Brosch R, Gordon SV, Marmiesse M, Brodin P, Buchrieser C, Eiglmeier K, Garnier T, Gutierrez C, Hewinson G, Kremer K: A new evolutionary scenario for the Mycobacterium tuberculosis complex. Proc Natl Acad Sci USA. 2002, 99 (6): 3684-3689. 10.1073/pnas.052548299.
Article
PubMed Central
CAS
PubMed
Google Scholar
Djelouadji Z, Raoult D, Drancourt M: Palaeogenomics of Mycobacterium tuberculosis: epidemic bursts with a degrading genome. Lancet Infect Dis. 2011, 11 (8): 641-650. 10.1016/S1473-3099(11)70093-7.
Article
PubMed
Google Scholar
Wirth T, Hildebrand F, Allix-Beguec C, Wolbeling F, Kubica T, Kremer K, van Soolingen D, Rusch-Gerdes S, Locht C, Brisse S: Origin, spread and demography of the Mycobacterium tuberculosis complex. PLoS Pathog. 2008, 4 (9): e1000160-10.1371/journal.ppat.1000160.
Article
PubMed Central
PubMed
Google Scholar
Smith NH, Gordon SV, de la Rua-Domenech R, Clifton-Hadley RS, Hewinson RG: Bottlenecks and broomsticks: the molecular evolution of Mycobacterium bovis. Nat Rev Microbiol. 2006, 4 (9): 670-681. 10.1038/nrmicro1472.
Article
CAS
PubMed
Google Scholar
Good M: Bovine tuberculosis eradication in Ireland. Irish Veterinary Journal. 2006, 59 (3): 154-162.
Google Scholar
More SJ, Good M: The tuberculosis eradication programme in Ireland: a review of scientific and policy advances since 1988. Vet Microbiol. 2006, 112 (2–4): 239-251.
Article
PubMed
Google Scholar
Pollock JM, Neill SD: Mycobacterium bovis infection and tuberculosis in cattle. Vet J. 2002, 163 (2): 115-127. 10.1053/tvjl.2001.0655.
Article
CAS
PubMed
Google Scholar
Harding CV, Boom WH: Regulation of antigen presentation by Mycobacterium tuberculosis: a role for Toll-like receptors. Nat Rev Microbiol. 2010, 8 (4): 296-307. 10.1038/nrmicro2321.
Article
PubMed Central
CAS
PubMed
Google Scholar
Kunnath-Velayudhan S, Gennaro ML: Immunodiagnosis of tuberculosis: a dynamic view of biomarker discovery. Clin Microbiol Rev. 2011, 24 (4): 792-805. 10.1128/CMR.00014-11.
Article
PubMed Central
CAS
PubMed
Google Scholar
Pollock JM, Welsh MD, McNair J: Immune responses in bovine tuberculosis: towards new strategies for the diagnosis and control of disease. Vet Immunol Immunopathol. 2005, 108 (1–2): 37-43.
Article
CAS
PubMed
Google Scholar
Waters WR, Palmer MV, Thacker TC, Davis WC, Sreevatsan S, Coussens P, Meade KG, Hope JC, Estes DM: Tuberculosis immunity: opportunities from studies with cattle. Clin Dev Immunol. 2011, 2011: 768542-
Article
PubMed Central
PubMed
Google Scholar
Sundaramurthy V, Pieters J: Interactions of pathogenic mycobacteria with host macrophages. Microbes Infect. 2007, 9 (14–15): 1671-1679.
Article
CAS
PubMed
Google Scholar
Meena LS, Rajni : Survival mechanisms of pathogenic Mycobacterium tuberculosis H37Rv. FEBS J. 2010, 277 (11): 2416-2427. 10.1111/j.1742-4658.2010.07666.x.
Article
CAS
PubMed
Google Scholar
Walzl G, Ronacher K, Hanekom W, Scriba TJ, Zumla A: Immunological biomarkers of tuberculosis. Nat Rev Immunol. 2011, 11 (5): 343-354. 10.1038/nri2960.
Article
CAS
PubMed
Google Scholar
MacHugh DE, Gormley E, Park SD, Browne JA, Taraktsoglou M, O’Farrelly C, Meade KG: Gene expression profiling of the host response to Mycobacterium bovis infection in cattle. Transbound Emerg Dis. 2009, 56 (6–7): 204-214.
