Professor Cathal Seoighe

PhD

 
researcher
 

Biography


After an undergraduate degree in Theoretical Physics (Trinity College Dublin, 1996), Cathal Seoighe undertook a PhD in Molecular Evolution/Bioinformatics, under the supervision of Ken Wolfe (Trinity College Dublin, awarded 2000). In 2000 he went to Cape Town, South Africa, working initially with the South African Medical Research Council on a national biotechnology strategy and at the South African National Bioinformatics Institute (SANBI), University of the Western Cape (UWC), as director of Bioinformatics training. In 2001 he began working full-time as a lecturer at UWC, before joining the University of Cape Town (UCT) in 2004 as Associate Professor. He returned to Ireland in 2001 as Stokes Professor of Bioinformatics in the School of Mathematics, Statistics and Applied Mathematics at NUI Galway. Although now motivated primarily by biological problems, he has a long-standing interest in the the intersection of the mathematical and biological sciences. In Cape Town he was involved in the establishment of the South African Centre for Epidemiological Modeling and Analysis (Sacema) and the African Institute of Mathematical Sciences (AIMS), representing UWC on the inaugural executive committee of the latter. Current research interests include probabilistic models of molecular evolution, transcriptomics and epigenetics. He is interested in the development of methods to analyze gene expression, mRNA splicing and epigenetic data and in understanding the impact of mutations on gene expression, particularly how human mutations responsible for complex diseases can lead to widespread perturbations of gene expression patterns.

Research Interests

Modeling molecular biological data, including gene expression, alternative mRNA splicing and the evolution of viruses, in particular HIV-1. In addition to computational biology research my group collaborates with lab-based scientists within and outside NUI Galway. Application areas include epigenetics of colon cancer and the DNA damage response, genome assembly and annotation and applications of next-generation genomics in developmental biology.

Research Projects

  Project Start Date End Date
IRC POSTGRADUATE THANH NGOC NGUYEN CATHAL SEOIGE 01-OCT-13 13-NOV-17
NEANDER 150 CATHAL SEOIGE 01-MAR-14 30-NOV-14
SFI Stokes Professorship - 07/SK/M1211b 01-JAN-09 31-AUG-16
QUANTATIVE T CELL IMMUNITY QUANTI CATHAL SEOIGE 01-MAY-13 30-NOV-17
TEAGASC THE DEVELOMENT OF A WEB-BASED ANNOTATION AND GENE FUNCTION TOOLS CATHAL SEOIGHE 01-OCT-10 31-DEC-13
IRCSET EMBARK CATHAL SEOIGHE TRUNG THONG NGUYEN 01-OCT-09 30-SEP-12
IRCSET PHD PROGRAMME IN BIOINFORMATICS AND SYSTEMS BIOLOGY CATHAL SEOIGHE GREP 01-SEP-09 31-DEC-15
MODELING HIV-1 IMMUNE MIGUEL LACARDA - C SEOIGHE 01-OCT-09 30-SEP-12
SFI RECOMB COMPARATIVE GENEOMICS WORKSHOP 10/CW/B1867 CATHAL SEOIGHE 01-APR-11 31-MAR-12

