Publications
Génomique
BERLAND, J.-L. ; DE CARVALHO, F. M. ; DE ALMEIDA, L. G. P. ; BABLISHVILI, N. ;
GAUTHIER, M. ; PARANHOS-BACCALA, G. ; DE VASCONCELOS, A. T. R. Draft Genome
Sequence of Mycobacterium tuberculosis Clinical Strain G-12-005. Genome
Announcements, v. 2, p. e00385-14-e00385-14, 2014. PDF available
LOBO, F. P.; GONCALVES, D. L.; ALVES, S. L.; Gerber, A. L.; DE VASCONCELOS, A. T. R.;
BASSO, L. C.; Franco, G. R.; SOARES, M. A.; CADETE, R. M.; ROSA, C. A.; STAMBUK, B.
U.. Draft Genome Sequence of the D-Xylose-Fermenting Yeast Spathaspora
arborariae UFMG-HM19.1AT. Genome Announcements, v. 2, p. e01163-13-e01163-13,
2014. PDF available
RAMOS, PABLO IVAN ; PICÃO, RENATA C ; ALMEIDA, LUIZ GONZAGA ; LIMA,
NICHOLAS COSTA ; GIRARDELLO, RAQUEL ; VIVAN, ANA CAROLINA ; XAVIER, DANILO
E ; Barcellos, Fernando G ; PELISSON, MARSILENI ; VESPERO, ELIANA C ; MÉDIGUE,
CLAUDINE ; Vasconcelos, Ana Tereza ; GALES, ANA C ; Nicolás, Marisa F .
Comparative analysis of the complete genome of KPC-2-producing Klebsiella
pneumoniae Kp13 reveals remarkable genome plasticity and a wide repertoire of
virulence and resistance mechanisms. BMC Genomics, v. 15, p. 54, 2014. PDF
available
STOCO, PATRÍCIA HERMES WAGNER, GLAUBER TALAVERA-LOPEZ, CARLOS GERBER,
ALEXANDRA ZAHA, Arnaldo THOMPSON, CLAUDIA ELIZABETH BARTHOLOMEU,
DANIELLA CASTANHEIRA LÜCKEMEYER, DÉBORA DENARDIN BAHIA, DIANA LORETO,
ELGION PRESTES, ELISA BEATRIZ LIMA, FÁBIO MITSUO RODRIGUES-LUIZ, GABRIELA
VALLEJO, GUSTAVO ADOLFO FILHO, JOSÉ FRANCO DA SILVEIRA SCHENKMAN, SÉRGIO
MONTEIRO, KARINA MARIANTE TYLER, KEVIN MORRIS ALMEIDA, LUIZ GONZAGA PAULA
DE ORTIZ, MAURO FREITAS CHIURILLO, MIGUEL ANGEL MORAES, MILENE HÖEHR DE
CUNHA, OBERDAN DE LIMA MENDONÇA-NETO, RONDON SILVA, ROSANE , et al. ;
Genome of the Avirulent Human-Infective Trypanosome-Trypanosoma rangeli. PLoS
Neglected Tropical Diseases (Online), v. 8, p. e3176, 2014. PDF available
GRISARD, E. C. ; TEIXEIRA, S. M. R. ; DE ALMEIDA, L. G. P. ; STOCO, P. H. ; Gerber, A. L. ;
TALAVERA-LOPEZ, C. ; LIMA, O. C. ; ANDERSSON, B. ; DE VASCONCELOS, A. T. R..
Trypanosoma cruzi Clone Dm28c Draft Genome Sequence. Genome
Announcements, v. 2, p. e01114-13-e01114-13, 2014. PDF available
MORILLO, VIVIANA ; ABREU, FERNANDA ; ARAUJO, ANA C. ; DE ALMEIDA, LUIZ G. P. ;
ENRICH-PRAST, ALEX ; FARINA, MARCOS; DE VASCONCELOS, ANA T. R. ; BAZYLINSKI,
DENNIS A. ; LINS, ULYSSES . Isolation, cultivation and genomic analysis of
magnetosome biomineralization genes of a new genus of South-seeking
magnetotactic cocci within the Alphaproteobacteria. Frontiers in Microbiology
(Online), v. 5, p. 1/12, 2014. PDF available
SIQUEIRA, ARTHUR FERNANDES ; ORMEÑO-ORRILLO, ERNESTO ; SOUZA, Rangel Celso ;
RODRIGUES, ELISETE PAINS ; ALMEIDA, LUIZ GONZAGA ; BARCELLOS, FERNANDO
GOMES ; BATISTA, JESIANE STEFÂNIA ; NAKATANI, ANDRE SHIGUEYOSHI ; MARTÍNEZROMERO, ESPERANZA ; Vasconcelos, Ana Tereza ; HUNGRIA, Mariangela.
