Micklem Lab

University of Cambridge


HumanMine: advanced data searching, analysis and cross-species comparison. 2022 Database Lyne R, Bazaga A, Butano D, Contrino S, Heimbach J, et al.
Translating synthetic natural language to database queries with a polyglot deep learning framework. 2021 Scientific reports Bazaga A, Gunwant N, Micklem G
Insights into olfactory ensheathing cell development from a laser-microdissection and transcriptome-profiling approach. 2020 Glia Perera SN, Williams RM, Lyne R, Stubbs O, Buehler DP, et al.
InterMineR: an R package for InterMine databases. 2019 Bioinformatics Kyritsis KA, Wang B, Sullivan J, Lyne R, Micklem G
Correction: esyN: Network Building, Sharing and Publishing. 2019 PloS one Bean DM, Heimbach J, Ficorella L, Micklem G, Oliver SG, et al.
Encompassing new use cases - level 3.0 of the HUPO-PSI format for molecular interactions. 2018 BMC bioinformatics Sivade Dumousseau M, Alonso-López D, Ammari M, Bradley G, Campbell NH, et al.
Comparative genomics of bdelloid rotifers: Insights from desiccating and nondesiccating species. 2018 PLoS biology Nowell RW, Almeida P, Wilson CG, Smith TP, Fontaneto D, et al.
The InterMine Android app: Cross-organism genomic data in your pocket. 2018 F1000Research Komkova D, Lyne R, Sullivan J, Yehudi Y, Micklem G
ComplexViewer: visualization of curated macromolecular complexes. 2017 Bioinformatics Combe CW, Sivade MD, Hermjakob H, Heimbach J, Meldal BHM, et al.
Correction for Guo et al., "Poly(A) Signals Located near the 5' End of Genes Are Silenced by a General Mechanism That Prevents Premature 3'-End Processing". 2017 Molecular and cellular biology Guo J, Garrett M, Micklem G, Brogna S
Empirical Bayes method for reducing false discovery rates of correlation matrices with block diagonal structure. 2017 BMC bioinformatics Pacini C, Ajioka JW, Micklem G
Insights into electrosensory organ development, physiology and evolution from a lateral line-enriched transcriptome. 2017 eLife Modrell MS, Lyne M, Carr AR, Zakon HH, Buckley D, et al.
Urinary Exosomes Contain MicroRNAs Capable of Paracrine Modulation of Tubular Transporters in Kidney. 2017 Scientific reports Gracia T, Wang X, Su Y, Norgett EE, Williams TL, et al.
ThaleMine: A Warehouse for Arabidopsis Data Integration and Discovery. 2017 Plant & cell physiology Krishnakumar V, Contrino S, Cheng CY, Belyaeva I, Ferlanti ES, et al.
Genomes of coral dinoflagellate symbionts highlight evolutionary adaptations conducive to a symbiotic lifestyle. 2016 Scientific reports Aranda M, Li Y, Liew YJ, Baumgarten S, Simakov O, et al.
Cross-organism analysis using InterMine. 2015 Genesis (New York, N.Y. : 2000) Lyne R, Sullivan J, Butano D, Contrino S, Heimbach J, et al.
Expression of multiple horizontally acquired genes is a hallmark of both vertebrate and invertebrate genomes. 2015 Genome biology Crisp A, Boschetti C, Perry M, Tunnacliffe A, Micklem G
toxoMine: an integrated omics data warehouse for Toxoplasma gondii systems biology research. 2015 Database Rhee DB, Croken MM, Shieh KR, Sullivan J, Micklem G, et al.
Araport: the Arabidopsis information portal. 2015 Nucleic acids research Krishnakumar V, Hanlon MR, Contrino S, Ferlanti ES, Karamycheva S, et al.
InterMine: extensive web services for modern biology. 2014 Nucleic acids research Kalderimis A, Lyne R, Butano D, Contrino S, Lyne M, et al.
esyN: network building, sharing and publishing. 2014 PloS one Bean DM, Heimbach J, Ficorella L, Micklem G, Oliver SG, et al.
BioJS DAGViewer: A reusable JavaScript component for displaying directed graphs. 2014 F1000Research Kalderimis A, Stepan R, Sullivan J, Lyne R, Lyne M, et al.
Identification of microRNAs in the coral Stylophora pistillata. 2014 PloS one Liew YJ, Aranda M, Carr A, Baumgarten S, Zoccola D, et al.
Integrating microRNA and mRNA expression profiling in Symbiodinium microadriaticum, a dinoflagellate symbiont of reef-building corals. 2013 BMC genomics Baumgarten S, Bayer T, Aranda M, Liew YJ, Carr A, et al.
Activity of a heptad of transcription factors is associated with stem cell programs and clinical outcome in acute myeloid leukemia. 2013 Blood Diffner E, Beck D, Gudgin E, Thoms JA, Knezevic K, et al.
The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies. 2013 Journal of biomedical semantics Katayama T, Wilkinson MD, Micklem G, Kawashima S, Yamaguchi A, et al.
metabolicMine: an integrated genomics, genetics and proteomics data warehouse for common metabolic disease research. 2013 Database Lyne M, Smith RN, Lyne R, Aleksic J, Hu F, et al.
InterMOD: integrated data and tools for the unification of model organism research. 2013 Scientific reports Sullivan J, Karra K, Moxon SA, Vallejos A, Motenko H, et al.
