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Items: 41

1.

Structure and function of the global topsoil microbiome.

Bahram M, Hildebrand F, Forslund SK, Anderson JL, Soudzilovskaia NA, Bodegom PM, Bengtsson-Palme J, Anslan S, Coelho LP, Harend H, Huerta-Cepas J, Medema MH, Maltz MR, Mundra S, Olsson PA, Pent M, Põlme S, Sunagawa S, Ryberg M, Tedersoo L, Bork P.

Nature. 2018 Aug;560(7717):233-237. doi: 10.1038/s41586-018-0386-6. Epub 2018 Aug 1.

PMID:
30069051
2.

Immediate start of antiretroviral, why not?

Matsuda EM, Coelho LPO, Ahagon CM, Campos IB, Brígido LFM.

Braz J Infect Dis. 2018 May - Jun;22(3):250-251. doi: 10.1016/j.bjid.2018.05.006. Epub 2018 Jun 22. No abstract available.

3.

Similarity of the dog and human gut microbiomes in gene content and response to diet.

Coelho LP, Kultima JR, Costea PI, Fournier C, Pan Y, Czarnecki-Maulden G, Hayward MR, Forslund SK, Schmidt TSB, Descombes P, Jackson JR, Li Q, Bork P.

Microbiome. 2018 Apr 19;6(1):72. doi: 10.1186/s40168-018-0450-3.

4.

Selective maternal seeding and environment shape the human gut microbiome.

Korpela K, Costea P, Coelho LP, Kandels-Lewis S, Willemsen G, Boomsma DI, Segata N, Bork P.

Genome Res. 2018 Apr;28(4):561-568. doi: 10.1101/gr.233940.117. Epub 2018 Mar 1.

5.

Subspecies in the global human gut microbiome.

Costea PI, Coelho LP, Sunagawa S, Munch R, Huerta-Cepas J, Forslund K, Hildebrand F, Kushugulova A, Zeller G, Bork P.

Mol Syst Biol. 2017 Dec 14;13(12):960. doi: 10.15252/msb.20177589.

6.

Quantitative 3D-imaging for cell biology and ecology of environmental microbial eukaryotes.

Colin S, Coelho LP, Sunagawa S, Bowler C, Karsenti E, Bork P, Pepperkok R, de Vargas C.

Elife. 2017 Oct 31;6. pii: e26066. doi: 10.7554/eLife.26066.

7.

High Prevalence of Drug Resistance Mutations Among Patients Failing First-Line Antiretroviral Therapy and Predictors of Virological Response 24 Weeks After Switch to Second-Line Therapy in São Paulo State, Brazil.

Matsuda EM, Coelho LPO, Romero GF, de Moraes MJ, Lopez-Lopes GIS, Morejon K, Campeas AE, Cabral GB, Brígido LFM.

AIDS Res Hum Retroviruses. 2017 Nov 27. doi: 10.1089/AID.2017.0052. [Epub ahead of print]

PMID:
28969448
8.

Towards standards for human fecal sample processing in metagenomic studies.

Costea PI, Zeller G, Sunagawa S, Pelletier E, Alberti A, Levenez F, Tramontano M, Driessen M, Hercog R, Jung FE, Kultima JR, Hayward MR, Coelho LP, Allen-Vercoe E, Bertrand L, Blaut M, Brown JRM, Carton T, Cools-Portier S, Daigneault M, Derrien M, Druesne A, de Vos WM, Finlay BB, Flint HJ, Guarner F, Hattori M, Heilig H, Luna RA, van Hylckama Vlieg J, Junick J, Klymiuk I, Langella P, Le Chatelier E, Mai V, Manichanh C, Martin JC, Mery C, Morita H, O'Toole PW, Orvain C, Patil KR, Penders J, Persson S, Pons N, Popova M, Salonen A, Saulnier D, Scott KP, Singh B, Slezak K, Veiga P, Versalovic J, Zhao L, Zoetendal EG, Ehrlich SD, Dore J, Bork P.

Nat Biotechnol. 2017 Nov;35(11):1069-1076. doi: 10.1038/nbt.3960. Epub 2017 Oct 2.

PMID:
28967887
9.

metaSNV: A tool for metagenomic strain level analysis.

Costea PI, Munch R, Coelho LP, Paoli L, Sunagawa S, Bork P.

PLoS One. 2017 Jul 28;12(7):e0182392. doi: 10.1371/journal.pone.0182392. eCollection 2017.

10.

Erratum to: Functional implications of microbial and viral gut metagenome changes in early stage L-DOPA-naïve Parkinson's disease patients.