Comparative genomics of Bradyrhizobium japonicum CPAC 15 and Bradyrhizobium
diazoefficiens CPAC 7: elite model strains for understanding symbiotic performance
with soybean. BMC Genomics, v. 15, p. 420, 2014. PDF available
ZULETA, LUIZ FERNANDO ; CUNHA, CLAÚDIO DE ; DE CARVALHO, FABÍOLA MARQUES ;
CIAPINA, LUCIANE PRIOLI ; SOUZA, Rangel Celso ; MERCANTE, FÁBIO MARTINS ; DE
FARIA, SERGIO MIANA ; BALDANI, JOSÉ IVO ; STRALIOTTO, ROSANGELA ; HUNGRIA,
Mariangela ; De Vasconcelos, Ana Tereza . The complete genome of Burkholderia
phenoliruptrix strain BR3459a, a symbiont of Mimosa flocculosa: highlighting the
coexistence of symbiotic and pathogenic genes. BMC Genomics, v. 15, p. 535, 2014.
PDF available
STAATS, CHARLEY CHRISTIAN ; JUNGES, ÂNGELA ; GUEDES, RAFAEL LUCAS ;
THOMPSON, CLAUDIA ELIZABETH ; DE MORAIS, GUILHERME LOSS ; BOLDO, JULIANO
TOMAZZONI ; DE ALMEIDA, LUIZ GONZAGA ; ANDREIS, FÁBIO CARRER ; GERBER,
ALEXANDRA LEHMKUHL ; SBARAINI, NICOLAU ; DA PAIXÃO, RANA LOUISE ; BROETTO,
LEONARDO ; LANDELL, MELISSA ; SANTI, LUCÉLIA ; DA SILVA, WALTER ORLANDO ;
SILVEIRA, CAROLINA PEREIRA ; SERRANO, THAIANE RISPOLI ; DE OLIVEIRA, EDER SILVA ;
KMETZSCH, LÍVIA ; VAINSTEIN, MARILENE HENNING ; De Vasconcelos, Ana Tereza;
SCHRANK, AUGUSTO. Comparative genome analysis of entomopathogenic fungi
reveals a complex set of secreted proteins. BMC Genomics, v. 15, p. 822, 2014. PDF
available
DA FONSECA, PAULO GS ; PAIVA, JORGE AP ; Almeida, Luiz GP ; Vasconcelos, Ana TR
; Freitas, Ana T . Empirical assessment of sequencing errors for high throughput
pyrosequencing data. BMC Research Notes, v. 6, p. 25, 2013. PDF available
TEIXEIRA, MARCUS M DE ALMEIDA, LUIZ GP KUBITSCHEK-BARREIRA, PAULA ALVES,
FERNANDA L KIOSHIMA, ÉRIKA S ABADIO, ANA KR FERNANDES, LARISSA
DERENGOWSKI, LORENA S FERREIRA, KAREN S Souza, Rangel C RUIZ, JERONIMO C DE
ANDRADE, NATHALIA C PAES, HUGO C NICOLA, ANDRÉ M ALBUQUERQUE, PATRÍCIA
GERBER, ALEXANDRA L MARTINS, VICENTE P PECONICK, LUISA DF NETO, ALAN
VIGGIANO CHAUCANEZ, CLAUDIA B SILVA, PATRÍCIA A CUNHA, OBERDAN L DE
OLIVEIRA, FABIANA FM DOS SANTOS, TAYNÁ C BARROS, AMANDA LN , et al.;
Comparative genomics of the major fungal agents of human and animal
Sporotrichosis: Sporothrix schenckii and Sporothrix brasiliensis. BMC Genomics, v. 15,
p. 943, 2014. PDF available
SIQUEIRA, F. M. ; THOMPSON, C. E. ; VIRGINIO, V. G. ; GONCHOROSKI, T. ; REOLON, L. ;
Almeida, Luiz G. P. ; FONSECA, M. M. ; SOUZA, Rangel Celso ; PROSDOCIMI, F. ;
SCHRANK, I. S. ; Bunselmeyer-Ferreira, H. ; Vasconcelos, Ana TR ; ZAHA, Arnaldo . New
insights on the biology of swine respiratory tract mycoplasmas from a comparative
genome analysis. BMC Genomics, v. 14, p. 175, 2013. PDF available
COSTA, M. O. C. ; BELTRAME, C. O. ; FERREIRA, F. A. ; BOTELHO, A. M. N. ; LIMA, N. C. B.
