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Items: 20

1.

ACES: a machine learning toolbox for clustering analysis and visualization.

Gao J, Sundström G, Moghadam BT, Zamani N, Grabherr MG.

BMC Genomics. 2018 Dec 27;19(1):964. doi: 10.1186/s12864-018-5300-y.

2.

Special Issue Introduction: The Wonders and Mysteries Next Generation Sequencing Technologies Help Reveal.

Grabherr MG, Kaminska B, Komorowski J.

Genes (Basel). 2018 Oct 18;9(10). pii: E505. doi: 10.3390/genes9100505.

3.

RNA-sequence data normalization through in silico prediction of reference genes: the bacterial response to DNA damage as case study.

Berghoff BA, Karlsson T, Källman T, Wagner EGH, Grabherr MG.

BioData Min. 2017 Sep 5;10:30. doi: 10.1186/s13040-017-0150-8. eCollection 2017.

4.

Combinatorial identification of DNA methylation patterns over age in the human brain.

Torabi Moghadam B, Dabrowski M, Kaminska B, Grabherr MG, Komorowski J.

BMC Bioinformatics. 2016 Sep 23;17(1):393.

5.

Serendipitous Meta-Transcriptomics: The Fungal Community of Norway Spruce (Picea abies).

Delhomme N, Sundström G, Zamani N, Lantz H, Lin YC, Hvidsten TR, Höppner MP, Jern P, Van de Peer Y, Lundeberg J, Grabherr MG, Street NR.

PLoS One. 2015 Sep 28;10(9):e0139080. doi: 10.1371/journal.pone.0139080. eCollection 2015.

6.

Whiteboard: a framework for the programmatic visualization of complex biological analyses.

Sundström G, Zamani N, Grabherr MG, Mauceli E.

Bioinformatics. 2015 Jun 15;31(12):2054-5. doi: 10.1093/bioinformatics/btv078. Epub 2015 Feb 5.

PMID:
25661541
7.

Modular and configurable optimal sequence alignment software: Cola.

Zamani N, Sundström G, Höppner MP, Grabherr MG.

Source Code Biol Med. 2014 Jun 9;9:12. doi: 10.1186/1751-0473-9-12. eCollection 2014.

8.

A universal genomic coordinate translator for comparative genomics.

Zamani N, Sundström G, Meadows JR, Höppner MP, Dainat J, Lantz H, Haas BJ, Grabherr MG.

BMC Bioinformatics. 2014 Jun 30;15:227. doi: 10.1186/1471-2105-15-227.

9.

The genomic landscape underlying phenotypic integrity in the face of gene flow in crows.

Poelstra JW, Vijay N, Bossu CM, Lantz H, Ryll B, Müller I, Baglione V, Unneberg P, Wikelski M, Grabherr MG, Wolf JB.

Science. 2014 Jun 20;344(6190):1410-4. doi: 10.1126/science.1253226.

10.

An improved canine genome and a comprehensive catalogue of coding genes and non-coding transcripts.

Hoeppner MP, Lundquist A, Pirun M, Meadows JR, Zamani N, Johnson J, Sundström G, Cook A, FitzGerald MG, Swofford R, Mauceli E, Moghadam BT, Greka A, Alföldi J, Abouelleil A, Aftuck L, Bessette D, Berlin A, Brown A, Gearin G, Lui A, Macdonald JP, Priest M, Shea T, Turner-Maier J, Zimmer A, Lander ES, di Palma F, Lindblad-Toh K, Grabherr MG.

PLoS One. 2014 Mar 13;9(3):e91172. doi: 10.1371/journal.pone.0091172. eCollection 2014.

11.

Unsupervised genome-wide recognition of local relationship patterns.

Zamani N, Russell P, Lantz H, Hoeppner MP, Meadows JR, Vijay N, Mauceli E, di Palma F, Lindblad-Toh K, Jern P, Grabherr MG.

BMC Genomics. 2013 May 24;14:347. doi: 10.1186/1471-2164-14-347.

12.

The genomic basis of adaptive evolution in threespine sticklebacks.

Jones FC, Grabherr MG, Chan YF, Russell P, Mauceli E, Johnson J, Swofford R, Pirun M, Zody MC, White S, Birney E, Searle S, Schmutz J, Grimwood J, Dickson MC, Myers RM, Miller CT, Summers BR, Knecht AK, Brady SD, Zhang H, Pollen AA, Howes T, Amemiya C; Broad Institute Genome Sequencing Platform & Whole Genome Assembly Team, Baldwin J, Bloom T, Jaffe DB, Nicol R, Wilkinson J, Lander ES, Di Palma F, Lindblad-Toh K, Kingsley DM.

