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Analyzing DNA methylation patterns in subjects diagnosed with schizophrenia using machine learning methods.

Torabi Moghadam B, Etemadikhah M, Rajkowska G, Stockmeier C, Grabherr M, Komorowski J, Feuk L, Carlström EL.

J Psychiatr Res. 2019 Jul;114:41-47. doi: 10.1016/j.jpsychires.2019.04.001. Epub 2019 Apr 2.


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.


Functional and evolutionary genomic inferences in Populus through genome and population sequencing of American and European aspen.

Lin YC, Wang J, Delhomme N, Schiffthaler B, Sundström G, Zuccolo A, Nystedt B, Hvidsten TR, de la Torre A, Cossu RM, Hoeppner MP, Lantz H, Scofield DG, Zamani N, Johansson A, Mannapperuma C, Robinson KM, Mähler N, Leitch IJ, Pellicer J, Park EJ, Van Montagu M, Van de Peer Y, Grabherr M, Jansson S, Ingvarsson PK, Street NR.

Proc Natl Acad Sci U S A. 2018 Nov 13;115(46):E10970-E10978. doi: 10.1073/pnas.1801437115. Epub 2018 Oct 29.


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.


Global characterization of the Dicer-like protein DrnB roles in miRNA biogenesis in the social amoeba Dictyostelium discoideum.

Liao Z, Kjellin J, Hoeppner MP, Grabherr M, Söderbom F.

RNA Biol. 2018;15(7):937-954. doi: 10.1080/15476286.2018.1481697. Epub 2018 Aug 21. Update in: RNA Biol. 2018;15(7):iii.


Comparative omics and feeding manipulations in chicken indicate a shift of the endocrine role of visceral fat towards reproduction.

Bornelöv S, Seroussi E, Yosefi S, Benjamini S, Miyara S, Ruzal M, Grabherr M, Rafati N, Molin AM, Pendavis K, Burgess SC, Andersson L, Friedman-Einat M.

BMC Genomics. 2018 Apr 26;19(1):295. doi: 10.1186/s12864-018-4675-0.


Reading and editing the Pleurodeles waltl genome reveals novel features of tetrapod regeneration.

Elewa A, Wang H, Talavera-López C, Joven A, Brito G, Kumar A, Hameed LS, Penrad-Mobayed M, Yao Z, Zamani N, Abbas Y, Abdullayev I, Sandberg R, Grabherr M, Andersson B, Simon A.

Nat Commun. 2017 Dec 22;8(1):2286. doi: 10.1038/s41467-017-01964-9.


Characterization of the Giardia intestinalis secretome during interaction with human intestinal epithelial cells: The impact on host cells.

Ma'ayeh SY, Liu J, Peirasmaki D, Hörnaeus K, Bergström Lind S, Grabherr M, Bergquist J, Svärd SG.

PLoS Negl Trop Dis. 2017 Dec 11;11(12):e0006120. doi: 10.1371/journal.pntd.0006120. eCollection 2017 Dec.


A practical guide to build de-novo assemblies for single tissues of non-model organisms: the example of a Neotropical frog.

Montero-Mendieta S, Grabherr M, Lantz H, De la Riva I, Leonard JA, Webster MT, Vilà C.

PeerJ. 2017 Sep 1;5:e3702. doi: 10.7717/peerj.3702. eCollection 2017.


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.


Evolution of the p53-MDM2 pathway.

Åberg E, Saccoccia F, Grabherr M, Ore WYJ, Jemth P, Hultqvist G.

BMC Evol Biol. 2017 Aug 3;17(1):177. doi: 10.1186/s12862-017-1023-y.


PiiL: visualization of DNA methylation and gene expression data in gene pathways.

Moghadam BT, Zamani N, Komorowski J, Grabherr M.

BMC Genomics. 2017 Aug 2;18(1):571. doi: 10.1186/s12864-017-3950-9.


Correspondence on Lovell et al.: identification of chicken genes previously assumed to be evolutionarily lost.

