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Faculty Profile

Aaron A.J. Golden, Ph.D.

Dr. Aaron A.J. Golden

Associate Professor, Department of Genetics

Research Associate Professor, Department of Mathematical Sciences, Yeshiva University


Professional Interests

Genome, Epigenome and Microbiome Informatics

The digitization of genetic information coupled with recent developments in high throughput sequencing technologies have revolutionized the life sciences, and the discipline of genetics in particular. The Golden Lab is dedicated to the development of innovative, scalable algorithms and software to process and interpret the vast amounts of data generated by these sequencing platforms and other high-throughput biological assays. We do this by combining many different strands in computational science ranging from algorithmic development, high-performance computing and hardware optimization, to the application of techniques in artificial intelligence and computer vision.

We actively collaborate with many members of the Einstein research community, on areas as diverse as aptamer design, metabolomic profiling, integrative epigenomics and probing the (truly) dark matter that are the numerous human microbiomes.

Much of the group's research relies on High-Performance Computing resources and hardware accelerators. Our symmetric multiprocessing cluster, 'Leo', is an SGI Altix UV1000 with 64-cpus, 4 Nvidia Tesla GPUs and 1.5TB of fully addressable RAM.  Leo is named for Leo Szilard, the Hungarian physicist and pioneering molecular biologist, who was one of Einstein’s closest friends and collaborators.


Selected Publications

Gupta, A., Ó Broin, P., Bao, Y., Pullman, J., Kamal, L., Ajaimy, M., Lubetzky, M., Colovai, A., Schwartz, D., de Boccardo, G., Golden, A., Akalin, E. `Clinical and molecular significance of microvascular inflammation in transplant kidney biopsies'. Kidney International, 2015 Sep 30. doi: 10.1038/ki.2015.276

Nabet, B., Ó Broin, P., Reyes, J.M., Shieh, K., Lin, C.Y., Will, C.M., Popovic, R., Ezponda, T., Bradner, J.E., Golden, A., Licht, J.D. `Deregulation of the Ras-Erk signaling axis modulates the enhancer landscape.', Cell Reports, 12, 1-14, 2015.

Delio, M., Patel, K., Maslov, A., Marion, R.W., McDonald, T.V., Cadoff, E.M., Golden, A., Greally, J.M., Vijg, J., Morrow, B., Montagna, C. `Development of a Targeted Multi-Disorder High-Throughput Sequencing Assay for the Effective Identification of Disease-Causing Variants'. PLoS ONE, 10, 7, 2015.

Rhee, D.B., Croken, M.M., Shieh, K.R., Sullivan, J., Micklem, G., Kim, K., Golden, A. `toxoMine: an integrated omics data warehouse for Toxoplasma gondii systems biology research'. Database (Oxford) 2015 Jun 30;2015:bav066. doi: 10.1093/database/bav066, 2015.

Kurland, I.J.∗, Ó Broin, P.∗, Golden, A.∗, Su, G., Meng, F., Liu, L., Mohney, R., Kulkarni, S., Guha, C. `Integrative Metabolic Signatures for Hepatic Radiation Injury'. (∗ denotes joint first author) PLoS ONE, 10, 6:e0124795, 2015.

Kamal, L., Ó Broin, P., Bao, Y., Ajaimy, M., Lubetzky, M., Gupta, A., de Boccardo, G., Pullman, J., Golden, A., Akalin, E. `Clinical, Histological, and Molecular Markers Associated With Allograft Loss in Transplant Glomerulopathy Patients'. Transplantation, 2015 Feb 11 (Epub ahead of print), 2015.

Ó Broin, P., Smith, T.J., Golden, A. `Alignment-free clustering of transcription factor binding motifs using a genetic-k-medoids approach'. BMC Bioinformatics 16(1):22, 2015.

Ó Broin, P., Hayde, N., Bao, Y., Calder, R.B., de Boccardo, G., Lubetzky, M., Ajaimy, M., Pullman, J., Colovai, A., Akalin, E., Golden, A. `A pathogenesis-based transcript signature in donor-specic antibody-positive kidney transplant patients with normal biopsies'. Genomics Data. 2(0):357-360, 2014.

Ó Broin, P., Vaitheesvaran, P., Saha, S., Hartil, K., Chen, E.I., Goldman, D., Fleming, W.H., Kurland, I.J., Guha, C., Golden, A., `Intestinal Microbiota Derived Metabolomic Blood Plasma Markers for Prior Radiation Injury', International Journal of Radiation OncologyBiologyPhysics, 91(2):360-367, 2015.

Wijetunga, N.A., Delahaye, F., Zhao, Y.M., Golden, A., Mar, J.C., Einstein, F.H., Greally, J.M., 'The meta-epigenomic structure of purified human stem cell populations is defined at cis-regulatory sequences', Nature Communications, 5:5195, 2014.

