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Items: 20

1.

Responses of the picoprasinophyte Micromonas commoda to light and ultraviolet stress.

Cuvelier ML, Guo J, Ortiz AC, van Baren MJ, Tariq MA, Partensky F, Worden AZ.

PLoS One. 2017 Mar 9;12(3):e0172135. doi: 10.1371/journal.pone.0172135. eCollection 2017.

2.

Identifying Aspects of the Post-Transcriptional Program Governing the Proteome of the Green Alga Micromonas pusilla.

Waltman PH, Guo J, Reistetter EN, Purvine S, Ansong CK, van Baren MJ, Wong CH, Wei CL, Smith RD, Callister SJ, Stuart JM, Worden AZ.

PLoS One. 2016 Jul 19;11(7):e0155839. doi: 10.1371/journal.pone.0155839. eCollection 2016.

3.

Evidence-based green algal genomics reveals marine diversity and ancestral characteristics of land plants.

van Baren MJ, Bachy C, Reistetter EN, Purvine SO, Grimwood J, Sudek S, Yu H, Poirier C, Deerinck TJ, Kuo A, Grigoriev IV, Wong CH, Smith RD, Callister SJ, Wei CL, Schmutz J, Worden AZ.

BMC Genomics. 2016 Mar 31;17:267. doi: 10.1186/s12864-016-2585-6.

4.

Intron Invasions Trace Algal Speciation and Reveal Nearly Identical Arctic and Antarctic Micromonas Populations.

Simmons MP, Bachy C, Sudek S, van Baren MJ, Sudek L, Ares M Jr, Worden AZ.

Mol Biol Evol. 2015 Sep;32(9):2219-35. doi: 10.1093/molbev/msv122. Epub 2015 May 20.

5.

Marine algae and land plants share conserved phytochrome signaling systems.

Duanmu D, Bachy C, Sudek S, Wong CH, Jiménez V, Rockwell NC, Martin SS, Ngan CY, Reistetter EN, van Baren MJ, Price DC, Wei CL, Reyes-Prieto A, Lagarias JC, Worden AZ.

Proc Natl Acad Sci U S A. 2014 Nov 4;111(44):15827-32. doi: 10.1073/pnas.1416751111. Epub 2014 Sep 29.

6.

Estimating the nucleotide diversity in Ceratodon purpureus (Ditrichaceae) from 218 conserved exon-primed, intron-spanning nuclear loci.

McDaniel SF, van Baren MJ, Jones KS, Payton AC, Quatrano RS.

Appl Plant Sci. 2013 Mar 28;1(4). pii: apps.1200387. doi: 10.3732/apps.1200387. eCollection 2013 Apr.

7.

The developmental transcriptome of Drosophila melanogaster.

Graveley BR, Brooks AN, Carlson JW, Duff MO, Landolin JM, Yang L, Artieri CG, van Baren MJ, Boley N, Booth BW, Brown JB, Cherbas L, Davis CA, Dobin A, Li R, Lin W, Malone JH, Mattiuzzo NR, Miller D, Sturgill D, Tuch BB, Zaleski C, Zhang D, Blanchette M, Dudoit S, Eads B, Green RE, Hammonds A, Jiang L, Kapranov P, Langton L, Perrimon N, Sandler JE, Wan KH, Willingham A, Zhang Y, Zou Y, Andrews J, Bickel PJ, Brenner SE, Brent MR, Cherbas P, Gingeras TR, Hoskins RA, Kaufman TC, Oliver B, Celniker SE.

Nature. 2011 Mar 24;471(7339):473-9. doi: 10.1038/nature09715. Epub 2010 Dec 22.

8.

The transcriptional diversity of 25 Drosophila cell lines.

Cherbas L, Willingham A, Zhang D, Yang L, Zou Y, Eads BD, Carlson JW, Landolin JM, Kapranov P, Dumais J, Samsonova A, Choi JH, Roberts J, Davis CA, Tang H, van Baren MJ, Ghosh S, Dobin A, Bell K, Lin W, Langton L, Duff MO, Tenney AE, Zaleski C, Brent MR, Hoskins RA, Kaufman TC, Andrews J, Graveley BR, Perrimon N, Celniker SE, Gingeras TR, Cherbas P.

Genome Res. 2011 Feb;21(2):301-14. doi: 10.1101/gr.112961.110. Epub 2010 Dec 22.

9.

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation.

Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L.

Nat Biotechnol. 2010 May;28(5):511-5. doi: 10.1038/nbt.1621. Epub 2010 May 2.

10.

The completion of the Mammalian Gene Collection (MGC).

