Publications

Papers in Journals

Highlighted are those with over 100 citations according to Google-Scholar, see public profile

    2018

  1. Ray S, Tillo D, Assad N, Ufot A, Deppmann C, Durell SR, Porollo A, Vinson C. Replacing C189 in the bZIP domain of Zta with S, T, V, or A changes DNA binding specificity to four types of double-stranded DNA. Biochem Biophys Res Commun. 2018 Jul 2;501(4):905-912. doi: 10.1016/j.bbrc.2018.05.080. Epub 2018 May 18. PubMed PMID: 29772230.
  2. Cushion MT, Limper AH, Porollo A, Saper V, Sinai AP, Weiss LM. The 14(th) International Workshops on Opportunistic Protists (IWOP 14). J Eukaryot Microbiol. 2018 May 3. doi: 10.1111/jeu.12631. [Epub ahead of print] PubMed PMID: 29722096.
  3. Cushion MT, Ashbaugh A, Hendrix K, Linke MJ, Tisdale N, Sayson SG, Porollo A. Gene Expression of Pneumocystis murina after Treatment with Anidulafungin Results in Strong Signals for Sexual Reproduction, Cell Wall Integrity, and Cell Cycle Arrest, Indicating a Requirement for Ascus Formation for Proliferation. Antimicrob Agents Chemother. 2018 Apr 26;62(5). pii: e02513-17. doi: 10.1128/AAC.02513-17. Print 2018 May. PubMed PMID: 29463544.
  4. Miller ML, Porollo A, Wert S. Ultrastructure of Highly Ordered Granules in Alveolar Type II Cells in Several Species. Anat Rec (Hoboken). 2018 Mar 15. doi: 10.1002/ar.23805. [Epub ahead of print] PubMed PMID: 29544026.
  5. Lombardo RC, Porollo A, Cnota JF, Hopkin RJ. Congenital heart disease and aortic arch variants associated with mutation in PHOX2B. Genet Med. 2018 Mar 15. doi: 10.1038/gim.2018.34. [Epub ahead of print] PubMed PMID: 29543228.
  6. Baker FN, Porollo A. CoeViz: A Web-Based Integrative Platform for Interactive Visualization of Large Similarity and Distance Matrices. Data (Basel). 2018 Mar;3(1). pii: 4. doi: 10.3390/data3010004. Epub 2018 Jan 13. PubMed PMID: 29423399; PubMed Central PMCID: PMC5798608.

    7. 2017

  7. Tillo D, Ray S, Syed KS, Gaylor MR, He X, Wang J, Assad N, Durell SR, Porollo A, Weirauch MT, Vinson C. The Epstein-Barr Virus B-ZIP Protein Zta Recognizes Specific DNA Sequences Containing 5-Methylcytosine and 5-Hydroxymethylcytosine. Biochemistry. 2017 Nov 28;56(47):6200-6210. doi: 10.1021/acs.biochem.7b00741. Epub 2017 Nov 10. PubMed PMID: 29072898.
  8. Litosh VA, Rochman M, Rymer JK, Porollo A, Kottyan LC, Rothenberg ME. Calpain-14 and its association with eosinophilic esophagitis. J Allergy Clin Immunol. 2017 Jun;139(6):1762-1771.e7. doi: 10.1016/j.jaci.2016.09.027. Epub 2017 Jan 25. Review. PubMed PMID: 28131390; PubMed Central PMCID: PMC5461191.
  9. 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.
  10. Caldwell JM, Collins MH, Kemme KA, Sherrill JD, Wen T, Rochman M, Stucke EM, Amin L, Tai H, Putnam PE, Jiménez-Dalmaroni MJ, Wormald MR, Porollo A, Abonia JP, Rothenberg ME. Cadherin 26 is an alpha integrin-binding epithelial receptor regulated during allergic inflammation. Mucosal immunology. 2017; 10(5):1190-1201. PubMed PMID: 28051089, PMCID: PMC5496811.

