Publications

Select Articles in Scientific Journals

Most recent

  • Ojha M, Smith NJ, Devine AJ, Joshi R, Goodman EM, Fan Q, Schuman R, Porollo A, Wells JM, Tiwary E, Batie MR, Gray J, Deshmukh H, Borchers MT, Ammerman SA, Varisco BM. Anti-CELA1 antibody KF4 prevents emphysema by inhibiting stretch- mediated remodeling. JCI Insight. 2024 Jan 9;9(1):e169189. doi: 10.1172/jci.insight.169189. PMID: 38193533.
  • Van Camp PJ, Prasath VBS, Haslam DB, Porollo A. MGS2AMR: a gene-centric mining of metagenomic sequencing data for pathogens and their antimicrobial resistance profile. Microbiome. 2023 Oct 13;11(1):223. doi: 10.1186/s40168-023-01674-z. PMID: 37833777; PMCID: PMC10571262.
  • Elliott KH, Balchand SK, Bonatto Paese CL, Chang CF, Yang Y, Brown KM, Rasicci DT, He H, Thorner K, Chaturvedi P, Murray SA, Chen J, Porollo A, Peterson KA, Brugmann SA. Identification of a heterogeneous and dynamic ciliome during embryonic development and cell differentiation. Development. 2023 Apr 15;150(8):dev201237. doi: 10.1242/dev.201237. Epub 2023 Apr 27. PMID: 36971348; PMCID: PMC10163354.
  • Tran C, Khadkikar S, Porollo A. Survey of Protein Sequence Embedding Models. Int J Mol Sci. 2023 Feb 14;24(4):3775. doi: 10.3390/ijms24043775. PMID: 36835188; PMCID: PMC9963412.
  • Marsili L, Davis JL, Espay AJ, Gilthorpe J, Williams C, Kauffman MA, Porollo A. SOD1-Related Cerebellar Ataxia and Motor Neuron Disease: Cp Variant as Functional Modifier? Cerebellum. 2023 Feb 9. doi: 10.1007/s12311-023-01527-3. Epub ahead of print. PMID: 36757662.

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. PMID: 21981924; PMCID: PMC3190169.
  • Porollo A, Meller J. Prediction-based fingerprints of protein-protein interactions. Proteins. 2007 Feb 15;66(3):630-45. 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. 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. 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. PMID: 32085478; PMCID: PMC7072858.
  • 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. PMID: 26956673; 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. PMID: 25370490; 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. PMID: 23904501; 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.