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<p><a id="headshot" href="lmr-cv"><img src="/core/assets/cbb/images/roberto-vera-alvarez.jpg" alt="Roberto Vera Alvarez, PhD" /></a>
<strong>Contact Information</strong><br />
Building 38A, Room 6S614-I<br />
8600 Rockville Pike MSC 6075<br />
Bethesda, MD 20894-6075<br />
Tel: +1-301-594-8079<br />
Fax: +1-301-480-2288<br />
<a href="mailto:veraalva@ncbi.nlm.nih.gov">veraalva@ncbi.nlm.nih.gov</a></p>
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<div id="ncbi-content-block-main">
<h1 id="roberto-vera-alvarez-phd">Roberto Vera Alvarez, PhD</h1>
<p>Senior Biostatistician, Computational Biology Branch<br />
<a href="/research/staff/landsman/">Bioinformatics of Chromatin Structure Group</a><br />
<a href="/">NCBI</a>, <a href="//www.nlm.nih.gov/">NLM</a>, <a href="//www.nih.gov/">NIH</a></p>
<h2 id="research-interests">Research Interests</h2>
<ul>
<li>Development of computational tools for the analysis of Next-Generation Sequencing (NGS) data.</li>
<li>Cancer diseases and its effect on the spliceosome.</li>
<li><em>In-silico</em> 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.</li>
<li>Integration of cloud computing technologies and bioinformatics tools and pipelines to process biomedical data.</li>
<li>Development of biological databases.</li>
<li>Development of web application to analyze and visualize biological data.</li>
</ul>
<h2 id="selected-publications">Selected Publications</h2>
<ul>
<li><strong>Vera R.</strong>, 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</li>
<li><strong>Vera R.</strong>, Mariño-Ramírez L., Landsman, D. (2020) Transcriptome annotation in the cloud: complexity, best practices and cost. GigaScience, 10(2), doi: 10.1093/gigascience/giaa163</li>
<li>Galperin MY, Wolf YI, Garushyants SK, <strong>Vera R</strong>, 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</li>
<li>Bai, J., Bandla, C., Guo, J., <strong>Vera, R.</strong>, 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</li>
<li>Galperin, M.Y., Wolf Y.I, Makarova K.S., <strong>Vera R.</strong>, 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</li>
<li>Zhang, N., Chen, Y., Lu, H., Zhao, F., <strong>Vera, R.</strong>, 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</li>
<li>Pongor, LS.; Gross, JM.; <strong>Vera, R.</strong> <em>et al</em>. (2020) BAMscale: quantification of next-generation sequencing peaks and generation of scaled coverage tracks. <em>Epigenetics &amp; Chromatin</em> 13(21). <a href="https://link.springer.com/article/10.1186/s13072-020-00343-x">[Full Text]</a></li>
<li>Allot A., Chen Q., Kim S., <strong>Vera, R.</strong>, Comeau DC., Wilbur WJ., Lu Z., (2019) LitSense: making sense of biomedical literature at sentence level. <em>Nucleic Acids Research</em>, 2019. 47(W1):W594W599. <a href="/pubmed/31020319">[PubMed]</a> <a href="https://academic.oup.com/nar/article-pdf/47/W1/W594/28880151/gkz289.pdf">[PDF]</a></li>
<li>Games, R.; Rodriguez, F.; Vidal, N.; Ramirez, S.; <strong>Vera, R.</strong>; Landsman D.; Mariño-Ramírez L. Banana (Musa acuminata) transcriptome profiling in response to rhizobacteria: Bacillus amyloliquefaciens Bs006 and Pseudomonas fluorescens Ps006. <em>BMC genomics</em>. 2019; 20(1):378. <a href="https://link.springer.com/content/pdf/10.1186/s12864-019-5763-5.pdf">[PDF]</a></li>
<li><strong>Vera, R.</strong>; Pongor, LS.; Mariño-Ramírez L.; Landsman D. TPMCalculator: one-step software to quantify mRNA abundance of genomic features, <em>Bioinformatics</em>. 2018; 35(11):1960-1962. <a href="https://academic.oup.com/bioinformatics/article-pdf/35/11/1960/28759311/bty896.pdf">[PDF]</a></li>
