Selected Publications

Our team has contributed to big data analyses and has co-authored several high-quality publications listed below:

1. VISTA Enhancer Browser: An updated database of tissue-specific developmental enhancers
   Nucleic Acids Research, 2024 (In Press)
2. BioTextQuest v2.0: An evolved tool for biomedical literature mining and concept discovery
   Comput Struct Biotechnol J. 2024 Aug 21:23:3247-3253. doi: 10.1016/j.csbj.2024.08.016. eCollection 2024 Dec. PMID:39279874
3. kmerDB: a database encompassing the set of genomic and proteomic sequence information of each species
   Comput Struct Biotechnol J. 2024 Apr 21;23:1919-1928. doi: 10.1016/j.csbj.2024.04.050., PMID:38711760 
4. SCALA: A complete solution for multimodal analysis of single-cell Next Generation Sequencing data  
   Comput Struct Biotechnol J.  2023 October 20. ISSN 2001-0370, https://doi.org/10.1016/j.csbj.2023.10.032.  PMID:38022693
5. Unraveling the functional dark matter through global metagenomics.
   Nature, 2023 Oct;622(7983):594-602. Epub 2023 Oct 11. https://doi.org/10.1038/s41586-023-06583-7, PMID:37821698
6. NMPFamsDB: A database of novel protein families from microbial metagenomes and metatranscriptomes
   Nucleic Acids Research 2023 Oct 9:gkad800. doi: 10.1093/nar/gkad800. PMID:37811892
7. FLAME (v2.0): advanced integration and interpretation of functional enrichment results from multiple sources
   Bioinformatics. 2023 Aug 1;39(8):btad490. doi: 10.1093/bioinformatics/btad490. PMID:37540207
8. Arena3Dweb: Interactive 3D visualization of multilayered networks supporting multiple directional information channels, clustering analysis and application integration
   NAR Genomics and Bioinformatics, Volume 5, Issue 2, June 2023, lqad053, https://doi.org/10.1093/nargab/lqad053 PMID:37260509 
9. Consolidated variant calling from Whole Exome Sequencing data using three variant callers
   STAR Protocols (Cell Press),  04 June 2022, Volume 3, Issue 2, https://doi.org/10.1016/j.xpro.2022.101418  PMID:35669050
10. The network makeup artist (NORMA-2.0): Distinguishing annotated groups in a network using innovative layout strategies
    Bioinformatics Advances, 13 May 2022;, vbac036, https://doi.org/10.1093/bioadv/vbac036  PMID:36699373
11. DARLING: A web application for detecting disease-related biomedical entity associations using literature mining  
    Biomolecules, 2022 Mar 30 , 12(4), 520; https://doi.org/10.3390/biom12040520 PMID:35454109
12. PREGO: A Literature and Data-Mining Resource to Associate Microorganisms, Biological Processes, and Environment Types
    Microorganisms, 2022, 10, 293. https://doi.org/10.3390/microorganisms10020293 PMID:35208748
13. OnTheFly2.0: a text-mining web application for automated biomedical entity recognition, document annotation, network and functional enrichment analysis
    NAR Genomics and Bioinformatics, Volume 3, Issue 4, December 2021, lqab090, https://doi.org/10.1093/nargab/lqab090  PMID: 34632381
14. Flame: A web tool for functional and literature enrichment analysis using multiple gene lists
    Biology,14 Jul 2021, 10(7), 665; https://doi.org/10.3390/biology10070665  PMID:34356520 
15. NORMA-The network makeup artist: a web tool for network annotation visualization
    Genomics Proteomics and Bioinformatics, 2021 Jun 22:S1672-0229(21)00130-3. doi: 10.1016/j.gpb.2021.02.005.  PMID:34171457
16. VICTOR: A visual analytics web application for comparing cluster sets
    Computers in Biology and Medicine, 8 June 2021, 104557, ISSN 0010-4825, https://doi.org/10.1016/j.compbiomed.2021.104557. PMID:34139436
17. ProteoSign v2: A faster and evolved user-friendly online tool for statistical analyses of differential proteomics 
    Nucleic Acids Res. 2021 May 8:gkab329. doi: 10.1093/nar/gkab329. PMID:33963869
18. Arena3Dweb: Interactive 3D visualization of multilayered networks
    Nucleic Acids Res., 2021 Apr 22:gkab278. doi: 10.1093/nar/gkab278. PMID:33885790
19. UniProt Related Documents (UniReD): assisting wet lab biologists in their quest on finding novel counterparts in a protein network.
    NAR Genomics and Bioinformatics, Volume 2, Issue 1, March 2020, lqaa005, https://doi.org/10.1093/nargab/lqaa005 PMID:33575553
20. HipMCL: A high-performance parallel implementation of the Markov clustering algorithm for large-scale networks.
    Nucleic Acids Research, 5 Jan 2018, https://doi.org/10.1093/nar/gkx1313, PMID:29315405 
21. NAP: The Network Analysis Profiler, a web tool for easier topological analysis and comparison of medium-scale biological networks
    BMC Research Notes, 2017, 10:278, DOI: 10.1186/s13104-017-2607-8 PMID:28705239 
22. ProteoSign: An end-user online differential proteomics statistical analysis platform.
    Nucleic Acids Research, 2017 May 17. doi: 10.1093/nar/gkx444. PMID:28520987 
23. Uncovering Earth's Virome
    Nature, 2016 Aug 17;536(7617):425-430. doi: 10.1038/nature19094. PMID:27533034