    11. 2016

  11. Baker FN, Cushion MT, Porollo A. A Quantitative Model to Estimate Drug Resistance in Pathogens. J Fungi (Basel). 2016 Dec;2(4). pii: 30. doi: 10.3390/jof2040030. PubMed PMID: 28018911; PubMed Central PMCID: PMC5179226.
  12. Cushion MT, Collins MS, Sesterhenn T, Porollo A, Vadukoot AK, Merino EJ. Functional Characterization of Pneumocystis carinii Inositol Transporter 1. MBio. 2016 Dec 13;7(6). pii: e01851-16. doi: 10.1128/mBio.01851-16. PubMed PMID: 27965450; PubMed Central PMCID: PMC5156303.
  13. Subramanian Vignesh K, Landero Figueroa JA, Porollo A, Divanovic S, Caruso JA, Deepe GS Jr. IL-4 Induces Metallothionein 3- and SLC30A4-Dependent Increase in Intracellular Zn(2+) that Promotes Pathogen Persistence in Macrophages. Cell Rep. 2016 Sep 20;16(12):3232-46. doi: 10.1016/j.celrep.2016.08.057. PubMed PMID: 27653687.
  14. 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.

    15. 2010-2015

  15. de Bruin C, Mericq V, Andrew SF, van Duyvenvoorde HA, Verkaik NS, Losekoot M, Porollo A, Garcia H, Kuang Y, Hanson D, Clayton P, van Gent DC, Wit JM, Hwa V, Dauber A. An XRCC4 splice mutation associated with severe short stature, gonadal failure, and early-onset metabolic syndrome. J Clin Endocrinol Metab. 2015 May;100(5):E789-98. doi: 10.1210/jc.2015-1098. Epub 2015 Mar 5. PubMed PMID: 25742519; PubMed Central PMCID: PMC4422886.
  16. Namjou B, Marsolo K, Caroll RJ, Denny JC, Ritchie MD, Verma SS, Lingren T, Porollo A, Cobb BL, Perry C, Kottyan LC, Rothenberg ME, Thompson SD, Holm IA, Kohane IS, Harley JB. Phenome-wide association study (PheWAS) in EMR-linked pediatric cohorts, genetically links PLCL1 to speech language development and IL5-IL13 to Eosinophilic Esophagitis. Front Genet. 2014 Nov 18;5:401. doi: 10.3389/fgene.2014.00401. eCollection 2014. PubMed PMID: 25477900; PubMed Central PMCID: PMC4235428.
  17. 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.
  18. Porollo A. EC2KEGG: a command line tool for comparison of metabolic pathways. Source Code Biol Med. 2014 Sep 2;9:19. doi: 10.1186/1751-0473-9-19. eCollection 2014. PubMed PMID: 25202338; PubMed Central PMCID: PMC4157228.
  19. Fechter K, Porollo A. MutaCYP: Classification of missense mutations in human cytochromes P450. BMC Med Genomics. 2014 Jul 30;7(1):47. PubMed PMID: 25073475; PubMed Central PMCID: PMC4119178.
  20. Subramanian Vignesh K, Landero Figueroa JA, Porollo A, Caruso JA, Deepe GS Jr. Zinc sequestration: arming phagocyte defense against fungal attack. PLoS Pathog. 2013 Dec;9(12):e1003815. doi: 10.1371/journal.ppat.1003815. Epub 2013 Dec 26. PubMed PMID: 24385902; PubMed Central PMCID: PMC3873440.
  21. Subramanian Vignesh K, Landero Figueroa JA, Porollo A, Caruso JA, Deepe GS Jr. Granulocyte macrophage-colony stimulating factor induced Zn sequestration enhances macrophage superoxide and limits intracellular pathogen survival. Immunity. 2013 Oct 17;39(4):697-710. doi: 10.1016/j.immuni.2013.09.006. PubMed PMID: 24138881; PubMed Central PMCID: PMC3841917.
  22. 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.
  23. Green JV, Orsborn KI, Zhang M, Tan QK, Greis KD, Porollo A, Andes DR, Long Lu J, Hostetter MK. Heparin-binding motifs and biofilm formation by Candida albicans. J Infect Dis. 2013 Nov 15;208(10):1695-704. doi: 10.1093/infdis/jit391. Epub 2013 Jul 31. PubMed PMID: 23904295.