; SOUZA, R. C. ; DE ALMEIDA, L. G. P. ; VASCONCELOS, A. T. R. ; Nicolas, M. F. ;
FIGUEIREDO, A. M. S.. Complete Genome Sequence of a Variant of the MethicillinResistant Staphylococcus aureus ST239 Lineage, Strain BMB9393, Displaying Superior
Ability To Accumulate ica-Independent Biofilm. Genome Announcements, v. 1, p.
e00576-13-e00576-13, 2013. PDF available
MARINOTTI, O. CERQUEIRA, G. C. ALMEIDA, L. G. P. Ferro, M. I. T. LORETO, E. L. S. ZAHA,
Arnaldo TEIXEIRA, S. M. R. WESPISER, A. R. SILVA, A. A. E. SCHLINDWEIN, A. D.
PACHECO, A. C. L. SILVA, A. L. C. GRAVELEY, B. R. WALENZ, B. P. LIMA, B. A. RIBEIRO,
C. A. G. NUNES-SILVA, C. G. CARVALHO, C. R. SOARES, C. M. A. MENEZES, C. B. A.
MATIOLLI, C. CAFFREY, D. ARAUJO, D. A. M. OLIVEIRA, D. M. GOLENBOCK, D. , et al. ;
The Genome of Anopheles darlingi, the main neotropical malaria vector. Nucleic
Acids Research (Online), p. 1-14, 2013. PDF available
MOTTA, M. C. M. MARTINS, A. C. A. SOUZA, S. S. CATTA-PRETA, C. M. C. SILVA, R. KLEIN,
C. C. ALMEIDA, L. G. P. CUNHA, O. L. Ciapina L P BROCCHI, M. COLABARDINI, A. C.
LIMA, B. A. MACHADO, C. R. SOARES, C. M. A. PROBST, C. M. MENEZES, C. B. A.
BARTHOLOMEU, D. C. GRADIA, D. F. PAVONI, D. P. GRISARD, E. C. FANTINATTIGARBOGGINI, F. MARCHINI, F. K. RODRIGUES-LUIZ, G. F. WAGNER, G. GOLDMAN, G.
H. , et al.; Predicting the Proteins of Angomonas deanei, Strigomonas culicis and Their
Respective Endosymbionts Reveals New Aspects of the Trypanosomatidae Family.
Plos One, v. 8, p. e60209, 2013. PDF available
LEFÈVRE, CHRISTOPHER T. ; TRUBITSYN, DENIS ; ABREU, FERNANDA ; KOLINKO,
SEBASTIAN ; JOGLER, CHRISTIAN ; DE ALMEIDA, LUIZ GONZAGA PAULA ; DE
VASCONCELOS, ANA TEREZA R. ; KUBE, MICHAEL ; REINHARDT, RICHARD ; LINS, ULYSSES
; PIGNOL, DAVID ; SCHÜLER, DIRK ; BAZYLINSKI, DENNIS A. ; GINET, NICOLAS .
Comparative Genomic Analysis of Magnetotactic Bacteria from the
Deltaproteobacteria Provides New Insights into Magnetite and Greigite
Magnetosome Genes Required for Magnetotaxis. Environmental Microbiology (Print),
v. s/n, p. n/a-n/a, 2013. PDF available
ABREU, FERNANDA ; MORILLO, VIVIANA ; NASCIMENTO, FABRÍCIA F ; WERNECK,
CLARISSA ; CANTÃO, MAURICIO EGIDIO ; CIAPINA, LUCIANE PRIOLI; DE ALMEIDA, LUIZ
GONZAGA PAULA ; LEFÈVRE, CHRISTOPHER T ;BAZYLINSKI, DENNIS A ; DE
VASCONCELOS, ANA TEREZA RIBEIRO ; LINS, ULYSSES . Deciphering unusual uncultured
magnetotactic multicellular prokaryotes through genomics. The ISME Journal (Print),
v. 8, p. 1055-1068, 2013. PDF available
Pablo I.P Ramos ; Renata C Picão ; Eliana C Vespero ; Marsileni Pelisson ; ZULETA, L. F.
