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Staff Profiles

Dr Pilib Ó Broin

B.A.,M.Sc.,PhD

Contact Details


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ADB-1017
Áras de Brún
Scoil na Matamaitice, na Staitisticí & na Matamaitice Feidhmí
Ollscoil na hÉireann Gaillimh
Bóthar na hOllscoile, Gaillimh, Éire

T: +353 91 49 2337
E: pilib.obroin@nuigalway.ie
W: http://maths.nuigalway.ie/biocluster/researchers/pilib/
 
researcher

Biography

Research Interests

  • Statistical machine learning & high-performance computing
  • Functional and biomedical genomics

Peer Reviewed Journals

  Year Publication
(2016) 'Structure and function of neonatal social communication in a genetic mouse model of autism spectrum disorders'
Tomohisa Takahashi, Shota Okabe, Pilib Ó Broin, Akira Nishi, Kenny Ye, Michael Beckert, Takeshi Izumi, Hiroaki Machida, Gina Kang, Jose L. Pena, Aaron Golden, Takefumi Kikusui, Noboru Hiroi (2016) 'Structure and function of neonatal social communication in a genetic mouse model of autism spectrum disorders'. Molecular Psychiatry, [Details]
(2015) 'Integrative Metabolic Signatures for Hepatic Radiation Injury'
Kurland, Irwin Jack* and Ó Broin, Pilib* and Golden, Aaron* and Su, Gang and Meng, Fan and Liu, Laibin and Mohney, Robert and Kulkarni, Shilpa and Guha, Chandan (2015) 'Integrative Metabolic Signatures for Hepatic Radiation Injury'. Plos One, 10 (6) [Details]
(2015) 'Deregulation of the Ras-Erk signaling axis modulates the enhancer landscape'
Nabet, Behnam and Ó Broin, Pilib and Reyes, Jaime M and Shieh, Kevin and Lin, Charles Y and Will, Christine M and Popovic, Relja and Ezponda, Teresa and Bradner, James E and Golden, Aaron A and others (2015) 'Deregulation of the Ras-Erk signaling axis modulates the enhancer landscape'. Cell Reports, 12 (8):1300-1313 [Details]
(2015) 'Intestinal Microbiota-Derived Metabolomic Blood Plasma Markers for Prior Radiation Injury'
Ó Broin, Pilib and Vaitheesvaran, Bhavapriya and Saha, Subhrajit and Hartil, Kirsten and Chen, Emily I and Goldman, Devorah and Fleming, William Harv and Kurland, Irwin J and Guha, Chandan and Golden, Aaron (2015) 'Intestinal Microbiota-Derived Metabolomic Blood Plasma Markers for Prior Radiation Injury'. International Journal Of Radiation Oncology Biology Physics, 91 (2):360-367 [Details]
(2015) 'RNA: DNA hybrids in the human genome have distinctive nucleotide characteristics, chromatin composition, and transcriptional relationships'
Nadel, Julie and Athanasiadou, Rodoniki and Lemetre, Christophe and Wijetunga, Neil Ari and Ó Broin, Pilib and Sato, Hanae and Zhang, Zhengdong and Jeddeloh, Jeffrey and Montagna, Cristina and Golden, Aaron and others (2015) 'RNA: DNA hybrids in the human genome have distinctive nucleotide characteristics, chromatin composition, and transcriptional relationships'. Epigenetics & Chromatin, [Details]
(2016) 'Clinical and molecular significance of microvascular inflammation in transplant kidney biopsies'
Gupta, Anjali and Ó Broin, Pilib and Bao, Yi and Pullman, James and Kamal, Layla and Ajaimy, Maria and Lubetzky, Michelle and Colovai, Adriana and Schwartz, Daniel and de Boccardo, Graciela and others (2016) 'Clinical and molecular significance of microvascular inflammation in transplant kidney biopsies'. Kidney Int, [Details]
(2015) 'Clinical, Histological, and Molecular Markers Associated With Allograft Loss in Transplant Glomerulopathy Patients'
Kamal, Layla and Ó Broin, Pilib and Bao, Yi and Ajaimy, Maria and Lubetzky, Michelle and Gupta, Anjali and de Boccardo, Graciela and Pullman, James and Golden, Aaron and Akalin, Enver (2015) 'Clinical, Histological, and Molecular Markers Associated With Allograft Loss in Transplant Glomerulopathy Patients'. Transplantation, [Details]
(2015) 'Alignment-free clustering of transcription factor binding motifs using a genetic-k-medoids approach'
Ó Broin, Pilib and Smith, Terry J and Golden, Aaron AJ (2015) 'Alignment-free clustering of transcription factor binding motifs using a genetic-k-medoids approach'. BMC Bioinformatics, 16 (1) [Details]
(2014) 'Increased intragraft rejection--associated gene transcripts in patients with donor-specific antibodies and normal biopsies'