  24. Syed K, Porollo A, Lam YW, Grimmett PE, Yadav JS. CYP63A2, a catalytically versatile fungal P450 monooxygenase capable of oxidizing higher-molecular-weight polycyclic aromatic hydrocarbons, alkylphenols, and alkanes. Appl Environ Microbiol. 2013 Apr;79(8):2692-702. doi: 10.1128/AEM.03767-12. Epub 2013 Feb 15. PubMed PMID: 23416995; PubMed Central PMCID: PMC3623170.
  25. Ma L, Tao Y, Duran A, Llado V, Galvez A, Barger JF, Castilla EA, Chen J, Yajima T, Porollo A, Medvedovic M, Brill LM, Plas DR, Riedl SJ, Leitges M, Diaz-Meco MT, Richardson AD, Moscat J. Control of nutrient stress-induced metabolic reprogramming by PKCzeta in tumorigenesis. Cell. 2013 Jan 31;152(3):599-611. doi: 10.1016/j.cell.2012.12.028. PubMed PMID: 23374352.
  26. Hu P, Chen X, Whitener RJ, Boder ET, Jones JO, Porollo A, Chen J, Zhao L. Effects of parabens on adipocyte differentiation. Toxicol Sci. 2013 Jan;131(1):56-70. doi: 10.1093/toxsci/kfs262. Epub 2012 Sep 5. PubMed PMID: 22956630; PubMed Central PMCID: PMC3621350.
  27. Porollo A, Meller J, Joshi Y, Jaiswal V, Smulian AG, Cushion MT. Analysis of current antifungal agents and their targets within the Pneumocystis carinii genome. Curr Drug Targets. 2012 Nov;13(12):1575-85. Review. PubMed PMID: 22934582.
  28. Ren K, Lu J, Porollo A, Du C. Tumor-suppressing function of caspase-2 requires catalytic site Cys-320 and site Ser-139 in mice. J Biol Chem. 2012 Apr 27;287(18):14792-802. doi: 10.1074/jbc.M112.347625. Epub 2012 Mar 6. PubMed PMID: 22396545; PubMed Central PMCID: PMC3340225.
  29. Syed K, Porollo A, Lam YW, Yadav JS. A fungal P450 (CYP5136A3) capable of oxidizing polycyclic aromatic hydrocarbons and endocrine disrupting alkylphenols: role of Trp(129) and Leu(324). PLoS One. 2011;6(12):e28286. doi: 10.1371/journal.pone.0028286. Epub 2011 Dec 2. PubMed PMID: 22164262; PubMed Central PMCID: PMC3229547.
  30. 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.
  31. Giridhar PV, Funk HM, Gallo CA, Porollo A, Mercer CA, Plas DR, Drew AF. Interleukin-6 receptor enhances early colonization of the murine omentum by upregulation of a mannose family receptor, LY75, in ovarian tumor cells. Clin Exp Metastasis. 2011 Dec;28(8):887-97. doi: 10.1007/s10585-011-9420-x. Epub 2011 Sep 2. PubMed PMID: 21887537.
  32. Biesiada J, Porollo A, Velayutham P, Kouril M, Meller J. Survey of public domain software for docking simulations and virtual screening. Hum Genomics. 2011 Jul;5(5):497-505. Review. PubMed PMID: 21807604; PubMed Central PMCID: PMC3525969.
  33. Lu G, Haider HKh, Porollo A, Ashraf M. Mitochondria-specific transgenic overexpression of connexin-43 simulates preconditioning-induced cytoprotection of stem cells. Cardiovasc Res. 2010 Nov 1;88(2):277-86. doi: 10.1093/cvr/cvq293. Epub 2010 Sep 10. PubMed PMID: 20833648; PubMed Central PMCID: PMC2952537.
  34. Porollo A, Meller J. POLYVIEW-MM: web-based platform for animation and analysis of molecular simulations. Nucleic Acids Res. 2010 Jul;38(Web Server issue):W662-6. doi: 10.1093/nar/gkq445. Epub 2010 May 26. PubMed PMID: 20504857; PubMed Central PMCID: PMC2896192.