Peer Reviewed Journals

  Year Publication
(2019) 'Insights from deconvolution of cell subtype proportions enhance the interpretation of functional genomic data'
Kong, Y,Rastogi, D,Seoighe, C,Greally, JM,Suzuki, M (2019) 'Insights from deconvolution of cell subtype proportions enhance the interpretation of functional genomic data'. Plos One, 14 [DOI] [Details]
(2019) 'Oligodendrocyte gene expression is reduced by and influences effects of chronic social stress in mice'
Cathomas, F;Azzinnari, D;Bergamini, G;Sigrist, H;Buerge, M;Hoop, V;Wicki, B;Goetze, L;Soares, S;Kukelova, D;Seifritz, E;Goebbels, S;Nave, KA;Ghandour, MS;Seoighe, C;Hildebrandt, T;Leparc, G;Klein, H;Stupka, E;Hengerer, B;Pryce, CR (2019) 'Oligodendrocyte gene expression is reduced by and influences effects of chronic social stress in mice'. Genes Brain And Behavior, 18 [DOI] [Details]
(2019) 'Insights from deconvolution of cell subtype proportions enhance the interpretation of functional genomic data'
Kong, Y;Rastogi, D;Seoighe, C;Greally, JM;Suzuki, M (2019) 'Insights from deconvolution of cell subtype proportions enhance the interpretation of functional genomic data'. Plos One, 14 [DOI] [Details]
(2018) 'DNA methylation haplotypes as cancer markers'
Seoighe, C; Tosh, N; Greally, J (2018) 'DNA methylation haplotypes as cancer markers'. Nature Genetics, 50 :1062-1063 [DOI] [Details]
(2018) 'Cancer expression quantitative trait loci (eQTLs) can be determined from heterogeneous tumor gene expression data by modeling variation in tumor purity'
Geeleher, P,Nath, A,Wang, F,Zhang, ZY,Barbeira, AN,Fessler, J,Grossman, RL,Seoighe, C,Huang, RS (2018) 'Cancer expression quantitative trait loci (eQTLs) can be determined from heterogeneous tumor gene expression data by modeling variation in tumor purity'. Genome Biol, 19 [DOI] [Details]
(2018) 'History by the numbers?'
Tosh, N; Ferguson, J; Seoighe, C (2018) 'History by the numbers?'. Proceedings Of The National Academy Of Sciences Of The United States Of America, [Details]
(2017) 'Inflammation-associated DNA methylation patterns in epithelium of ulcerative colitis'
Barnicle, A,Seoighe, C,Greally, JM,Golden, A,Egan, LJ (2017) 'Inflammation-associated DNA methylation patterns in epithelium of ulcerative colitis'. Epigenetics, 12 :591-606 [DOI] [Details]
(2017) 'Inference of Candidate Germline Mutator Loci in Humans from Genome-Wide Haplotype Data'
Seoighe, C,Scally, A (2017) 'Inference of Candidate Germline Mutator Loci in Humans from Genome-Wide Haplotype Data'. Plos Genetics, 13 [DOI] [Details]
(2017) 'Inflammation-associated DNA methylation patterns in epithelium of ulcerative colitis'
Barnicle, A. and Seoighe, C. and Greally, J. M. and Golden, A. and Egan, L. J. (2017) 'Inflammation-associated DNA methylation patterns in epithelium of ulcerative colitis'. Epigenetics, 12 (8):591-606 [Details]
(2017) 'Allele-specific splicing effects on DKKL1 and ZNF419 transcripts in HeLa cells'
Martin, G,Selcuklu, SD,Schouest, K,Nembaware, V,McKeown, PC,Seoighe, C,Spillane, C (2017) 'Allele-specific splicing effects on DKKL1 and ZNF419 transcripts in HeLa cells'. Gene, 598 :107-112 [DOI] [Details]
(2016) 'Differential DNA methylation patterns of homeobox genes in proximal and distal colon epithelial cells'
Barnicle, A,Seoighe, C,Golden, A,Greally, JM,Egan, LJ (2016) 'Differential DNA methylation patterns of homeobox genes in proximal and distal colon epithelial cells'. Physiological Genomics, 48 :257-273 [DOI] [Details]
(2016) 'Intron Length Coevolution across Mammalian Genomes'
Keane, PA,Seoighe, C (2016) 'Intron Length Coevolution across Mammalian Genomes'. Molecular Biology And Evolution, 33 :2682-2691 [DOI] [Details]
(2016) 'Impact of the Choice of Normalization Method on Molecular Cancer Class Discovery Using Nonnegative Matrix Factorization'
Yang, HX,Seoighe, C (2016) 'Impact of the Choice of Normalization Method on Molecular Cancer Class Discovery Using Nonnegative Matrix Factorization'. Plos One, 11 [DOI] [Details]
(2016) 'LymAnalyzer: a tool for comprehensive analysis of next generation sequencing data of T cell receptors and immunoglobulins'
Yu, YX,Ceredig, R,Seoighe, C (2016) 'LymAnalyzer: a tool for comprehensive analysis of next generation sequencing data of T cell receptors and immunoglobulins'. Nucleic Acids Research, 44 [DOI] [Details]
(2016) 'Human newborn bacille Calmette-Guérin vaccination and risk of tuberculosis disease: A case-control study'
H.A. Fletcher et all. (2016) 'Human newborn bacille Calmette-Guérin vaccination and risk of tuberculosis disease: A case-control study'. BMC Medicine, 14 (11) [DOI] [Details]
(2016) 'Consistency in large pharmacogenomic studies'
Geeleher, P. and Gamazon, E.R. and Seoighe, C. and Cox, N.J. and Huang, R.S. (2016) 'Consistency in large pharmacogenomic studies'. Nature, 540 (76317631) [DOI] [Details]
(2016) 'Impact of the Choice of Normalization Method on Molecular Cancer Class Discovery Using Nonnegative Matrix Factorization'
Yang, HX;Seoighe, C (2016) 'Impact of the Choice of Normalization Method on Molecular Cancer Class Discovery Using Nonnegative Matrix Factorization'. Plos One, 11 [DOI] [Details]
(2015) 'Promiscuous mRNA splicing under the control of AIRE in medullary thymic epithelial cells'
Keane, P,Ceredig, R,Seoighe, C (2015) 'Promiscuous mRNA splicing under the control of AIRE in medullary thymic epithelial cells'. Bioinformatics, 31 :986-990 [DOI] [Details]
(2015) 'RNA:DNA hybrids in the human genome have distinctive nucleotide characteristics, chromatin composition, and transcriptional relationships'
Nadel, J,Athanasiadou, R,Lemetre, C,Wijetunga, NA,Broin, PO,Sato, H,Zhang, ZD,Jeddeloh, J,Montagna, C,Golden, A,Seoighe, C,Greally, JM (2015) 'RNA:DNA hybrids in the human genome have distinctive nucleotide characteristics, chromatin composition, and transcriptional relationships'. Epigenetics & Chromatin, 8 [DOI] [Details]
