Contact Information
Building 38A, Room 6S614-I
8600 Rockville Pike MSC 6075
Bethesda, MD 20894-6075
Tel: +1-301-594-8079
Fax: +1-301-480-2288
[email protected]
Roberto Vera Alvarez, PhD
Senior Biostatistician, Computational Biology Branch
Bioinformatics of Chromatin Structure Group
NCBI, NLM, NIH
Research Interests
- Development of computational tools for the analysis of Next-Generation Sequencing (NGS) data.
- Cancer diseases and its effect on the spliceosome.
- In-silico methodologies for the identification of new relevant cancer targets which could lead to the development of new drugs or to the improvement of the existent ones.
- Integration of cloud computing technologies and bioinformatics tools and pipelines to process biomedical data.
- Development of biological databases.
- Development of web application to analyze and visualize biological data.
Selected Publications
- Vera R., Pongor L.S., Mariño-Ramírez L., Landsman, D. (2020) PM4NGS, a project management framework for Next-Generation Sequencing data analysis. GigaScience, 10(1), doi: 10.1093/gigascience/giaa141
- Vera R., Mariño-Ramírez L., Landsman, D. (2020) Transcriptome annotation in the cloud: complexity, best practices and cost. GigaScience, 10(2), doi: 10.1093/gigascience/giaa163
- Galperin MY, Wolf YI, Garushyants SK, Vera R, Koonin EV. Non-essential ribosomal proteins in bacteria and archaea identified using COGs. J Bacteriol. 2021 Mar 22;203(11):e00058-21. doi: 10.1128/JB.00058-21
- Bai, J., Bandla, C., Guo, J., Vera, R., Vizcaíno, J., Bai, M., Moreno, P., Grüning, B., Sallou, O., Perez-Riverol, Y. (2020) BioContainers Registry: searching for bioinformatics tools, packages and containers. J Proteome Res. 2021 Apr 2;20(4):2056-2061. doi: 10.1021/acs.jproteome.0c00904
- Galperin, M.Y., Wolf Y.I, Makarova K.S., Vera R., Landsman, D., Koonin E.V. (2020) COG database update: Focus on microbial diversity, model organisms, and widespread pathogens. Nucleic Acids Research, gkaa1018, https://doi.org/10.1093/nar/gkaa1018
- Zhang, N., Chen, Y., Lu, H., Zhao, F., Vera, R., Goncearenco, A., Panchenko, A.R., Li, M. (2020) MutaBind2: Predicting the Impacts of Single and Multiple Mutations on Protein-Protein Interactions. iScience. 23(3): 100939. doi: 10.1016/j.isci.2020.100939
- Pongor, LS.; Gross, JM.; Vera, R. et al. (2020) BAMscale: quantification of next-generation sequencing peaks and generation of scaled coverage tracks. Epigenetics & Chromatin 13(21). [Full Text]
- Allot A., Chen Q., Kim S., Vera, R., Comeau DC., Wilbur WJ., Lu Z., (2019) LitSense: making sense of biomedical literature at sentence level. Nucleic Acids Research, 2019. 47(W1):W594–W599. [PubMed] [PDF]
- Games, R.; Rodriguez, F.; Vidal, N.; Ramirez, S.; Vera, R.; Landsman D.; Mariño-Ramírez L. Banana (Musa acuminata) transcriptome profiling in response to rhizobacteria: Bacillus amyloliquefaciens Bs006 and Pseudomonas fluorescens Ps006. BMC genomics. 2019; 20(1):378. [PDF]
- Vera, R.; Pongor, LS.; Mariño-Ramírez L.; Landsman D. TPMCalculator: one-step software to quantify mRNA abundance of genomic features, Bioinformatics. 2018; 35(11):1960-1962. [PDF]
- Vera, R.; Shan, L.; Landsman, D.; Ovcharenko, I. SNPDelScore: combining multiple methods to score deleterious effects of noncoding mutations in the human genome. Bioinformatics. 2017; 34(2):289-291. [PDF]
- Vera, R.; Vidal N.; Garzón-Martínez G.; Barrero LS.; Landsman D.; Mariño-Ramírez L. Workflow and web application for annotating NCBI BioProject transcriptome data. Database (Oxford). 2017; (1): bax008. [PDF]
- Shan, L.; Vera, R.; Sharan, R.; Landsman, D.; Ovcharenko, I. Quantifying deleterious effects of regulatory variants. Nucleic Acids Research. 2017; 45(5):2307-2317. [PubMed] [PDF]
- Ligeti, B.; Vera, R.; Juhász, J.; Pongor, S. CX, DPX and PCW (2016): Web servers for the visualization of interior and protruding regions of protein structures in 3D and 1D. Springer Protocols: Predicting Protein Secondary Structure and Other One-dimensional Structural Properties. 2016. [PDF]
- Ligeti, B.; Pénzváltó, Z.; Vera, R.; Győrffy, B.; Pongor, S. A Network-Based Target Overlap Score for Characterizing Drug Combinations: High Correlation with Cancer Clinical Trial Results. PLoS One. 2015; 10 (9), e0129267. [PubMed] [PDF]
- Vera, R., Pongor, LS.; Ligeti, B. Fast and Sensitive Alignment of Microbial Whole Genome Sequencing Reads to Large Sequence Datasets on a Desktop PC: Application to Metagenomic Datasets and Pathogen Identification. PLoS ONE. 2014; 9(7): e103441. [PubMed] [PDF]
- Vera, R.; Perez-Riverol, Y.; Perez, S.; Ligeti, B.; Kertész-Farkas, A.; Pongor, S. JBioWH: an open-source Java framework for bioinformatics data integration. Database (Oxford). 2013. [PubMed] [PDF]
- Perez-Riverol, Y; Vera, R.; Mazola, Y; Mussachio, A. A Parallel Systematic-Monte Carlo Algorithm for exploring Conformational Space. Curr Top in Med Chem. 2012; 12(16): 1790-1796. [PubMed]