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Mathematical and Statistical Sciences

Dr Pilib Ó Broin

B.A.,M.Sc.,PhD

Contact Details

Lecturer
SCHOOL OF MATHEMATICS, STATISTIC
& APPLIED MATHEMATICS
NUI GALWAY
E: PILIB.OBROIN@nuigalway.ie
 
researcher
 

Biography

2004-2006: Graduate researcher, Computational Intelligence Research Group (CIRG), NUIG
2006-2009: Doctoral researcher, National Centre for Biomedical Engineering Science (NCBES), NUIG
2009-2015: Bioinformatician, Department of Genetics (Div. of Computational Genetics), Albert Einstein College of Medicine, New York
 2015-to date: Lecturer (Bioinformatics/Biomedical Genomics), School of Mathematical & Statistical Sciences, NUIG

Research Interests

I am a PI in the Bioinformatics and Biostatistics Research Cluster where my group is primarily interested in the development and application of statistical/machine learning methods with a particular focus on genomics applications in immunology, cancer and neuroscience. My research has been funded by SFI, HRB, IRC, and the European Commission.


Research Projects

  Project Start Date End Date
Ulysses 2019 - Elucidating the functional consequences of differing cell type subpopulations in hematopoietic stem and progenitor cells stem and progenitor cells 01-MAY-20 30-APR-21
EC (ERASMUS+) - HPC-based Computational BioMedicine 01-JAN-20 01-DEC-20
SFI (Opportunistic Fund) - HPC Cluster for Bioinformatics and Data Science 01-JAN-18 01-DEC-18
HRB (NCI Summer Curriculum) - Molecular prevention of Cancer 01-JAN-17 01-DEC-17
GEMINI - PILIP O' BROIN STUDENT ACCOUNT - INTAKE 1 - SFI FUNDS 01-JAN-20 31-AUG-28
GENERAL RESEARCH ACCOUNT PILIB Ó BROIN 01-JUL-16 30-JUN-26
GALWAY GENOMICS GENERAL RESEARCH ACCOUNT 01-JUL-16 30-JUN-26

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]

