Ariel Aptekmann

Bioinformatician at Hackensack Meridian Hospital Center for Discovery and Innovation

Research Expertise

Computational biology
bioinformatics
metagenomics
evolution
Genetics
Infectious Diseases
Public Health, Environmental and Occupational Health
Inorganic Chemistry
Organic Chemistry
Physical and Theoretical Chemistry
Computer Science Applications
Spectroscopy
Molecular Biology
Catalysis
Computational Mathematics
Computational Theory and Mathematics
Biochemistry
Statistics and Probability
Ecology, Evolution, Behavior and Systematics
Microbiology
Biophysics
Atmospheric Science

About

I am a bioinformatician and researcher in computational biology. My research focuses on the application of machine learning and data analysis to understand the molecular basis of disease. I also work on developing novel software tools for data management and analysis.

Publications

Molecular link between auxin and ROS-mediated polar growth

Proceedings of the National Academy of Sciences / May 01, 2017

Mangano, S., Denita-Juarez, S. P., Choi, H.-S., Marzol, E., Hwang, Y., Ranocha, P., Velasquez, S. M., Borassi, C., Barberini, M. L., Aptekmann, A. A., Muschietti, J. P., Nadra, A. D., Dunand, C., Cho, H.-T., & Estevez, J. M. (2017). Molecular link between auxin and ROS-mediated polar growth. Proceedings of the National Academy of Sciences, 114(20), 5289–5294. https://doi.org/10.1073/pnas.1701536114

Quantifying structural relationships of metal-binding sites suggests origins of biological electron transfer

Science Advances / Jan 14, 2022

Bromberg, Y., Aptekmann, A. A., Mahlich, Y., Cook, L., Senn, S., Miller, M., Nanda, V., Ferreiro, D. U., & Falkowski, P. G. (2022). Quantifying structural relationships of metal-binding sites suggests origins of biological electron transfer. Science Advances, 8(2). https://doi.org/10.1126/sciadv.abj3984

Apoplastic class III peroxidases PRX62 and PRX69 promote Arabidopsis root hair growth at low temperature

Nature Communications / Mar 14, 2022

Pacheco, J. M., Ranocha, P., Kasulin, L., Fusari, C. M., Servi, L., Aptekmann, Ariel. A., Gabarain, V. B., Peralta, J. M., Borassi, C., Marzol, E., Rodríguez-Garcia, D. R., del Carmen Rondón Guerrero, Y., Sardoy, M. C., Ferrero, L., Botto, J. F., Meneses, C., Ariel, F., Nadra, A. D., Petrillo, E., … Estevez, J. M. (2022). Apoplastic class III peroxidases PRX62 and PRX69 promote Arabidopsis root hair growth at low temperature. Nature Communications, 13(1). https://doi.org/10.1038/s41467-022-28833-4

Deep learning of a bacterial and archaeal universal language of life enables transfer learning and illuminates microbial dark matter

Nature Communications / May 11, 2022

Hoarfrost, A., Aptekmann, A., Farfañuk, G., & Bromberg, Y. (2022). Deep learning of a bacterial and archaeal universal language of life enables transfer learning and illuminates microbial dark matter. Nature Communications, 13(1). https://doi.org/10.1038/s41467-022-30070-8

Decoding the effects of synonymous variants

Nucleic Acids Research / Nov 30, 2021

Zeng, Z., Aptekmann, A. A., & Bromberg, Y. (2021). Decoding the effects of synonymous variants. Nucleic Acids Research, 49(22), 12673–12691. https://doi.org/10.1093/nar/gkab1159

Core promoter information content correlates with optimal growth temperature

Scientific Reports / Jan 22, 2018

Aptekmann, A. A., & Nadra, A. D. (2018). Core promoter information content correlates with optimal growth temperature. Scientific Reports, 8(1). https://doi.org/10.1038/s41598-018-19495-8

Ecology theory disentangles microbial dichotomies

Environmental Microbiology / Sep 05, 2023

Couso, L. L., Soler‐Bistué, A., Aptekmann, A. A., & Sánchez, I. E. (2023). Ecology theory disentangles microbial dichotomies. Environmental Microbiology. Portico. https://doi.org/10.1111/1462-2920.16495