Hayde, Nicole and Ó Broin, Pilib and Bao, Yi and de Boccardo, Graciela and Lubetzky, Michelle and Ajaimy, Maria and Pullman, James and Colovai, Adriana and Golden, Aaron and Akalin, Enver (2014) 'Increased intragraft rejection--associated gene transcripts in patients with donor-specific antibodies and normal biopsies'. Kidney Int, [Details]
(2014) 'A pathogenesis-based transcript signature in donor-specific antibody-positive kidney transplant patients with normal biopsies'
O Broin, P and Hayde, N and Bao, Y and Ye, B and Calder, RB and de Boccardo, G and Lubetzky, M and Ajaimy, M and Pullman, J and Colovai, A and others (2014) 'A pathogenesis-based transcript signature in donor-specific antibody-positive kidney transplant patients with normal biopsies'. Genomics Data, 2 :357-360 [Details]
(2014) 'Genomics of BK viremia in kidney transplant recipients'
Lubetzky, Michelle and Bao, Yi and Ó Broin, Pilib and Marfo, Kwaku and Ajaimy, Maria and Aljanabi, Aws and de Boccardo, Graciela and Golden, Aaron and Akalin, Enver (2014) 'Genomics of BK viremia in kidney transplant recipients'. Transplantation, 97 (4):451-456 [Details]
(2014) 'Role of the tumor suppressor IQGAP2 in metabolic homeostasis: possible link between diabetes and cancer'
Vaitheesvaran, B and Hartil, K and Navare, A and Zheng, C and Ó Broin, P and Golden, A and Guha, C and Lee, WN and Kurland, IJ and Bruce, JE (2014) 'Role of the tumor suppressor IQGAP2 in metabolic homeostasis: possible link between diabetes and cancer'. Metabolomics, :1-18 [Details]
(2012) 'The Wasp System: an open source environment for managing and analyzing genomic data'
McLellan, Andrew S and Dubin, Robert A and Jing, Qiang and Ó Broin, Pilib and Moskowitz, David and Suzuki, Masako and Calder, R Brent and Hargitai, Joseph and Golden, Aaron and Greally, John M (2012) 'The Wasp System: an open source environment for managing and analyzing genomic data'. Genomics, 100 (6):345-351 [Details]
(2012) 'The Einstein Genome Gateway using WASP-A High Throughput Multi-Layered Life Sciences Portal for XSEDE'
Golden, A and McLellan, AS and Dubin, RA and Jing, Q and Ó Broin, P and Moskowitz, D and Zhang, Z and Suzuki, M and Hargitai, J and Calder, RB and others (2012) 'The Einstein Genome Gateway using WASP-A High Throughput Multi-Layered Life Sciences Portal for XSEDE'. Stud Health Technol Inform, 175 :182-191 [Details]
(2011) 'Allele-specific transcriptional elongation regulates monoallelic expression of the IGF2BP1 gene'
Thomas, Brandon J and Rubio, Eric D and Krumm, Niklas and Ó Broin, Pilib and Bomsztyk, Karol and Welcsh, Piri and Greally, John M and Golden, Aaron A and Krumm, Anton (2011) 'Allele-specific transcriptional elongation regulates monoallelic expression of the IGF2BP1 gene'. Epigenetics & Chromatin, 4 [Details]
(2010) 'WASP: Wiki-based automated sequence processor for epigenomics and genomics applications'
Dubin, R and Jing, Q and Ó Broin, P and Calder, B and Moskowitz, D and Suzuki, M and Greally, J and McLellan, A (2010) 'WASP: Wiki-based automated sequence processor for epigenomics and genomics applications'. Journal of biomolecular techniques: JBT, 21 (3 Suppl) [Details]
(2009) 'Institutional Profile: The Einstein Center for Epigenomics: studying the role of epigenomic dysregulation in human disease'
McLellan, Andrew S and Dubin, Robert A and Jing, Qiang and Maqbool, Shahina B and Olea, Raul and Westby, Gael and Ó Broin, Pilib and Fazzari, Melissa J and Zheng, Deyou and Suzuki, Masako and others (2009) 'Institutional Profile: The Einstein Center for Epigenomics: studying the role of epigenomic dysregulation in human disease'. Epigenomics, 1 (1):33-38 [Details]
(2009) 'An integrated genome screen identifies the Wnt signaling pathway as a major target of WT1'
Kim, Marianne K-H and McGarry, Thomas J and Ó Broin, Pilib and Flatow, Jared M and Golden, Aaron A-J and Licht, Jonathan D (2009) 'An integrated genome screen identifies the Wnt signaling pathway as a major target of WT1'. Proceedings Of The National Academy Of Sciences Of The United States Of America, 106 (27):11154-11159 [Details]
(2007) 'An evolutionary approach to deception in multi-agent systems'
Ó Broin, Pilib and O'Riordan, Colm (2007) 'An evolutionary approach to deception in multi-agent systems'. Artificial Intelligence Review, 27 (4):257-271 [Details]