Peer Reviewed Journals

  Year Publication
(2022) 'Loss of MMR and TGFBR2 increases the susceptibility to microbiota-dependent inflammation-associated colon cancer'
Tosti, Elena and Almeida, Ana S and Tran, Tam TT and e Silva, Mariel Barbachan and Broin, Pilib \'O and Dubin, Robert and Chen, Ken and Beck, Amanda P and Mclellan, Andrew S and Vilar-Sanchez, Eduardo and others (2022) 'Loss of MMR and TGFBR2 increases the susceptibility to microbiota-dependent inflammation-associated colon cancer'. Cellular and Molecular Gastroenterology and Hepatology, [Details]
(2022) 'Comparing the XGBoost machine learning algorithm to polygenic scoring for the prediction of intelligence based on genotype data'
Fahey, Laura and Morris, Derek W and Broin, Pilib O (2022) 'Comparing the XGBoost machine learning algorithm to polygenic scoring for the prediction of intelligence based on genotype data'. bioRxiv, [Details]
(2022) 'Thirteen independent genetic loci associated with preserved processing speed in a study of cognitive resilience in 330,097 individuals in the UK Biobank'
Fitzgerald, Joan and Fahey, Laura and Holleran, Laurena and \'O Broin, Pilib and Donohoe, Gary and Morris, Derek W (2022) 'Thirteen independent genetic loci associated with preserved processing speed in a study of cognitive resilience in 330,097 individuals in the UK Biobank'. Genes, 13 (1) [Details]
(2022) 'Single-cell characterisation of the hematopoietic bone marrow interactome in health and disease'
Ennis, Sarah and Conforte, Alessandra and Cichocka, Tatiana and Dhami, Sukhraj Pal and Nicholson, Pamela and Krebs, Philippe and Broin, Pilib O and Szegezdi, Eva (2022) 'Single-cell characterisation of the hematopoietic bone marrow interactome in health and disease'. bioRxiv, [Details]
(2022) 'Potential biomarkers of Acute Ischemic Stroke etiology revealed by mass spectrometry-based proteomic characterization of formalin-fixed paraffin-embedded blood clots'
Rossi, Rosanna and Mereuta, Oana Madalina and Silva, Mariel Barbachan E and Gil, Sara Molina and Douglas, Andrew and Pandit, Abhay and Gilvarry, Michael and McCarthy, Ray and O'connell, Shane and Tierney, Ciara and others (2022) 'Potential biomarkers of Acute Ischemic Stroke etiology revealed by mass spectrometry-based proteomic characterization of formalin-fixed paraffin-embedded blood clots'. Frontiers in neurology, 13 [Details]
(2021) 'DOME: recommendations for supervised machine learning validation in biology'
Walsh, Ian and Fishman, Dmytro and Garcia-Gasulla, Dario and Titma, Tiina and Pollastri, Gianluca and Harrow, Jennifer and Psomopoulos, Fotis E and Tosatto, Silvio CE (2021) 'DOME: recommendations for supervised machine learning validation in biology'. Nature methods, 18 (10):1122-1127 [Details]
(2021) 'Computational identification of variables in neonatal vocalizations predictive for postpubertal social behaviors in a mouse model of 16p11. 2 deletion'
Nakamura, Mitsuteru and Ye, Kenny and Yamauchi, Takahira and Hoeppner, Daniel J and Fayyazuddin, Amir and Kang, Gina and Yuda, Emi A and Nagashima, Masako and Enomoto, Shingo and Hiramoto, Takeshi and others (2021) 'Computational identification of variables in neonatal vocalizations predictive for postpubertal social behaviors in a mouse model of 16p11. 2 deletion'. Molecular psychiatry, 26 (11):6578-6588 [Details]
(2021) 'Deep Learning of Histopathological Features for the Prediction of Tumour Molecular Genetics'
Murchan, Pierre and \'O’Brien, Cathal and O’Connell, Shane and McNevin, Ciara S and Baird, Anne-Marie and Sheils, Orla and \'O Broin, Pilib and Finn, Stephen P (2021) 'Deep Learning of Histopathological Features for the Prediction of Tumour Molecular Genetics'. Diagnostics, 11 (8) [Details]
(2021) 'Genes influenced by MEF2C contribute to neurodevelopmental disease via gene expression changes that affect multiple types of cortical excitatory neurons'
