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An RNA-Seq Protocol for Differential Expression Analysis.

Owens NDL, De Domenico E, Gilchrist MJ.

Cold Spring Harb Protoc. 2019 Jun 3;2019(6):pdb.prot098368. doi: 10.1101/pdb.prot098368.


New methods for computational decomposition of whole-mount in situ images enable effective curation of a large, highly redundant collection of Xenopus images.

Patrushev I, James-Zorn C, Ciau-Uitz A, Patient R, Gilchrist MJ.

PLoS Comput Biol. 2018 Aug 29;14(8):e1006077. doi: 10.1371/journal.pcbi.1006077. eCollection 2018 Aug.


Planning to halve Gram-negative bloodstream infection: getting to grips with healthcare-associated Escherichia coli bloodstream infection sources.

Otter JA, Galletly TJ, Davies F, Hitchcock J, Gilchrist MJ, Dyakova E, Mookerjee S, Holmes AH, Brannigan ET.

J Hosp Infect. 2019 Feb;101(2):129-133. doi: 10.1016/j.jhin.2018.07.033. Epub 2018 Jul 27.


Editorial: The Xenopus laevis genome.

Harland RM, Gilchrist MJ.

Dev Biol. 2017 Jun 15;426(2):139-142. doi: 10.1016/j.ydbio.2017.04.016. Epub 2017 Apr 27. No abstract available.


A catalog of Xenopus tropicalis transcription factors and their regional expression in the early gastrula stage embryo.

Blitz IL, Paraiso KD, Patrushev I, Chiu WTY, Cho KWY, Gilchrist MJ.

Dev Biol. 2017 Jun 15;426(2):409-417. doi: 10.1016/j.ydbio.2016.07.002. Epub 2016 Jul 28.


Developmentally regulated long non-coding RNAs in Xenopus tropicalis.

Forouzmand E, Owens NDL, Blitz IL, Paraiso KD, Khokha MK, Gilchrist MJ, Xie X, Cho KWY.

Dev Biol. 2017 Jun 15;426(2):401-408. doi: 10.1016/j.ydbio.2016.06.016. Epub 2016 Jul 12.


Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development.

Owens NDL, Blitz IL, Lane MA, Patrushev I, Overton JD, Gilchrist MJ, Cho KWY, Khokha MK.

Cell Rep. 2016 Jan 26;14(3):632-647. doi: 10.1016/j.celrep.2015.12.050. Epub 2016 Jan 7.


A Database of microRNA Expression Patterns in Xenopus laevis.

Ahmed A, Ward NJ, Moxon S, Lopez-Gomollon S, Viaut C, Tomlinson ML, Patrushev I, Gilchrist MJ, Dalmay T, Dotlic D, Münsterberg AE, Wheeler GN.

PLoS One. 2015 Oct 27;10(10):e0138313. doi: 10.1371/journal.pone.0138313. eCollection 2015.


Antimicrobial stewardship: are we failing in cross-specialty clinical engagement?

Rawson TM, Moore LS, Gilchrist MJ, Holmes AH.

J Antimicrob Chemother. 2016 Feb;71(2):554-9. doi: 10.1093/jac/dkv337. Epub 2015 Oct 23.


The Xenopus ORFeome: A resource that enables functional genomics.

Grant IM, Balcha D, Hao T, Shen Y, Trivedi P, Patrushev I, Fortriede JD, Karpinka JB, Liu L, Zorn AM, Stukenberg PT, Hill DE, Gilchrist MJ.

Dev Biol. 2015 Dec 15;408(2):345-57. doi: 10.1016/j.ydbio.2015.09.004. Epub 2015 Sep 29.


Molecular asymmetry in the 8-cell stage Xenopus tropicalis embryo described by single blastomere transcript sequencing.

De Domenico E, Owens ND, Grant IM, Gomes-Faria R, Gilchrist MJ.