(2015) 'A Genomic Portrait of Haplotype Diversity and Signatures of Selection in Indigenous Southern African Populations'
Chimusa ER, Meintjies A, Tchanga M, Mulder N, Seoighe C, Soodyall H, Ramesar R (2015) 'A Genomic Portrait of Haplotype Diversity and Signatures of Selection in Indigenous Southern African Populations'. Plos Genetics, [Details]
(2015) 'Seq-ing improved gene expression estimates from microarrays using machine learning'
Korir, PK,Geeleher, P,Seoighe, C (2015) 'Seq-ing improved gene expression estimates from microarrays using machine learning'. BMC Bioinformatics, 16 [DOI] [Details]
(2015) 'The Contribution of William King to the Early Development of Palaeoanthropology'
Murray J, Nasheuer HP, Seoighe C, McCormack GP, Williams DM, Harper DAT (2015) 'The Contribution of William King to the Early Development of Palaeoanthropology'. Irish Journal Of Earth Sciences, 33 :1-16 [Details]
(2014) 'Genome-wide Variant Discovery Using Sequence Assembly, Mapping and Population-wide Analysis'
Coughlan, S,Barreira, S,Seoighe, C,Downing, T,Bishop, OT (2014) 'Genome-wide Variant Discovery Using Sequence Assembly, Mapping and Population-wide Analysis'. Bioinformatics And Data Analysis In Microbiology, :51-80 [Details]
(2014) 'Genome-wide Variant Discovery Using Sequence Assembly, Mapping and Population-wide Analysis'
Coughlan, S;Barreira, S;Seoighe, C;Downing, T (2014) 'Genome-wide Variant Discovery Using Sequence Assembly, Mapping and Population-wide Analysis'. Bioinformatics And Data Analysis In Microbiology, :51-80 [Details]
(2014) 'Inference of Allele-Specific Expression from RNA-seq Data'
Korir, PK,Seoighe, C,Spillane, C,McKeown, PC (2014) 'Inference of Allele-Specific Expression from RNA-seq Data'. Methods Mol Biol, 1112 :49-69 [DOI] [Details]
(2014) 'The miRNAome of the postpartum dairy cow liver in negative energy balance'
Fatima, A,Lynn, DJ,O'Boyle, P,Seoighe, C,Morris, D (2014) 'The miRNAome of the postpartum dairy cow liver in negative energy balance'. BMC Genomics, 15 [DOI] [Details]
(2014) 'Population Genetics Inference for Longitudinally-Sampled Mutants Under Strong Selection'
Lacerda, M,Seoighe, C (2014) 'Population Genetics Inference for Longitudinally-Sampled Mutants Under Strong Selection'. Genetics, 198 [DOI] [Details]
(2014) 'Co-acting gene networks predict TRAIL responsiveness of tumour cells with high accuracy'
O'Reilly, P,Ortutay, C,Gernon, G,O'Connell, E,Seoighe, C,Boyce, S,Serrano, L,Szegezdi, E (2014) 'Co-acting gene networks predict TRAIL responsiveness of tumour cells with high accuracy'. BMC Genomics, 15 [DOI] [Details]
(2014) 'Inference of Allele-Specific Expression from RNA-seq Data'
Korir, PK;Seoighe, C (2014) 'Inference of Allele-Specific Expression from RNA-seq Data'. Methods in Molecular Biology, 1112 :49-69 [DOI] [Details]
(2013) 'The shared genomic architecture of human nucleolar organizer regions'
Floutsakou, I,Agrawal, S,Nguyen, TT,Seoighe, C,Ganley, ARD,McStay, B (2013) 'The shared genomic architecture of human nucleolar organizer regions'. Genome Research, 23 :2003-2012 [DOI] [Details]
(2013) 'Integrative Analysis of mRNA Expression and Half-Life Data Reveals Trans-Acting Genetic Variants Associated with Increased Expression of Stable Transcripts'
Nguyen, TT,Seoighe, C (2013) 'Integrative Analysis of mRNA Expression and Half-Life Data Reveals Trans-Acting Genetic Variants Associated with Increased Expression of Stable Transcripts'. Plos One, 8 [DOI] [Details]
(2013) 'CellMix: a comprehensive toolbox for gene expression deconvolution'
Gaujoux, R,Seoighe, C (2013) 'CellMix: a comprehensive toolbox for gene expression deconvolution'. Bioinformatics, 29 :2211-2212 [DOI] [Details]
(2013) 'Gene-set analysis is severely biased when applied to genome-wide methylation data'
Geeleher, P,Hartnett, L,Egan, LJ,Golden, A,Ali, RAR,Seoighe, C (2013) 'Gene-set analysis is severely biased when applied to genome-wide methylation data'. Bioinformatics, 29 :1851-1857 [DOI] [Details]
(2013) 'Comparison of Viral Env Proteins from Acute and Chronic Infections with Subtype C Human Immunodeficiency Virus Type 1 Identifies Differences in Glycosylation and CCR5 Utilization and Suggests a New Strategy for Immunogen Design'
Ping, LH,Joseph, SB,Anderson, JA,Abrahams, MR,Salazar-Gonzalez, JF,Kincer, LP,Treurnicht, FK,Arney, L,Ojeda, S,Zhang, M,Keys, J,Potter, EL,Chu, HT,Moore, P,Salazar, MG,Iyer, S,Jabara, C,Kirchherr, J,Mapanje, C,Ngandu, N,Seoighe, C,Hoffman, I,Gao, F,Tang, YY,Labranche, C,Lee, B,Saville, A,Vermeulen, M,Fiscus, S,Morris, L,Karim, SA,Haynes, BF,Shaw, GM,Korber, BT,Hahn, BH,Cohen, MS,Montefiori, D,Williamson, C,Swanstrom, R (2013) 'Comparison of Viral Env Proteins from Acute and Chronic Infections with Subtype C Human Immunodeficiency Virus Type 1 Identifies Differences in Glycosylation and CCR5 Utilization and Suggests a New Strategy for Immunogen Design'. J Virol, 87 :7218-7233 [DOI] [Details]
(2013) 'Identification of broadly neutralizing antibody epitopes in the HIV-1 envelope glycoprotein using evolutionary models'
Lacerda, M,Moore, PL,Ngandu, NK,Seaman, M,Gray, ES,Murrell, B,Krishnamoorthy, M,Nonyane, M,Madiga, M,Wibmer, CK,Sheward, D,Bailer, RT,Gao, HM,Greene, KM,Karim, SSA,Mascola, JR,Korber, BTM,Montefiori, DC,Morris, L,Williamson, C,Seoighe, C (2013) 'Identification of broadly neutralizing antibody epitopes in the HIV-1 envelope glycoprotein using evolutionary models'. Virology Journal, 10 [DOI] [Details]
(2013) 'Rapid, complex adaptation of transmitted HIV-1 full-length genomes in subtype C-infected individuals with differing disease progression'
Abrahams, MR,Treurnicht, FK,Ngandu, NK,Goodier, SA,Marais, JC,Bredell, H,Thebus, R,Rosa, DD,Mlisana, K,Seoighe, C,Karim, SA,Gray, CM,Williamson, C (2013) 'Rapid, complex adaptation of transmitted HIV-1 full-length genomes in subtype C-infected individuals with differing disease progression'. AIDS (London, England), 27 :507-518 [DOI] [Details]
