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Items: 1 to 20 of 25

1.

A variant by any name: quantifying annotation discordance across tools and clinical databases.

Yen JL, Garcia S, Montana A, Harris J, Chervitz S, Morra M, West J, Chen R, Church DM.

Genome Med. 2017 Jan 26;9(1):7. doi: 10.1186/s13073-016-0396-7.

2.

Achieving high-sensitivity for clinical applications using augmented exome sequencing.

Patwardhan A, Harris J, Leng N, Bartha G, Church DM, Luo S, Haudenschild C, Pratt M, Zook J, Salit M, Tirch J, Morra M, Chervitz S, Li M, Clark M, Garcia S, Chandratillake G, Kirk S, Ashley E, Snyder M, Altman R, Bustamante C, Butte AJ, West J, Chen R.

Genome Med. 2015 Jul 16;7:71. doi: 10.1186/s13073-015-0197-4. eCollection 2015.

3.

Exome sequencing in 32 patients with anophthalmia/microphthalmia and developmental eye defects.

Slavotinek AM, Garcia ST, Chandratillake G, Bardakjian T, Ullah E, Wu D, Umeda K, Lao R, Tang PL, Wan E, Madireddy L, Lyalina S, Mendelsohn BA, Dugan S, Tirch J, Tischler R, Harris J, Clark MJ, Chervitz S, Patwardhan A, West JM, Ursell P, de Alba Campomanes A, Schneider A, Kwok PY, Baranzini S, Chen RO.

Clin Genet. 2015 Nov;88(5):468-73. doi: 10.1111/cge.12543. Epub 2015 Jan 6.

4.

Variant priorization and analysis incorporating problematic regions of the genome.

Patwardhan A, Clark M, Morgan A, Chervitz S, Pratt M, Bartha G, Chandratillake G, Garcia S, Leng N, Chen R.

Pac Symp Biocomput. 2014:277-87.

5.

Data standards for Omics data: the basis of data sharing and reuse.

Chervitz SA, Deutsch EW, Field D, Parkinson H, Quackenbush J, Rocca-Serra P, Sansone SA, Stoeckert CJ Jr, Taylor CF, Taylor R, Ball CA.

Methods Mol Biol. 2011;719:31-69. doi: 10.1007/978-1-61779-027-0_2. Review.

6.

Genoviz Software Development Kit: Java tool kit for building genomics visualization applications.

Helt GA, Nicol JW, Erwin E, Blossom E, Blanchard SG Jr, Chervitz SA, Harmon C, Loraine AE.

BMC Bioinformatics. 2009 Aug 25;10:266. doi: 10.1186/1471-2105-10-266.

8.

An open letter on microarray data from the MGED Society.

Ball C, Brazma A, Causton H, Chervitz S, Edgar R, Hingamp P, Matese JC, Icahn C, Parkinson H, Quackenbush J, Ringwald M, Sansone SA, Sherlock G, Spellman P, Stoeckert C, Tateno Y, Taylor R, White J, Winegarden N; Microarray Gene Expression Data (MGED) Society.

Microbiology. 2004 Nov;150(Pt 11):3522-4. No abstract available.

PMID:
15528642
9.

Standards for microarray data: an open letter.

Ball C, Brazma A, Causton H, Chervitz S, Edgar R, Hingamp P, Matese JC, Parkinson H, Quackenbush J, Ringwald M, Sansone SA, Sherlock G, Spellman P, Stoeckert C, Tateno Y, Taylor R, White J, Winegarden N; MGED Society.

Environ Health Perspect. 2004 Aug;112(12):A666-7. No abstract available.

10.

Submission of microarray data to public repositories.

Ball CA, Brazma A, Causton H, Chervitz S, Edgar R, Hingamp P, Matese JC, Parkinson H, Quackenbush J, Ringwald M, Sansone SA, Sherlock G, Spellman P, Stoeckert C, Tateno Y, Taylor R, White J, Winegarden N.