G. ; ALMEIDA, L. G. P. ; Alexandra L. Gerber ; VASCONCELOS, A. T. R. ; GALES, A. C. ;
Nicolás, Marisa F . Pyrosequencing-based analysis reveals a novel capsular gene
cluster in a KPC-producing Klebsiella pneumoniae clinical isolate identified in Brazil.
BMC Microbiology (Online), v. 12, p. 173, 2012. PDF available.
CUNHA, C. O. ; ZULETA, L. F. G. ; ALMEIDA, L. G. P. ; Ciapina L P ; BORGES, W. L. ;
PITARD, R. M. ; BALDANI, J. I. ; STRALIOTTO, R. ; FARIA, M. ; HUNGRIA, Mariangela ;
CAVADA, B. S. ; MERCANTE, F. M. ; VASCONCELOS, A. T. R. . Complete genome
sequence of Burkholderia phenoliruptrix BR3459a (= CLA1), a heat-tolerant nitrogenfixing symbiont of Mimosa flocculosa. Journal of Bacteriology (Print), v. 194, p. 66756676, 2012. PDF available
ORMENO-ORRILLO, E. ; MENNA, P. ; ALMEIDA, L. G. P. ; OLLERO, F. J. ; Nicolás, Marisa
F. ; RODRIGUES, E. P. ; NAKATANI, A. S. ; BATISTA, J. S. S. ; CHUEIRE, L. M. O. ; SOUZA,
Rangel Celso ; VASCONCELOS, A. T. R. ; MEGIAS M. ; HUNGRIA, Mariangela ;
MARTINEZ-ROMERO, E. Genomic basis of broad host range and environmental
adaptability of Rhizobium tropici CIAT 899 and Rhizobium sp. PRF 81 which are used
in inoculants for common bean (Phaseolus vulgaris L.). BMC Genomics, v. 13, p. 735,
2012. PDF available
Sant'Anna, Fernando H ; Almeida, Luiz GP ; Cecagno, Ricardo ; Reolon, Luciano A ;
Siqueira, Franciele M ; Machado, Maicon RS ; Vasconcelos, Ana TR ; Schrank, Irene S
. Genomic insights into the versatility of the plant growth-promoting bacterium
Azospirillum amazonense. BMC Genomics, v. 12, p. 409, 2011. PDF available
Lanzarotti, E. ; Pellizza, L. ; Bercovich, A. ; Foti, M. ; Coria, S. H. ; Vazquez, S. C. ;
Ruberto, L. ; Hernandez, E. A. ; Dias, R. L. ; Mac Cormack, W. P. ; Cicero, D. O. ; Smal,
C. ; Nicolas, M. F. ; VASCONCELOS, A. T. R. ; Marti, M. A. ; Turjanski, A. G. . Draft
Genome Sequence of Bizionia argentinensis, Isolated from Antarctic Surface Water.
Journal of Bacteriology (Print), v. 193, p. 6797-6798, 2011. PDF available
Silveira, A. C. G. ; Robertson, K. L. ; Lin, B. ; Wang, Z. ; Vora, G. J. ; VASCONCELOS, A. T.
R. ; Thompson, F. L. . Identification of non-coding RNAs in environmental vibrios.
Microbiology (Reading), p. 1, 2010. PDF available
Carvalho, Fabiola M ; Souza, Rangel C ; Barcellos, Fernando G ; HUNGRIA,
Mariangela ; Vasconcelos, Ana Tereza R . Genomic and evolutionary comparisons of
diazotrophic and pathogenic bacteria of the order Rhizobiales. BMC Microbiology
(Online), v. 10, p. 37, 2010.
PDF available
Mendes, Nuno D ; Freitas, Ana T ; Vasconcelos, Ana T ; Sagot, Marie-France .