Bedarf JR, Hildebrand F, Coelho LP, Sunagawa S, Bahram M, Goeser F, Bork P, Wüllner U.

Genome Med. 2017 Jun 29;9(1):61. doi: 10.1186/s13073-017-0451-z. No abstract available.

11.

Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper.

Huerta-Cepas J, Forslund K, Coelho LP, Szklarczyk D, Jensen LJ, von Mering C, Bork P.

Mol Biol Evol. 2017 Aug 1;34(8):2115-2122. doi: 10.1093/molbev/msx148.

12.

Functional implications of microbial and viral gut metagenome changes in early stage L-DOPA-naïve Parkinson's disease patients.

Bedarf JR, Hildebrand F, Coelho LP, Sunagawa S, Bahram M, Goeser F, Bork P, Wüllner U.

Genome Med. 2017 Apr 28;9(1):39. doi: 10.1186/s13073-017-0428-y. Erratum in: Genome Med. 2017 Jun 29;9(1):61.

13.

Undiagnosed acute HIV infection identified through RNA testing of pooled serum samples obtained during a dengue outbreak in São Paulo, Brazil.

Matsuda EM, Colpas DR, Campos NC, Coelho LP, Carmo AM, Brígido LF.

Rev Soc Bras Med Trop. 2017 Jan-Feb;50(1):110-112. doi: 10.1590/0037-8682-0370-2016.

14.

MOCAT2: a metagenomic assembly, annotation and profiling framework.

Kultima JR, Coelho LP, Forslund K, Huerta-Cepas J, Li SS, Driessen M, Voigt AY, Zeller G, Sunagawa S, Bork P.

Bioinformatics. 2016 Aug 15;32(16):2520-3. doi: 10.1093/bioinformatics/btw183. Epub 2016 Apr 8.

15.

Plankton networks driving carbon export in the oligotrophic ocean.

Guidi L, Chaffron S, Bittner L, Eveillard D, Larhlimi A, Roux S, Darzi Y, Audic S, Berline L, Brum J, Coelho LP, Espinoza JCI, Malviya S, Sunagawa S, Dimier C, Kandels-Lewis S, Picheral M, Poulain J, Searson S; Tara Oceans coordinators, Stemmann L, Not F, Hingamp P, Speich S, Follows M, Karp-Boss L, Boss E, Ogata H, Pesant S, Weissenbach J, Wincker P, Acinas SG, Bork P, de Vargas C, Iudicone D, Sullivan MB, Raes J, Karsenti E, Bowler C, Gorsky G.

Nature. 2016 Apr 28;532(7600):465-470. doi: 10.1038/nature16942. Epub 2016 Feb 10.

16.

Gene expression changes in the salivary glands of Anopheles coluzzii elicited by Plasmodium berghei infection.

Pinheiro-Silva R, Borges L, Coelho LP, Cabezas-Cruz A, Valdés JJ, do Rosário V, de la Fuente J, Domingos A.

Parasit Vectors. 2015 Sep 23;8:485. doi: 10.1186/s13071-015-1079-8.

17.

Transmission of a multidrug-resistant HIV-1 from an occupational exposure, in São Paulo, Brazil.

López-Lopes GI, Coelho LP, Hornke L, Volpato AP, Lopércio AP, Cabral GB, Ferreira JL, Domingues CS, Brígido LF.

AIDS. 2015 Jul 31;29(12):1580-3. doi: 10.1097/QAD.0000000000000751. No abstract available.

PMID:
26244399
18.

Glucagon induces airway smooth muscle relaxation by nitric oxide and prostaglandin E₂.

Insuela DB, Daleprane JB, Coelho LP, Silva AR, e Silva PM, Martins MA, Carvalho VF.

J Endocrinol. 2015 Jun;225(3):205-17. doi: 10.1530/JOE-14-0648.

19.

Ocean plankton. Structure and function of the global ocean microbiome.

Sunagawa S, Coelho LP, Chaffron S, Kultima JR, Labadie K, Salazar G, Djahanschiri B, Zeller G, Mende DR, Alberti A, Cornejo-Castillo FM, Costea PI, Cruaud C, d'Ovidio F, Engelen S, Ferrera I, Gasol JM, Guidi L, Hildebrand F, Kokoszka F, Lepoivre C, Lima-Mendez G, Poulain J, Poulos BT, Royo-Llonch M, Sarmento H, Vieira-Silva S, Dimier C, Picheral M, Searson S, Kandels-Lewis S; Tara Oceans coordinators, Bowler C, de Vargas C, Gorsky G, Grimsley N, Hingamp P, Iudicone D, Jaillon O, Not F, Ogata H, Pesant S, Speich S, Stemmann L, Sullivan MB, Weissenbach J, Wincker P, Karsenti E, Raes J, Acinas SG, Bork P.