Cosgrove, Donna and Whitton, Laura and Fahey, Laura and \'O Broin, Pilib and Donohoe, Gary and Morris, Derek W (2021) 'Genes influenced by MEF2C contribute to neurodevelopmental disease via gene expression changes that affect multiple types of cortical excitatory neurons'. Human Molecular Genetics, 30 (11):961-970 [Details]
(2021) 'Transcriptional regulation of neonatal neural stem cells is a determinant of social behavior'
Hiramoto, Takeshi and Boku, Shuken and Kang, Gina and Abe, Seiji and e Silva, Mariel Barbachan and Tanigaki, Kenji and Nagashima, Masako and Ye, Kenny and Yamauchi, Takahira and Michurina, Tatyana V and others (2021) 'Transcriptional regulation of neonatal neural stem cells is a determinant of social behavior'. bioRxiv, [Details]
(2021) 'Magnetic Resonance Imaging-based Deep Learning Predictive Models of Brain Disorders: A Systematic Review of Modelling Practices, Transparency, and Interpretability'
O'Connell, Shane and Cannon, Dara M and Broin, Pilib O (2021) 'Magnetic Resonance Imaging-based Deep Learning Predictive Models of Brain Disorders: A Systematic Review of Modelling Practices, Transparency, and Interpretability'. medRxiv, [Details]
(2020) 'Genes regulated byBCL11Bduring T-cell development are enriched for de novo mutations found in schizophrenia patients'
Fahey, L,Donohoe, G,Ó Broin, P,Morris, DW (2020) 'Genes regulated byBCL11Bduring T-cell development are enriched for de novo mutations found in schizophrenia patients'. American Journal Of Medical Genetics Part B-Neuropsychiatric Genetics, [DOI] [ARAN Link] [Details]
(2020) 'Genes regulated by BCL11B during T-cell development are enriched for de novo mutations found in schizophrenia patients'
Fahey, Laura and Donohoe, Gary and Broin, Pilib \'O and Morris, Derek W (2020) 'Genes regulated by BCL11B during T-cell development are enriched for de novo mutations found in schizophrenia patients'. American Journal of Medical Genetics Part B: Neuropsychiatric Genetics, 183 (6):370-379 [Details]
(2016) 'Clinical and molecular significance of microvascular inflammation in transplant kidney biopsies'
Gupta, Anjali and Broin, Pilib \'O 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 international, 89 (1):217-225 [Details]
(2016) 'Structure and function of neonatal social communication in a genetic mouse model of autism'
Takahashi T;Okabe S;Broin PÓ;Nishi A;Ye K;Beckert MV;Izumi T;Machida A;Kang G;Abe S;Pena JL;Golden A;Kikusui T;Hiroi N; (2016) 'Structure and function of neonatal social communication in a genetic mouse model of autism'. Molecular Psychiatry, 21 (9):1208-1214 [DOI] [Details]
(2015) 'Alignment-free clustering of transcription factor binding motifs using a genetic-k-medoids approach'
Broin, Pilib \'O 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]
(2015) 'Clinical, histological, and molecular markers associated with allograft loss in transplant glomerulopathy patients'
Kamal, Layla and Broin, Pilib \'O 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, 99 (9):1912-1918 [Details]
(2014) 'A pathogenesis-based transcript signature in donor-specific antibody-positive kidney transplant patients with normal biopsies'
Ó 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]
(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 Broin, Pilib \'O 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 O 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 Broin, Pilib \'O 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 O’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) 'An integrated genome screen identifies the Wnt signaling pathway as a major target of WT1'
Kim, Marianne K-H and McGarry, Thomas J and Broin, Pilib \'O 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, 106 (27):11154-11159 [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 Broin, Pilib \'O 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]