Combination of measures distinguishes pre-miRNAs from other stem-loops in the
genome of the newly sequenced Anopheles darlingi. BMC Genomics, v. 11, p. 529,
2010. PDF available
Pinto, Fabiana G. S. ; Chueire, Ligia M. O. ; Vasconcelos, Ana Tereza R. ; Nicolás,
Marisa F. ; Almeida, Luiz G. P. ; Souza, Rangel C. ; Menna, Pâmela ; Barcellos,
Fernando G. ; Megías, Manuel ; HUNGRIA, Mariangela . Novel genes related to
nodulation, secretion systems, and surface structures revealed by a genome draft of
Rhizobium tropici strain PRF 81. Functional & Integrative Genomics, p. 1-8, 2009. PDF
available
GODOY, L ; VASCONCELOS, A. T. R. ; CHUEIRE, L ; SOUZA, R ; NICOLAS, M ;
BARCELLOS, F ; HUNGRIA, M . Genomic panorama of Bradyrhizobium japonicum
CPAC 15, a commercial inoculant strain largely established in Brazilian soils and
belonging to the same serogroup as USDA 123. Soil Biology & Biochemistry, p. 1-11,
2008. PDF available
GONZALEZ, A. ; Gonzalez-Gonzalez E. ; ESPINOSA, V. ; VASCONCELOS, A. T. R. ;
COLLADO-VIDES, J. . Impact of Transcription Units rearrangement on the evolution of
the regulatory network of gamma-proteobacteria. BMC Genomics, v. 9, p. 1-18,
2008. PDF available
Souza, Rangel Celso ; ALMEIDA, Darcy Fontoura de ; ZAHA, Arnaldo ; Morais, David
Anderson de Lima ; Vasconcelos, Ana Tereza Ribeiro de. In search of essentiality:
Mollicute-specific genes shared by twelve genomes. Genetics and Molecular
Biology, v. 30, p. 169-173, 2007. PDF available
ALarCON, F. ; VASCONCELOS, A. T. R. ; lucia Yim ; ZAHA, Arnaldo . Genes involved in
cell division in mycoplasmas. Genetics and Molecular Biology, v. 30, p. 174-181, 2007.
PDF available
Brocchi, Marcelo ; Vasconcelos, Ana Tereza Ribeiro de ; ZAHA, Arnaldo. Restrictionmodification systems in Mycoplasma spp. Genetics and Molecular Biology, v. 30, p.
236-244, 2007. PDF available
VEIGA, D. F. ; VICENTE, F.F.R. ; FUENTE A, L. ; MAIA, M. A. G. M. ; VASCONCELOS, A. T.
R. Genome-wide partialcorrelation analysis of Escherichia coli Microarray Data.
Genetics and Molecular Research, v. 6, p. 730-742, 2007. No PDF available
VASCONCELOS, A. T. R. . Swine and Poultry Pathogens: the Complete Genome
Sequences of Two Strains of Mycoplasma hyopneumoniae and a Strain of
Mycoplasma synoviae. Journal of Bacteriology, Inglaterra, v. 187, n.16, p. 5568-5577,
2005.
ESPINOSA, V ; GONZALEZ, A ; VASCONCELOS, A ; HUERTA, A ; COLLADOVIDES, J .
Comparative Studies of Transcriptional Regulation Mechanisms in a Group of Eight
Gamma-proteobacterial Genomes. Journal of Molecular Biology, Inglaterra, v. 354,
p. 184-199, 2005. PDF available
SIMPSON, Andrew John George ; CAMARGO, Anamaria ; FERRO, Jesus Aparecido ;
PARRA, Jucara ; VASCONCELOS, A. T. R. . Coordinated, Network Based Research as
a Strategic Component of Science in Brazil. Genetics and Molecular Research, v. 3,
n.1, p. 18-25, 2004. PDF available
OLIVEIRA, Marcio Ferreira da Silva ; MENDES, Daniele Quintella ; FERRARI, Luciana
Itida ; VASCONCELOS, A. T. R. . Ribosome Binding Site recognition using neural
networks.. Genetics and Molecular Biology, v. 27, n.4, p. 644-650, 2004. PDF available
CARRARO, Dirce Maria ; CAMARGO, Anamaria ; SALIM, Anna Christina M ; ALMEIDA,
Luiz Gonzaga Paula ; COSTA, Gisele Cavalcante da ; VASCONCELOS, A. T. R. ;
SIMPSON, Andrew John George . Closure of rRNA related gaps in the
Chromobacterium violaceum Genome with the PCR Assisted Contig Extension
(PACE) Protocol. Genetics and Molecular Research, v. 3, n.1, p. 53-63, 2004. PDF
available
HUNGRIA, Mariangela ; NICOLÁS, Marisa Fabiana ; GUIMARÃES, Claudia Teixeira ;
JARDIM, Sílvia Neto ; GOMES, Eliane Aparecida ; VASCONCELOS, A. T. R. . Tolerance
to Stresses and Environmental Adaptability of Chromobacterium violaceum.