Article
CAS
PubMed
Google Scholar
Widdison S, Watson M, Coffey TJ: Early response of bovine alveolar macrophages to infection with live and heat-killed Mycobacterium bovis. Dev Comp Immunol. 2011, 35 (5): 580-591. 10.1016/j.dci.2011.01.001.
Article
CAS
PubMed
Google Scholar
Meade KG, Gormley E, Doyle MB, Fitzsimons T, O’Farrelly C, Costello E, Keane J, Zhao Y, MacHugh DE: Innate gene repression associated with Mycobacterium bovis infection in cattle: toward a gene signature of disease. BMC Genomics. 2007, 8: 400-10.1186/1471-2164-8-400.
Article
PubMed Central
PubMed
Google Scholar
Kabara E, Kloss CC, Wilson M, Tempelman RJ, Sreevatsan S, Janagama H, Coussens PM: A large-scale study of differential gene expression in monocyte-derived macrophages infected with several strains of Mycobacterium avium subspecies paratuberculosis. Brief Funct Genomics. 2010, 9 (3): 220-237. 10.1093/bfgp/elq009.
Article
CAS
PubMed
Google Scholar
MacHugh D, Taraktsoglou M, Killick K, Nalpas N, Browne J, Park S, Hokamp K, Gormley E, Magee D: Pan-genomic analysis of bovine monocyte-derived macrophage gene expression in response to in vitro infection with Mycobacterium avium subspecies paratuberculosis. Vet Res. 2012, 43 (1): 25-10.1186/1297-9716-43-25.
Article
PubMed Central
CAS
PubMed
Google Scholar
Magee DA, Taraktsoglou M, Killick KE, Nalpas NC, Browne JA, Park SDE, Conlon KM, Lynn DJ, Hokamp K, Gordon SV: Global gene expression and systems biology analysis of bovine monocyte-derived macrophages in response to in vitro challenge with Mycobacterium bovis. PLoS One. 2012, 7 (2): e32034-10.1371/journal.pone.0032034.
Article
PubMed Central
CAS
PubMed
Google Scholar
Killick KE, Browne JA, Park SD, Magee DA, Martin I, Meade KG, Gordon SV, Gormley E, O’Farrelly C, Hokamp K: Genome-wide transcriptional profiling of peripheral blood leukocytes from cattle infected with Mycobacterium bovis reveals suppression of host immune genes. BMC Genomics. 2011, 12 (1): 611-10.1186/1471-2164-12-611.
Article
PubMed Central
CAS
PubMed
Google Scholar
Wilhelm BT, Landry JR: RNA-Seq-quantitative measurement of expression through massively parallel RNA-sequencing. Methods. 2009, 48 (3): 249-257. 10.1016/j.ymeth.2009.03.016.
Article
CAS
PubMed
Google Scholar
Ozsolak F, Milos PM: RNA sequencing: advances, challenges and opportunities. Nat Rev Genet. 2011, 12 (2): 87-98. 10.1038/nrg2934.
Article
PubMed Central
CAS
PubMed
Google Scholar
Roy NC, Altermann E, Park ZA, McNabb WC: A comparison of analog and next-generation transcriptomic tools for mammalian studies. Brief Funct Genomics. 2011, 10 (3): 135-150. 10.1093/bfgp/elr005.
Article
CAS
PubMed
Google Scholar
Behar SM, Martin CJ, Booty MG, Nishimura T, Zhao X, Gan HX, Divangahi M, Remold HG: Apoptosis is an innate defense function of macrophages against Mycobacterium tuberculosis. Mucosal Immunol. 2011, 4 (3): 279-287. 10.1038/mi.2011.3.
Article
PubMed Central
CAS
PubMed
Google Scholar
GeneChip® Bovine Genome Array data sheet. http://media.affymetrix.com/support/technical/datasheets/bovine_datasheet.pdf,
Chen H, Liu Z, Gong S, Wu X, Taylor WL, Williams RW, Matta SG, Sharp BM: Genome-wide gene expression profiling of nucleus accumbens neurons projecting to ventral pallidum using both microarray and transcriptome sequencing. Frontiers in neuroscience. 2011, 5: 98-
Article
PubMed Central
PubMed
Google Scholar
Su Z, Li Z, Chen T, Li QZ, Fang H, Ding D, Ge W, Ning B, Hong H, Perkins RG: Comparing next-generation sequencing and microarray technologies in a toxicological study of the effects of aristolochic acid on rat kidneys. Chem Res Toxicol. 2011, 24 (9): 1486-1493. 10.1021/tx200103b.