(2007) 'An evolutionary approach to deception in multi-agent systems'
Broin, Pilib \'O and O’Riordan, Colm (2007) 'An evolutionary approach to deception in multi-agent systems'. Artificial Intelligence Review, 27 (4):257-271 [Details]
(2020) 'Genes influenced by MEF2C contribute to neurodevelopmental disease via gene expression changes that affect multiple types of cortical excitatory neurons'
Cosgrove D;Whitton L;Fahey L;Ó Broin P;Donohoe G;Morris DW; (2020) 'Genes influenced by MEF2C contribute to neurodevelopmental disease via gene expression changes that affect multiple types of cortical excitatory neurons'. Human Molecular Genetics, [DOI] [ARAN Link] [Details]
(2019) 'Molecular signatures and clinical outcomes of transplant glomerulopathy stratified by microvascular inflammation and donor-specific antibody'
Lubetzky, Michelle and Hayde, Nicole and Ó Broin, Pilib and Ajaimy, Maria and Bao, Yi and Mohammed, Omar and Schwartz, Daniel and Pullman, James and Akalin, Enver (2019) 'Molecular signatures and clinical outcomes of transplant glomerulopathy stratified by microvascular inflammation and donor-specific antibody'. Clinical Transplantation, 33 (3) [Details]
(2019) 'Optimal targeting of BCL-family proteins in head and neck squamous cell carcinoma requires inhibition of both BCL-xL and MCL-1'
Ow, Thomas J and Fulcher, Cory D and Thomas, Carlos and Ó Broin, Pilib and L\'opez, Andrea and Reyna, Denis E and Smith, Richard V and Sarta, Catherine and Prystowsky, Michael B and Schlecht, Nicolas F and others (2019) 'Optimal targeting of BCL-family proteins in head and neck squamous cell carcinoma requires inhibition of both BCL-xL and MCL-1'. Oncotarget, 10 (4) [Details]
(2018) 'Computational analysis of neonatal mouse ultrasonic vocalization'
\'O Broin, Pilib and Beckert, Michael V and Takahashi, Tomohisa and Izumi, Takeshi and Ye, Kenny and Kang, Gina and Pouso, Patricia and Topolski, Mackenzie and Pena, Jose L and Hiroi, Noboru (2018) 'Computational analysis of neonatal mouse ultrasonic vocalization'. Current protocols in mouse biology, 8 (2) [Details]
(2017) 'Resveratrol Improves Vascular Function and Mitochondrial Number but Not Glucose Metabolism in Older Adults'
Pollack, Rena M and Barzilai, Nir and Anghel, Valentin and Kulkarni, Ameya S and Golden, Aaron and Ó Broin, Pilib and Sinclair, David A and Bonkowski, Michael S and Coleville, Alexander J and Powell, Danielle and others (2017) 'Resveratrol Improves Vascular Function and Mitochondrial Number but Not Glucose Metabolism in Older Adults'. The journals of gerontology. Series A, Biological sciences and medical sciences, [Details]
(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]
(2016) 'LPA receptor activity is basal specific and coincident with early pregnancy and involution during mammary gland postnatal development'
Acosta, Deanna and Bagchi, Susmita and Ó Broin, Pilib and Hollern, Daniel and Racedo, Silvia E and Morrow, Bernice and Sellers, Rani S and Greally, John M and Golden, Aaron and Andrechek, Eran and others (2016) 'LPA receptor activity is basal specific and coincident with early pregnancy and involution during mammary gland postnatal development'. Scientific Reports, 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) '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):22-34 [DOI] [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, 99 (9):1912-1918 [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]
(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]
(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, 10 (5):920-937 [DOI] [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 International, 86 (3):600-609 [DOI] [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]