Vaitheesvaran, B., Hartil, K., Navare A., Zheng, C., Ó Broin, P., Golden, A., Guha, C., Kurland, I.J., Bruce, J. E. `Linking the gap between diabetes and cancer with IQGAP2: Role of the tumor suppressor in metabolic homeostasis.' Metabolomics 10(5):920-37, 2014.

Hayde, N, Broin, PO, Bao, Y, de Boccardo, G, Lubetzky, M, Ajaimy, M, Pullman, J, Colovai, A, Golden, A, Akalin, `Increased intragraft rejection-associated gene transcripts in patients with donor-specific antibodies and normal biopsies' Kidney International, 86(3):600-9, 2014.

Sparano, J.A., Golden, A.,A.J., Montagna, C., 'Translating the TCGA Breast Cancer Results into Clinical Practice: Searching for Therapeutic Clues' Oncology Journal, Dec 15 2013.

December 15, 2013

Lubetzky, M., Bao, Y., ´O Broin, P., Marfo, K., Ajaimy, M., Aljanabi, A., de Boccardo, G., Golden, A., Akalin, E., ’Genomics of BK Viremia in Kidney Transplant Recipients’ Transplantation,Dec 4 2013.

Golden, A., Djorgovski, S.G., Greally, J.M., ‘Astrogenomics: big data, old problems, old solutions?’ Genome Biology, 14:129, 2013.

Rhee, D., Calder, R.B., Shieh, K., ´O Broin, P., Hargitai, J., Golden, A., ‘’Spring through the gateway’: deploying genomic workflows with XSEDE’, XSEDE ’13 Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to Discovery, ACM New York, NY, USA, 2013.

Geeleher, P., Egan, L.J., Hartnett, L., Golden, A., Seoighe, C., ’Severe Bias in Gene-Set Analysis Applied to High-throughput Methylation Data', Bioinformatics. 2013 Aug 1;29(15):1851-7.

Geeleher, P., Huang, R.S., Gamazon, E.R., Golden, A., Seoighe, C. ’The regulatory effect of miRNAs is a heritable genetic trait in humans’ BMC Genomics, 13:383, 2012.

Agoni, L., Golden, A., Guha, C., Lenz, J. ‘Neanderthal and Denisovan Retroviruses’, Current Biology, 22, 11:R437-8, 2012

McLellan, A.S., Dubin, R.A., Jing, Q., ´O Broin, P., Moskowitz, D., Suzuki, M., Calder, R.B., Hargitai, J., Golden, A., Greally, J.M. ’The Wasp System: an open source environment for managing and analyzing genomic data.’ Genomics, 100(6);354-51, 2012.

Golden, A., McLellan, A.S., Dubin, R.A., Jing, Q., ´O Broin, P., Moskowitz, D., Xhang, Z., Suzuki, M., Hargitai, J., Calder, R.B., Greally, J.M., ‘The Einstein Genome Gateway using WASP - A High Throughput Multi-Layered Life Sciences Portal for XSEDE’, Proceedings of the 4th International Workshop on Science Gateways for Life Sciences, IOS Press, Amsterdam, 2012

Thomas, B.J., Rubio, E.D., Krumm, N., Ó Broin, P., Bomsztyk, K., Welsch, P., Greally, J.M., Golden, A.A., Krumm, A.’Allele-specifc transcriptional elongation regulates monoallelic expression of the IGF2BP1 gene’, Epigenetics and Chromatin, 4:14, 2011

Kim, M.K.-H., McGarry, T.J., Ó Broin, P., Flatow, J.M., Golden, A. A.-J., Licht, J.D.  ‘An Integrated Genome Screen Identifies The Wnt Signalling Pathway as a Major Target of WT1’, Proceedings of the National Academy of Sciences,106(27):11154-9, 2009

Geeleher, P., Morris, D., Hinde, J.P., Golden, A. (2009), BioconductorBuntu - a Linux Distribution that Implements a Web-Based DNA Microarray Analysis Server, Bioinformatics, 25(11):1438-9, 2009

N McCoy, S Mahony, Golden, A., ‘Gene Prediction in Metagenomic Libraries Using the Self-Organising Map and High Performance Computing Techniques’, Distributed and Grid Computing in Computational Biology, Vol 4360 (Springer), Lecture Notes in Computer Science, 2007


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More Information About Dr. Aaron Golden

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Albert Einstein College of Medicine
Jack and Pearl Resnick Campus
1300 Morris Park Avenue
Van Etten, Room B-B04
Bronx, NY 10461

Tel: 718.839.7219

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