Michael J Gilchrist - Publications

Publications (33)

XB-PERS-960

Publications By Michael J Gilchrist

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Genomics Methods for Xenopus Embryos and Tissues., Gilchrist MJ, Cho KWY, Veenstra GJC., Cold Spring Harb Protoc. May 1, 2020; 2020 (5): 097915.
Transcriptomics and Proteomics Methods for Xenopus Embryos and Tissues., Gilchrist MJ, Veenstra GJC, Cho KWY., Cold Spring Harb Protoc. February 3, 2020; 2020 (2): 098350.
An RNA-Seq Protocol for Differential Expression Analysis., Owens NDL, De Domenico E, Gilchrist MJ., Cold Spring Harb Protoc. June 3, 2019; 2019 (6):
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. August 2, 2018; 14 (8): e1006077.
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. June 15, 2017; 426 (2): 401-408.
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. June 15, 2017; 426 (2): 409-417.
Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development., Owens ND, Blitz IL, Lane MA, Patrushev I, Overton JD, Gilchrist MJ, Cho KW, Khokha MK., Cell Rep. January 26, 2016; 14 (3): 632-47.
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. December 15, 2015; 408 (2): 252-68.
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. December 15, 2015; 408 (2): 345-57.
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. January 1, 2015; 145 (3-4): 187-91.
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. January 1, 2015; 10 (10): e0138313.
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. May 1, 2014; 141 (9): 1927-39.
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. September 26, 2013; 4 (6): 1185-96.
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. May 28, 2013; 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. January 1, 2013; 5 (6): 1087-98.
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. November 21, 2012; 13 649.
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. April 1, 2012; 72 (4): 491-506.
From expression cloning to gene modeling: the development of Xenopus gene sequence resources., Gilchrist MJ., Genesis. March 1, 2012; 50 (3): 143-54.
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. January 20, 2012; 21 (2): 181-90.
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. January 1, 2012; 7 (3): e33346.
Databases of gene expression in Xenopus development., Gilchrist MJ, Pollet N., Methods Mol Biol. January 1, 2012; 917 319-45.
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. November 15, 2011; 11 70.
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. April 30, 2010; 328 (5978): 633-6.
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. October 1, 2009; 19 (10): 1766-75.
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. June 1, 2009; 238 (6): 1379-88.
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. January 1, 2009; 53 (1): 37-43.
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. October 17, 2008; 9 442.
Defining synphenotype groups in Xenopus tropicalis by use of antisense morpholino oligonucleotides., Rana AA, Collart C, Gilchrist MJ, Smith JC., PLoS Genet. November 17, 2006; 2 (11): e193.
A Xenopus tropicalis oligonucleotide microarray works across species using RNA from Xenopus laevis., Chalmers AD, Goldstone K, Smith JC, Gilchrist M, Amaya E, Papalopulu N., Mech Dev. March 1, 2005; 122 (3): 355-63.
Microarray-based identification of VegT targets in Xenopus., Taverner NV, Kofron M, Shin Y, Kabitschke C, Gilchrist MJ, Wylie C, Cho KW, Heasman J, Smith JC., Mech Dev. March 1, 2005; 122 (3): 333-54.
Identification of novel genes affecting mesoderm formation and morphogenesis through an enhanced large scale functional screen in Xenopus., Chen JA, Voigt J, Gilchrist M, Papalopulu N, Amaya E., Mech Dev. March 1, 2005; 122 (3): 307-31.
Expression cloning screening of a unique and full-length set of cDNA clones is an efficient method for identifying genes involved in Xenopus neurogenesis., Voigt J, Chen JA, Gilchrist M, Amaya E, Papalopulu N., Mech Dev. March 1, 2005; 122 (3): 289-306.
Defining a large set of full-length clones from a Xenopus tropicalis EST project., Gilchrist MJ, Zorn AM, Voigt J, Smith JC, Papalopulu N, Amaya E., Dev Biol. July 15, 2004; 271 (2): 498-516.