PLoS Biol. 2004 Sep;2(9):E317. Epub 2004 Aug 31. No abstract available.

11.

The Bioperl toolkit: Perl modules for the life sciences.

Stajich JE, Block D, Boulez K, Brenner SE, Chervitz SA, Dagdigian C, Fuellen G, Gilbert JG, Korf I, Lapp H, Lehväslaiho H, Matsalla C, Mungall CJ, Osborne BI, Pocock MR, Schattner P, Senger M, Stein LD, Stupka E, Wilkinson MD, Birney E.

Genome Res. 2002 Oct;12(10):1611-8.

12.

Design and implementation of microarray gene expression markup language (MAGE-ML).

Spellman PT, Miller M, Stewart J, Troup C, Sarkans U, Chervitz S, Bernhart D, Sherlock G, Ball C, Lepage M, Swiatek M, Marks WL, Goncalves J, Markel S, Iordan D, Shojatalab M, Pizarro A, White J, Hubley R, Deutsch E, Senger M, Aronow BJ, Robinson A, Bassett D, Stoeckert CJ Jr, Brazma A.

Genome Biol. 2002 Aug 23;3(9):RESEARCH0046. Epub 2002 Aug 23.

13.

Comparative genomics of the eukaryotes.

Rubin GM, Yandell MD, Wortman JR, Gabor Miklos GL, Nelson CR, Hariharan IK, Fortini ME, Li PW, Apweiler R, Fleischmann W, Cherry JM, Henikoff S, Skupski MP, Misra S, Ashburner M, Birney E, Boguski MS, Brody T, Brokstein P, Celniker SE, Chervitz SA, Coates D, Cravchik A, Gabrielian A, Galle RF, Gelbart WM, George RA, Goldstein LS, Gong F, Guan P, Harris NL, Hay BA, Hoskins RA, Li J, Li Z, Hynes RO, Jones SJ, Kuehl PM, Lemaitre B, Littleton JT, Morrison DK, Mungall C, O'Farrell PH, Pickeral OK, Shue C, Vosshall LB, Zhang J, Zhao Q, Zheng XH, Lewis S.

Science. 2000 Mar 24;287(5461):2204-15.

14.

Expanding yeast knowledge online.

Dolinski K, Ball CA, Chervitz SA, Dwight SS, Harris MA, Roberts S, Roe T, Cherry JM, Botstein D.

Yeast. 1998 Dec;14(16):1453-69. Review.

15.

Comparison of the complete protein sets of worm and yeast: orthology and divergence.

Chervitz SA, Aravind L, Sherlock G, Ball CA, Koonin EV, Dwight SS, Harris MA, Dolinski K, Mohr S, Smith T, Weng S, Cherry JM, Botstein D.

Science. 1998 Dec 11;282(5396):2022-8. Review.

16.

Using the Saccharomyces Genome Database (SGD) for analysis of protein similarities and structure.

Chervitz SA, Hester ET, Ball CA, Dolinski K, Dwight SS, Harris MA, Juvik G, Malekian A, Roberts S, Roe T, Scafe C, Schroeder M, Sherlock G, Weng S, Zhu Y, Cherry JM, Botstein D.

Nucleic Acids Res. 1999 Jan 1;27(1):74-8.

17.

SGD: Saccharomyces Genome Database.

Cherry JM, Adler C, Ball C, Chervitz SA, Dwight SS, Hester ET, Jia Y, Juvik G, Roe T, Schroeder M, Weng S, Botstein D.

Nucleic Acids Res. 1998 Jan 1;26(1):73-9.

18.

Yeast as a model organism.

Botstein D, Chervitz SA, Cherry JM.

Science. 1997 Aug 29;277(5330):1259-60. No abstract available.

19.
20.

Molecular mechanism of transmembrane signaling by the aspartate receptor: a model.

Chervitz SA, Falke JJ.

Proc Natl Acad Sci U S A. 1996 Mar 19;93(6):2545-50.

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