Conference Publications

  Year Publication
(2021) 2021 IEEE Congress on Evolutionary Computation (CEC)
e Silva, Mariel Barbachan and Narloch, Pedro Henrique and Dorn, Marcio and Broin, Pilib \'O (2021) Optimisation of Cancer Status Prediction Pipelines using Bio-Inspired Computing 2021 IEEE Congress on Evolutionary Computation (CEC) , pp.442-449 [Details]
(2017) AMERICAN JOURNAL OF TRANSPLANTATION
Ajaimy, M and O Broin, P and Bao, Y and Akalin, E (2017) Molecular Significance of Peritubular Capillaritis in Early Transplant Kidney Biopsies of Donor-Specific Antibody Negative Patients AMERICAN JOURNAL OF TRANSPLANTATION , pp.532-532 [Details]
(2017) AMERICAN JOURNAL OF TRANSPLANTATION
Lubetzky, M and Hayde, N and O Broin, P and Bao, Y and Akalin, E (2017) Clinical and Molecular Significance of Microvascular Inflammation Negative Transplant Glomerulopathy AMERICAN JOURNAL OF TRANSPLANTATION , pp.532-532 [Details]
(2017) AMERICAN JOURNAL OF TRANSPLANTATION
Kamal, L and O Broin, P and Lubetzky, M and Bao, Y and Akalin, E (2017) A Molecular Approach to Chronic Rejection: Antibody or T-Cell Mediated? AMERICAN JOURNAL OF TRANSPLANTATION , pp.345-345 [Details]
(2015) 2015 American Transplant Congress
Ajaimy M, Ó Broin P, Bao Y, Lindower J, Golden A, Akalin E (2015) Differential Intragraft Gene Expression Profiles in Patients With Sterile Leukocyturia 2015 American Transplant Congress [Details]
(2015) 2015 American Transplant Congress
Akten, S and Ajaimy, M and Ó Broin, P and Bao, Y and Golden, A and Akalin, E (2015) Increased Cytotoxic and Regulatory T Cell and B Cell Associated Gene Transcripts in Transplant Kidney Biopsies With Non-Specific IFTA and Interstitial Inflammation 2015 American Transplant Congress Philadelpha, PA, , 02-MAY-15 - 06-MAY-15 [Details]
(2014) The World Transplant Congress 2014
Ajaimy, M and Ó Broin, P and Bao, Y and Golden, A and Akalin, E (2014) Effects of Prolonged Cold Ischemia On Intragraft Gene Expression Profiles The World Transplant Congress 2014 San Francisco, CA, , 27-JUL-14 - 31-JUL-14 [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 Broin, Pilib \'O and Shieh, Kevin and Golden, Aaron (2013) 'Spring through the gateway': deploying genomic workflows with XSEDE . In: Nancy Wilkins-Diehr eds. Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to Discovery San Diego, CA, , 22-JUL-13 - 25-JUL-13 , pp.30 (1)-30 (4) [Details]
(2020) 2020 IEEE Congress on Evolutionary Computation (CEC)
M. B. e. Silva and P. Ó Broin (2020) An optimised ensemble for antibody-mediated rejection status prediction in kidney transplant patients 2020 IEEE Congress on Evolutionary Computation (CEC) , pp.1-8 [Details]
(2020) NEUROPSYCHOPHARMACOLOGY
Nakamura, Mitsuteru and Ye, Kenny and Barbachan e Silva, Mariel and Yamauchi, Takahira and Hoeppner, Daniel and Fayyazuddin, Amir and Kang, Gina and Nagashima, Masako and Enomoto, Shingo and Hiramoto, Takeshi and others (2020) A Computationally-Identifiable Dimensional Structure in Neonatal Social Communication Predicts Post-Pubertal Social Behaviors in a Mouse Model of 16p11. 2 Deletion NEUROPSYCHOPHARMACOLOGY , pp.214-214 [Details]
(2019) AMERICAN JOURNAL OF TRANSPLANTATION
Liriano-Ward, LF and Barbachan e Silva, M and Azzi, Y and Ajaimy, A and Cambell, A and Graham, J and Rocca, J and Pynadath, C and Nair, G and Andacoglu, O and others (2019) Infectious Complications in Kidney Transplant Recipients Age 65 and Older AMERICAN JOURNAL OF TRANSPLANTATION , pp.731-731 [Details]
(2018) AMERICAN JOURNAL OF TRANSPLANTATION
Akalin, E and Bao, Y and Bontha, V and Silva, ME and Ajaimy, M and Broin, PO and Mas, V (2018) Molecular Assessment of Pre-Implantation Donor Biopsies: Effects of Prolonged Cold Ischemia Time and Development of Delayed Graft Function AMERICAN JOURNAL OF TRANSPLANTATION , pp.403-404 [Details]
(2017) HUMAN HEREDITY
Fahey, Laura and Morris, Derek and Broin, Pilib O (2017) The Contribution of BCL11B Related Biology to Schizophrenia and Cognition HUMAN HEREDITY , pp.231-231 [Details]
(2016) AMERICAN JOURNAL OF TRANSPLANTATION
Lubetzky, M and Broin, PO and Bao, Y and Akalin, E (2016) Molecular Significance of Microvascular Inflammation and C4d Negative Transplant Glomerulopathy AMERICAN JOURNAL OF TRANSPLANTATION , pp.224-225 [Details]
(2015) AMERICAN JOURNAL OF TRANSPLANTATION
Ajaimy, M and Broin, PO and Bao, Y and Lindower, J and Golden, A and Akalin, E (2015) Differential Intragraft Gene Expression Profiles in Patients With Sterile Leukocyturia AMERICAN JOURNAL OF TRANSPLANTATION [Details]
(2015) AMERICAN JOURNAL OF TRANSPLANTATION
Akten, S and Ajaimy, M and Broin, PO and Bao, Y and Golden, A and Akalin, E (2015) Increased Cytotoxic and Regulatory T Cell and B Cell Associated Gene Transcripts in Transplant Kidney Biopsies With Non-Specific IFTA and Interstitial Inflammation AMERICAN JOURNAL OF TRANSPLANTATION [Details]
(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) 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 . In: Lathrop, S. and Alameda, J eds. Proceedings of the 2014 Annual Conference on Extreme Science and Engineering Discovery Environment Atlanta, GA, , 13-JUL-14 - 18-JUL-14 , pp.27(1)-27(4) [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]