    35. 2000-2009

  35. Korolev VL, Pivina TS, Porollo AA, Petukhova TV, Sheremetev AB, Ivshin VP. Differentiation of the molecular structures of nitro compounds as the basis for simulation of their thermal destruction processes. Russ Chem Rev. 2009; 78: 945-969.
  36. Porollo A, Meller J. Versatile annotation and publication quality visualization of protein complexes using POLYVIEW-3D. BMC Bioinformatics. 2007 Aug 29;8:316. PubMed PMID: 17727718; PubMed Central PMCID: PMC1978507.
  37. Cushion MT, Smulian AG, Slaven BE, Sesterhenn T, Arnold J, Staben C, Porollo A, Adamczak R, Meller J. Transcriptome of Pneumocystis carinii during fulminate infection: carbohydrate metabolism and the concept of a compatible parasite. PLoS One. 2007 May 9;2(5):e423. PubMed PMID: 17487271; PubMed Central PMCID: PMC1855432.
  38. Slaven BE, Meller J, Porollo A, Sesterhenn T, Smulian AG, Cushion MT. Draft assembly and annotation of the Pneumocystis carinii genome. J Eukaryot Microbiol. 2006;53 Suppl 1:S89-91. PubMed PMID: 17169080.
  39. Slaven BE, Porollo A, Sesterhenn T, Smulian AG, Cushion MT, Meller J. Large-scale characterization of introns in the Pneumocystis carinii genome. J Eukaryot Microbiol. 2006;53 Suppl 1:S151-3. PubMed PMID: 17169040.
  40. Porollo A, Meller J. Prediction-based fingerprints of protein-protein interactions. Proteins. 2007 Feb 15;66(3):630-45. PubMed PMID: 17152079.
  41. Cao B, Porollo A, Adamczak R, Jarrell M, Meller J. Enhanced recognition of protein transmembrane domains with prediction-based structural profiles. Bioinformatics. 2006 Feb 1;22(3):303-9. Epub 2005 Nov 17. PubMed PMID: 16293670.
  42. Korolev VL, Petukhova TV, Pivina TS, Porollo AA, Sheremetev AB, Souponitsky KYu, Ivshin VP. Thermal Decomposition Mechanisms of Nitro-1,2,4-triazoles: A Theoretical Study. Rus Chem Bul. 2006; 55: 1388-1410.
  43. Wagner M, Adamczak R, Porollo A, Meller J. Linear regression models for solvent accessibility prediction in proteins. J Comput Biol. 2005 Apr;12(3):355-69. PubMed PMID: 15857247.
  44. 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.
  45. Adamczak R, Porollo A, Meller J. Accurate prediction of solvent accessibility using neural networks-based regression. Proteins. 2004 Sep 1;56(4):753-67. PubMed PMID: 15281128.
  46. Porollo AA, Adamczak R, Meller J. POLYVIEW: a flexible visualization tool for structural and functional annotations of proteins. Bioinformatics. 2004 Oct 12;20(15):2460-2. Epub 2004 Apr 8. PubMed PMID: 15073023.

    47. 1990-1999

  47. Porollo AA, Lushnikov DE, Pivina TS, Ivshin VP, Zefirov NS. Computer Simulation of Thermal Decomposition Reactions of Alkyl Nitrates. Rus Chem Bul. 1999; 48: 1845-1857.
  48. Porollo AA, Lushnikov DE, Pivina TS, Ivshin VP. Computer Representation and Generation of Possible Pathways for Thermal Decomposition Reactions of Organic Compounds. J Mol Struc (THEOCHEM). 1997; 391: 117-124.

Book Chapters

  1. 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.
  2. 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.
  3. 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.