<li><strong>Vera, R.</strong>; Shan, L.; Landsman, D.; Ovcharenko, I. SNPDelScore: combining multiple methods to score deleterious effects of noncoding mutations in the human genome. <em>Bioinformatics</em>. 2017; 34(2):289-291. <a href="https://academic.oup.com/bioinformatics/article-pdf/34/2/289/25114261/btx583.pdf">[PDF]</a></li>
<li><strong>Vera, R.</strong>; Vidal N.; Garzón-Martínez G.; Barrero LS.; Landsman D.; Mariño-Ramírez L. Workflow and web application for annotating NCBI BioProject transcriptome data. <em>Database (Oxford)</em>. 2017; (1): bax008. <a href="https://academic.oup.com/database/article-pdf/2017/1/bax008/13628704/bax008.pdf">[PDF]</a></li>
<li>Shan, L.; <strong>Vera, R.</strong>; Sharan, R.; Landsman, D.; Ovcharenko, I. Quantifying deleterious effects of regulatory variants. <em>Nucleic Acids Research</em>. 2017; 45(5):2307-2317. <a href="/pubmed/26989147">[PubMed]</a> <a href="https://academic.oup.com/nar/article-pdf/45/5/2307/16667333/gkw1263.pdf">[PDF]</a></li>
<li>Ligeti, B.; <strong>Vera, R.</strong>; 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. <em>Springer Protocols: Predicting Protein Secondary Structure and Other One-dimensional Structural Properties</em>. 2016. <a href="https://link.springer.com/content/pdf/10.1007%2F978-1-4939-6406-2.pdf">[PDF]</a></li>
<li>Ligeti, B.; Pénzváltó, Z.; <strong>Vera, R.</strong>; Győrffy, B.; Pongor, S. A Network-Based Target Overlap Score for Characterizing Drug Combinations: High Correlation with Cancer Clinical Trial Results. <em>PLoS One</em>. 2015; 10 (9), e0129267. <a href="/pubmed/26047322">[PubMed]</a> <a href="http://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0129267&amp;type=printable">[PDF]</a></li>
<li><strong>Vera, R.</strong>, 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. <em>PLoS ONE</em>. 2014; <strong>9</strong>(7): e103441. <a href="/pubmed/26989147">[PubMed]</a> <a href="https://academic.oup.com/nar/article-pdf/45/5/2307/16667333/gkw1263.pdf">[PDF]</a></li>
<li><strong>Vera, R.</strong>; Perez-Riverol, Y.; Perez, S.; Ligeti, B.; Kertész-Farkas, A.; Pongor, S. JBioWH: an open-source Java framework for bioinformatics data integration. <em>Database (Oxford)</em>. 2013. <a href="/pubmed/26989147">[PubMed]</a> <a href="https://academic.oup.com/nar/article-pdf/45/5/2307/16667333/gkw1263.pdf">[PDF]</a></li>
<li>Perez-Riverol, Y; <strong>Vera, R.</strong>; Mazola, Y; Mussachio, A. A Parallel Systematic-Monte Carlo Algorithm for exploring Conformational Space. <em>Curr Top in Med Chem</em>. 2012; 12(16): 1790-1796. <a href="/pubmed/26989147">[PubMed]</a></li>
</ul>
<h2 id="google-citations"><a href="https://scholar.google.com/citations?user=X9OKjuEAAAAJ&amp;hl=en">Google Citations</a></h2>
<h2 id="linkedin-profile"><a href="https://www.linkedin.com/in/robertoveraalvarez/">LinkedIn Profile</a></h2>
<h2 id="researchgate-profile"><a href="https://www.researchgate.net/profile/Roberto_Vera_Alvarez">ResearchGate Profile</a><a href="https://scholar.google.com/citations?user=X9OKjuEAAAAJ&amp;hl=en"> </a></h2>
<h2 id="research-group">Research Group</h2>
<ul>
<li><a href="/research/staff/landsman/">David Landsman</a></li>
<li><a href="mailto:iris.zhu@nih.gov">Iris Zhou</a></li>
</ul>
<h2 id="links">Links</h2>
<ul>
<li><a href="https://pm4ngs.readthedocs.io/">PM4NGS</a></li>
<li><a href="https://github.com/ncbi/cwl-ngs-workflows-cbb">CWL workflows</a></li>
<li><a href="https://pypi.org/project/goenrichment/0.0.10a3/">GO Enrichment</a></li>
<li><a href="https://pypi.org/project/jupyterngsplugin/">jupyterngsplugin</a></li>
<li><a href="https://github.com/ncbi/TPMCalculator">TPMCalculator</a></li>
<li><a href="/snpdelscore">SNPDelScore</a></li>
<li><a href="/research/physalis">PhysalisDB</a></li>
<li><a href="/projects/banana/">BananaDB</a></li>
<li><a href="https://github.com/ncbi/dcode-cape">CAPE</a></li>
</ul>
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