Article
CAS
PubMed
Google Scholar
Lesho E, Forestiero FJ, Hirata MH, Hirata RD, Cecon L, Melo FF, Paik SH, Murata Y, Ferguson EW, Wang Z: Transcriptional responses of host peripheral blood cells to tuberculosis infection. Tuberculosis (Edinb). 2011, 91 (5): 390-399. 10.1016/j.tube.2011.07.002.
Article
CAS
Google Scholar
Bradford JR, Hey Y, Yates T, Li Y, Pepper SD, Miller CJ: A comparison of massively parallel nucleotide sequencing with oligonucleotide microarrays for global transcription profiling. BMC Genomics. 2010, 11: 282-10.1186/1471-2164-11-282.
Article
PubMed Central
PubMed
Google Scholar
Liu S, Lin L, Jiang P, Wang D, Xing Y: A comparison of RNA-Seq and high-density exon array for detecting differential gene expression between closely related species. Nucleic Acids Res. 2011, 39 (2): 578-588. 10.1093/nar/gkq817.
Article
PubMed Central
CAS
PubMed
Google Scholar
Marioni JC, Mason CE, Mane SM, Stephens M, Gilad Y: RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Res. 2008, 18 (9): 1509-1517. 10.1101/gr.079558.108.
Article
PubMed Central
CAS
PubMed
Google Scholar
Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q: Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotech. 2011, 29 (7): 644-652. 10.1038/nbt.1883.
Article
CAS
Google Scholar
Garber M, Grabherr MG, Guttman M, Trapnell C: Computational methods for transcriptome annotation and quantification using RNA-seq. Nat Meth. 2011, 8 (6): 469-477. 10.1038/nmeth.1613.
Article
CAS
Google Scholar
Toung JM, Morley M, Li M, Cheung VG: RNA-sequence analysis of human B-cells. Genome Res. 2011, 21 (6): 991-998. 10.1101/gr.116335.110.
Article
PubMed Central
CAS
PubMed
Google Scholar
Tarazona S, Garcia-Alcalde F, Dopazo J, Ferrer A, Conesa A: Differential expression in RNA-seq: a matter of depth. Genome Res. 2011, 21 (12): 2213-2223. 10.1101/gr.124321.111.
Article
PubMed Central
CAS
PubMed
Google Scholar
Wang Y, Ghaffari N, Johnson CD, Braga-Neto UM, Wang H, Chen R, Zhou H: Evaluation of the coverage and depth of transcriptome by RNA-Seq in chickens. BMC Bioinformatics. 2011, 12 (Suppl 10): S5-10.1186/1471-2105-12-S10-S5.
Article
CAS
Google Scholar
Blanco FC, Soria M, Bianco MV, Bigi F: Transcriptional response of peripheral blood mononuclear cells from cattle infected with Mycobacterium bovis. PLoS One. 2012, 7 (7): e41066-10.1371/journal.pone.0041066.
Article
PubMed Central
CAS
PubMed
Google Scholar
Mirrakhimov AE, Kerimkulova AS, Lunegova OS, Moldokeeva CB, Zalesskaya YV, Abilova SS, Sovhozova NA, Aldashev AA, Mirrakhimov EM: An association between TRP64ARG polymorphism of the B3 adrenoreceptor gene and some metabolic disturbances. Cardiovasc Diabetol. 2011, 10: 89-10.1186/1475-2840-10-89.
Article
PubMed Central
CAS
PubMed
Google Scholar
Lirussi F, Rakotoniaina Z, Madani S, Goirand F, Breuiller-Fouche M, Leroy MJ, Sagot P, Morrison JJ, Dumas M, Bardou M: ADRB3 adrenergic receptor is a key regulator of human myometrial apoptosis and inflammation during chorioamnionitis. Biol Reprod. 2008, 78 (3): 497-505. 10.1095/biolreprod.107.064444.
Article
CAS
PubMed
Google Scholar
Yu JJ, Gaffen SL: Interleukin-17: a novel inflammatory cytokine that bridges innate and adaptive immunity. Front Biosci. 2008, 13: 170-177. 10.2741/2667.