(2013) 'Gene-set analysis is severely biased when applied to genome-wide methylation data'
Geeleher, P. and Hartnett, L. and Egan, L. J. and Golden, A. and Raja Ali, R. A. and Seoighe, C. (2013) 'Gene-set analysis is severely biased when applied to genome-wide methylation data'. Bioinformatics, 29 (15):1851-1857 [Details]
(2013) 'Identification of broadly neutralizing antibody epitopes in the HIV-1 envelope glycoprotein using evolutionary models'
Lacerda, M;Moore, PL;Ngandu, NK;Seaman, M;Gray, ES;Murrell, B;Krishnamoorthy, M;Nonyane, M;Madiga, M;Wibmer, CK;Sheward, D;Bailer, RT;Gao, HM;Greene, KM;Karim, SSA;Mascola, JR;Korber, BTM;Montefiori, DC;Morris, L;Williamson, C;Seoighe, C (2013) 'Identification of broadly neutralizing antibody epitopes in the HIV-1 envelope glycoprotein using evolutionary models'. Virology Journal, 10 [DOI] [Details]
(2013) 'Gene-set analysis is severely biased when applied to genome-wide methylation data'
Geeleher, P;Hartnett, L;Egan, LJ;Golden, A;Ali, RAR;Seoighe, C (2013) 'Gene-set analysis is severely biased when applied to genome-wide methylation data'. Bioinformatics, 29 :1851-1857 [DOI] [Details]
(2013) 'Rapid, complex adaptation of transmitted HIV-1 full-length genomes in subtype C-infected individuals with differing disease progression'
Abrahams, MR;Treurnicht, FK;Ngandu, NK;Goodier, SA;Marais, JC;Bredell, H;Thebus, R;Rosa, DD;Mlisana, K;Seoighe, C;Karim, SA;Gray, CM;Williamson, C (2013) 'Rapid, complex adaptation of transmitted HIV-1 full-length genomes in subtype C-infected individuals with differing disease progression'. Aids, 27 :507-518 [DOI] [Details]
(2013) 'The shared genomic architecture of human nucleolar organizer regions'
Floutsakou, I;Agrawal, S;Nguyen, TT;Seoighe, C;Ganley, ARD;McStay, B (2013) 'The shared genomic architecture of human nucleolar organizer regions'. Genome Research, 23 :2003-2012 [DOI] [Details]
(2013) 'Integrative Analysis of mRNA Expression and Half-Life Data Reveals Trans-Acting Genetic Variants Associated with Increased Expression of Stable Transcripts'
Nguyen, TT;Seoighe, C (2013) 'Integrative Analysis of mRNA Expression and Half-Life Data Reveals Trans-Acting Genetic Variants Associated with Increased Expression of Stable Transcripts'. Plos One, 8 [DOI] [Details]
(2013) 'Comparison of Viral Env Proteins from Acute and Chronic Infections with Subtype C Human Immunodeficiency Virus Type 1 Identifies Differences in Glycosylation and CCR5 Utilization and Suggests a New Strategy for Immunogen Design'
Ping, LH;Joseph, SB;Anderson, JA;Abrahams, MR;Salazar-Gonzalez, JF;Kincer, LP;Treurnicht, FK;Arney, L;Ojeda, S;Zhang, M;Keys, J;Potter, EL;Chu, HT;Moore, P;Salazar, MG;Iyer, S;Jabara, C;Kirchherr, J;Mapanje, C;Ngandu, N;Seoighe, C;Hoffman, I;Gao, F;Tang, YY;Labranche, C;Lee, B;Saville, A;Vermeulen, M;Fiscus, S;Morris, L;Karim, SA;Haynes, BF;Shaw, GM;Korber, BT;Hahn, BH;Cohen, MS;Montefiori, D;Williamson, C;Swanstrom, R (2013) 'Comparison of Viral Env Proteins from Acute and Chronic Infections with Subtype C Human Immunodeficiency Virus Type 1 Identifies Differences in Glycosylation and CCR5 Utilization and Suggests a New Strategy for Immunogen Design'. Virology Journal, 87 :7218-7233 [DOI] [Details]
(2013) 'CellMix: a comprehensive toolbox for gene expression deconvolution'
Gaujoux, R;Seoighe, C (2013) 'CellMix: a comprehensive toolbox for gene expression deconvolution'. Bioinformatics, 29 :2211-2212 [DOI] [Details]
(2012) 'The Hidden Geometries of the Arabidopsis thaliana Epidermis'
Staff, L,Hurd, P,Reale, L,Seoighe, C,Rockwood, A,Gehring, C (2012) 'The Hidden Geometries of the Arabidopsis thaliana Epidermis'. Plos One, 7 [DOI] [Details]
(2012) 'The Hidden Geometries of the Arabidopsis thaliana Epidermis'
Staff, L;Hurd, P;Reale, L;Seoighe, C;Rockwood, A;Gehring, C (2012) 'The Hidden Geometries of the Arabidopsis thaliana Epidermis'. Plos One, 7 [DOI] [Details]
(2012) 'Semi-supervised Nonnegative Matrix Factorization for gene expression deconvolution: A case study'
Gaujoux, R;Seoighe, C (2012) 'Semi-supervised Nonnegative Matrix Factorization for gene expression deconvolution: A case study'. Infection Genetics And Evolution, 12 :913-921 [DOI] [Details]
(2012) 'The regulatory effect of miRNAs is a heritable genetic trait in humans'
Geeleher, P;Huang, RS;Gamazon, ER;Golden, A;Seoighe, C (2012) 'The regulatory effect of miRNAs is a heritable genetic trait in humans'. BMC Genomics, 13 [DOI] [Details]
(2012) 'The regulatory effect of miRNAs is a heritable genetic trait in humans'
Geeleher, P. and Huang, S. R. and Gamazon, E. R. and Golden, A. and Seoighe, C. (2012) 'The regulatory effect of miRNAs is a heritable genetic trait in humans'. BMC Genomics, 13 [Details]
(2012) 'Semi-supervised Nonnegative Matrix Factorization for gene expression deconvolution: A case study'
Gaujoux, R,Seoighe, C (2012) 'Semi-supervised Nonnegative Matrix Factorization for gene expression deconvolution: A case study'. Infection Genetics And Evolution, 12 :913-921 [DOI] [Details]
(2012) 'The regulatory effect of miRNAs is a heritable genetic trait in humans'
Geeleher, P,Huang, RS,Gamazon, ER,Golden, A,Seoighe, C (2012) 'The regulatory effect of miRNAs is a heritable genetic trait in humans'. BMC Genomics, 13 [DOI] [Details]
(2011) 'Inhibition of Human BK Polyomavirus Replication by Small Noncoding RNAs'
Tikhanovich, I,Liang, B,Seoighe, C,Folk, WR,Nasheuer, HP (2011) 'Inhibition of Human BK Polyomavirus Replication by Small Noncoding RNAs'. J Virol, 85 :6930-6940 [DOI] [Details]
(2011) 'Investigating the effect of paralogs on microarray gene-set analysis'
Faure, AJ,Seoighe, C,Mulder, NJ (2011) 'Investigating the effect of paralogs on microarray gene-set analysis'. BMC Bioinformatics, 12 [DOI] [Details]
(2011) 'Is there evidence of optimisation for carbon efficiency in plant proteomes?'
Jankovic, B,Seoighe, C,Alqurashi, M,Gehring, C (2011) 'Is there evidence of optimisation for carbon efficiency in plant proteomes?'. Plant Biology, 13 :831-834 [DOI] [Details]