Book Chapters

  Year Publication
(2013) 'Chromatin Signature'
Thomas, Brandon J and Rubio, Eric D and Krumm, Niklas and Ó Broin, Pilib and Bomsztyk, Karol and Welcsh, Piri and Greally, John M and Golden, Aaron A and Krumm, Anton (2013) 'Chromatin Signature' In: Epigenetics, environment, and genes. New Jersey: CRC Press. [Details]

Conference Publications

  Year Publication
(2015) ASTRO
D.J. Mark, R. Kabarriti, P. Ó Broin, T.J. Belbin, T. Harris, M.B. Prystowsky, M. Haigentz, R.V. Smith, T.J. Ow, C. Guha, M.K. Garg (2015) Gene Expression Biomarkers for Radiation Toxicity With a Focus on Mucositis in Head and Neck Cancers ASTRO [Details]
(2014) TRANSPLANTATION
Gupta, A and Ó Broin, P and Bao, Y and Golden, A and Akalin, E (2014) Clinical and Molecular Significance of Microcirculation Inflammation in Transplant Kidney Biopsies TRANSPLANTATION , pp.139-139 [Details]
(2014) Proceedings of the 2014 Annual Conference on Extreme Science and Engineering Discovery Environment
Shieh, Kevin and Ó Broin, Pilib and Rhee, David and Levy, Matthew and Golden, Aaron (2014) Using SAGA and the Open Science Grid to Search for Aptamers Proceedings of the 2014 Annual Conference on Extreme Science and Engineering Discovery Environment [Details]
(2014) HEPATOLOGY
Sharma, Yogeshwar and Tchaikovskaya, Tatyana and Viswanathan, Preeti and Rhee, David B and Ó Broin, Pilib and Gorbacheva, Tatyana and Maslov, Alexander Y and Golden, Aaron and Gupta, Sanjeev (2014) Characterization of Exosomal microRNA (miRNA) Content Following Hepatic Injury And Roles in Cytoprotection After Uptake of Exosomes By Injured Hepatocytes HEPATOLOGY , pp.825-826 [Details]
(2014) TRANSPLANTATION
Kamal, L and Ó Broin, P and Bao, Y and Golden, A and Akalin, E (2014) Increased Intragraft Endothelial Cell and Interferon-gamma Associated Transcripts and Banff Chronic Allograft Glomerulopathy (cg) Score Predict the Graft Loss in Transplant Glomerulopathy TRANSPLANTATION , pp.468-469 [Details]
(2013) Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to Discovery
Rhee, David and Hargitai, Joseph and Calder, R Brent and Ó Broin, Pilib and Shieh, Kevin and Golden, Aaron (2013) 'Spring through the gateway': deploying genomic workflows with XSEDE Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to Discovery [Details]