Science. 2015 May 22;348(6237):1261359. doi: 10.1126/science.1261359.

20.

Transmitted Drug Resistance Among Recently Diagnosed Adults and Children in São Paulo, Brazil.

Guimarães PM, Ferreira JL, Coelho LP, Cavalcanti Jde S, Lopes GI, Matsuda EM, Almeida FJ, Almeida VC, Campeas AE, Junior LC, Brígido LF; Sa˜o Paulo Salvage Workgroup.

AIDS Res Hum Retroviruses. 2015 Dec;31(12):1219-24. doi: 10.1089/AID.2014.0354. Epub 2015 May 4.

PMID:
25826640
21.

Automatic determination of NET (neutrophil extracellular traps) coverage in fluorescent microscopy images.

Coelho LP, Pato C, Friães A, Neumann A, von Köckritz-Blickwede M, Ramirez M, Carriço JA.

Bioinformatics. 2015 Jul 15;31(14):2364-70. doi: 10.1093/bioinformatics/btv156. Epub 2015 Mar 19.

PMID:
25792554
22.

High degree of concordance between flow cytometry and geno2pheno methods for HIV-1 tropism determination in proviral DNA.

Torres AJ, Brígido LF, Abrahão MH, Angelo AL, de Jesus Ferreira G, Coelho LP, Ferreira JL, Jorge CR, Netto EM, Brites C.

Braz J Infect Dis. 2015 Mar-Apr;19(2):163-9. doi: 10.1016/j.bjid.2014.11.007. Epub 2015 Feb 18.

23.

An HIV-1 transmission case possibly associated with manicure care.

Matsuda EM, Coelho LP, Pimentel VF, Onias HB, Brigido LF.

AIDS Res Hum Retroviruses. 2014 Nov;30(11):1150-3. doi: 10.1089/aid.2014.0264.

PMID:
25354026
24.

Genotypic tropism prediction from paired cell and plasma using single and replicate sequences.

Coelho LP, Ferreira JL, Cabral GB, Guimarães PM, Brigido LF.

AIDS Res Hum Retroviruses. 2014 Jul;30(7):711-6. doi: 10.1089/AID.2013.0258. Epub 2014 Apr 24.

PMID:
24673579
25.

Metagenomic insights into the human gut resistome and the forces that shape it.

Forslund K, Sunagawa S, Coelho LP, Bork P.

Bioessays. 2014 Mar;36(3):316-29. doi: 10.1002/bies.201300143. Epub 2014 Jan 29. Review.

PMID:
24474281
26.

Host-cell sensors for Plasmodium activate innate immunity against liver-stage infection.

Liehl P, Zuzarte-Luís V, Chan J, Zillinger T, Baptista F, Carapau D, Konert M, Hanson KK, Carret C, Lassnig C, Müller M, Kalinke U, Saeed M, Chora AF, Golenbock DT, Strobl B, Prudêncio M, Coelho LP, Kappe SH, Superti-Furga G, Pichlmair A, Vigário AM, Rice CM, Fitzgerald KA, Barchet W, Mota MM.

Nat Med. 2014 Jan;20(1):47-53. doi: 10.1038/nm.3424. Epub 2013 Dec 22.

27.

Metagenomic species profiling using universal phylogenetic marker genes.

Sunagawa S, Mende DR, Zeller G, Izquierdo-Carrasco F, Berger SA, Kultima JR, Coelho LP, Arumugam M, Tap J, Nielsen HB, Rasmussen S, Brunak S, Pedersen O, Guarner F, de Vos WM, Wang J, Li J, Doré J, Ehrlich SD, Stamatakis A, Bork P.

Nat Methods. 2013 Dec;10(12):1196-9. doi: 10.1038/nmeth.2693. Epub 2013 Oct 20.

PMID:
24141494
28.

Mangiferin prevents guinea pig tracheal contraction via activation of the nitric oxide-cyclic GMP pathway.

Vieira AB, Coelho LP, Insuela DB, Carvalho VF, dos Santos MH, Silva PM, Martins MA.

PLoS One. 2013 Aug 8;8(8):e71759. doi: 10.1371/journal.pone.0071759. eCollection 2013. Erratum in: PLoS One. 2013;8(9). doi:10.1371/annotation/48d07c62-084f-4c46-b8cf-564ff59f1bd4.

29.

Determining the subcellular location of new proteins from microscope images using local features.

Coelho LP, Kangas JD, Naik AW, Osuna-Highley E, Glory-Afshar E, Fuhrman M, Simha R, Berget PB, Jarvik JW, Murphy RF.