Conference Contributions

  Year Publication
(2015) The 66th Annual Meeting of the American Association for the Study of Liver Diseases,
Sharma, Yogeshwar and Tchaikovskaya, Tatyana and Viswana-than, Preeti and Rhee, David and Broin, Pilib and Gorbacheva, Tatyana and Maslov, Alexander and Golden, Aaron and Gupta, Sanjeev (2015) Characterization of Exosomal microRNA (miRNA) Content Following Hepatic Injury And Roles in Cytoprotection After Uptake of Exosomes By Injured Hepatocytes. [Poster Presentation], The 66th Annual Meeting of the American Association for the Study of Liver Diseases, Boston , 13-NOV-15 - 17-NOV-15. [Details]
(2015) 2015 American Transplant Congress,
Ajaimy M, Ó Broin P, Bao Y, Lindower J, Golden A, Akalin E (2015) Differential Intragraft Gene Expression Profiles in Patients With Sterile Leukocyturia. [Refereed Abstracts], 2015 American Transplant Congress, Philadelpha, PA , 02-MAY-15 - 06-MAY-15. [Details]
(2015) The 66th Annual Meeting of the American Association for the Study of Liver Diseases,
Sharma, Yogeshwar and Tchaikovskaya, Tatyana and Viswanathan, Preeti and Rogler, Charles and Rhee, David and Broin, Pilib and Quispe, Wilber and Maslov, Alexander and Golden, Aaron and Gupta, Sanjeev (2015) Therapeutic Potential in Toxic Liver Injury of Exosomes Isolated from Healthy or Diseased Donors Depends on their Content with Capacity to Beneficially Regulate Cellular Gene Expression: 515. [Poster Presentation], The 66th Annual Meeting of the American Association for the Study of Liver Diseases, Boston , 13-NOV-15 - 17-NOV-15. [Details]
(2015) 2015 American Transplant Congress,
Kamal, L and Ó Broin, P and Bao, Y and Golden, A and Akalin, E (2015) Molecular Features of Isolated Arteriolar Hyalinosis in Renal Transplant Biopsies. [Refereed Abstracts], 2015 American Transplant Congress, Philadelpha, PA , 02-MAY-15 - 06-MAY-15. [Details]
(2015) 2015 American Transplant Congress,
Ajaimy, M and Ó Broin, P and Lubetzky, M and Bao, Y and Golden, A and Akalin, E (2015) Molecular Features of Kidney Transplant Biopsies Without Allograft Injury in Relation With Type of Induction Therapy. [Published Abstract], 2015 American Transplant Congress, Philadelpha, PA , 02-MAY-15 - 06-MAY-15. [Details]
(2014) The World Transplant Congress 2014,
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. [Refereed Abstracts], The World Transplant Congress 2014, San Francisco, CA , 27-JUL-14 - 31-JUL-14. [Details]
(2007) Intelligent Systems in Molecular Biology/European Conference on Computational Biology (ISMB/ECCB 2007),
Golden, A and Ó Broin, P and Mahony, S and Krumm, A and Greally, J (2007) Optimum Transcription Factor Binding Site Model Selection from a Self-Organising Map ChIP-chip Case Study. [Poster Presentation], Intelligent Systems in Molecular Biology/European Conference on Computational Biology (ISMB/ECCB 2007), Vienna, Austria , 21-JUL-07 - 25-JUL-07. [Details]
(2008) Virtual Insititute of Bioinformatics Éire (VIBE 2008),
Ó Broin, P and Smith, TJ, and Golden, Aaron (2008) Generating Familial Binding Profiles by Genetic Algorithm. [Poster Presentation], Virtual Insititute of Bioinformatics Éire (VIBE 2008), Maynooth , 12-SEP-08 - 12-SEP-08. [Details]
(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]
(2015) Virtual Institute of Bioinformatics, Éire (VIBE),
Pilib Ó Broin, Noboru Hiroi, Aaron Golden (2015) ChIPSOM: Improved de novo motif discovery using a self- organizing map - a Tbx1 case study. [Oral Presentation], Virtual Institute of Bioinformatics, Éire (VIBE), Dublin , 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]

Professional Associations

  Association Function From / To
Irish Society of Human Genetics (ISHG) Member /
Marie Curie Alumni Association Member /
European Society of Human Genetics (ESHG) Member /
European Association for Cancer Research (EACR) Member /
International Society for Computational Biology (ISCB) Member /
The Virtual Institute of Bioinformatics & Evolution (VIBE) Member /

Patents

  Patent Number Title Granted
US Patent 11,092,591 Host and intestinal microbiota derived metabolomic blood plasma signature for prior radiation injury