Nature. 2012 Apr 4;484(7392):55-61. doi: 10.1038/nature10944.

13.

Artificially designed promoters: understanding the role of spatial features and canonical binding sites in transcription.

Baumann M, Höppner MP, Meier M, Pontiller J, Ernst W, Grabherr R, Mauceli E, Grabherr MG.

Bioeng Bugs. 2012 Mar-Apr;3(2):120-3. doi: 10.4161/bbug.18530. Epub 2012 Mar 1.

14.

Exploiting nucleotide composition to engineer promoters.

Grabherr MG, Pontiller J, Mauceli E, Ernst W, Baumann M, Biagi T, Swofford R, Russell P, Zody MC, Di Palma F, Lindblad-Toh K, Grabherr RM.

PLoS One. 2011;6(5):e20136. doi: 10.1371/journal.pone.0020136. Epub 2011 May 18.

15.

Computational methods for transcriptome annotation and quantification using RNA-seq.

Garber M, Grabherr MG, Guttman M, Trapnell C.

Nat Methods. 2011 Jun;8(6):469-77. doi: 10.1038/nmeth.1613. Epub 2011 May 27. Review. Erratum in: Nat Methods. 2011 Jun;8(6):following 477.

PMID:
21623353
16.

Genome sequencing and assembly.

Grabherr MG, Mauceli E, Ma LJ.

Methods Mol Biol. 2011;722:1-9. doi: 10.1007/978-1-61779-040-9_1.

PMID:
21590409
17.

Full-length transcriptome assembly from RNA-Seq data without a reference genome.

Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, Chen Z, Mauceli E, Hacohen N, Gnirke A, Rhind N, di Palma F, Birren BW, Nusbaum C, Lindblad-Toh K, Friedman N, Regev A.

Nat Biotechnol. 2011 May 15;29(7):644-52. doi: 10.1038/nbt.1883.

18.

Obligate biotrophy features unraveled by the genomic analysis of rust fungi.

Duplessis S, Cuomo CA, Lin YC, Aerts A, Tisserant E, Veneault-Fourrey C, Joly DL, Hacquard S, Amselem J, Cantarel BL, Chiu R, Coutinho PM, Feau N, Field M, Frey P, Gelhaye E, Goldberg J, Grabherr MG, Kodira CD, Kohler A, Kües U, Lindquist EA, Lucas SM, Mago R, Mauceli E, Morin E, Murat C, Pangilinan JL, Park R, Pearson M, Quesneville H, Rouhier N, Sakthikumar S, Salamov AA, Schmutz J, Selles B, Shapiro H, Tanguay P, Tuskan GA, Henrissat B, Van de Peer Y, Rouzé P, Ellis JG, Dodds PN, Schein JE, Zhong S, Hamelin RC, Grigoriev IV, Szabo LJ, Martin F.

Proc Natl Acad Sci U S A. 2011 May 31;108(22):9166-71. doi: 10.1073/pnas.1019315108. Epub 2011 May 2.

19.

Genome-wide synteny through highly sensitive sequence alignment: Satsuma.

Grabherr MG, Russell P, Meyer M, Mauceli E, Alföldi J, Di Palma F, Lindblad-Toh K.

Bioinformatics. 2010 May 1;26(9):1145-51. doi: 10.1093/bioinformatics/btq102. Epub 2010 Mar 5.

20.

Genomic analysis of the basal lineage fungus Rhizopus oryzae reveals a whole-genome duplication.

Ma LJ, Ibrahim AS, Skory C, Grabherr MG, Burger G, Butler M, Elias M, Idnurm A, Lang BF, Sone T, Abe A, Calvo SE, Corrochano LM, Engels R, Fu J, Hansberg W, Kim JM, Kodira CD, Koehrsen MJ, Liu B, Miranda-Saavedra D, O'Leary S, Ortiz-Castellanos L, Poulter R, Rodriguez-Romero J, Ruiz-Herrera J, Shen YQ, Zeng Q, Galagan J, Birren BW, Cuomo CA, Wickes BL.

PLoS Genet. 2009 Jul;5(7):e1000549. doi: 10.1371/journal.pgen.1000549. Epub 2009 Jul 3.

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