Bioinformatic
1. Cytoscape: a software environment for integrated models of biomolecular interaction networks.
Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T.
Genome Res. 2003 Nov;13(11):2498-504.
2. KEGG – Kyoto Encyclopedia of Genes and Genomes
Kanehisa M, Sato Y, Kawashima M, Furumichi M, Tanabe M. KEGG as a reference resource for gene and protein annotation. Nucleic Acids Res. 2016 Jan 4;44(D1):D457-62.
Predictions
Proteins. 1998 Dec 1;33(4):460-74.
Predicting peptides that bind to MHC molecules using supervised learning of hidden Markov models.
Mamitsuka H1.
Bioconductor packages
Multidrug-resistant
1. Hocquet D, Muller A, Bertrand X.
What happens in hospitals does not stay in hospitals: antibiotic-resistant bacteria in hospital wastewater systems. J Hosp Infect. 2016 Aug;93(4):395-402.
D.O. Santoro, A.M. Cardoso, F.H. Coutinho, L.H. Pinto, R.P. Vieira, R.M. Albano, M.M. Clementino
Diversity and antibiotic resistance profiles of Pseudomonads from a hospital wastewater treatment plant
2 November 2015
Keith S. Kaye, Jason M. Pogue
Infections Caused by Resistant Gram-Negative Bacteria: Epidemiology and Management
24 October 2015
Daniela Jones-Dias, Vera Manageiro, Manuela Caniça
Influence of agricultural practice on mobile bla genes: IncI1-bearing CTX-M, SHV, CMY and TEM in Escherichia coli from intensive farming soils
14 October 2015
T.P.G. Chagas, L.M. Seki, J.C. Cury, J.A.L. Oliveira, A.M.R. Dávila, D.M. Silva, M.D. Asensi
Multiresistance, beta-lactamase-encoding genes and bacterial diversity in hospital wastewater in Rio de Janeiro, Brazil
4 July 2011
T. Tängdén, C. G. Giske
Global dissemination of extensively drug-resistant carbapenemase-producing Enterobacteriaceae: clinical perspectives on detection, treatment and infection control
27 January 2015
C. Lee Ventola, MS The Antibiotic Resistance Crisis. Part 1: Causes and Threats. P T. 2015 Apr; 40(4): 277–283.PMCID: PMC4378521
Imunnology
Trypanosoma cruzi immunology
1. http://www.msc.es/biblioPublic/publicaciones/recursos_propios/resp/revista_cdrom/vol87/Suplemento_Chagas/RS87C_Chagas.pdf
Trypanosoma cruzi evolution
1. Trypanosoma cruzi: um parasita, dois parasitas ou vários parasitas da doença
de chagas?
Trypanosoma cruzi: one parasite, two parasites or several parasites of chagas disease?
Bianca Zingales. Revista da Biologia (2011) 6b: 44-48
2. Differentiation of Trypanosoma cruzi I (TcI) and T. cruzi II (TcII) genotypes using genes encoding serine carboxypeptidases.
de Araújo CA, Mayer C, Waniek PJ, Azambuja P, Jansen AM. Parasitol Res. 2016 Jul 28.
Braz J Med Biol Res. 2011 Feb;44(2):84-90. Epub 2011 Jan 14.
Evasion of immune responses by Trypanosoma cruzi, the etiological agent of Chagas disease.
DosReis GA1.
Cardoso MS1, Reis-Cunha JL1, Bartholomeu DC1. Evasion of the Immune Response by Trypanosoma cruzi during Acute Infection. Front Immunol. 2016 Jan 18;6:659. doi: 10.3389/fimmu.2015.00659. eCollection 2015.
Infect Immun. 2005 Oct;73(10):6974-80.
Toll-like receptor 2 regulates interleukin-1beta-dependent cardiomyocyte hypertrophy triggered by Trypanosoma cruzi.
Petersen CA1, Krumholz KA, Burleigh BA.
