Bioinformatics Talks and Journal Club: All from NUIG welcome to attend
Bioinformatics seminars - Tim Downing, NUI, Galway
Bioinformatics Talks and Journal Club Timetable
Thursdays at 2pm in Aras de Brun room ADB-1019 (1st floor)
All researchers with an interest in bioinformatics are encouraged to come, and to present
This series includes research talks, journal club presentations and any other bioinformatics-related contributions
Planned talks:
11th Dec 2014: Paul Cherry - Research Talk. Seaweed-derived prebiotics: Dietary modulation of the gut microbiome.
Previous Journal Clubs and talks:
4th Dec 2014: Ngoc T Nguyen - Journal Club. Paper by Gerashchenko and Gladyshev (2014) in Nucleic Acids Res Translation inhibitors cause abnormalities in ribosome profiling experiments.
27th Nov 2014: Haixuan Yang - Research Talk. Protein function prediction.
20th Nov 2014: Cathal Seoighe - Journal Club. Paper by Necsulea and Kaessmann (2014) in Nature Reviews Genetics Evolutionary dynamics of coding and non-coding transcriptomes.
13th Nov 2014: Alan Barnicle - Journal Club. Paper by Wagner et al (2014) in Genome Biology The relationship between DNA methylation, genetic and expression inter-individual variation in untransformed human fibroblasts.
6th Nov 2014: Peter Keane - Journal Club. Paper by Sansom et al (2014) in Genome Research Population and single cell genomics reveal the Aire-dependency, relief from Polycomb silencing and distribution of self-antigen expression in thymic epithelia.
30th Oct 2014: Tim Downing - Research Talk. Escherichia coli ST131 genomes from long-term care facilities highlight subtype displacement and pervasive recombination.
23rd Oct 2014: Simone Coughlan - Research Talk. Genomic and transcriptomic signatures of oxacillin resistance in Staphylococcus aureus.
16th Oct 2014: Sofia Barreira - Journal Club. Paper by Salmela and Rivals (2014) in BioinformaticsLoRDEC: accurate and efficient long read error correction.
9th Oct 2014: Reetu Tuteja - Journal Club. Paper by Gossmann et al (2013) in Mol Biol EvolSelection-driven evolution of sex-biased genes is consistent with sexual selection in Arabidopsis thaliana.
2nd Oct 2014: Laleh Kazemzadeh - Journal Club. Paper by Zhou et al (2013) in Plos OnePredicting Protein-Protein Interactions by the Mirrortree Methods: Possibilities and Limitations.
25th Sept 2014: Liam Doonan - Journal Club. Paper by Fang et al (2014) in Cell Reports Adaptations to a subterranean environment and longevity revealed by the analysis of mole rat genomes.
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10th July 2014: Yaxuan Yu - Journal Club. Paper by Thomas et al (2013) in BioinformaticsDecombinator: a tool for fast, efficient gene assignment in T-cell receptor sequences using a finite state machine.
3rd July 2014: NUI Galway Research Event
26th June 2014: Estienne Swart - Research Talk: "Genetic and epigenetic control of targeted DNA deletion in Paramecium"
19th June 2014: Ngoc T Nguyen- Journal Club. Paper by Rapakoulia et al (2014) in BioinformaticsEnsembleGASVR: a novel ensemble method for classifying missense single nucleotide polymorphisms.
12th June 2014: Haixuan Yang - Journal Club. Paper by Mei and Key (2011) in IEEE International Geoscience and Remote Sensing SymposiumMinimum endmember-wise distance constrained Nonnegative Matrix Factorization for Spectral Mixture Analysis of hyperspectral images.
5th June 2014: Alan Barnicle - Journal Club. Paper by Liu et al (2014) in The American Journal of Human GeneticsGeMes, Clusters of DNA Methylation under Genetic Control, Can Inform Genetic and Epigenetic Analysis of Disease.
29th May 2014: Cathal Seoighe - Research Talk: "Inference of germline mutation rate polymorphism from genome-wide haplotype data"
22nd May 2014: Lida Fallah - Research Talk: "Modelling Heterogenous Populations under Joint Progressive Type-II Censoring"
15th May 2014: Peter Keane - Journal Club. Paper by Guilgur et al (2014) in nRequirement for highly efficient pre-mRNA splicing during Drosophila early embryonic development.
8th May 2014: Tim Downing - Journal Club. Paper by Sankararaman et al (2014) in NatureThe genomic landscape of Neanderthal ancestry in present-day humans. See also Resurrecting surviving Neandertal lineages from modern human genomes.
24th April 2014: Simone Coughlan - Journal Club. Paper by Hunt et al (2013) in Genome BiologyREAPR: a universal tool for genome assembly evaluation.
17th April 2014: Sofia Barreira - Journal Club. Paper by Jin et al (2013) in NatureA high-resolution map of the three-dimensional chromatin interactome in human cells.
10th April 2014: Liam Doonan. Research Talk: Stem Cell Transcriptome Analysis in Hydractinia.
3rd April 2014: Yaxuan Yu. Research Talk: Bioinformatics Pipelines for TCR Sequencing Data Analysis.
27th March 2014: Ngoc T Nguyen. Research Talk: Sequencing-based metagenomics in mining genes encoding lignocellulolytic enzymes from termite-gut microbiota.
20th March 2014: Tom Weber School seminar at 3.45pm. Quantifying the length and variance of the eukaryotic cell cycle phases by a stochastic model and dual nucleoside pulse labelling.