(2011) 'Induced stem cell neoplasia in a cnidarian by ectopic expression of a POU domain transcription factor'
Millane, RC;Kanska, J;Duffy, DJ;Seoighe, C;Cunningham, S;Plickert, G;Frank, U (2011) 'Induced stem cell neoplasia in a cnidarian by ectopic expression of a POU domain transcription factor'. Development , 138 :2429-2439 [DOI] [Details]
(2011) 'Is there evidence of optimisation for carbon efficiency in plant proteomes?'
Jankovic, B;Seoighe, C;Alqurashi, M;Gehring, C (2011) 'Is there evidence of optimisation for carbon efficiency in plant proteomes?'. Plant Biology, 13 :831-834 [DOI] [Details]
(2011) 'Immune and Genetic Correlates of Vaccine Protection Against Mucosal Infection by SIV in Monkeys'
Letvin, NL;Rao, SS;Montefiori, DC;Seaman, MS;Sun, Y;Lim, SY;Yeh, WW;Asmal, M;Gelman, RS;Shen, L;Whitney, JB;Seoighe, C;Lacerda, M;Keating, S;Norris, PJ;Hudgens, MG;Gilbert, PB;Buzby, AP;Mach, LV;Zhang, JR;Balachandran, H;Shaw, GM;Schmidt, SD;Todd, JP;Dodson, A;Mascola, JR;Nabel, GJ (2011) 'Immune and Genetic Correlates of Vaccine Protection Against Mucosal Infection by SIV in Monkeys'. Science Translational Medicine, 3 [DOI] [Details]
(2011) 'Investigating the effect of paralogs on microarray gene-set analysis'
Faure, AJ;Seoighe, C;Mulder, NJ (2011) 'Investigating the effect of paralogs on microarray gene-set analysis'. BMC Bioinformatics, 12 [DOI] [Details]
(2011) 'Inhibition of Human BK Polyomavirus Replication by Small Noncoding RNAs'
Tikhanovich, I;Liang, B;Seoighe, C;Folk, WR;Nasheuer, HP (2011) 'Inhibition of Human BK Polyomavirus Replication by Small Noncoding RNAs'. Virology Journal, 85 :6930-6940 [DOI] [Details]
(2011) 'Evidence for intron length conservation in a set of mammalian genes associated with embryonic development'
Seoighe, C, Korir, P (2011) 'Evidence for intron length conservation in a set of mammalian genes associated with embryonic development'. BMC Bioinformatics, 12(Suppl 9):S16 [Details]
(2010) 'Adaptive changes in HIV-1 subtype C proteins during early infection are driven by changes in HLA-associated immune pressure'
Treurnicht FK, Seoighe C, Martin DP, Wood N, Abrahams MR, Rosa Dde A, Bredell H, Woodman Z, Hide W, Mlisana K, Karim SA, Gray CM, Williamson C. (2010) 'Adaptive changes in HIV-1 subtype C proteins during early infection are driven by changes in HLA-associated immune pressure'. Virology, [Details]
(2010) 'Genome-wide analysis of the structure of the South African Coloured Population in the Western Cape'
de Wit, E,Delport, W,Rugamika, CE,Meintjes, A,Moller, M,van Helden, PD,Seoighe, C,Hoal, EG (2010) 'Genome-wide analysis of the structure of the South African Coloured Population in the Western Cape'. Human Genetics, 128 :145-153 [DOI] [Details]
(2010) 'A flexible R package for nonnegative matrix factorization'
Gaujoux, R;Seoighe, C (2010) 'A flexible R package for nonnegative matrix factorization'. BMC Bioinformatics, 11 [DOI] [Details]
(2010) 'Epitope Discovery with Phylogenetic Hidden Markov Models'
Lacerda, M;Scheffler, K;Seoighe, C (2010) 'Epitope Discovery with Phylogenetic Hidden Markov Models'. Molecular Biology And Evolution, 27 :1212-1220 [DOI] [Details]
(2010) 'Heritability in the Efficiency of Nonsense-Mediated mRNA Decay in Humans'
Seoighe, C;Gehring, C (2010) 'Heritability in the Efficiency of Nonsense-Mediated mRNA Decay in Humans'. Plos One, 5 [DOI] [Details]
(2010) 'A flexible R package for nonnegative matrix factorization'
Gaujoux, R,Seoighe, C (2010) 'A flexible R package for nonnegative matrix factorization'. BMC Bioinformatics, 11 [DOI] [Details]
(2010) 'Epitope Discovery with Phylogenetic Hidden Markov Models'
Lacerda, M,Scheffler, K,Seoighe, C (2010) 'Epitope Discovery with Phylogenetic Hidden Markov Models'. Molecular Biology And Evolution, 27 :1212-1220 [DOI] [Details]
(2010) 'Genome-wide analysis of the structure of the South African Coloured Population in the Western Cape'
de Wit, E;Delport, W;Rugamika, CE;Meintjes, A;Moller, M;van Helden, PD;Seoighe, C;Hoal, EG (2010) 'Genome-wide analysis of the structure of the South African Coloured Population in the Western Cape'. Human Genetics, 128 :145-153 [DOI] [Details]
(2010) 'Heritability in the Efficiency of Nonsense-Mediated mRNA Decay in Humans'
Seoighe, C,Gehring, C (2010) 'Heritability in the Efficiency of Nonsense-Mediated mRNA Decay in Humans'. Plos One, 5 [DOI] [Details]
(2009) 'Quantitating the multiplicity of infection with human immunodeficiency virus type 1 subtype C reveals a non-poisson distribution of transmitted variants'
Abrahams MR, Anderson JA, Giorgi EE, Seoighe C, Mlisana K, Ping LH, Athreya GS, Treurnicht FK, Keele BF, Wood N, Salazar-Gonzalez JF, Bhattacharya T, Chu H, Hoffman I, Galvin S, Mapanje C, Kazembe P, Thebus R, Fiscus S, Hide W, Cohen MS, Karim SA, Haynes BF, Shaw GM, Hahn BH, Korber BT, Swanstrom R, Williamson C; CAPRISA Acute Infection Study Team; Center for HIV-AIDS Vaccine Immunology Consortium. (2009) 'Quantitating the multiplicity of infection with human immunodeficiency virus type 1 subtype C reveals a non-poisson distribution of transmitted variants'. J Virol, [Details]
(2009) 'Association Between the 4 bp Proinsulin Gene Insertion Polymorphism (IVS-69) and Body Composition in Black South African Women'
Berman, P;Collins, M;Baumgarten, I;Seoighe, C;Jennings, CL;Joffe, Y;Lambert, EV;Levitt, NS;Faulenbach, MV;Kahn, SE;Goedecke, JH (2009) 'Association Between the 4 bp Proinsulin Gene Insertion Polymorphism (IVS-69) and Body Composition in Black South African Women'. Obesity, 17 :1298-1300 [DOI] [Details]
(2009) 'HIV Evolution in Early Infection: Selection Pressures, Patterns of Insertion and Deletion, and the Impact of APOBEC'
Wood, N;Bhattacharya, T;Keele, BF;Giorgi, E;Liu, M;Gaschen, B;Daniels, M;Ferrari, G;Haynes, BF;McMichael, A;Shaw, GM;Hahn, BH;Korber, B;Seoighe, C (2009) 'HIV Evolution in Early Infection: Selection Pressures, Patterns of Insertion and Deletion, and the Impact of APOBEC'. Plos Pathogens, 5 [DOI] [Details]