Bornelöv S, Seroussi E, Yosefi S, Pendavis K, Burgess SC, Grabherr M, Friedman-Einat M, Andersson L.

Genome Biol. 2017 Jun 14;18(1):112. doi: 10.1186/s13059-017-1231-1.


microTaboo: a general and practical solution to the k-disjoint problem.

Al-Jaff M, Sandström E, Grabherr M.

BMC Bioinformatics. 2017 May 2;18(1):228. doi: 10.1186/s12859-017-1644-6.


Thrombocytopaenia after aortic valve replacement with stented, stentless and sutureless bioprostheses.

Stanger O, Grabherr M, Gahl B, Longnus S, Meinitzer A, Fiedler M, Tevaearai H, Carrel T.

Eur J Cardiothorac Surg. 2017 Feb 1;51(2):340-346. doi: 10.1093/ejcts/ezw295. No abstract available.


Interactions of Freshwater Cyanobacteria with Bacterial Antagonists.

Osman OA, Beier S, Grabherr M, Bertilsson S.

Appl Environ Microbiol. 2017 Mar 17;83(7). pii: e02634-16. doi: 10.1128/AEM.02634-16. Print 2017 Apr 1.


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.


Freedom SOLO-Associated Thrombocytopaenia is Valve-Dependent and Not Due to In Vitro Pseudothrombocytopaenia.

Stanger O, Gahl B, Grabherr M, Krausler R, Longnus S, Meinitzer A, Cadamuro J.

Heart Lung Circ. 2017 Mar;26(3):268-275. doi: 10.1016/j.hlc.2016.07.002. Epub 2016 Aug 16.


Coordinated Changes in Gene Expression Throughout Encystation of Giardia intestinalis.

Einarsson E, Troell K, Hoeppner MP, Grabherr M, Ribacke U, Svärd SG.

PLoS Negl Trop Dis. 2016 Mar 25;10(3):e0004571. doi: 10.1371/journal.pntd.0004571. eCollection 2016 Mar.


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.


Draft Genome Sequence of the Cellulolytic Fungus Chaetomium globosum.

Cuomo CA, Untereiner WA, Ma LJ, Grabherr M, Birren BW.

Genome Announc. 2015 Feb 26;3(1). pii: e00021-15. doi: 10.1128/genomeA.00021-15.


Evolution of Darwin's finches and their beaks revealed by genome sequencing.

Lamichhaney S, Berglund J, Almén MS, Maqbool K, Grabherr M, Martinez-Barrio A, Promerová M, Rubin CJ, Wang C, Zamani N, Grant BR, Grant PR, Webster MT, Andersson L.

Nature. 2015 Feb 19;518(7539):371-5. doi: 10.1038/nature14181. Epub 2015 Feb 11.


Function of Isolated Pancreatic Islets From Patients at Onset of Type 1 Diabetes: Insulin Secretion Can Be Restored After Some Days in a Nondiabetogenic Environment In Vitro: Results From the DiViD Study.

Krogvold L, Skog O, Sundström G, Edwin B, Buanes T, Hanssen KF, Ludvigsson J, Grabherr M, Korsgren O, Dahl-Jørgensen K.

Diabetes. 2015 Jul;64(7):2506-12. doi: 10.2337/db14-1911. Epub 2015 Feb 12.


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.


Genome and physiology of the ascomycete filamentous fungus Xeromyces bisporus, the most xerophilic organism isolated to date.

Leong SL, Lantz H, Pettersson OV, Frisvad JC, Thrane U, Heipieper HJ, Dijksterhuis J, Grabherr M, Pettersson M, Tellgren-Roth C, Schnürer J.

Environ Microbiol. 2015 Feb;17(2):496-513. doi: 10.1111/1462-2920.12596. Epub 2014 Oct 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.


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.


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.


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.


Broad-scale phylogenomics provides insights into retrovirus-host evolution.

Hayward A, Grabherr M, Jern P.

Proc Natl Acad Sci U S A. 2013 Dec 10;110(50):20146-51. doi: 10.1073/pnas.1315419110. Epub 2013 Nov 25.


