COG database update: focus on microbial diversity, model organisms, and widespread pathogens von Galperin, Michael Y, Wolf, Yuri I, Makarova, Kira S, Vera Alvarez, Roberto, Landsman, David, Koonin, Eugene V

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TPMCalculator: one-step software to quantify mRNA abundance of genomic features von Vera Alvarez, Roberto, Pongor, Lorinc Sandor, Mariño-Ramírez, Leonardo, Landsman, David

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ElasticBLAST: accelerating sequence search via cloud computing von Camacho, Christiam, Boratyn, Grzegorz M, Joukov, Victor, Vera Alvarez, Roberto, Madden, Thomas L

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BioContainers: an open-source and community-driven framework for software standardization von da Veiga Leprevost, Felipe, Grüning, Björn A, Alves Aflitos, Saulo, Röst, Hannes L, Uszkoreit, Julian, Barsnes, Harald, Vaudel, Marc, Moreno, Pablo, Gatto, Laurent, Weber, Jonas, Bai, Mingze, Jimenez, Rafael C, Sachsenberg, Timo, Pfeuffer, Julianus, Vera Alvarez, Roberto, Griss, Johannes, Nesvizhskii, Alexey I, Perez-Riverol, Yasset

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LitSense: making sense of biomedical literature at sentence level von Allot, Alexis, Chen, Qingyu, Kim, Sun, Vera Alvarez, Roberto, Comeau, Donald C, Wilbur, W John, Lu, Zhiyong

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COG database update 2024 von Galperin, Michael Y, Vera Alvarez, Roberto, Karamycheva, Svetlana, Makarova, Kira S, Wolf, Yuri I, Landsman, David, Koonin, Eugene V

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Nonessential Ribosomal Proteins in Bacteria and Archaea Identified Using Clusters of Orthologous Genes von Galperin, Michael Y, Wolf, Yuri I, Garushyants, Sofya K, Vera Alvarez, Roberto, Koonin, Eugene V

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Banana (Musa acuminata) transcriptome profiling in response to rhizobacteria: Bacillus amyloliquefaciens Bs006 and Pseudomonas fluorescens Ps006 von Gamez, Rocío M, Rodríguez, Fernando, Vidal, Newton Medeiros, Ramirez, Sandra, Vera Alvarez, Roberto, Landsman, David, Mariño-Ramírez, Leonardo

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BioContainers Registry: Searching Bioinformatics and Proteomics Tools, Packages, and Containers von Bai, Jingwen, Bandla, Chakradhar, Guo, Jiaxin, Vera Alvarez, Roberto, Bai, Mingze, Vizcaíno, Juan Antonio, Moreno, Pablo, Grüning, Björn, Sallou, Olivier, Perez-Riverol, Yasset

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PM4NGS, a project management framework for next-generation sequencing data analysis von Vera Alvarez, Roberto, Pongor, Lorinc, Mariño-Ramírez, Leonardo, Landsman, David

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GTax: improving de novo transcriptome assembly by removing foreign RNA contamination von Alvarez, Roberto Vera, Landsman, David

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Aberrant spliceosome activity via elevated intron retention and upregulation and phosphorylation of SF3B1 in chronic lymphocytic leukemia von Kashyap, Manoj Kumar, Karathia, Hiren, Kumar, Deepak, Vera Alvarez, Roberto, Forero-Forero, Jose Vicente, Moreno, Eider, Lujan, Juliana Velez, Amaya-Chanaga, Carlos Ivan, Vidal, Newton Medeiros, Yu, Zhe, Ghia, Emanuela M., Lengerke-Diaz, Paula A., Achinko, Daniel, Choi, Michael Y., Rassenti, Laura Z., Mariño-Ramírez, Leonardo, Mount, Stephen M., Hannenhalli, Sridhar, Kipps, Thomas J., Castro, Januario E.

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Conservation and Evolution of the Sporulation Gene Set in Diverse Members of the Firmicutes von Galperin, Michael Y, Yutin, Natalya, Wolf, Yuri I, Vera Alvarez, Roberto, Koonin, Eugene V

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MutaBind2: Predicting the Impacts of Single and Multiple Mutations on Protein-Protein Interactions von Zhang, Ning, Chen, Yuting, Lu, Haoyu, Zhao, Feiyang, Alvarez, Roberto Vera, Goncearenco, Alexander, Panchenko, Anna R., Li, Minghui

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Workflow and web application for annotating NCBI BioProject transcriptome data von Vera Alvarez, Roberto, Medeiros Vidal, Newton, Garzón-Martínez, Gina A., Barrero, Luz S., Landsman, David, Mariño-Ramírez, Leonardo

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Transcriptome annotation in the cloud: complexity, best practices, and cost von Alvarez, Roberto Vera, Mariño-Ramírez, Leonardo, Landsman, David

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Census of solo LuxR genes in prokaryotic genomes von Hudaiberdiev, Sanjarbek, Choudhary, Kumari S, Vera Alvarez, Roberto, Gelencsér, Zsolt, Ligeti, Balázs, Lamba, Doriano, Pongor, Sándor

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BAMscale: quantification of next-generation sequencing peaks and generation of scaled coverage tracks von Pongor, Lorinc S, Gross, Jacob M, Vera Alvarez, Roberto, Murai, Junko, Jang, Sang-Min, Zhang, Hongliang, Redon, Christophe, Fu, Haiqing, Huang, Shar-Yin, Thakur, Bhushan, Baris, Adrian, Marino-Ramirez, Leonardo, Landsman, David, Aladjem, Mirit I, Pommier, Yves

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SNPDelScore: combining multiple methods to score deleterious effects of noncoding mutations in the human genome von Alvarez, Roberto Vera, Li, Shan, Landsman, David, Ovcharenko, Ivan

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Quantifying deleterious effects of regulatory variants von Li, Shan, Alvarez, Roberto Vera, Sharan, Roded, Landsman, David, Ovcharenko, Ivan

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