(2009) 'HIV Evolution in Early Infection: Selection Pressures, Patterns of Insertion and Deletion, and the Impact of APOBEC'
Wood, N,Bhattacharya, T,Keele, BF,Giorgi, E,Liu, M,Gaschen, B,Daniels, M,Ferrari, G,Haynes, BF,McMichael, A,Shaw, GM,Hahn, BH,Korber, B,Seoighe, C (2009) 'HIV Evolution in Early Infection: Selection Pressures, Patterns of Insertion and Deletion, and the Impact of APOBEC'. Plos Pathogens, 5 [DOI] [Details]
(2009) 'Evidence of HIV-1 adaptation to host HLA alleles following chimp-to-human transmission'
Ngandu, NK;Seoighe, C;Scheffler, K (2009) 'Evidence of HIV-1 adaptation to host HLA alleles following chimp-to-human transmission'. Virology Journal, 6 [DOI] [Details]
(2009) 'Association Between the 4 bp Proinsulin Gene Insertion Polymorphism (IVS-69) and Body Composition in Black South African Women'
Berman, P,Collins, M,Baumgarten, I,Seoighe, C,Jennings, CL,Joffe, Y,Lambert, EV,Levitt, NS,Faulenbach, MV,Kahn, SE,Goedecke, JH (2009) 'Association Between the 4 bp Proinsulin Gene Insertion Polymorphism (IVS-69) and Body Composition in Black South African Women'. Obesity, 17 :1298-1300 [DOI] [Details]
(2009) 'Evidence of HIV-1 adaptation to host HLA alleles following chimp-to-human transmission'
Ngandu, NK,Seoighe, C,Scheffler, K (2009) 'Evidence of HIV-1 adaptation to host HLA alleles following chimp-to-human transmission'. Virology Journal, 6 [DOI] [Details]
(2009) 'Duplication of the Asymmetric Leaves1/Rough Sheath 2/Phantastica (ARP) gene precedes the explosive radiation of the Ruschioideae'
Illing N, Klak C, Johnson C, Brito D, Negrao N, Baine F, van Kets V, Ramchurn KR, Seoighe C, Roden L. (2009) 'Duplication of the Asymmetric Leaves1/Rough Sheath 2/Phantastica (ARP) gene precedes the explosive radiation of the Ruschioideae'. Dev Genes Evol, [Details]
(2009) 'Human Immunodeficiency Virus-Specific Gamma Interferon Enzyme-Linked Immunospot Assay Responses Targeting Specific Regions of the Proteome during Primary Subtype C Infection Are Poor Predictors of the Course of Viremia and Set Point'
Gray, C.M., Mlotshwa, M., Riou, C., Mathebula, T., de Assis Rosa, D., Mashishi, T., Seoighe, C., Ngandu, N., van Loggerenberg, F., Morris, L., Mlisana, K., Williamson, C., Karim, S.A. (2009) 'Human Immunodeficiency Virus-Specific Gamma Interferon Enzyme-Linked Immunospot Assay Responses Targeting Specific Regions of the Proteome during Primary Subtype C Infection Are Poor Predictors of the Course of Viremia and Set Point'. J Virol, 83 (1):470-478 [Details]
(2008) 'Identification and Characterization of Transmitted and Early Founder Virus Envelopes in Primary HIV-1 Infection'
Keele, B.F., Giorgi, E.E., Salazar-Gonzalez, J.F., Decker, J.M., Pham, K.T., Salazar, M.G., Sun, C., Grayson, T., Wang, S., Li, H., Wei, X., Jiang, C., Kirchherr, J.L., Gao, F., Anderson, J.A., Ping, L., Swanstrom, R., Tomaras, G.D., Blattner, W.A., Goepfert, P.A., Kilby, M., Saag, M.S., Delwart, E.L., Busch, M.P., Cohen, M.S., Montefiori, D.C., Haynes, B.F., Gaschen, B., Athreya, G.S., Lee, H.Y., Wood, N., Seoighe, C., Perelson, A.S., Bhattacharya, T., Korber, B.T., Hahn, B.H., Shaw, G.M. (2008) 'Identification and Characterization of Transmitted and Early Founder Virus Envelopes in Primary HIV-1 Infection'. Proc Natl Acad Sci U S A, 105 (21):7552-7557 [Details]
(2008) 'Models of coding sequence evolution'
Delport, W., Scheffler, K., Seoighe, C. (2008) 'Models of coding sequence evolution'. Brief Bioinform, [Details]
(2008) 'Genome-wide survey of allele-specific splicing in humans'
Nembaware, V,Lupindo, B,Schouest, K,Spillane, C,Scheffler, K,Seoighe, C (2008) 'Genome-wide survey of allele-specific splicing in humans'. BMC Genomics, 9 [DOI] [Details]
(2008) 'Frequent toggling between alternative amino acids is driven by selection in HIV-1'
Delport, W., Scheffler, K., Seoighe, C. (2008) 'Frequent toggling between alternative amino acids is driven by selection in HIV-1'. PLoS Pathog, 4 (12) [Details]
(2008) 'Extensive purifying selection acting on synonymous sites in HIV-1 Group M sequences'
Ngandu NK, Scheffler K, Moore P, Woodman Z, Martin D, Seoighe C. (2008) 'Extensive purifying selection acting on synonymous sites in HIV-1 Group M sequences'. Virol J, 2008 Dec 23;5:160 [Details]
(2008) 'MScanner: a classifier for retrieving Medline citations'
Poulter, G.L., Rubin, D.L., Altman, R.B., Seoighe, C. (2008) 'MScanner: a classifier for retrieving Medline citations'. BMC Bioinformatics, 9 (1) [Details]
(2008) 'Transmission of HIV-1 CTL escape variants provides HLA-mismatched recipients with a survival advantage'
D.R. Chopera, D.R., Woodman, Z., Mlisana, K., Mlotshwa, M., Martin, D.P., Seoighe, C., Treurnicht, F., Assis de Rosa, D., Hide, W., Abdool Karim, S., Gray, C.M., Williamson, C., The CAPRISA 002 study team (2008) 'Transmission of HIV-1 CTL escape variants provides HLA-mismatched recipients with a survival advantage'. PLoS Pathogens p. e1000033, 4 (3) [Details]
(2007) 'Protein kinase C delta is essential for optimal macrophage-mediated phagosomal containment of Listeria monocytogenes'
Schwegmann, A., Guler, R., Cutler, A.J., Arendse, B., Horsnell, W.G., Flemming, A., Kottmann, A.H., Ryan, G., Hide, W., Leitges, M., Seoighe, C., Brombacher, F. (2007) 'Protein kinase C delta is essential for optimal macrophage-mediated phagosomal containment of Listeria monocytogenes'. Proc Natl Acad Sci U S A, 104 (41):16251-16256 [Details]
(2007) 'Comparative evolutionary analysis of the FoxG1 transcription factor from diverse vertebrates identifies conserved recognition sites for microRNA regulation'
Bredenkamp, N., Seoighe, C., Illing, N. (2007) 'Comparative evolutionary analysis of the FoxG1 transcription factor from diverse vertebrates identifies conserved recognition sites for microRNA regulation'. Dev. Genes Evol, [Details]