Dev Biol. 2015 Dec 15;408(2):252-68. doi: 10.1016/j.ydbio.2015.06.010. Epub 2015 Jun 19.


A pipeline for the systematic identification of non-redundant full-ORF cDNAs for polymorphic and evolutionary divergent genomes: Application to the ascidian Ciona intestinalis.

Gilchrist MJ, Sobral D, Khoueiry P, Daian F, Laporte B, Patrushev I, Matsumoto J, Dewar K, Hastings KE, Satou Y, Lemaire P, Rothbächer U.

Dev Biol. 2015 Aug 15;404(2):149-63. doi: 10.1016/j.ydbio.2015.05.014. Epub 2015 May 27.


A New Nomenclature of Xenopus laevis Chromosomes Based on the Phylogenetic Relationship to Silurana/Xenopus tropicalis.

Matsuda Y, Uno Y, Kondo M, Gilchrist MJ, Zorn AM, Rokhsar DS, Schmid M, Taira M.

Cytogenet Genome Res. 2015;145(3-4):187-91. doi: 10.1159/000381292. Epub 2015 Apr 8.


Homogeneity of antimicrobial policy, yet heterogeneity of antimicrobial resistance: antimicrobial non-susceptibility among 108,717 clinical isolates from primary, secondary and tertiary care patients in London.

Moore LS, Freeman R, Gilchrist MJ, Gharbi M, Brannigan ET, Donaldson H, Livermore DM, Holmes AH.

J Antimicrob Chemother. 2014 Dec;69(12):3409-22. doi: 10.1093/jac/dku307. Epub 2014 Aug 12.


Activation of the aryl hydrocarbon receptor dampens the severity of inflammatory skin conditions.

Di Meglio P, Duarte JH, Ahlfors H, Owens ND, Li Y, Villanova F, Tosi I, Hirota K, Nestle FO, Mrowietz U, Gilchrist MJ, Stockinger B.

Immunity. 2014 Jun 19;40(6):989-1001. doi: 10.1016/j.immuni.2014.04.019. Epub 2014 Jun 5.


Transcriptional regulation of Caenorhabditis elegans FOXO/DAF-16 modulates lifespan.

Bansal A, Kwon ES, Conte D Jr, Liu H, Gilchrist MJ, MacNeil LT, Tissenbaum HA.

Longev Healthspan. 2014 Apr 23;3:5. doi: 10.1186/2046-2395-3-5. eCollection 2014.


High-resolution analysis of gene activity during the Xenopus mid-blastula transition.

Collart C, Owens ND, Bhaw-Rosun L, Cooper B, De Domenico E, Patrushev I, Sesay AK, Smith JN, Smith JC, Gilchrist MJ.

Development. 2014 May;141(9):1927-39. doi: 10.1242/dev.102012.


In vivo T-box transcription factor profiling reveals joint regulation of embryonic neuromesodermal bipotency.

Gentsch GE, Owens ND, Martin SR, Piccinelli P, Faial T, Trotter MW, Gilchrist MJ, Smith JC.

Cell Rep. 2013 Sep 26;4(6):1185-96. doi: 10.1016/j.celrep.2013.08.012. Epub 2013 Sep 19.


Efficient high-throughput sequencing of a laser microdissected chromosome arm.

Seifertova E, Zimmerman LB, Gilchrist MJ, Macha J, Kubickova S, Cernohorska H, Zarsky V, Owens ND, Sesay AK, Tlapakova T, Krylov V.

BMC Genomics. 2013 May 28;14:357. doi: 10.1186/1471-2164-14-357.


A large pseudoautosomal region on the sex chromosomes of the frog Silurana tropicalis.

Bewick AJ, Chain FJ, Zimmerman LB, Sesay A, Gilchrist MJ, Owens ND, Seifertova E, Krylov V, Macha J, Tlapakova T, Kubickova S, Cernohorska H, Zarsky V, Evans BJ.

