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Items: 49

1.

Metallothionein 3 Controls the Phenotype and Metabolic Programming of Alternatively Activated Macrophages.

Chowdhury D, Alrefai H, Landero Figueroa JA, Candor K, Porollo A, Fecher R, Divanovic S, Deepe GS Jr, Subramanian Vignesh K.

Cell Rep. 2019 Jun 25;27(13):3873-3886.e7. doi: 10.1016/j.celrep.2019.05.093.

2.

The S52F FOXF1 Mutation Inhibits STAT3 Signaling and Causes Alveolar Capillary Dysplasia.

Pradhan A, Dunn A, Ustiyan V, Bolte C, Wang G, Whitsett JA, Zhang Y, Porollo A, Hu YC, Xiao R, Szafranski P, Shi D, Stankiewicz P, Kalin TV, Kalinichenko VV.

Am J Respir Crit Care Med. 2019 Jun 14. doi: 10.1164/rccm.201810-1897OC. [Epub ahead of print]

PMID:
31199666
3.

The bZIP mutant CEBPB (V285A) has sequence specific DNA binding propensities similar to CREB1.

Ray S, Ufot A, Assad N, Singh J, Durell SR, Porollo A, Tillo D, Vinson C.

Biochim Biophys Acta Gene Regul Mech. 2019 Apr;1862(4):486-492. doi: 10.1016/j.bbagrm.2019.02.002. Epub 2019 Feb 27.

PMID:
30825655
4.

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.

Ray S, Tillo D, Assad N, Ufot A, Deppmann C, Durell SR, Porollo A, Vinson C.

Biochem Biophys Res Commun. 2018 Jul 2;501(4):905-912. doi: 10.1016/j.bbrc.2018.05.080. Epub 2018 May 18.

5.

The 14th International Workshops on Opportunistic Protists (IWOP 14).

Cushion MT, Limper AH, Porollo A, Saper VE, Sinai AP, Weiss LM.

J Eukaryot Microbiol. 2018 Nov;65(6):934-939. doi: 10.1111/jeu.12631. Epub 2018 May 25.

PMID:
29722096
6.

Ultrastructure of Highly Ordered Granules in Alveolar Type II Cells in Several Species.

Miller ML, Porollo A, Wert S.

Anat Rec (Hoboken). 2018 Mar 15;301(7):1290-1302. doi: 10.1002/ar.23805. [Epub ahead of print]

7.

Congenital heart disease and aortic arch variants associated with mutation in PHOX2B.

Lombardo RC, Porollo A, Cnota JF, Hopkin RJ.

Genet Med. 2018 Dec;20(12):1538-1543. doi: 10.1038/gim.2018.34. Epub 2018 Mar 15.

PMID:
29543228
8.

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.

Cushion MT, Ashbaugh A, Hendrix K, Linke MJ, Tisdale N, Sayson SG, Porollo A.

Antimicrob Agents Chemother. 2018 Apr 26;62(5). pii: e02513-17. doi: 10.1128/AAC.02513-17. Print 2018 May.

9.

CoeViz: A Web-Based Integrative Platform for Interactive Visualization of Large Similarity and Distance Matrices.

Baker FN, Porollo A.

Data (Basel). 2018 Mar;3(1). pii: 4. doi: 10.3390/data3010004. Epub 2018 Jan 13.

10.

The Epstein-Barr Virus B-ZIP Protein Zta Recognizes Specific DNA Sequences Containing 5-Methylcytosine and 5-Hydroxymethylcytosine.

Tillo D, Ray S, Syed KS, Gaylor MR, He X, Wang J, Assad N, Durell SR, Porollo A, Weirauch MT, Vinson C.

Biochemistry. 2017 Nov 28;56(47):6200-6210. doi: 10.1021/acs.biochem.7b00741. Epub 2017 Nov 10.

11.

Calpain-14 and its association with eosinophilic esophagitis.

Litosh VA, Rochman M, Rymer JK, Porollo A, Kottyan LC, Rothenberg ME.

J Allergy Clin Immunol. 2017 Jun;139(6):1762-1771.e7. doi: 10.1016/j.jaci.2016.09.027. Epub 2017 Jan 25. Review.

12.

A fast and robust protocol for metataxonomic analysis using RNAseq data.

Cox JW, Ballweg RA, Taft DH, Velayutham P, Haslam DB, Porollo A.

Microbiome. 2017 Jan 19;5(1):7. doi: 10.1186/s40168-016-0219-5.

13.

Cadherin 26 is an alpha integrin-binding epithelial receptor regulated during allergic inflammation.

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.

Mucosal Immunol. 2017 Sep;10(5):1190-1201. doi: 10.1038/mi.2016.120. Epub 2017 Jan 4.

14.

A Quantitative Model to Estimate Drug Resistance in Pathogens.

Baker FN, Cushion MT, Porollo A.

J Fungi (Basel). 2016 Dec;2(4). pii: 30. doi: 10.3390/jof2040030. Epub 2016 Dec 5.

15.

Functional Characterization of Pneumocystis carinii Inositol Transporter 1.