InterMine: a flexible data warehouse system for the integration and analysis of heterogeneous biological data. 2012 Bioinformatics Smith RN, Aleksic J, Butano D, Carr A, Contrino S, et al.
Multiple functionally divergent and conserved copies of alpha tubulin in bdelloid rotifers. 2012 BMC evolutionary biology Eyres I, Frangedakis E, Fontaneto D, Herniou EA, Boschetti C, et al.
Biochemical diversification through foreign gene expression in bdelloid rotifers. 2012 PLoS genetics Boschetti C, Carr A, Crisp A, Eyres I, Wang-Koh Y, et al.
YeastMine--an integrated data warehouse for Saccharomyces cerevisiae data as a multipurpose tool-kit. 2012 Database Balakrishnan R, Park J, Karra K, Hitz BC, Binkley G, et al.
modMine: flexible access to modENCODE data. 2012 Nucleic acids research Contrino S, Smith RN, Butano D, Carr A, Hu F, et al.
MicroRNAs dysregulated in breast cancer preferentially target key oncogenic pathways. 2011 Molecular bioSystems Lim WK, Micklem G
The impact of quantitative optimization of hybridization conditions on gene expression analysis. 2011 BMC bioinformatics Sykacek P, Kreil DP, Meadows LA, Auburn RP, Fischer B, et al.
Poly(A) signals located near the 5' end of genes are silenced by a general mechanism that prevents premature 3'-end processing. 2011 Molecular and cellular biology Guo J, Garrett M, Micklem G, Brogna S
The modENCODE Data Coordination Center: lessons in harvesting comprehensive experimental details. 2011 Database Washington NL, Stinson EO, Perry MD, Ruzanov P, Contrino S, et al.
Identification of functional elements and regulatory circuits by Drosophila modENCODE. 2010 Science Roy S, Ernst J, Kharchenko PV, Kheradpour P, Negre N, et al.
Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. 2010 Science Gerstein MB, Lu ZJ, Van Nostrand EL, Cheng C, Arshinoff BI, et al.
Identification and analysis of serpin-family genes by homology and synteny across the 12 sequenced Drosophilid genomes. 2009 BMC genomics Garrett M, Fullaondo A, Troxler L, Micklem G, Gubb D
Unlocking the secrets of the genome. 2009 Nature Celniker SE, Dillon LA, Gerstein MB, Gunsalus KC, Henikoff S, et al.
Phylogenetic and genomewide analyses suggest a functional relationship between kayak, the Drosophila fos homolog, and fig, a predicted protein phosphatase 2c nested within a kayak intron. 2007 Genetics Hudson SG, Garrett MJ, Carlson JW, Micklem G, Celniker SE, et al.
Bayesian modelling of shared gene function. 2007 Bioinformatics Sykacek P, Clarkson R, Print C, Furlong R, Micklem G
FlyMine: an integrated database for Drosophila and Anopheles genomics. 2007 Genome biology Lyne R, Smith R, Rutherford K, Wakeling M, Varley A, et al.
Prospero acts as a binary switch between self-renewal and differentiation in Drosophila neural stem cells. 2006 Developmental cell Choksi SP, Southall TD, Bossing T, Edoff K, de Wit E, et al.
A friendly statistics package for microarray analysis. 2005 Bioinformatics Sykacek P, Furlong RA, Micklem G
Regions of human chromosome 2 (2q32-q35) and mouse chromosome 1 show synteny with the pufferfish genome (Fugu rubripes). 1997 Genomics Schofield JP, Elgar G, Greystrong J, Lye G, Deadman R, et al.
Sequence comparison of human and yeast telomeres identifies structurally distinct subtelomeric domains. 1997 Human molecular genetics Flint J, Bates GP, Clark K, Dorman A, Willingham D, et al.
The relationship between chromosome structure and function at a human telomeric region. 1997 Nature genetics Flint J, Thomas K, Micklem G, Raynham H, Clark K, et al.
The BRC repeats are conserved in mammalian BRCA2 proteins. 1997 Human molecular genetics Bignell G, Micklem G, Stratton MR, Ashworth A, Wooster R
Molecular cloning of tissue-specific transcripts of a transketolase-related gene: implications for the evolution of new vertebrate genes. 1996 Genomics Coy JF, Dübel S, Kioschis P, Thomas K, Micklem G, et al.
Identification of the breast cancer susceptibility gene BRCA2. 1995 Nature Wooster R, Bignell G, Lancaster J, Swift S, Seal S, et al.
Comparative sequence analysis of the human and pufferfish Huntington's disease genes. 1995 Nature genetics Baxendale S, Abdulla S, Elgar G, Buck D, Berks M, et al.
The sequence complexity of exons trapped from the mouse genome. 1994 Current biology Nehls M, Pfeifer D, Micklem G, Schmoor C, Boehm T
Dissecting the temporal requirements for homeotic gene function. 1994 Development Castelli-Gair J, Greig S, Micklem G, Akam M
Structure and expression of the Huntington's disease gene: evidence against simple inactivation due to an expanded CAG repeat. 1994 Somatic cell and molecular genetics Ambrose CM, Duyao MP, Barnes G, Bates GP, Lin CS, et al.
Yeast origin recognition complex is involved in DNA replication and transcriptional silencing. 1993 Nature Micklem G, Rowley A, Harwood J, Nasmyth K, Diffley JF
A yeast silencer contains sequences that can promote autonomous plasmid replication and transcriptional activation. 1987 Cell Brand AH, Micklem G, Nasmyth K