Genome Biol Evol. 2013;5(6):1087-98. doi: 10.1093/gbe/evt073.


Exon capture and bulk segregant analysis: rapid discovery of causative mutations using high-throughput sequencing.

del Viso F, Bhattacharya D, Kong Y, Gilchrist MJ, Khokha MK.

BMC Genomics. 2012 Nov 21;13:649. doi: 10.1186/1471-2164-13-649.


Databases of gene expression in Xenopus development.

Gilchrist MJ, Pollet N.

Methods Mol Biol. 2012;917:319-45. doi: 10.1007/978-1-61779-992-1_19.


Rsx is a metatherian RNA with Xist-like properties in X-chromosome inactivation.

Grant J, Mahadevaiah SK, Khil P, Sangrithi MN, Royo H, Duckworth J, McCarrey JR, VandeBerg JL, Renfree MB, Taylor W, Elgar G, Camerini-Otero RD, Gilchrist MJ, Turner JM.

Nature. 2012 Jul 12;487(7406):254-8. doi: 10.1038/nature11171.


Genomic targets of Brachyury (T) in differentiating mouse embryonic stem cells.

Evans AL, Faial T, Gilchrist MJ, Down T, Vallier L, Pedersen RA, Wardle FC, Smith JC.

PLoS One. 2012;7(3):e33346. doi: 10.1371/journal.pone.0033346. Epub 2012 Mar 30.


From expression cloning to gene modeling: the development of Xenopus gene sequence resources.

Gilchrist MJ.

Genesis. 2012 Mar;50(3):143-54. doi: 10.1002/dvg.22008. Epub 2012 Feb 16. Review.


A large scale screen for neural stem cell markers in Xenopus retina.

Parain K, Mazurier N, Bronchain O, Borday C, Cabochette P, Chesneau A, Colozza G, El Yakoubi W, Hamdache J, Locker M, Gilchrist MJ, Pollet N, Perron M.

Dev Neurobiol. 2012 Apr;72(4):491-506. doi: 10.1002/dneu.20973.


Genome-wide analysis of gene expression during Xenopus tropicalis tadpole tail regeneration.

Love NR, Chen Y, Bonev B, Gilchrist MJ, Fairclough L, Lea R, Mohun TJ, Paredes R, Zeef LA, Amaya E.

BMC Dev Biol. 2011 Nov 15;11:70. doi: 10.1186/1471-213X-11-70.


Widespread transcription in an amphibian oocyte relates to its reprogramming activity on transplanted somatic nuclei.

Simeoni I, Gilchrist MJ, Garrett N, Armisen J, Gurdon JB.

Stem Cells Dev. 2012 Jan 20;21(2):181-90. doi: 10.1089/scd.2011.0162. Epub 2011 Jun 15.


The ANISEED database: digital representation, formalization, and elucidation of a chordate developmental program.

Tassy O, Dauga D, Daian F, Sobral D, Robin F, Khoueiry P, Salgado D, Fox V, Caillol D, Schiappa R, Laporte B, Rios A, Luxardi G, Kusakabe T, Joly JS, Darras S, Christiaen L, Contensin M, Auger H, Lamy C, Hudson C, Rothbächer U, Gilchrist MJ, Makabe KW, Hotta K, Fujiwara S, Satoh N, Satou Y, Lemaire P.

Genome Res. 2010 Oct;20(10):1459-68. doi: 10.1101/gr.108175.110. Epub 2010 Jul 20.


A study of alternative splicing in the pig.

Nygard AB, Cirera S, Gilchrist MJ, Gorodkin J, Jørgensen CB, Fredholm M.

BMC Res Notes. 2010 May 5;3:123. doi: 10.1186/1756-0500-3-123.


The genome of the Western clawed frog Xenopus tropicalis.