MGC Project Team, Temple G, Gerhard DS, Rasooly R, Feingold EA, Good PJ, Robinson C, Mandich A, Derge JG, Lewis J, Shoaf D, Collins FS, Jang W, Wagner L, Shenmen CM, Misquitta L, Schaefer CF, Buetow KH, Bonner TI, Yankie L, Ward M, Phan L, Astashyn A, Brown G, Farrell C, Hart J, Landrum M, Maidak BL, Murphy M, Murphy T, Rajput B, Riddick L, Webb D, Weber J, Wu W, Pruitt KD, Maglott D, Siepel A, Brejova B, Diekhans M, Harte R, Baertsch R, Kent J, Haussler D, Brent M, Langton L, Comstock CL, Stevens M, Wei C, van Baren MJ, Salehi-Ashtiani K, Murray RR, Ghamsari L, Mello E, Lin C, Pennacchio C, Schreiber K, Shapiro N, Marsh A, Pardes E, Moore T, Lebeau A, Muratet M, Simmons B, Kloske D, Sieja S, Hudson J, Sethupathy P, Brownstein M, Bhat N, Lazar J, Jacob H, Gruber CE, Smith MR, McPherson J, Garcia AM, Gunaratne PH, Wu J, Muzny D, Gibbs RA, Young AC, Bouffard GG, Blakesley RW, Mullikin J, Green ED, Dickson MC, Rodriguez AC, Grimwood J, Schmutz J, Myers RM, Hirst M, Zeng T, Tse K, Moksa M, Deng M, Ma K, Mah D, Pang J, Taylor G, Chuah E, Deng A, Fichter K, Go A, Lee S, Wang J, Griffith M, Morin R, Moore RA, Mayo M, Munro S, Wagner S, Jones SJ, Holt RA, Marra MA, Lu S, Yang S, Hartigan J, Graf M, Wagner R, Letovksy S, Pulido JC, Robison K, Esposito D, Hartley J, Wall VE, Hopkins RF, Ohara O, Wiemann S.

Genome Res. 2009 Dec;19(12):2324-33. doi: 10.1101/gr.095976.109. Epub 2009 Sep 18.

11.

Using N-SCAN or TWINSCAN to predict gene structures in genomic DNA sequences.

van Baren MJ, Koebbe BC, Brent MR.

Curr Protoc Bioinformatics. 2007 Dec;Chapter 4:Unit 4.8. doi: 10.1002/0471250953.bi0408s20.

PMID:
18428682
12.

Iterative gene prediction and pseudogene removal improves genome annotation.

van Baren MJ, Brent MR.

Genome Res. 2006 May;16(5):678-85.

13.

The PCR suite.

van Baren MJ, Heutink P.

Bioinformatics. 2004 Mar 1;20(4):591-3. Epub 2004 Jan 29.

PMID:
14751986
14.

Mutations in the DJ-1 gene associated with autosomal recessive early-onset parkinsonism.

Bonifati V, Rizzu P, van Baren MJ, Schaap O, Breedveld GJ, Krieger E, Dekker MC, Squitieri F, Ibanez P, Joosse M, van Dongen JW, Vanacore N, van Swieten JC, Brice A, Meco G, van Duijn CM, Oostra BA, Heutink P.

Science. 2003 Jan 10;299(5604):256-9. Epub 2002 Nov 21.

15.

Disruption of a long-range cis-acting regulator for Shh causes preaxial polydactyly.

Lettice LA, Horikoshi T, Heaney SJ, van Baren MJ, van der Linde HC, Breedveld GJ, Joosse M, Akarsu N, Oostra BA, Endo N, Shibata M, Suzuki M, Takahashi E, Shinka T, Nakahori Y, Ayusawa D, Nakabayashi K, Scherer SW, Heutink P, Hill RE, Noji S.

Proc Natl Acad Sci U S A. 2002 May 28;99(11):7548-53.

16.

A double RING-H2 domain in RNF32, a gene expressed during sperm formation.

van Baren MJ, van der Linde HC, Breedveld GJ, Baarends WM, Rizzu P, de Graaff E, Oostra BA, Heutink P.

Biochem Biophys Res Commun. 2002 Mar 22;292(1):58-65.

PMID:
11890671
17.

Hemimelic extra toes and Hammer toe are distinct mutations that show a genetic interaction.

Heus HC, Luijsterburg AJ, van Baren MJ, Breedveld GJ, Joosse MN, Nieuwenhuizen IM, Vermeij-Keers C, Oostra BA, Heutink P.

Mamm Genome. 2001 Jan;12(1):77-9. No abstract available.

PMID:
11178748
18.

Acheiropodia is caused by a genomic deletion in C7orf2, the human orthologue of the Lmbr1 gene.

Ianakiev P, van Baren MJ, Daly MJ, Toledo SP, Cavalcanti MG, Neto JC, Silveira EL, Freire-Maia A, Heutink P, Kilpatrick MW, Tsipouras P.

Am J Hum Genet. 2001 Jan;68(1):38-45. Epub 2000 Nov 22.

19.

Construction of a detailed physical and transcript map of the FTDP-17 candidate region on chromosome 17q21.

Froelich S, Houlden H, Rizzu P, Chakraverty S, Baker M, Kwon J, Nowotny P, Isaacs A, Nowotny V, Wauters E, van Baren MJ, Oostra BA, Hardy J, Lannfelt L, Goate A, Hutton M, Lendon CL, Heutink P.

Genomics. 1999 Sep 1;60(2):129-36.

PMID:
10486204
20.

A physical and transcriptional map of the preaxial polydactyly locus on chromosome 7q36.

Heus HC, Hing A, van Baren MJ, Joosse M, Breedveld GJ, Wang JC, Burgess A, Donnis-Keller H, Berglund C, Zguricas J, Scherer SW, Rommens JM, Oostra BA, Heutink P.

Genomics. 1999 May 1;57(3):342-51.

PMID:
10329000

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