Gravina HD1, Antonelli L, Gazzinelli RT, Ropert C. Differential use of TLR2 and TLR9 in the regulation of immune responses during the infection with Trypanosoma cruzi. PLoS One. 2013 May 1;8(5):e63100. doi: 10.1371/journal.pone.0063100. Print 2013.
Trypanosoma cruzi isolation and triatomine
1. Fernandes CD1, Murta SM, Cerávolo IP, Krug LP, Vidigal PG, Steindel M, Nardi N, Romanha AJ. Characterization of Trypanosoma cruzi strains isolated from chronic chagasic patients, triatomines and opossums naturally infected from the State of Rio Grande do Sul, Brazil. Mem Inst Oswaldo Cruz. 1997 May-Jun;92(3):343-51.
2. Ribeiro AR1, Mendonça VJ2, Alves RT3, Martinez I2, Araújo RF4, Mello F5, da Rosa JA2. Trypanosoma cruzi strains from triatomine collected in Bahia and Rio Grande do Sul, Brazil. Rev Saude Publica. 2014 Apr;48(2):295-302.
3. Ribeiro AR1, Oliveira RC2, Ceretti Junior W3, Lima L4, Almeida LA5, Nascimento JD1, Teixeira MM4, Rosa JA5. Trypanosoma cruzi isolated from a triatomine found in one of the biggest metropolitan areas of Latin America. Rev Soc Bras Med Trop. 2016 Apr;49(2):183-9. doi: 10.1590/0037-8682-0366-2015.
4. Lauricella MA1, Stariolo RL, Riarte AR, Segura EL, Gürtler RE. Distribution and pathogenicity of Trypanosoma cruzi isolated from peridomestic populations of Triatoma infestans and Triatoma guasayana from rural Western Argentina. Mem Inst Oswaldo Cruz. 2005 Apr;100(2):123-9.
5. Barbosa-Silva AN1, Câmara AC1, Martins K1, Nunes DF2, Oliveira PI1, Azevedo PR3, Chiari E2, Galvão LM1. Characteristics of Triatomine infestation and natural Trypanosoma cruzi infection in the State of Rio Grande do Norte, Brazil. Rev Soc Bras Med Trop. 2016 Feb;49(1):57-67.
Márcio Costa Vinhaesa et al. Assessing the vulnerability of Brazilian municipalities to the vectorial transmission of Trypanosoma cruzi using multi-criteria decision analysis
Acta Tropical. Volume 137, September 2014, Pages 105–110
Biedermann T1, Zimmermann S, Himmelrich H, Gumy A, Egeter O, Sakrauski AK, Seegmüller I, Voigt H, Launois P, Levine AD, Wagner H, Heeg K, Louis JA, Röcken M. IL-4 instructs TH1 responses and resistance to Leishmania major in susceptible BALB/c mice. Nat Immunol. 2001 Nov;2(11):1054-60.
Hurdayal R1, Brombacher F2.The role of IL-4 and IL-13 in cutaneous Leishmaniasis. Immunol Lett. 2014 Oct;161(2):179-83. doi: 10.1016/j.imlet.2013.12.022. Epub 2014 Jan 8.
Immunology Letters 99 (2005) 17–23
Review
T helper (h)1/Th2 and Leishmania: paradox rather than paradigm
James Alexander ∗, Karen Bryson
M. T. M. Roberts Current understandings on the immunology of leishmaniasis and recent developments in prevention and treatment
Sacks D1, Noben-Trauth N. The immunology of susceptibility and resistance to Leishmania major in mice. Nat Rev Immunol. 2002 Nov;2(11):845-58.
Matthews DJ1, Emson CL, McKenzie GJ, Jolin HE, Blackwell JM, McKenzie AN. IL-13 is a susceptibility factor for Leishmania major infection. J Immunol. 2000 Feb 1;164(3):1458-62.