Hellsten U, Harland RM, Gilchrist MJ, Hendrix D, Jurka J, Kapitonov V, Ovcharenko I, Putnam NH, Shu S, Taher L, Blitz IL, Blumberg B, Dichmann DS, Dubchak I, Amaya E, Detter JC, Fletcher R, Gerhard DS, Goodstein D, Graves T, Grigoriev IV, Grimwood J, Kawashima T, Lindquist E, Lucas SM, Mead PE, Mitros T, Ogino H, Ohta Y, Poliakov AV, Pollet N, Robert J, Salamov A, Sater AK, Schmutz J, Terry A, Vize PD, Warren WC, Wells D, Wills A, Wilson RK, Zimmerman LB, Zorn AM, Grainger R, Grammer T, Khokha MK, Richardson PM, Rokhsar DS.

Science. 2010 Apr 30;328(5978):633-6. doi: 10.1126/science.1183670.


Abundant and dynamically expressed miRNAs, piRNAs, and other small RNAs in the vertebrate Xenopus tropicalis.

Armisen J, Gilchrist MJ, Wilczynska A, Standart N, Miska EA.

Genome Res. 2009 Oct;19(10):1766-75. doi: 10.1101/gr.093054.109. Epub 2009 Jul 23.


Factors associated with rabid animals since the introduction of raccoon rabies variant in Massachusetts, 1992-2007.

Wang X, Smole S, DeMaria A, Gilchrist MJ.

Vector Borne Zoonotic Dis. 2010 Apr;10(3):275-81. doi: 10.1089/vbz.2009.0002.


Database of queryable gene expression patterns for Xenopus.

Gilchrist MJ, Christensen MB, Bronchain O, Brunet F, Chesneau A, Fenger U, Geach TJ, Ironfield HV, Kaya F, Kricha S, Lea R, Massé K, Néant I, Paillard E, Parain K, Perron M, Sinzelle L, Souopgui J, Thuret R, Ymlahi-Ouazzani Q, Pollet N.

Dev Dyn. 2009 Jun;238(6):1379-88. doi: 10.1002/dvdy.21940.


A gene regulatory network directed by zebrafish No tail accounts for its roles in mesoderm formation.

Morley RH, Lachani K, Keefe D, Gilchrist MJ, Flicek P, Smith JC, Wardle FC.

Proc Natl Acad Sci U S A. 2009 Mar 10;106(10):3829-34. doi: 10.1073/pnas.0808382106. Epub 2009 Feb 18.


Identification of direct T-box target genes in the developing zebrafish mesoderm.

Garnett AT, Han TM, Gilchrist MJ, Smith JC, Eisen MB, Wardle FC, Amacher SL.

Development. 2009 Mar;136(5):749-60. doi: 10.1242/dev.024703. Epub 2009 Jan 21.


Sequence assembly.

Scheibye-Alsing K, Hoffmann S, Frankel A, Jensen P, Stadler PF, Mang Y, Tommerup N, Gilchrist MJ, Nygård AB, Cirera S, Jørgensen CB, Fredholm M, Gorodkin J.

Comput Biol Chem. 2009 Apr;33(2):121-36. doi: 10.1016/j.compbiolchem.2008.11.003. Epub 2008 Dec 6. Review.


Loss of REEP4 causes paralysis of the Xenopus embryo.

Argasinska J, Rana AA, Gilchrist MJ, Lachani K, Young A, Smith JC.

Int J Dev Biol. 2009;53(1):37-43. doi: 10.1387/ijdb.072542ja.


Evading the annotation bottleneck: using sequence similarity to search non-sequence gene data.

Gilchrist MJ, Christensen MB, Harland R, Pollet N, Smith JC, Ueno N, Papalopulu N.

BMC Bioinformatics. 2008 Oct 17;9:442. doi: 10.1186/1471-2105-9-442.


In vivo imaging of oskar mRNA transport reveals the mechanism of posterior localization.

Zimyanin VL, Belaya K, Pecreaux J, Gilchrist MJ, Clark A, Davis I, St Johnston D.