Selected Abstracts, Posters, and Oral Presentations

  1. Baker FN, Maltbie N, Hirschfeld J, Porollo A (2018) Metalloproteome landscape from the amino acid covariance perspective. 26th International Conference on Intelligent Systems for Molecular Biology (ISMB2018), Chicago, IL, USA. (International; Oral and poster presentation)
  2. Porollo A, Cox JW, Sesterhenn TM, Collins MS, Ficker L, Nikeya T, Salomonis N, Cushion MT (2017) Functional Genomics of the Mouse Model of Pneumocystis Pneumonia. International Workshop on Opportunistic Protists (IWOP-2017), Cincinnati, OH, USA. (International; Oral presentation)
  3. Cox JW, Porollo A (2017) vKLAT: A High-Throughput Alignment Tool for Mapping Shotgun Reads to Reference Database with Variants. Great Lakes Bioinformatics Conference 2017 (GLBIO2017), Chicago, IL, USA. (International; Oral presentation)
  4. Baker FN, Porollo A (2016) A covariance-based model to estimate antimicrobial drug resistance. The Protein Society 30th Annual Symposium, Baltimore, MD, USA. (International; Poster)
  5. Baker FN, Porollo A (2016) Prediction of Metal Binding Sites in Proteins Using Coevolution Data. Great Lakes Bioinformatics Conference 2016 (GLBIO2016), Toronto, ON, Canada. (International; Oral presentation)
  6. Cox JW, Ballweg RA, Velayutham P, Haslam DB, Porollo A (2016) An Accurate RNAseq-based Protocol for Metagenomic Taxonomy Classification. Great Lakes Bioinformatics Conference 2016 (GLBIO2016), Toronto, ON, Canada. (International; Poster)
  7. Baker FN, Porollo A (2015) Comparative Analysis of Gene Expression Profiles Perturbed by Lupus Inducing Drugs. Great Lakes Bioinformatics Conference 2015 (GLBIO2015), West Lafayette, IN, USA.
  8. Cox J, Cushion MT, Porollo A (2015) On Optimizing a Computational Pipeline for Analysis of Lung Microbiome. Great Lakes Bioinformatics Conference 2015 (GLBIO2015), West Lafayette, IN, USA.
  9. A. Porollo, JS Yadav (2014) Rational engineering of the fungal P450 monooxygenase CYP5136A3 to improve its oxidizing activity toward polycyclic aromatic hydrocarbons. Great Lakes Bioinformatics Conference 2014 (GLBIO2014), Cincinnati, OH, USA.
  10. A. Porollo, M.S. Collins, M.T. Cushion (2013) Toward Deciphering Metabolic Strategies of the Obligate Fungal Pathogen Pneumocystis carinii. 6th Annual RECOMB/ISCB Conference on Regulatory and Systems Genomics, Toronto, ON, Canada.
  11. A. Porollo (2012) Towards Improved Sequence-based Prediction of Protein-Protein Interaction Sites. Great Lakes Bioinformatics Conference (GLBIO 2012), Ann Arbor, MI, USA.
  12. A. Porollo, J. Meller (2010) POLYVIEW: Web-based Platform for Protein Structure Analysis and Visualization. 18th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB2010), Boston, MA, USA.
  13. M. Phatak, B. Cao, R. Adamczak, A. Porollo, M. Wagner, J. Meller (2010) Prediction of interaction sites in membrane proteins. Ohio Collaborative Conference on Bioinformatics (OCCBIO'10), Columbus, OH, USA.
  14. A. Porollo, M.S. Collins, M.T. Cushion (2010) QSAR study of new inhibitors for Pneumocystis carinii oxidosqualene cyclase. 11th International Workshops for Opportunistic Protists (IWOP'10), Hilo, HI, USA.
  15. A. Porollo, S.-M. Ho (2009) Bioinformatics insights into androgen signaling pathways: Identification of alternative points of disruption and intervention. 9th International Congress of Andrology (ICA`09), Barcelona, Spain.
  16. G. Lu, H.Kh. Haider, A. Porollo, M. Ashraf (2009) Mitochondrial Connexin-43 Shares A Common BH3 Motif With Bcl-2 Family Members To Impart Cytoprotection In Preconditioned Sca-1+ Cells Via Regulation Of Cytochrome-C Release. American Heart Association Resuscitation Science Symposium (AHA-ReSS'09), Orlando, FL, USA.
  17. A. Porollo, J. Chen, J.O. Jones, M.I. Diamond, P.G. Green, N.A. Gee, A.J. Conley, A.J. Duleba, B.L. Lasley (2009) Possible mechanisms in triclocarban disruption of endocrine function. The Endocrine Society's Annual Meeting (ENDO 09), Washington, DC, USA.
  18. A. Porollo, B. Cao, J. Meller (2007) Biases in Lipid Accessibility Prediction Can Be Used for the Recognition of Protein Interaction Interfaces in Soluble Proteins. Proceedings of International Conference on Bioinformatics & Computational Biology (BIOCOMP'07 / WORLDCOMP'07), Las Vegas, NV, USA, P 439-445.
  19. A. Porollo, R. Adamczak, M. Wagner, J. Meller (2003) Maximum Feasibility Approach for Consensus Classifiers: Applications to Protein Structure Prediction. Proceedings of 2nd International Conference on CIRAS (Computational Intelligence, Robotics and Autonomous Systems), Singapore, P 120 (1-6).
  20. A.A. Porollo, T.S. Pivina, V.P. Ivshin (1998) Theoretical Technique for Modeling of 1,3,3-Trinitroazetidine (TNAZ) Thermal Decomposition. Proceedings of 24th International Pyrotechnics Seminar, Monterey, USA, P. 445-455.
  21. A.A. Porollo (1997) Computer-aided modeling of the processes of nitramines thermal decomposition. Proceedings of Research Conference "Advances in chemistry of organic compounds of nitrogen", St.-Peterburg, Russia, P. 16.
 

Last modified: Tue Jul 3 10:13:58 EDT 2018