Efficient cellular fractionation improves RNA sequencing analysis of mature and nascent transcripts from human tissues.

Zaghlool A, Ameur A, Nyberg L, Halvardson J, Grabherr M, Cavelier L, Feuk L.

BMC Biotechnol. 2013 Nov 13;13:99. doi: 10.1186/1472-6750-13-99.


De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis.

Haas BJ, Papanicolaou A, Yassour M, Grabherr M, Blood PD, Bowden J, Couger MB, Eccles D, Li B, Lieber M, MacManes MD, Ott M, Orvis J, Pochet N, Strozzi F, Weeks N, Westerman R, William T, Dewey CN, Henschel R, LeDuc RD, Friedman N, Regev A.

Nat Protoc. 2013 Aug;8(8):1494-512. doi: 10.1038/nprot.2013.084. Epub 2013 Jul 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.


Population-scale sequencing reveals genetic differentiation due to local adaptation in Atlantic herring.

Lamichhaney S, Martinez Barrio A, Rafati N, Sundström G, Rubin CJ, Gilbert ER, Berglund J, Wetterbom A, Laikre L, Webster MT, Grabherr M, Ryman N, Andersson L.

Proc Natl Acad Sci U S A. 2012 Nov 20;109(47):19345-50. doi: 10.1073/pnas.1216128109. Epub 2012 Nov 7.


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.


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.


The genome of the green anole lizard and a comparative analysis with birds and mammals.

Alföldi J, Di Palma F, Grabherr M, Williams C, Kong L, Mauceli E, Russell P, Lowe CB, Glor RE, Jaffe JD, Ray DA, Boissinot S, Shedlock AM, Botka C, Castoe TA, Colbourne JK, Fujita MK, Moreno RG, ten Hallers BF, Haussler D, Heger A, Heiman D, Janes DE, Johnson J, de Jong PJ, Koriabine MY, Lara M, Novick PA, Organ CL, Peach SE, Poe S, Pollock DD, de Queiroz K, Sanger T, Searle S, Smith JD, Smith Z, Swofford R, Turner-Maier J, Wade J, Young S, Zadissa A, Edwards SV, Glenn TC, Schneider CJ, Losos JB, Lander ES, Breen M, Ponting CP, Lindblad-Toh K.

Nature. 2011 Aug 31;477(7366):587-91. doi: 10.1038/nature10390.


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.


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.


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.


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.


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.


Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium.

Ma LJ, van der Does HC, Borkovich KA, Coleman JJ, Daboussi MJ, Di Pietro A, Dufresne M, Freitag M, Grabherr M, Henrissat B, Houterman PM, Kang S, Shim WB, Woloshuk C, Xie X, Xu JR, Antoniw J, Baker SE, Bluhm BH, Breakspear A, Brown DW, Butchko RA, Chapman S, Coulson R, Coutinho PM, Danchin EG, Diener A, Gale LR, Gardiner DM, Goff S, Hammond-Kosack KE, Hilburn K, Hua-Van A, Jonkers W, Kazan K, Kodira CD, Koehrsen M, Kumar L, Lee YH, Li L, Manners JM, Miranda-Saavedra D, Mukherjee M, Park G, Park J, Park SY, Proctor RH, Regev A, Ruiz-Roldan MC, Sain D, Sakthikumar S, Sykes S, Schwartz DC, Turgeon BG, Wapinski I, Yoder O, Young S, Zeng Q, Zhou S, Galagan J, Cuomo CA, Kistler HC, Rep M.

Nature. 2010 Mar 18;464(7287):367-73. doi: 10.1038/nature08850.


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.


Identification of repetitive elements in the genome of Oreochromis niloticus: tilapia repeat masker.

Shirak A, Grabherr M, Di Palma F, Lindblad-Toh K, Hulata G, Ron M, Kocher TD, Seroussi E.

Mar Biotechnol (NY). 2010 Apr;12(2):121-5. doi: 10.1007/s10126-009-9236-8. Epub 2009 Nov 21.