Cell. 2008 Sep 5;134(5):843-53. doi: 10.1016/j.cell.2008.06.053.


Maternal Argonaute 2 is essential for early mouse development at the maternal-zygotic transition.

Lykke-Andersen K, Gilchrist MJ, Grabarek JB, Das P, Miska E, Zernicka-Goetz M.

Mol Biol Cell. 2008 Oct;19(10):4383-92. doi: 10.1091/mbc.E08-02-0219. Epub 2008 Aug 13.


Piwi and piRNAs act upstream of an endogenous siRNA pathway to suppress Tc3 transposon mobility in the Caenorhabditis elegans germline.

Das PP, Bagijn MP, Goldstein LD, Woolford JR, Lehrbach NJ, Sapetschnig A, Buhecha HR, Gilchrist MJ, Howe KL, Stark R, Matthews N, Berezikov E, Ketting RF, Tavaré S, Miska EA.

Mol Cell. 2008 Jul 11;31(1):79-90. doi: 10.1016/j.molcel.2008.06.003. Epub 2008 Jun 19.


Prdm1- and Sox6-mediated transcriptional repression specifies muscle fibre type in the zebrafish embryo.

von Hofsten J, Elworthy S, Gilchrist MJ, Smith JC, Wardle FC, Ingham PW.

EMBO Rep. 2008 Jul;9(7):683-9. doi: 10.1038/embor.2008.73. Epub 2008 Jun 6.


Modelling and measuring single cell RNA expression levels find considerable transcriptional differences among phenotypically identical cells.

Subkhankulova T, Gilchrist MJ, Livesey FJ.

BMC Genomics. 2008 Jun 3;9:268. doi: 10.1186/1471-2164-9-268.


SNP-finding in pig mitochondrial ESTs.

Scheibye-Alsing K, Cirera S, Gilchrist MJ, Fredholm M, Gorodkin J.

Anim Genet. 2008 Apr;39(2):193-5. doi: 10.1111/j.1365-2052.2007.01694.x. Epub 2008 Feb 6.


EST analysis on pig mitochondria reveal novel expression differences between developmental and adult tissues.

Scheibye-Alsing K, Cirera S, Gilchrist MJ, Fredholm M, Gorodkin J.

BMC Genomics. 2007 Oct 11;8:367.


Detection of RNA structures in porcine EST data and related mammals.

Seemann SE, Gilchrist MJ, Hofacker IL, Stadler PF, Gorodkin J.

BMC Genomics. 2007 Sep 10;8:316.


Porcine transcriptome analysis based on 97 non-normalized cDNA libraries and assembly of 1,021,891 expressed sequence tags.

Gorodkin J, Cirera S, Hedegaard J, Gilchrist MJ, Panitz F, Jørgensen C, Scheibye-Knudsen K, Arvin T, Lumholdt S, Sawera M, Green T, Nielsen BJ, Havgaard JH, Rosenkilde C, Wang J, Li H, Li R, Liu B, Hu S, Dong W, Li W, Yu J, Wang J, Staefeldt HH, Wernersson R, Madsen LB, Thomsen B, Hornshøj H, Bujie Z, Wang X, Wang X, Bolund L, Brunak S, Yang H, Bendixen C, Fredholm M.

Genome Biol. 2007;8(4):R45.


The potential role of concentrated animal feeding operations in infectious disease epidemics and antibiotic resistance.

Gilchrist MJ, Greko C, Wallinga DB, Beran GW, Riley DG, Thorne PS.

Environ Health Perspect. 2007 Feb;115(2):313-6. Epub 2006 Nov 14.


Defining synphenotype groups in Xenopus tropicalis by use of antisense morpholino oligonucleotides.

Rana AA, Collart C, Gilchrist MJ, Smith JC.

PLoS Genet. 2006 Nov 17;2(11):e193. Epub 2006 Oct 4.

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