Article
CAS
PubMed
Google Scholar
Molenaar AJ, Harris DP, Rajan GH, Pearson ML, Callaghan MR, Sommer L, Farr VC, Oden KE, Miles MC, Petrova RS: The acute-phase protein serum amyloid A3 is expressed in the bovine mammary gland and plays a role in host defence. Biomarkers. 2009, 14 (1): 26-37. 10.1080/13547500902730714.
Article
CAS
PubMed
Google Scholar
Bettler B, Kaupmann K, Mosbacher J, Gassmann M: Molecular structure and physiological functions of GABA(B) receptors. Physiol Rev. 2004, 84 (3): 835-867. 10.1152/physrev.00036.2003.
Article
CAS
PubMed
Google Scholar
Chapman RW, Hey JA, Rizzo CA, Bolser DC: GABAB receptors in the lung. Trends Pharmacol Sci. 1993, 14 (1): 26-29. 10.1016/0165-6147(93)90110-6.
Article
CAS
PubMed
Google Scholar
Dicpinigaitis PV, Dobkin JB, Rauf K, Aldrich TK: Inhibition of capsaicin-induced cough by the gamma-aminobutyric acid agonist baclofen. J Clin Pharmacol. 1998, 38 (4): 364-367. 10.1002/j.1552-4604.1998.tb04436.x.
Article
CAS
PubMed
Google Scholar
Halbleib JM, Nelson WJ: Cadherins in development: cell adhesion, sorting, and tissue morphogenesis. Genes Dev. 2006, 20 (23): 3199-3214. 10.1101/gad.1486806.
Article
CAS
PubMed
Google Scholar
Kadarmideen HN, Ali AA, Thomson PC, Muller B, Zinsstag J: Polymorphisms of the SLC11A1 gene and resistance to bovine tuberculosis in African Zebu cattle. Anim Genet. 2011, 42 (6): 656-658. 10.1111/j.1365-2052.2011.02203.x.
Article
CAS
PubMed
Google Scholar
Somia NV, Schmitt MJ, Vetter DE, Van Antwerp D, Heinemann SF, Verma IM: LFG: an anti-apoptotic gene that provides protection from Fas-mediated cell death. Proc Natl Acad Sci USA. 1999, 96 (22): 12667-12672. 10.1073/pnas.96.22.12667.
Article
PubMed Central
CAS
PubMed
Google Scholar
Roberts RC, Peden AA, Buss F, Bright NA, Latouche M, Reilly MM, Kendrick-Jones J, Luzio JP: Mistargeting of SH3TC2 away from the recycling endosome causes Charcot-Marie-Tooth disease type 4C. Hum Mol Genet. 2010, 19 (6): 1009-1018. 10.1093/hmg/ddp565.
Article
PubMed Central
CAS
PubMed
Google Scholar
Halaas O, Steigedal M, Haug M, Awuh JA, Ryan L, Brech A, Sato S, Husebye H, Cangelosi GA, Akira S: Intracellular Mycobacterium avium intersect transferrin in the Rab11(+) recycling endocytic pathway and avoid lipocalin 2 trafficking to the lysosomal pathway. J Infect Dis. 2010, 201 (5): 783-792. 10.1086/650493.
Article
PubMed Central
PubMed
Google Scholar
Stendel C, Roos A, Kleine H, Arnaud E, Ozcelik M, Sidiropoulos PN, Zenker J, Schupfer F, Lehmann U, Sobota RM: SH3TC2, a protein mutant in Charcot-Marie-Tooth neuropathy, links peripheral nerve myelination to endosomal recycling. Brain. 2010, 133 (Pt 8): 2462-2474.
Article
PubMed
Google Scholar
Wang F, Hu S, Liu W, Qiao Z, Gao Y, Bu Z: Deep-sequencing analysis of the mouse transcriptome response to infection with Brucella melitensis strains of differing virulence. PLoS One. 2011, 6 (12): e28485-10.1371/journal.pone.0028485.
Article
PubMed Central
CAS
PubMed
Google Scholar
‘t Hoen PA, Ariyurek Y, Thygesen HH, Vreugdenhil E, Vossen RH, de Menezes RX, Boer JM, van Ommen GJ, den Dunnen JT: Deep sequencing-based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms. Nucleic Acids Res. 2008, 36 (21): e141-10.1093/nar/gkn705.