Conference Contributions

  Year Publication
(2015) American Association of Cancer Research Annual Meeting (AACR 2015),
Behnam Nabet, Pilib Ó Broin, Jaime M. Reyes, Kevin Shieh, Charles Y. Lin, Christine M. Will, Relja Popovic, Teresa Ezponda, James E. Bradner, Aaron A. Golden, and Jonathan D. Licht. (2015) Deregulation of the Ras-Erk signaling axis modulates the enhancer landscape. [Poster Presentation (Refereed)], American Association of Cancer Research Annual Meeting (AACR 2015), Philadelphia , 01-JAN-15 - 01-JAN-15. [Details]
(2014) 5th Annual Symposium in Computational Biology & Innovation,
Pilib Ó Broin, Tomohisa Takahashi, Shota Okabe, Akira Nishi, Takeshi Izumi, Michael Beckert, Gina Kang, Jose L. Pena, Kenji Tanigaki, Takefumi Kikusui, Noboru Hiroi, and Aaron Golden (2014) Analysis of Ultrasonic Mouse Vocalizations in a 22q11.2DS-associated Mouse Model of Autism Spectrum Disorder. [Poster Presentation (Refereed)], 5th Annual Symposium in Computational Biology & Innovation, Dublin , 01-JAN-14 - 01-JAN-14. [Details]
(2014) 2014 Annual Conference on Extreme Science and Engineering Discovery Environment (XSEDE2014),
David B. Rhee, Kevin Shieh, Pilib Ó Broin, Raquel G. Gur, Aaron Golden (2014) The International Brain and Behavior Consortium Genomics Gateway. [Poster Presentation (Refereed)], 2014 Annual Conference on Extreme Science and Engineering Discovery Environment (XSEDE2014), New York , 01-JAN-14 - 01-JAN-14. [Details]
(2013) 40th Annual Meeting of the European Radiation Research Society (ERR2013),
Pilib Ó Broin, Irwin J. Kurland, Aaron Golden, and Chandan Guha (2013) Metabolic Biomarkers for Radiation-Induced Liver Damage in Mice. [Poster Presentation (Refereed)], 40th Annual Meeting of the European Radiation Research Society (ERR2013), Dublin , 01-JAN-13 - 01-JAN-13. [Details]
(2012) 4th International Workshop on Science Gateways for Life Sciences (IWSG-Life 2012),
Aaron Golden, Andrew S. McLellan, Robert A. Dubin, Qiang Jing, Pilib Ó Broin, David Moskowitz, Zhengdong Zhang, Masako Suzuki, Joseph Hargitai, R. Brent Calder, and John M. Greally (2012) The Einstein Science Gateway using WASP: A High Throughput Multi-Layered Life Sciences Portal for XSEDE. [Poster Presentation (Refereed)], 4th International Workshop on Science Gateways for Life Sciences (IWSG-Life 2012), Amsterdam , 01-JAN-12 - 01-JAN-12. [Details]
(2012) 8th Annual International Meeting of the Metabolomics Society (Metabolomics 2012),
Irwin J. Kurland, Pilib Ó Broin, Aaron Golden, Bhavapriya Vaitheesvaran, Kirsten Hartil, Subhrajit Saha, and Chandan Guha (2012) Integrative Metabolic Signatures for Radiation Induced Damage. [Poster Presentation (Refereed)], 8th Annual International Meeting of the Metabolomics Society (Metabolomics 2012), Washington D.C , 01-JAN-12 - 01-JAN-12. [Details]
(2012) American Association for Cancer Research Annual Meeting (AACR 2012),
Leleesha Samaraweera, Pilib Ó Broin, Lingling Liu, Masako Suzuki, Susan Band Horwitz, and Hayley M. McDaid (2012) Senescence Reversion Contributes to Acquired Drug Resistance. [Poster Presentation (Refereed)], American Association for Cancer Research Annual Meeting (AACR 2012), Chicago , 01-JAN-12 - 01-JAN-12. [Details]
(2012) RegGenSIG, Intelligent Systems in Molecular Biology (ISMB 2012),
Pilib Ó Broin, Terry Smith, and Aaron Golden (2012) A Non-Tree Based Approach to Automated Construction of Familial Binding Profiles. [Poster Presentation (Refereed)], RegGenSIG, Intelligent Systems in Molecular Biology (ISMB 2012), Long Beach, CA , 01-JAN-12 - 01-JAN-12. [Details]
(2008) Virtual Insititute of Bioinformatics Éire (VIBE 2008),
Pilib Ó Broin, Terry Smith, and Aaron Golden (2008) Generating Familial Binding Profiles by Genetic Algorithm. [Poster Presentation (Refereed)], Virtual Insititute of Bioinformatics Éire (VIBE 2008), Maynooth , 01-JAN-08 - 01-JAN-08. [Details]
(2008) RECOMB Regulatory Genomics (RECOMB 2008),
Pilib Ó Broin, Terry Smith, and Aaron Golden (2008) An Evolutionary Approach to Multiple Alignment of Transcription Factor Binding Motifs. [Poster Presentation (Refereed)], RECOMB Regulatory Genomics (RECOMB 2008), Boston , 01-JAN-08 - 01-JAN-08. [Details]
(2007) Intelligent Systems in Molecular Biology/European Conference on Computational Biology (ISMB/ECCB 2007),
Aaron Golden, Pilib Ó Broin, Shaun Mahony, Anton Krumm, and John Greally (2007) Optimum Transcription Factor Binding Site Model Selection from a Self­-Organising Map ChIP-­chip Case Study. [Poster Presentation (Refereed)], Intelligent Systems in Molecular Biology/European Conference on Computational Biology (ISMB/ECCB 2007), Vienna , 01-JAN-07 - 01-JAN-07. [Details]
(2007) 18th Irish Conference on Artificial Intelligence and Cognitive Science (AICS 2007),
Pilib Ó Broin and Colm O'Riordan (2007) Evolving a hybrid deceptive strategy for the repeated English auction. [Conference Paper], 18th Irish Conference on Artificial Intelligence and Cognitive Science (AICS 2007), Dublin , 01-JAN-07 - 01-JAN-07. [Details]
(2006) 17th Irish Conference on Artificial Intelligence and Cognitive Science (AICS 2006),
Pilib Ó Broin and Colm O'Riordan (2006) Deception in multi­agent auctions: an evolutionary approach. [Conference Paper], 17th Irish Conference on Artificial Intelligence and Cognitive Science (AICS 2006), Belfast , 01-JAN-06 - 01-JAN-06. [Details]