffoon S, Twigger SN, Dratz EA.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W638-44.

21.

ChromSorter PC: a database of chromosomal regions associated with human prostate cancer.

Etim A, Zhou G, Wen X, Liu H, Ruotti V, Twigger S, Jin W, Matysiak B, Mathis J, Tonellato PJ, Datta MW.

BMC Genomics. 2004 Apr 28;5(1):27.

22.

Integrative genomics: in silico coupling of rat physiology and complex traits with mouse and human data.

Twigger SN, Nie J, Ruotti V, Yu J, Chen D, Li D, Mathis J, Narayanasamy V, Gopinath GR, Pasko D, Shimoyama M, De La Cruz N, Bromberg S, Kwitek AE, Jacob HJ, Tonellato PJ.

Genome Res. 2004 Apr;14(4):651-60.

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