Article
PubMed Central
PubMed
Google Scholar
Grigoriadis A, Oliver GR, Tanney A, Kendrick H, Smalley MJ, Jat P, Neville AM: Identification of differentially expressed sense and antisense transcript pairs in breast epithelial tissues. BMC Genomics. 2009, 10: 324-10.1186/1471-2164-10-324.
Article
PubMed Central
PubMed
Google Scholar
Yelin R, Dahary D, Sorek R, Levanon EY, Goldstein O, Shoshan A, Diber A, Biton S, Tamir Y, Khosravi R: Widespread occurrence of antisense transcription in the human genome. Nat Biotechnol. 2003, 21 (4): 379-386. 10.1038/nbt808.
Article
CAS
PubMed
Google Scholar
Galante PA, Vidal DO, de Souza JE, Camargo AA, de Souza SJ: Sense-antisense pairs in mammals: functional and evolutionary considerations. Genome Biol. 2007, 8 (3): R40-10.1186/gb-2007-8-3-r40.
Article
PubMed Central
PubMed
Google Scholar
Zhang Y, Liu XS, Liu QR, Wei L: Genome-wide in silico identification and analysis of cis natural antisense transcripts (cis-NATs) in ten species. Nucleic Acids Res. 2006, 34 (12): 3465-3475. 10.1093/nar/gkl473.
Article
PubMed Central
CAS
PubMed
Google Scholar
Katayama S, Tomaru Y, Kasukawa T, Waki K, Nakanishi M, Nakamura M, Nishida H, Yap CC, Suzuki M, Kawai J: Antisense transcription in the mammalian transcriptome. Science. 2005, 309 (5740): 1564-1566.
Article
PubMed
Google Scholar
Werner A, Carlile M, Swan D: What do natural antisense transcripts regulate?. RNA Biol. 2009, 6 (1): 43-48. 10.4161/rna.6.1.7568.
Article
CAS
PubMed
Google Scholar
Werner A, Sayer JA: Naturally occurring antisense RNA: function and mechanisms of action. Curr Opin Nephrol Hypertens. 2009, 18 (4): 343-349. 10.1097/MNH.0b013e32832cb982.
Article
CAS
PubMed
Google Scholar
Werner A, Swan D: What are natural antisense transcripts good for?. Biochem Soc Trans. 2010, 38 (4): 1144-1149. 10.1042/BST0381144.
Article
PubMed Central
CAS
PubMed
Google Scholar
Lapidot M, Pilpel Y: Genome-wide natural antisense transcription: coupling its regulation to its different regulatory mechanisms. EMBO Rep. 2006, 7 (12): 1216-1222. 10.1038/sj.embor.7400857.
Article
PubMed Central
CAS
PubMed
Google Scholar
Lasa I, Toledo-Arana A, Dobin A, Villanueva M, de los Mozos IR, Vergara-Irigaray M, Segura V, Fagegaltier D, Penades JR, Valle J: Genome-wide antisense transcription drives mRNA processing in bacteria. Proc Natl Acad Sci USA. 2011, 108 (50): 20172-20177. 10.1073/pnas.1113521108.
Article
PubMed Central
CAS
PubMed
Google Scholar
Faghihi MA, Wahlestedt C: Regulatory roles of natural antisense transcripts. Nat Rev Mol Cell Biol. 2009, 10 (9): 637-643. 10.1038/nrm2738.
Article
PubMed Central
CAS
PubMed
Google Scholar
Esterhuyse MM, Linhart HG, Kaufmann SH: Can the battle against tuberculosis gain from epigenetic research?. Trends Microbiol. 2012, 20 (5): 220-226. 10.1016/j.tim.2012.03.002.
Article
CAS
PubMed
Google Scholar
Guida A, Lindstadt C, Maguire SL, Ding C, Higgins DG, Corton NJ, Berriman M, Butler G: Using RNA-seq to determine the transcriptional landscape and the hypoxic response of the pathogenic yeast Candida parapsilosis. BMC Genomics. 2011, 12: 628-10.1186/1471-2164-12-628.