(2006) 'Robust inference of positive selection from recombining coding sequences'
Scheffler, K., Martin, D.P., Seoighe, C. (2006) 'Robust inference of positive selection from recombining coding sequences'. Bioinformatics, 22 (20):2493-2499 [Details]
(2006) 'Maximum likelihood inference of imprinting and allele-specific expression from EST data'
Seoighe, C., Nembaware, V., Scheffler, K. (2006) 'Maximum likelihood inference of imprinting and allele-specific expression from EST data'. Bioinformatics, 22 (24):3032-3039 [Details]
(2005) 'Allele-specific transcript isoforms in human'
Nembaware, V., Wolfe, K.H., Bettoni, F., Kelso, J., Seoighe, C. (2005) 'Allele-specific transcript isoforms in human'. FEBS Lett, 577 (01-Feb):233-238 [Details]
(2005) 'Low power to detect asymmetric divergence of duplicated genes'
Seoighe, C., Scheffler, K. (2005) 'Low power to detect asymmetric divergence of duplicated genes'. Proceedings of the RECOMB 2005 International Workshop on Comparative Genomics, [Details]
(2005) 'Detecting molecular evidence of positive Darwinian selection'
Scheffler, K., Seoighe, C. (2005) 'Detecting molecular evidence of positive Darwinian selection'. In Information Processing and Living Systems, [Details]
(2005) 'A bayesian model comparison approach to inferring positive selection'
Scheffler, K., Seoighe, C. (2005) 'A bayesian model comparison approach to inferring positive selection'. Molecular Biology & Evolution, 22 (12):2531-2540 [Details]
(2005) 'Gametophytic Selection in Arabidopsis thaliana Supports the Selective Model of Intron'
Seoighe, C., Gehring, C., Hurst, L.D. (2005) 'Gametophytic Selection in Arabidopsis thaliana Supports the Selective Model of Intron'. Length Reduction. PLoS Genet, 1 (2) [Details]
(2004) 'Molecular mimicry of a plant signaling molecule enables pathogen control of plant homeostasis'
Nembaware, V., Said, M., Seoighe, C., Gehring, C.A. (2004) 'Molecular mimicry of a plant signaling molecule enables pathogen control of plant homeostasis'. BMC Evolution Biol, 4 (1) [Details]
(2004) 'Genome duplication led to highly selective expansion of the Arabidopsis thaliana proteome'
Seoighe, C., Gehring, C. (2004) 'Genome duplication led to highly selective expansion of the Arabidopsis thaliana proteome'. Trends in Genetics, 20 (10):461-464 [Details]
(2004) 'FRAGS: estimation of coding sequence substitution rates from fragmentary data'
Swart, E.C., Hide, W.H., Seoighe, C. (2004) 'FRAGS: estimation of coding sequence substitution rates from fragmentary data'. Bioinformatics, 5 (1) [Details]
(2004) 'The incidence of HIV-1 dual infection and its association with increased viral load set point in a cohort of subtype C infected female sex-workers'
Grobler, J., Gray, C.M., Rademeyer,C., Seoighe, C., Ramjee, G., Karim, S.A., Morris, L., Williamson, C. (2004) 'The incidence of HIV-1 dual infection and its association with increased viral load set point in a cohort of subtype C infected female sex-workers'. Journal of Infectious Disease, 190 [Details]
(2003) 'Significantly different patterns of amino acid replacement after gene duplication as compared to after speciation'
Seoighe, C., Johnston, C.R., Shields, D.C. (2003) 'Significantly different patterns of amino acid replacement after gene duplication as compared to after speciation'. Mol Biol Evol, 20 (4):484-490 [Details]
(2003) 'Turning the clock back on ancient genome duplication'
Seoighe, C. (2003) 'Turning the clock back on ancient genome duplication'. Curr Opin Genet Dev, 13 (6):636-643 [Details]
(2002) 'Impact of the presence of paralogues on sequence divergence in a set of mouse-human orthologues'
Nembaware, V., Crum, K., Kelso, J.F., Seoighe, C. (2002) 'Impact of the presence of paralogues on sequence divergence in a set of mouse-human orthologues'. Genome Res, 12 (9):1370-1376 [Details]
(2002) 'Expansin-like molecules: Novel functions derived from common domains'
Ludidi N.N., Heazlewood J.L., Seoighe C., Irving H.R., Gehring C.A. (2002) 'Expansin-like molecules: Novel functions derived from common domains'. Journal of Molecular Evolution, 54 (5):587-594 [Details]
(2001) 'The contribution of exon-skipping events on chromosome 22 to protein coding diversity'
Hide, W.A., Babenko, V.N., van Heusden, P.A., Seoighe, C., Kelso, J.F. (2001) 'The contribution of exon-skipping events on chromosome 22 to protein coding diversity'. Genome Res, 11 (11):1848-1853 [Details]
(2000) 'Prevalence of small inversions in yeast gene order evolution'
Seoighe, C., Federspiel, N., Jones, T., Hansen, N., Bivolarovic, V., Surzycki, R., Tamse, R., Komp, C., Huizar, L., Davis, R.W., Scherer, S., Tait, E., Shaw, D.J., Harris, D., Murphy, L., Oliver, K., Taylor, K., Rajandream, M.A., Barrell, B.G., Wolfe, K.H. (2000) 'Prevalence of small inversions in yeast gene order evolution'. Proc Natl Acad Sci U S A, [Details]
(1999) 'G+C content along and among Saccharomyces cerevisiae chromosomes'
Bradnam, K.R., Seoighe, C., Sharp, P.M., Wolfe, K.H. (1999) 'G+C content along and among Saccharomyces cerevisiae chromosomes'. Mol. Biol. Evol, [Details]
(1999) 'Yeast genome evolution in the post genome era'
Seoighe, C., Wolfe, K.H. (1999) 'Yeast genome evolution in the post genome era'. Curr Opin Microbiol. Review, 2 (5):548-554 [Details]
(1999) 'Updated map of duplicated regions in the yeast genome'
Seoighe, C., Wolfe, K.H. (1999) 'Updated map of duplicated regions in the yeast genome'. Gene, 238 (1):253-261 [Details]
(1998) 'Extent of genomic rearrangement after genome duplication in yeast'
Seoighe, C., Wolfe, K.H. (1998) 'Extent of genomic rearrangement after genome duplication in yeast'. Proc. Natl. Acad. Sci. USA 95, :4447-4452 [Details]
(1998) 'Evolution of gene order and chromosome number in Saccharomyces, Kluyveromyces and related fungi'
Keogh, R.S., Seoighe, C., Wolfe, K.H. (1998) 'Evolution of gene order and chromosome number in Saccharomyces, Kluyveromyces and related fungi'. Yeast, 14 :443-457 [Details]