Committees

  Committee Function From / To
Coiste Straitéiseach na Gaeilge Ball 20-OCT-21 /
Student Discipline Appeals Board Member 01-SEP-21 /
Academic Council Member 01-SEP-21 /
School of Mathematical & Statistical Sciences Athena SWAN Bronze Award SAT Member 01-SEP-19 / 01-SEP-21
MSc Chemoinformatics and Toxicology Programme Board Member 01-SEP-18 /
MSc Computational Genomics/Genomics Data Science Programme Board Chair 01-SEP-17 /
MSc Clinical Neuroscience Programme Board Member 01-SEP-16 /
MSc Biomedical Genomics Programme Board Chair 01-SEP-16 /
School of Mathematical & Statistical Sciences Research and Graduate Studies Committee Member 01-SEP-16 /
School of Mathematical & Statistical Sciences Learning, Teaching & Assessmnet Committee Member 01-SEP-15 / 01-SEP-16

Education

  Year Institution Qualification Subject
2014 NUIG PhD Bioinformatics
2003 NUIG BA Arts (Irish & Information Technology)
2006 NUIG MSc Computer Science (Software Design & Development)
2018 NUIG PgCert Teaching & Learning in Higher Education

Reviews

  Journal Role
BMC Bioinformatics Reviewer
Plos One Reviewer
Journal Of Psychiatric Research Reviewer
Lung Cancer Reviewer
Evolutionary Bioinformatics Reviewer
BMC Systems Biology Reviewer
Bioinformatics Reviewer
Briefings In Bioinformatics Reviewer

Teaching Interests

Medical genomics, genomics data analysis, bioinformatics

Recent Postgraduate Students

  Graduation Name Degree Primary Supervisor
2020 Ruth Colleran MSc (Biomedical Genomics)
2022 Clodagh Murray MSc (Biomedical Genomics)
2022 Gabriel Darcy MSc (Computational Genomics)
2017 Áine Duffy MSc (Biomedical Genomics)
2020 Eamon McAndrew MSc (Biomedical Genomics)
2019 Shane O¿Connell MSc (Biomedical Genomics)
2017 Dina Zhyschynska MSc (Biomedical Genomics)
2019 Brian Fennesey MSc (Biomedical Genomics)
2019 Shane Crinion MSc (Biomedical Genomics)
2021 Eric Tornabell MSc (Computational Genomics)
2020 Ruth Colleran MSc (Biomedical Genomics)
2018 Dona Shaju MSc (Biomedical Genomics)
2021 Conor O¿Donoghue MSc (Computational Genomics)
2021 Oisin McCaffrey MSc (Biomedical Genomics)
2018 Cathal King MSc (Computational Genomics)
2019 Sarah Collins MSc (Biomedical Genomics)
2017 Siraj Alharti MSc (Biomedical Genomics)
2017 Stephen Smith MSc (Biomedical Genomics)
2020 Srija Pidaparthi MSc (Biomedical Genomics)
2021 Claire Coleman MSc (Biomedical Genomics)
2019 Sarah Ennis MSc (Biomedical Genomics)
2018 Elissa Quinn MSc (Biomedical Genomics)
2017 Gemma Hyland MSc (Biomedical Genomics)
2020 Martin Gordon MSc (Biomedical Genomics)

Current Postgraduate Students (Research)

  Student Degree Type Type
Sarah Ennis Doctorate - Structured PhD (Science) Supervisor
Shane O Connell Doctorate - Structured PhD (Science) Supervisor
Mariel Barbachan E Silva Doctorate - Structured PhD (Science) Supervisor
Laura Fahey Doctorate - Structured PhD (Science) Co-supervisor (1)
Barry Digby Doctorate - Structured PhD (Science) Supervisor

Modules Taught

  Term/Year Module Title Module Code Subject / Desc
2015-16 Introduction to Bioinformatics MA324
2016- Genomics Data Analysis I MA5111
2015-16 Genomics Analysis MA570
2016- Genomics Research Project MA5105
2016- Medical Genomics 1 MA5106
2015-16 Introduction to Programming for Biology MA170
2016- Genomics Data Analysis II MA5112