Article
PubMed Central
CAS
PubMed
Google Scholar
Fasold M, Binder H: Estimating RNA-quality using GeneChip microarrays. BMC Genomics. 2012, 13 (1): 186-10.1186/1471-2164-13-186.
Article
PubMed Central
CAS
PubMed
Google Scholar
Fang Z, Martin JA, Wang Z: Statistical methods for identifying differentially expressed genes in RNA-Seq experiments. Cell & bioscience. 2012, 2 (1): 26-10.1186/2045-3701-2-26.
Article
CAS
Google Scholar
Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B: Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods. 2008, 5 (7): 621-628. 10.1038/nmeth.1226.
Article
CAS
PubMed
Google Scholar
Robinson MD, McCarthy DJ, Smyth GK: edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2010, 26 (1): 139-140. 10.1093/bioinformatics/btp616.
Article
PubMed Central
CAS
PubMed
Google Scholar
Smyth GK: Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol. 2004, 3: Article3-
PubMed
Google Scholar
Nookaew I, Papini M, Pornputtapong N, Scalcinati G, Fagerberg L, Uhlen M, Nielsen J: A comprehensive comparison of RNA-seq-based transcriptome analysis from reads to differential gene expression and cross-comparison with microarrays: a case study in Saccharomyces cerevisiae. Nucleic Acids Res. 2012, 40 (20): 10084-10097. 10.1093/nar/gks804.
Article
PubMed Central
CAS
PubMed
Google Scholar
Ferrero E, Biswas P, Vettoretto K, Ferrarini M, Uguccioni M, Piali L, Leone BE, Moser B, Rugarli C, Pardi R: Macrophages exposed to Mycobacterium tuberculosis release chemokines able to recruit selected leucocyte subpopulations: focus on gammadelta cells. Immunology. 2003, 108 (3): 365-374. 10.1046/j.1365-2567.2003.01600.x.
Article
PubMed Central
CAS
PubMed
Google Scholar
Langmead B, Trapnell C, Pop M, Salzberg SL: Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009, 10 (3): R25-10.1186/gb-2009-10-3-r25.
Article
PubMed Central
PubMed
Google Scholar
Trapnell C, Pachter L, Salzberg SL: TopHat: discovering splice junctions with RNA-Seq. Bioinformatics. 2009, 25 (9): 1105-1111. 10.1093/bioinformatics/btp120.
Article
PubMed Central
CAS
PubMed
Google Scholar
R Development Core Team: R: A language and environment for statistical computing. 2011, Austria: R Foundation for Statistical Computing Vienna
Google Scholar
Robinson MD, Oshlack A: A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biol. 2010, 11 (3): R25-10.1186/gb-2010-11-3-r25.
Article
PubMed Central
PubMed
Google Scholar
Benjamini Y, Hochberg Y: Controlling the false discovery rate - a practical and powerful approach to multiple testing. J Roy Stat Soc B Met. 1995, 57 (1): 289-300.
Google Scholar
Wilson CL, Miller CJ: Simpleaffy: a BioConductor package for Affymetrix Quality Control and data analysis. Bioinformatics. 2005, 21 (18): 3683-3685. 10.1093/bioinformatics/bti605.
Article
CAS
PubMed
Google Scholar
Wu ZJ, Irizarry RA, Gentleman R, Martinez-Murillo F, Spencer F: A model-based background adjustment for oligonucleotide expression arrays. J Am Stat Assoc. 2004, 99 (468): 909-917. 10.1198/016214504000000683.
Article
Google Scholar
Hochreiter S, Clevert DA, Obermayer K: A new summarization method for affymetrix probe level data. Bioinformatics. 2006, 22 (8): 943-949. 10.1093/bioinformatics/btl033.
Article
CAS
PubMed
Google Scholar
Talloen W, Clevert DA, Hochreiter S, Amaratunga D, Bijnens L, Kass S, Gohlmann HWH: I/NI-calls for the exclusion of non-informative genes: a highly effective filtering tool for microarray data. Bioinformatics. 2007, 23 (21): 2897-2902. 10.1093/bioinformatics/btm478.
Article
CAS
PubMed
Google Scholar
Durinck S, Spellman PT, Birney E, Huber W: Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt. Nat Protoc. 2009, 4 (8): 1184-1191. 10.1038/nprot.2009.97.
Article
PubMed Central
CAS
PubMed
Google Scholar