Cushion MT, Collins MS, Sesterhenn T, Porollo A, Vadukoot AK, Merino EJ.

MBio. 2016 Dec 13;7(6). pii: e01851-16. doi: 10.1128/mBio.01851-16.

16.

IL-4 Induces Metallothionein 3- and SLC30A4-Dependent Increase in Intracellular Zn(2+) that Promotes Pathogen Persistence in Macrophages.

Subramanian Vignesh K, Landero Figueroa JA, Porollo A, Divanovic S, Caruso JA, Deepe GS Jr.

Cell Rep. 2016 Sep 20;16(12):3232-3246. doi: 10.1016/j.celrep.2016.08.057.

17.

CoeViz: a web-based tool for coevolution analysis of protein residues.

Baker FN, Porollo A.

BMC Bioinformatics. 2016 Mar 8;17:119. doi: 10.1186/s12859-016-0975-z.

18.

An XRCC4 splice mutation associated with severe short stature, gonadal failure, and early-onset metabolic syndrome.

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.

J Clin Endocrinol Metab. 2015 May;100(5):E789-98. doi: 10.1210/jc.2015-1098. Epub 2015 Mar 5.

19.

Phenome-wide association study (PheWAS) in EMR-linked pediatric cohorts, genetically links PLCL1 to speech language development and IL5-IL13 to Eosinophilic Esophagitis.

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.

Front Genet. 2014 Nov 18;5:401. doi: 10.3389/fgene.2014.00401. eCollection 2014.

20.

Comparative genomics of pneumocystis species suggests the absence of genes for myo-inositol synthesis and reliance on inositol transport and metabolism.

Porollo A, Sesterhenn TM, Collins MS, Welge JA, Cushion MT.

MBio. 2014 Nov 4;5(6):e01834. doi: 10.1128/mBio.01834-14.

21.

EC2KEGG: a command line tool for comparison of metabolic pathways.

Porollo A.

Source Code Biol Med. 2014 Sep 2;9:19. doi: 10.1186/1751-0473-9-19. eCollection 2014.

22.

MutaCYP: Classification of missense mutations in human cytochromes P450.

Fechter K, Porollo A.

BMC Med Genomics. 2014 Jul 30;7:47. doi: 10.1186/1755-8794-7-47.

23.

Zinc sequestration: arming phagocyte defense against fungal attack.

Subramanian Vignesh K, Landero Figueroa JA, Porollo A, Caruso JA, Deepe GS Jr.

PLoS Pathog. 2013;9(12):e1003815. doi: 10.1371/journal.ppat.1003815. Epub 2013 Dec 26. Review. No abstract available.

24.

Granulocyte macrophage-colony stimulating factor induced Zn sequestration enhances macrophage superoxide and limits intracellular pathogen survival.

Subramanian Vignesh K, Landero Figueroa JA, Porollo A, Caruso JA, Deepe GS Jr.

Immunity. 2013 Oct 17;39(4):697-710. doi: 10.1016/j.immuni.2013.09.006.

25.

Rational engineering of the fungal P450 monooxygenase CYP5136A3 to improve its oxidizing activity toward polycyclic aromatic hydrocarbons.

Syed K, Porollo A, Miller D, Yadav JS.

Protein Eng Des Sel. 2013 Sep;26(9):553-7. doi: 10.1093/protein/gzt036. Epub 2013 Jul 31.

26.

Heparin-binding motifs and biofilm formation by Candida albicans.

Green JV, Orsborn KI, Zhang M, Tan QK, Greis KD, Porollo A, Andes DR, Long Lu J, Hostetter MK.

J Infect Dis. 2013 Nov 15;208(10):1695-704. doi: 10.1093/infdis/jit391. Epub 2013 Jul 31.

27.

CYP63A2, a catalytically versatile fungal P450 monooxygenase capable of oxidizing higher-molecular-weight polycyclic aromatic hydrocarbons, alkylphenols, and alkanes.

Syed K, Porollo A, Lam YW, Grimmett PE, Yadav JS.

Appl Environ Microbiol. 2013 Apr;79(8):2692-702. doi: 10.1128/AEM.03767-12. Epub 2013 Feb 15.

28.

Control of nutrient stress-induced metabolic reprogramming by PKCζ in tumorigenesis.

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.

Cell. 2013 Jan 31;152(3):599-611. doi: 10.1016/j.cell.2012.12.028.

29.

Effects of parabens on adipocyte differentiation.

Hu P, Chen X, Whitener RJ, Boder ET, Jones JO, Porollo A, Chen J, Zhao L.

Toxicol Sci. 2013 Jan;131(1):56-70. doi: 10.1093/toxsci/kfs262. Epub 2012 Sep 5.

30.

On setting up and assessing docking simulations for virtual screening.

Biesiada J, Porollo A, Meller J.

Methods Mol Biol. 2012;928:1-16. doi: 10.1007/978-1-62703-008-3_1.

PMID:
22956129
31.

Analysis of current antifungal agents and their targets within the Pneumocystis carinii genome.

