Publications

Select Articles in Scientific Journals

Most recent

  • Van Camp PJ, Porollo A. SEQ2MGS: an effective tool for generating realistic artificial metagenomes from the existing sequencing data. NAR Genom Bioinform. 2022 Jul 25;4(3):lqac050. doi: 10.1093/nargab/lqac050. PMID: 35899079; PMCID: PMC9310082.
  • Ray S, Tillo D, Assad N, Ufot A, Porollo A, Durell SR, Vinson C. Altering the Double-Stranded DNA Specificity of the bZIP Domain of Zta with Site-Directed Mutagenesis at N182. ACS Omega. 2021 Dec 28;7(1):129-139. doi: 10.1021/acsomega.1c04148. PMID: 35036684; PMCID: PMC8756438.
  • Chowdhury D, Gardner JC, Satpati A, Nookala S, Mukundan S, Porollo A, Landero Figueroa JA, Subramanian Vignesh K. Metallothionein 3-Zinc Axis Suppresses Caspase-11 Inflammasome Activation and Impairs Antibacterial Immunity. Front Immunol. 2021 Nov 12;12:755961. doi: 10.3389/fimmu.2021.755961. PMID: 34867993; PMCID: PMC8633875.
  • Brusilovsky M, Rochman M, Rochman Y, Caldwell JM, Mack LE, Felton JM, Habel JE, Porollo A, Pasare C, Rothenberg ME. Environmental allergens trigger type 2 inflammation through ripoptosome activation. Nat Immunol. 2021 Oct;22(10):1316-1326. doi: 10.1038/s41590-021-01011-2. Epub 2021 Sep 16. PMID: 34531562; PMCID: PMC8487942.
  • Corcoran D, Maltbie N, Sudalairaj S, Baker FN, Hirschfeld J, Porollo A. CoeViz 2: Protein Graphs Derived from Amino Acid Covariance. Front Bioinform. 2021;1:653681. doi: 10.3389/fbinf.2021.653681. Epub 2021 Jun 24. PMID: 35694032; PMCID: PMC9187035.
  • Cushion MT, Tisdale-Macioce N, Sayson SG, Porollo A. The Persistent Challenge of Pneumocystis Growth Outside the Mammalian Lung: Past and Future Approaches. Front Microbiol. 2021 May 20;12:681474. doi: 10.3389/fmicb.2021.681474. PMID: 34093506; PMCID: PMC8174303.

Most cited (over 300 citations)

  • Duran A, Amanchy R, Linares JF, Joshi J, Abu-Baker S, Porollo A, Hansen M, Moscat J, Diaz-Meco MT. p62 is a key regulator of nutrient sensing in the mTORC1 pathway. Mol Cell. 2011 Oct 7;44(1):134-46. doi: 10.1016/j.molcel.2011.06.038. PubMed PMID: 21981924; PubMed Central PMCID: PMC3190169.
  • Porollo A, Meller J. Prediction-based fingerprints of protein-protein interactions. Proteins. 2007 Feb 15;66(3):630-45. PubMed PMID: 17152079.
  • Adamczak R, Porollo A, Meller J. Combining prediction of secondary structure and solvent accessibility in proteins. Proteins. 2005 May 15;59(3):467-75. PubMed PMID: 15768403.
  • Adamczak R, Porollo A, Meller J. Accurate prediction of solvent accessibility using neural networks-based regression. Proteins. 2004 Sep 1;56(4):753-67. doi: 10.1002/prot.20176. PMID: 15281128.

Other representative articles

  • Van Camp PJ, Haslam DB, Porollo A. Prediction of Antimicrobial Resistance in Gram-Negative Bacteria From Whole-Genome Sequencing Data. Front Microbiol. 2020 May 25;11:1013. doi: 10.3389/fmicb.2020.01013. PMID: 32528441; PMCID: PMC7262952.
  • Van Camp PJ, Haslam DB, Porollo A. Bioinformatics Approaches to the Understanding of Molecular Mechanisms in Antimicrobial Resistance. Int J Mol Sci. 2020 Feb 18;21(4). pii: E1363. doi: 10.3390/ijms21041363. Review. PubMed PMID: 32085478; PubMed Central PMCID: PMC7072858.
  • Cox JW, Ballweg RA, Taft DH, Velayutham P, Haslam DB, Porollo A. A fast and robust protocol for metataxonomic analysis using RNAseq data. Microbiome. 2017 Jan 19;5(1):7. doi: 10.1186/s40168-016-0219-5. PubMed PMID: 28103917; PubMed Central PMCID: PMC5244565.
  • Baker FN, Porollo A. CoeViz: a web-based tool for coevolution analysis of protein residues. BMC Bioinformatics. 2016 Mar 8;17(1):119. doi: 10.1186/s12859-016-0975-z. PubMed PMID: 26956673; PubMed Central PMCID: PMC4782369.
  • Porollo A, Sesterhenn TM, Collins MS, Welge JA, Cushion MT. Comparative Genomics of Pneumocystis Species Suggests the Absence of Genes for myo-Inositol Synthesis and Reliance on Inositol Transport and Metabolism. MBio. 2014 Nov 4;5(6). pii: e01834-14. doi: 10.1128/mBio.01834-14. PubMed PMID: 25370490; PubMed Central PMCID: PMC4222102.
  • Syed K, Porollo A, Miller D, Yadav JS. Rational engineering of the fungal P450 monooxygenase CYP5136A3 to improve its oxidizing activity toward polycyclic aromatic hydrocarbons. Protein Eng Des Sel. 2013 Sep;26(9):553-7. doi: 10.1093/protein/gzt036. Epub 2013 Jul 31. PubMed PMID: 23904501; PubMed Central PMCID: PMC3751181.

Book Chapters

  • Porollo A, Cushion MT. Advances in Genomics Research of Pneumocystis Species. In: Reference Module in Life Sciences; J. Nosanchuk, ed. Elsevier 2020; pp. 1-8.
  • Biesiada J, Porollo A, Meller J. On setting up and assessing docking simulations for virtual screening. In: Rational Drug Design - Methods and Protocols; Y. Zheng, ed. Springer 2012; 928: pp. 1-16.
  • Porollo A, Meller J. Computational Methods for Prediction of Protein-Protein Interaction Sites. In: Protein-Protein Interactions - Computational and Experimental Tools; W. Cai and H. Hong, Eds. InTech 2012; 472: pp. 3-26.
  • Swaminathan K, Adamczak R, Porollo A, Meller J. Enhanced prediction of conformational flexibility and phosphorylation in proteins. In: Advances in Computational Biology, Advances in Experimental Medicine and Biology; H.R. Arabnia, Ed. Springer 2010; 680: pp. 307-319.