Genomics Methods for Xenopus Embryos and Tissues., Gilchrist MJ, Cho KWY, Veenstra GJC., Cold Spring Harb Protoc. May 1, 2020; 2020 (5): 097915.

Transcriptomics and Proteomics Methods for Xenopus Embryos and Tissues., Gilchrist MJ, Veenstra GJC, Cho KWY., Cold Spring Harb Protoc. February 3, 2020; 2020 (2): 098350.

An RNA-Seq Protocol for Differential Expression Analysis., Owens NDL, De Domenico E, Gilchrist MJ., Cold Spring Harb Protoc. June 3, 2019; 2019 (6):

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. August 2, 2018; 14 (8): e1006077.

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. June 15, 2017; 426 (2): 401-408.

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. June 15, 2017; 426 (2): 409-417.

Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development., Owens ND, Blitz IL, Lane MA, Patrushev I, Overton JD, Gilchrist MJ, Cho KW, Khokha MK., Cell Rep. January 26, 2016; 14 (3): 632-47.

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. December 15, 2015; 408 (2): 252-68.

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. December 15, 2015; 408 (2): 345-57.

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. January 1, 2015; 145 (3-4): 187-91.

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. January 1, 2015; 10 (10): e0138313.

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. May 1, 2014; 141 (9): 1927-39.

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. September 26, 2013; 4 (6): 1185-96.

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. May 28, 2013; 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. January 1, 2013; 5 (6): 1087-98.

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. November 21, 2012; 13 649.

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. April 1, 2012; 72 (4): 491-506.

From expression cloning to gene modeling: the development of Xenopus gene sequence resources., Gilchrist MJ., Genesis. March 1, 2012; 50 (3): 143-54.

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. January 20, 2012; 21 (2): 181-90.

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. January 1, 2012; 7 (3): e33346.

Databases of gene expression in Xenopus development., Gilchrist MJ, Pollet N., Methods Mol Biol. January 1, 2012; 917 319-45.

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. November 15, 2011; 11 70.

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. April 30, 2010; 328 (5978): 633-6.

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. October 1, 2009; 19 (10): 1766-75.

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. June 1, 2009; 238 (6): 1379-88.

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. January 1, 2009; 53 (1): 37-43.

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. October 17, 2008; 9 442.

Defining synphenotype groups in Xenopus tropicalis by use of antisense morpholino oligonucleotides., Rana AA, Collart C, Gilchrist MJ, Smith JC., PLoS Genet. November 17, 2006; 2 (11): e193.

A Xenopus tropicalis oligonucleotide microarray works across species using RNA from Xenopus laevis., Chalmers AD, Goldstone K, Smith JC, Gilchrist M, Amaya E, Papalopulu N., Mech Dev. March 1, 2005; 122 (3): 355-63.

Microarray-based identification of VegT targets in Xenopus., Taverner NV, Kofron M, Shin Y, Kabitschke C, Gilchrist MJ, Wylie C, Cho KW, Heasman J, Smith JC., Mech Dev. March 1, 2005; 122 (3): 333-54.

Identification of novel genes affecting mesoderm formation and morphogenesis through an enhanced large scale functional screen in Xenopus., Chen JA, Voigt J, Gilchrist M, Papalopulu N, Amaya E., Mech Dev. March 1, 2005; 122 (3): 307-31.

Expression cloning screening of a unique and full-length set of cDNA clones is an efficient method for identifying genes involved in Xenopus neurogenesis., Voigt J, Chen JA, Gilchrist M, Amaya E, Papalopulu N., Mech Dev. March 1, 2005; 122 (3): 289-306.

Defining a large set of full-length clones from a Xenopus tropicalis EST project., Gilchrist MJ, Zorn AM, Voigt J, Smith JC, Papalopulu N, Amaya E., Dev Biol. July 15, 2004; 271 (2): 498-516.

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