Felizardo TC1, Gaspar-Elsas MI, Lima GM, Abrahamsohn IA. Lack of signaling by IL-4 or by IL-4/IL-13 has more attenuating effects on Leishmania amazonensis dorsal skin–than on footpad-infected mice. Exp Parasitol. 2012 Jan;130(1):48-57. doi: 10.1016/j.exppara.2011.09.015. Epub 2011 Oct 12.
Buxbaum LU1, Uzonna JE, Goldschmidt MH, Scott P. Control of New World cutaneous leishmaniasis is IL-12 independent but STAT4 dependent. Eur J Immunol. 2002 Nov;32(11):3206-15.
Trypanosoma cruzi evolution
Mem Inst Oswaldo Cruz. 2003 Jan;98(1):1-12. Epub 2003 Apr 9.
Should Trypanosoma cruzi be called “cruzi” complex? a review of the parasite diversity and the potential of selecting population after in vitro culturing and mice infection.
Devera R1, Fernandes O, Coura JR.
Esther Von Stebut. Leishmaniasis. JDDG 26 February 2015. http://onlinelibrary.wiley.com/doi/10.1111/ddg.12595/full
Alvar J1, Vélez ID, Bern C, Herrero M, Desjeux P, Cano J, Jannin J, den Boer M; WHO Leishmaniasis Control Team.Leishmaniasis worldwide and global estimates of its incidence. PLoS One. 2012;7(5):e35671. doi: 10.1371/journal.pone.0035671. Epub 2012 May 31.
Sites – Bioinfo
ANN
1. http://neuralnetworksanddeeplearning.com/chap4.html
2. http://cs231n.github.io/neural-networks-1/
SNP
1. https://onlinecourses.science.psu.edu/stat555/node/106
ASD
1. Abrahams BS1, Arking DE, Campbell DB, Mefford HC, Morrow EM, Weiss LA, Menashe I, Wadkins T, Banerjee-Basu S, Packer A. SFARI Gene 2.0: a community-driven knowledgebase for the autism spectrum disorders (ASDs). Mol Autism. 2013 Oct 3;4(1):36. doi: 10.1186/2040-2392-4-36.
2. Cotney J1, Muhle RA2, Sanders SJ3, Liu L4, Willsey AJ3, Niu W2, Liu W1, Klei L5, Lei J4, Yin J1, Reilly SK1, Tebbenkamp AT6, Bichsel C6, Pletikos M6, Sestan N6, Roeder K7, State MW8, Devlin B5, Noonan JP1.
The autism-associated chromatin modifier CHD8 regulates other autism risk genes during human neurodevelopment. Nat Commun. 2015 Mar 10;6:6404. doi: 10.1038/ncomms7404.
GP63 – Leishmanolysin
PLoS One. 2014 Apr 15;9(4):e95007. doi: 10.1371/journal.pone.0095007. eCollection 2014.
Absence of metalloprotease GP63 alters the protein content of Leishmania exosomes.
Hassani K1, Shio MT1, Martel C1, Faubert D2, Olivier M1.
Subcell Biochem. 2014;74:253-70. doi: 10.1007/978-94-007-7305-9_11.
GP63 function in the interaction of trypanosomatids with the invertebrate host: facts and prospects.
d’Avila-Levy CM1, Altoé EC, Uehara LA, Branquinha MH, Santos AL.
An Acad Bras Cienc. 2006 Dec;78(4):687-714.
The ubiquitous gp63-like metalloprotease from lower trypanosomatids: in the search for a function.
Santos AL1, Branquinha MH, D’Avila-Levy CM.
Front Cell Infect Microbiol. 2012 May 16;2:72. doi: 10.3389/fcimb.2012.00072. eCollection 2012.
Impact of Leishmania metalloprotease GP63 on macrophage signaling.
Isnard A1, Shio MT, Olivier M.
Microbes Infect. 2012 Dec;14(15):1377-89. doi: 10.1016/j.micinf.2012.05.014. Epub 2012 Jun 6.
Leishmania virulence factors: focus on the metalloprotease GP63.
Olivier M1, Atayde VD, Isnard A, Hassani K, Shio MT.