A finely tuned interplay between calcium binding, ionic strength and pH modulates conformational and oligomerization equilibria in the Respiratory Syncytial Virus Matrix (M) protein

Archives of Biochemistry and Biophysics / Nov 01, 2022

Esperante, S. A., Alvarez-Paggi, D., Salgueiro, M., Desimone, M. F., de Oliveira, G. A. P., Arán, M., García-Pardo, J., Aptekmann, A. A., Ventura, S., Alonso, L. G., & de Prat-Gay, G. (2022). A finely tuned interplay between calcium binding, ionic strength and pH modulates conformational and oligomerization equilibria in the Respiratory Syncytial Virus Matrix (M) protein. Archives of Biochemistry and Biophysics, 731, 109424. https://doi.org/10.1016/j.abb.2022.109424

PhISCO: a simple method to infer phenotypes from protein sequences

Oct 23, 2022

Berthet, A. S. H., Aptekmann, A. A., Tejero, J., Sánchez, I. E., Noguera, M. E., & Roman, E. A. (2022). PhISCO: a simple method to infer phenotypes from protein sequences. https://doi.org/10.1101/2022.10.23.511734

Illuminating the Microbial Dark Matter Driving Energy Transformations in the Environment with a Universal Language of Life

Goldschmidt2021 abstracts / Jan 01, 2021

Hoarfrost, A., Aptekmann, A., Farfañuk, G., Falkowski, P., & Bromberg, Y. (2021). Illuminating the Microbial Dark Matter Driving Energy Transformations in the Environment with a Universal Language of Life. Goldschmidt2021 Abstracts. https://doi.org/10.7185/gold2021.4886

Dark Matter of the Transcription Factor Binding Site Motif Universe

Feb 16, 2021

Aptekmann, A. A., Bulavka, D., Nadra, A. D., & Sánchez, I. E. (2021). Dark Matter of the Transcription Factor Binding Site Motif Universe. https://doi.org/10.21203/rs.3.rs-199537/v1

ANÁLISIS DE LOS FLUJOS EXTREMOS DE ELECTRONES ENERGÉTICOS EN EL CINTURÓN DE RADIACIÓN EXTERIOR Y EN LA ANOMALÍA MAGNÉTICA DEL ATLÁNTICO SUR

Meteorologica / Jun 01, 2021

Lanabere, V., & Dasso, S. (2021). ANÁLISIS DE LOS FLUJOS EXTREMOS DE ELECTRONES ENERGÉTICOS EN EL CINTURÓN DE RADIACIÓN EXTERIOR Y EN LA ANOMALÍA MAGNÉTICA DEL ATLÁNTICO SUR. Meteorologica, 46(2), e006–e006. https://doi.org/10.24215/1850468xe006

NAC1 directs CEP1-CEP3 peptidase expression and modulates root hair growth in Arabidopsis

Mar 17, 2023

Rodríguez-García, D. R., Guerrero, Y. del C. R., Ferrero, L., Rossi, A. H., Miglietta, E. A., Aptekmann, A. A., Marzol, E., Pacheco, J. M., Carignani, M., Gabarain, V. B., Lopez, L. E., Dominguez, G. D., Borassi, C., Sánchez-Serrano, J. J., Xu, L., Nadra, A. D., Rojo, E., Ariel, F., & Estevez, J. M. (2023). NAC1 directs CEP1-CEP3 peptidase expression and modulates root hair growth in Arabidopsis. https://doi.org/10.1101/2023.03.15.532802

mebipred: identifying metal-binding potential in protein sequence

Bioinformatics / May 27, 2022

Aptekmann, A. A., Buongiorno, J., Giovannelli, D., Glamoclija, M., Ferreiro, D. U., & Bromberg, Y. (2022). mebipred: identifying metal-binding potential in protein sequence. Bioinformatics, 38(14), 3532–3540. https://doi.org/10.1093/bioinformatics/btac358

Class III Peroxidases PRX01, PRX44, and PRX73 Control Root Hair Growth in Arabidopsis thaliana