13th March 2014: Haixuan Yang. Research Talk:
6th March 2014: Alan Barnicle. Research Talk: Genome wide DNA methylation patterns across diverse cell lineages in colonic pinch biopsies.
27th February 2014: External talk by John Greally from the Einstein College of Medicine, NY, USA.
13th February 2014: Attia Fatima. Research Talk: Analysis of hepatic micro RNA expression in postpartum dairy cows in negative energy balance.
6th February 2014: Cathal Seoighe. Journal Club. Capturing Heterogeneity in Gene Expression Studies by Surrogate Variable Analysis and Reference-Free Cell Mixture Adjustments in Analysis of DNA Methylation Data
30th January 2014: Peter Keane. Research Talk.
16th January 2014: Paul Korir. Research Talk: Estimation and analysis of gene expression and alternative splicing: perspectives from development and disease.
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12th December 2013: Tim Downing. Research Talk: Genomic confirmation of hybridisation and recent inbreeding in a vector-isolated Leishmania population. Plos Genetics.
28th November 2013: Sofia Barreira. Research Talk: Genomic architecture of human nucleolar organiser regions
28th November 2013: Simone Coughlan. Research Talk: Harnessing related species and samples data to create and optimise draft genome sequences for Leishmania species.
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7th November 2013: Thong T Nguyen "Novel Insights into Chromatin Structure and Gene Regulation through Integrative Analysis of High Throughput Genomics Data"- Viva.
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3rd & 10th October 2013: Liam Doonan - Journal Club. Paper by Onal et al (2012) in the EMBO JournalGene expression of pluripotency determinants is conserved between mammalian and planarian stem cells
26th September 2013: Simone Coughlan - Journal Club. Paper by O'Rawe et al (2013) in Genome MedicineLow concordance of multiple variant-calling pipelines: practical implications for exome and genome sequencing
19th September 2013: Alan Barnicle - Journal Club. Paper by Varley et al (2013) in Genome ResearchDynamic DNA methylation across diverse human cell lines and tissues
12th September 2013: Tim Downing - Journal Club. Paper by Lawson et al (2012) in Plos GeneticsInference of population structure using dense haplotype data
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18th July 2013: Reetu Tuteja - Journal Club. Paper by Reme and Tautz (2013) BMC GenomicsPhylogenetic patterns of emergence of new genes support a model of frequent de novo evolution
4th July 2013: Laleh Kazemzadeh - Journal Club. Paper by Li et al (2012) BMC Systems BiologyA new essential protein discovery method based on the integration of protein-protein interaction and gene expression data
20th June 2013: Martin Braud - Journal Club. Paper by Leclercq et al (2013) in Nucleic Acids ResearchComputational prediction of the localization of microRNAs within their pre-miRNA
13th June 2013: Sofia Barreira - Journal Club. Paper by Hansen et al (2010) in PNASSequencing newly replicated DNA reveals widespread plasticity in human replication timing
6th June 2013: Thong Nguyen Trung - Journal Club. Paper by Wu et al (2013) in NatureVariation and genetic control of protein abundance in humans
23rd May 2013: Peter Keane - Journal Club. Paper by Gelfman et al (2013) in Genome ResearchDNA-methylation effect on costranscriptional splicing is dependent on GC architecture of the exon-intron structure
16th May 2013: Attia Fatima - Journal Club. Paper by Han et al (2013) in Physical BiologyPhysical model of the immune response of bacteria against bacteriophage through the adaptive CRISPR-Cas immune system
9th May 2013: Haixuan Yang- Journal Club. Paper by Wang et al 2012 in Nature BiotechnologyThree-dimensional reconstruction of protein networks provides insight into human genetic disease
25th April 2013: Paul Korir - Journal Club. Paper by Feng et al (2012) in PLoS Computational BiologyDetecting DNA Modifications from SMRT Sequencing Data by Modeling Sequence Context Dependence of Polymerase Kinetic
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7th March 2013: Cathal Seoighe - Journal Club. Papers by Lynch (2009) in PNAS Rate, molecular spectrum, and consequences of human mutation
Kong et al (2012) in NatureRate of de novo mutations and the importance of father's age to disease risk
14th February 2013: Simone Coughlan - Journal Club. Paper by Rahman et al (2012) in Genome BiologyCGAL:computing genome assembly likelihoods
17th January 2013: Tim Downing - Journal Club. Papers by Papasaikas & Valcarcel (2012) in Science Splicing in 4D
Barbosa-Morais et al (2012) in ScienceThe Evolutionary Landscape of Alternative Splicing in Vertebrate Species
Merkin et al (2012) in ScienceEvolutionary Dynamics of Gene
and Isoform Regulation in Mammalian Tissues
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13th December 2012: Peter Keane - Journal Club. Paper by Miyao et al (2012) in ImmunityPlasticity of Foxp3(+) T cells reflects promiscuous Foxp3 expression in conventional T cells but not reprogramming of regulatory T cells
4th October 2012: Sofia Barreira - Journal Club. Paper by Bresler et al (2012) in BioinformaticsTelescoper: de novo assembly of highly repetitive regions
18th July 2012: Peter Keane - Journal Club. Paper by Ip et al (2011) in Genome ResearchGlobal impact of RNA polymerase II elongation inhibition on alternative splicing regulation
Contact: tim.downing@nuigalway.ie
Rota:
Peter Keane
Lida Fallah
Cathal Seoighe
Alan Barnicle
Haixuan Yang
Ngoc T Nguyen
Yaxuan Yu
Liam Doonan
Laleh Kazemzadeh
Reetu Tuteja
Sofia Barreira
Simone Coughlan