High-throughput sequencing of microdissected chromosomal regions.

Weise A, Timmermann B, Grabherr M, Werber M, Heyn P, Kosyakova N, Liehr T, Neitzel H, Konrat K, Bommer C, Dietrich C, Rajab A, Reinhardt R, Mundlos S, Lindner TH, Hoffmann K.

Eur J Hum Genet. 2010 Apr;18(4):457-62. doi: 10.1038/ejhg.2009.196. Epub 2009 Nov 4.


Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans.

Haas BJ, Kamoun S, Zody MC, Jiang RH, Handsaker RE, Cano LM, Grabherr M, Kodira CD, Raffaele S, Torto-Alalibo T, Bozkurt TO, Ah-Fong AM, Alvarado L, Anderson VL, Armstrong MR, Avrova A, Baxter L, Beynon J, Boevink PC, Bollmann SR, Bos JI, Bulone V, Cai G, Cakir C, Carrington JC, Chawner M, Conti L, Costanzo S, Ewan R, Fahlgren N, Fischbach MA, Fugelstad J, Gilroy EM, Gnerre S, Green PJ, Grenville-Briggs LJ, Griffith J, Grünwald NJ, Horn K, Horner NR, Hu CH, Huitema E, Jeong DH, Jones AM, Jones JD, Jones RW, Karlsson EK, Kunjeti SG, Lamour K, Liu Z, Ma L, Maclean D, Chibucos MC, McDonald H, McWalters J, Meijer HJ, Morgan W, Morris PF, Munro CA, O'Neill K, Ospina-Giraldo M, Pinzón A, Pritchard L, Ramsahoye B, Ren Q, Restrepo S, Roy S, Sadanandom A, Savidor A, Schornack S, Schwartz DC, Schumann UD, Schwessinger B, Seyer L, Sharpe T, Silvar C, Song J, Studholme DJ, Sykes S, Thines M, van de Vondervoort PJ, Phuntumart V, Wawra S, Weide R, Win J, Young C, Zhou S, Fry W, Meyers BC, van West P, Ristaino J, Govers F, Birch PR, Whisson SC, Judelson HS, Nusbaum C.

Nature. 2009 Sep 17;461(7262):393-8. doi: 10.1038/nature08358. Epub 2009 Sep 9.


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.


Evolution of pathogenicity and sexual reproduction in eight Candida genomes.

Butler G, Rasmussen MD, Lin MF, Santos MA, Sakthikumar S, Munro CA, Rheinbay E, Grabherr M, Forche A, Reedy JL, Agrafioti I, Arnaud MB, Bates S, Brown AJ, Brunke S, Costanzo MC, Fitzpatrick DA, de Groot PW, Harris D, Hoyer LL, Hube B, Klis FM, Kodira C, Lennard N, Logue ME, Martin R, Neiman AM, Nikolaou E, Quail MA, Quinn J, Santos MC, Schmitzberger FF, Sherlock G, Shah P, Silverstein KA, Skrzypek MS, Soll D, Staggs R, Stansfield I, Stumpf MP, Sudbery PE, Srikantha T, Zeng Q, Berman J, Berriman M, Heitman J, Gow NA, Lorenz MC, Birren BW, Kellis M, Cuomo CA.

Nature. 2009 Jun 4;459(7247):657-62. doi: 10.1038/nature08064.


A cis-acting regulatory mutation causes premature hair graying and susceptibility to melanoma in the horse.

Rosengren Pielberg G, Golovko A, Sundström E, Curik I, Lennartsson J, Seltenhammer MH, Druml T, Binns M, Fitzsimmons C, Lindgren G, Sandberg K, Baumung R, Vetterlein M, Strömberg S, Grabherr M, Wade C, Lindblad-Toh K, Pontén F, Heldin CH, Sölkner J, Andersson L.

Nat Genet. 2008 Aug;40(8):1004-9. doi: 10.1038/ng.185. Epub 2008 Jul 20.


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