Conference Publications

  Year Publication
(2011) BMC BIOINFORMATICS
Seoighe, C;Korir, PK (2011) Evidence for intron length conservation in a set of mammalian genes associated with embryonic development BMC BIOINFORMATICS [DOI] [Details]
(2011) Evidence for intron length conservation in a set of mammalian genes associated with embryonic development
Seoighe, C,Korir, PK (2011) BMC BIOINFORMATICS Evidence for intron length conservation in a set of mammalian genes associated with embryonic development [DOI] [Details]

Abstract

  Year Publication
(2016) Genomics of Hydractinia: Characterizing and Determining the Biological Relevance of Highly Repetitive Regions.
Barreira, S,Mcstay, B,Seoighe, C,Baxevanis, AD (2016) Genomics of Hydractinia: Characterizing and Determining the Biological Relevance of Highly Repetitive Regions. Abstract [Details]
(2014) A Tale of Two Hydractinia Genomes: Comparative Genomics of Two Sister Hydrozoan Species.
Schnitzler, CE,Sanders, SM,Plickert, G,Seoighe, C,Buss, L,Wolfsberg, TG,Nicotra, M,Mullikin, JC,Cartwright, P,Frank, U,Baxevanis, AD (2014) A Tale of Two Hydractinia Genomes: Comparative Genomics of Two Sister Hydrozoan Species. Abstract [Details]
(2011) Reduction of Founder Virus in Vaccinated Monkeys After Mucosal SIV Challenge.
Whitney, JB,Rolland, M,Lacerda, M,Hraber, PT,DeCamp, A,Luedemann, C,Rao, SS,Mascola, JR,Korber, B,Nabel, GJ,Gilbert, P,Seoighe, C,Letvin, NL (2011) Reduction of Founder Virus in Vaccinated Monkeys After Mucosal SIV Challenge. Abstract [Details]

Meeting

  Year Publication
(2013) Analysis of the IL-6/STAT3 signalling pathway and DNA methylation patterns in patients with IBD.
Ali, RAR,Hartnett, L,Geeleher, P,Seoighe, C,Golden, A,Egan, L (2013) Analysis of the IL-6/STAT3 signalling pathway and DNA methylation patterns in patients with IBD. Meeting [Details]
(2012) Analysis of the interleukin-6/STAT3 signalling pathway and DNA methylation patterns in patients with short or long duration of IBD.
Ali, RAR,Harnett, L,Newell, J,Golden, A,Geeleher, P,Seoighe, C,Egan, L (2012) Analysis of the interleukin-6/STAT3 signalling pathway and DNA methylation patterns in patients with short or long duration of IBD. Meeting [Details]
(2011) Identification of Amino Acid Residues in HIV-1 Envelope Targeted by Plasma Broadly Neutralizing Antibodies using Evolutionary Models.
Lacerda, M,Moore, PL,Ngandu, N,Gray, ES,Wibmer, K,Nonyane, M,Sheward, D,Korber, BT,Montefiori, DC,Williamson, C,Morris, L,Seoighe, C (2011) Identification of Amino Acid Residues in HIV-1 Envelope Targeted by Plasma Broadly Neutralizing Antibodies using Evolutionary Models. Meeting [Details]
(2011) REDUCTION OF FOUNDER/TRANSMITTED VIRUS IN VACCINATED MONKEYS AFTER MUCOSAL SIVE660 CHALLENGE.
Whitney, JB,Lacerda, M,Luedemann, C,Hraber, P,Rao, SS,Mascola, JR,Nabel, GJ,Korber, B,Seoighe, C,Letvin, NL (2011) REDUCTION OF FOUNDER/TRANSMITTED VIRUS IN VACCINATED MONKEYS AFTER MUCOSAL SIVE660 CHALLENGE. Meeting [Details]