Bioinformatics. 2013 Sep 15;29(18):2343-9. doi: 10.1093/bioinformatics/btt392. Epub 2013 Jul 8.

30.

Two for one: cyclic AMP mediates the anti-inflammatory and anti-spasmodic properties of the non-anesthetic lidocaine analog JMF2-1.

Olsen PC, Coelho LP, da Costa JC, Cordeiro RS, Silva PM, Martins MA.

Eur J Pharmacol. 2012 Apr 5;680(1-3):102-7. doi: 10.1016/j.ejphar.2012.01.040. Epub 2012 Feb 4.

31.

Evaluation of genotypic prediction of HIV-1 tropism using population sequencing of replicates.

Ferreira JL, Coelho LP, Rodrigues R, Cabral GB, Cavalcanti Jde S, Guimaraes PM, Brigido LF.

J Virol Methods. 2012 Feb;179(2):325-9. doi: 10.1016/j.jviromet.2011.11.018. Epub 2011 Nov 26.

32.

Concordance of HIV type 1 tropism phenotype to predictions using web-based analysis of V3 sequences: composite algorithms may be needed to properly assess viral tropism.

Cabral GB, Ferreira JL, Coelho LP, Fonsi M, Estevam DL, Cavalcanti JS, Brígido LF.

AIDS Res Hum Retroviruses. 2012 Jul;28(7):734-8. doi: 10.1089/AID.2011.0251. Epub 2011 Dec 2.

33.

Structured Literature Image Finder: Parsing Text and Figures in Biomedical Literature.

Ahmed A, Arnold A, Coelho LP, Kangas J, Sheikh AS, Xing E, Cohen W, Murphy RF.

Web Semant. 2010 Jul 1;8(2-3):151-154.

34.

Quantifying the distribution of probes between subcellular locations using unsupervised pattern unmixing.

Coelho LP, Peng T, Murphy RF.

Bioinformatics. 2010 Jun 15;26(12):i7-12. doi: 10.1093/bioinformatics/btq220.

35.

Automated image analysis for high-content screening and analysis.

Shariff A, Kangas J, Coelho LP, Quinn S, Murphy RF.

J Biomol Screen. 2010 Aug;15(7):726-34. doi: 10.1177/1087057110370894. Epub 2010 May 20. Review.

PMID:
20488979
36.

Cell cycle dependence of protein subcellular location inferred from static, asynchronous images.

Buck TE, Rao A, Coelho LP, Fuhrman MH, Jarvik JW, Berget PB, Murphy RF.

Conf Proc IEEE Eng Med Biol Soc. 2009;2009:1016-9. doi: 10.1109/IEMBS.2009.5332888.

37.

NUCLEAR SEGMENTATION IN MICROSCOPE CELL IMAGES: A HAND-SEGMENTED DATASET AND COMPARISON OF ALGORITHMS.

Coelho LP, Shariff A, Murphy RF.

Proc IEEE Int Symp Biomed Imaging. 2009;5193098:518-521.

38.

NFAT1 transcription factor regulates pulmonary allergic inflammation and airway responsiveness.

Fonseca BP, Olsen PC, Coelho LP, Ferreira TP, Souza HS, Martins MA, Viola JP.

Am J Respir Cell Mol Biol. 2009 Jan;40(1):66-75. doi: 10.1165/rcmb.2007-0102OC. Epub 2008 Jul 29.

PMID:
18664642
39.

7-Epiclusianone, a tetraprenylated benzophenone, relaxes airway smooth muscle through activation of the nitric oxide-cGMP pathway.

Coelho LP, Serra MF, Pires AL, Cordeiro RS, Rodrigues e Silva PM, dos Santos MH, Martins MA.

J Pharmacol Exp Ther. 2008 Oct;327(1):206-14. doi: 10.1124/jpet.108.138032. Epub 2008 Jun 30.

40.

Antianaphylactic properties of 7-epiclusianone, a tetraprenylated benzophenone isolated from Garcinia brasiliensis.

Neves JS, Coelho LP, Cordeiro RS, Veloso MP, Rodrigues e Silva PM, dos Santos MH, Martins MA.

Planta Med. 2007 Jun;73(7):644-9. Epub 2007 Jun 11.

PMID:
17562491
41.

Antinociceptive properties of ethanolic extract and fractions of Pterodon pubescens Benth. seeds.

Coelho LP, Reis PA, de Castro FL, Gayer CR, da Silva Lopes C, da Costa e Silva MC, de Carvalho Sabino KC, Todeschini AR, Coelho MG.

J Ethnopharmacol. 2005 Apr 8;98(1-2):109-16.

PMID:
15763371

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