International Journal of Molecular Sciences / May 11, 2022

Marzol, E., Borassi, C., Carignani Sardoy, M., Ranocha, P., Aptekmann, A. A., Bringas, M., Pennington, J., Paez-Valencia, J., Martínez Pacheco, J., Rodríguez-Garcia, D. R., Rondón Guerrero, Y. del C., Peralta, J. M., Fleming, M., Mishler-Elmore, J. W., Mangano, S., Blanco-Herrera, F., Bedinger, P. A., Dunand, C., Capece, L., … Estevez, J. M. (2022). Class III Peroxidases PRX01, PRX44, and PRX73 Control Root Hair Growth in Arabidopsis thaliana. International Journal of Molecular Sciences, 23(10), 5375. https://doi.org/10.3390/ijms23105375

Transcription factor specificity limits the number of DNA-binding motifs

PLOS ONE / Jan 28, 2022

Aptekmann, A. A., Bulavka, D., Nadra, A. D., & Sánchez, I. E. (2022). Transcription factor specificity limits the number of DNA-binding motifs. PLOS ONE, 17(1), e0263307. https://doi.org/10.1371/journal.pone.0263307

mebipred: identifying metal-binding potential in protein sequences.

Aug 13, 2021

Aptekmann, A. A., Buongiorno, J., Giovannelli, D., Glamoclija, M., Ferreiro, D. U., & Bromberg, Y. (2021). mebipred: identifying metal-binding potential in protein sequences. https://doi.org/10.1101/2021.08.12.456141

Transcriptomic analysis and molecular docking reveal genes involved in the response of Aedes aegypti larvae to an essential oil extracted from Eucalyptus

PLOS Neglected Tropical Diseases / Jul 16, 2021

Sierra, I., Latorre-Estivalis, J. M., Traverso, L., Gonzalez, P. V., Aptekmann, A., Nadra, A. D., Masuh, H., & Ons, S. (2021). Transcriptomic analysis and molecular docking reveal genes involved in the response of Aedes aegypti larvae to an essential oil extracted from Eucalyptus. PLOS Neglected Tropical Diseases, 15(7), e0009587. https://doi.org/10.1371/journal.pntd.0009587

Decoding the effects of synonymous variants

May 22, 2021

Zeng, Z., Aptekmann, A. A., & Bromberg, Y. (2021). Decoding the effects of synonymous variants. https://doi.org/10.1101/2021.05.20.445019

Thousands of protein linear motif classes may still be undiscovered

PLOS ONE / May 03, 2021

Bulavka, D., Aptekmann, A. A., Méndez, N. A., Krick, T., & Sánchez, I. E. (2021). Thousands of protein linear motif classes may still be undiscovered. PLOS ONE, 16(5), e0248841. https://doi.org/10.1371/journal.pone.0248841

Shedding Light on Microbial Dark Matter with A Universal Language of Life

Dec 24, 2020

Hoarfrost, A., Aptekmann, A., Farfañuk, G., & Bromberg, Y. (2020). Shedding Light on Microbial Dark Matter with A Universal Language of Life. https://doi.org/10.1101/2020.12.23.424215

Computational Approaches for Unraveling the Effects of Variation in the Human Genome and Microbiome

Annual Review of Biomedical Data Science / Jul 20, 2020

Zhu, C., Miller, M., Zeng, Z., Wang, Y., Mahlich, Y., Aptekmann, A., & Bromberg, Y. (2020). Computational Approaches for Unraveling the Effects of Variation in the Human Genome and Microbiome. Annual Review of Biomedical Data Science, 3(1), 411–432. https://doi.org/10.1146/annurev-biodatasci-030320-041014

The molecular link between auxin and ROS-Mediated polar root hair growth

Mar 14, 2017

Mangano, S., Denita-Juarez, S. P., Choi, H.-S., Marzol, E., Hwang, Y., Ranocha, P., Velasquez, S. M., Borassi, C., Barberini, M. L., Aptekmann, A. A., Muschietti, J. P., Nadra, A. D., Dunand, C., Cho, H.-T., & Estevez, J. M. (2017). The molecular link between auxin and ROS-Mediated polar root hair growth. https://doi.org/10.1101/116517

Education

University of Buenos Aires

PhD, Biological Chemistry, Bioinformatics / February, 2018

Buenos Aires

Rutgers, The State University of New Jersey

Postdoc, Computational Biology / March, 2021

New Brunswick, New Jersey, United States of America

Experience

Hackensack Meridian Hospital Center for Discovery and Innovation

Bioinformatician / March, 2021Present

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