Porollo A, Meller J, Joshi Y, Jaiswal V, Smulian AG, Cushion MT.

Curr Drug Targets. 2012 Nov;13(12):1575-85. Review.

32.

Tumor-suppressing function of caspase-2 requires catalytic site Cys-320 and site Ser-139 in mice.

Ren K, Lu J, Porollo A, Du C.

J Biol Chem. 2012 Apr 27;287(18):14792-802. doi: 10.1074/jbc.M112.347625. Epub 2012 Mar 6.

33.

A fungal P450 (CYP5136A3) capable of oxidizing polycyclic aromatic hydrocarbons and endocrine disrupting alkylphenols: role of Trp(129) and Leu(324).

Syed K, Porollo A, Lam YW, Yadav JS.

PLoS One. 2011;6(12):e28286. doi: 10.1371/journal.pone.0028286. Epub 2011 Dec 2.

34.

p62 is a key regulator of nutrient sensing in the mTORC1 pathway.

Duran A, Amanchy R, Linares JF, Joshi J, Abu-Baker S, Porollo A, Hansen M, Moscat J, Diaz-Meco MT.

Mol Cell. 2011 Oct 7;44(1):134-46. doi: 10.1016/j.molcel.2011.06.038.

35.

Interleukin-6 receptor enhances early colonization of the murine omentum by upregulation of a mannose family receptor, LY75, in ovarian tumor cells.

Giridhar PV, Funk HM, Gallo CA, Porollo A, Mercer CA, Plas DR, Drew AF.

Clin Exp Metastasis. 2011 Dec;28(8):887-97. doi: 10.1007/s10585-011-9420-x. Epub 2011 Sep 2.

PMID:
21887537
36.

Survey of public domain software for docking simulations and virtual screening.

Biesiada J, Porollo A, Velayutham P, Kouril M, Meller J.

Hum Genomics. 2011 Jul;5(5):497-505. Review.

37.

Enhanced prediction of conformational flexibility and phosphorylation in proteins.

Swaminathan K, Adamczak R, Porollo A, Meller J.

Adv Exp Med Biol. 2010;680:307-19. doi: 10.1007/978-1-4419-5913-3_35.

PMID:
20865514
38.

Mitochondria-specific transgenic overexpression of connexin-43 simulates preconditioning-induced cytoprotection of stem cells.

Lu G, Haider HKh, Porollo A, Ashraf M.

Cardiovasc Res. 2010 Nov 1;88(2):277-86. doi: 10.1093/cvr/cvq293. Epub 2010 Sep 10.

39.

POLYVIEW-MM: web-based platform for animation and analysis of molecular simulations.

Porollo A, Meller J.

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W662-6. doi: 10.1093/nar/gkq445. Epub 2010 May 26.

40.
41.

Transcriptome of Pneumocystis carinii during fulminate infection: carbohydrate metabolism and the concept of a compatible parasite.

Cushion MT, Smulian AG, Slaven BE, Sesterhenn T, Arnold J, Staben C, Porollo A, Adamczak R, Meller J.

PLoS One. 2007 May 9;2(5):e423.

42.

Draft assembly and annotation of the Pneumocystis carinii genome.

Slaven BE, Meller J, Porollo A, Sesterhenn T, Smulian AG, Cushion MT.

J Eukaryot Microbiol. 2006;53 Suppl 1:S89-91. No abstract available.

PMID:
17169080
43.

Large-scale characterization of introns in the Pneumocystis carinii genome.

Slaven BE, Porollo A, Sesterhenn T, Smulian AG, Cushion MT, Meller J.

J Eukaryot Microbiol. 2006;53 Suppl 1:S151-3. No abstract available.

PMID:
17169040
44.

Prediction-based fingerprints of protein-protein interactions.

Porollo A, Meller J.

Proteins. 2007 Feb 15;66(3):630-45.

PMID:
17152079
45.

Enhanced recognition of protein transmembrane domains with prediction-based structural profiles.

Cao B, Porollo A, Adamczak R, Jarrell M, Meller J.

Bioinformatics. 2006 Feb 1;22(3):303-9. Epub 2005 Nov 17.

PMID:
16293670
46.

Linear regression models for solvent accessibility prediction in proteins.

Wagner M, Adamczak R, Porollo A, Meller J.

J Comput Biol. 2005 Apr;12(3):355-69.

PMID:
15857247
47.

Combining prediction of secondary structure and solvent accessibility in proteins.

Adamczak R, Porollo A, Meller J.

Proteins. 2005 May 15;59(3):467-75.

PMID:
15768403
48.

Accurate prediction of solvent accessibility using neural networks-based regression.

Adamczak R, Porollo A, Meller J.

Proteins. 2004 Sep 1;56(4):753-67.

PMID:
15281128
49.

POLYVIEW: a flexible visualization tool for structural and functional annotations of proteins.

Porollo AA, Adamczak R, Meller J.

Bioinformatics. 2004 Oct 12;20(15):2460-2. Epub 2004 Apr 8.

PMID:
15073023

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