Genetics and Molecular Research, v. 3, n.1, p. 102-16, 2004. PDF available
GRANGEIRO, Thalles Barbosa ; JORGE, Daniel Macedo de Melo ; BEZERRA, Walderly
Melgaço ; VASCONCELOS, A. T. R. ; SIMPSON, Andrew John George . Transport
Genes of Chromobacterium violaceum: An Overview. Genetics and Molecular
Research, v. 3, n.1, p. 117-133, 2004. PDF available
CARRARO, Dirce Maria ; CAMARGO, Anamaria ; SALIM, Anna Christina M ; MAIA, M.
A. G. M. ; VASCONCELOS, A. T. R. ; SIMPSON, Andrew John George . PCR Assisted
Contig Extension - PACE: a Stepwise Strategy for Bacterial Genome Closure.
BioTechniques, Estados Unidos, v. 34, n.3, p. 626-632, 2003. No PDF available
Vasconcelos, Ana T ; BRASILEIRO, Rede Genoma ; Simpson, A. J. G. ; VASCONCELOS,
A. T. R. . The complete genome sequence of Chromobacterium violaceum reveals
remarkable and exploitable bacterial adaptability. PNAS. Proceedings of the
National Academy of Sciences of the United States of America, v. 100, n.20, p. 1166011665, 2003. PDF available
VASCONCELOS, A. T. R. ; MAIA, M. A. G. M. ; ALMEIDA, Darcy Fontoura de . Short
interrupted palindromes on the extragenic DNA of Escherichia coli K-12, Haemophilus
influenzae Rd and Neisseria meningitidis Z2491. Bioinformatics, Inglaterra, v. 16, p. 110, 2000. PDF available
LOMBA, M. ; VASCONCELOS, A. T. R. ; PACHECO, A. B. ; ALMEIDA, Darcy Fontoura de.
Identification of yebG as a DNA damage inducible Escherichia coli gene. Fems
Microbiology Letters, Inglaterra, v. 156, n.1, p. 119-122, 1997. No PDF available
VASCONCELOS, A. T. R. ; SILVA, R. ; ALMEIDA, Darcy Fontoura de. Analysis of enteric
bacteria SOS operator sequences and description of potencial DNA damageinducible genes. Brazilian Journal Of Genetics, v. 19, n.2, p. 189-196, 1996. PDF
available
Transcriptomique
SALGADO, LEONARDO RIPPEL ; KOOP, DANIELA MARTINS ; PINHEIRO, DANIEL GUARIZ ;
RIVALLAN, RONAN ; LE GUEN, VINCENT ; NICOLÁS, Marisa Fabiana ; DE ALMEIDA, LUIZ
GONZAGA ; ROCHA, VIVIANI RIBEIRO ; MAGALHÃES, MILENA ; GERBER, ALEXANDRA
LEHMKUHL ; FIGUEIRA, ANTONIO ; CASCARDO, JÚLIO CÉZAR ; DE VASCONCELOS,
ANATEREZA RIBEIRO ; SILVA, WILSON ARAÚJO ; COUTINHO, LUIZ LEHMANN ; GARCIA,
DOMINIQUE . De novo transcriptome analysis of Hevea brasiliensis tissues by RNA-seq
and screening for molecular markers. BMC Genomics, v. 15, p. 236, 2014. PDF
available
JUNGES, ÂNGELA; BOLDO, JULIANO TOMAZZONI; SOUZA, BÁRBARA KUNZLER; GUEDES,
RAFAEL LUCAS MUNIZ; SBARAINI, NICOLAU ; KMETZSCH, LÍVIA; THOMPSON, CLAUDIA
ELIZABETH; STAATS, CHARLEY CHRISTIAN; DE ALMEIDA, LUIS GONZAGA PAULA; DE
VASCONCELOS, ANA TEREZA RIBEIRO; VAINSTEIN, MARILENE HENNING; SCHRANK,
AUGUSTO. Genomic Analyses and Transcriptional Profiles of the Glycoside Hydrolase
Family 18 Genes of the Entomopathogenic Fungus Metarhizium anisopliae. Plos One,
v. 9, p. e107864, 2014. PDF available
SIQUEIRA, FRANCIELE MABONI ; GERBER, ALEXANDRA LEHMKUHL ; GUEDES, RAFAEL
LUCAS MUNIZ ; ALMEIDA, LUIZ GONZAGA ; SCHRANK, IRENE SILVEIRA ; Vasconcelos,
Ana Tereza Ribeiro ; ZAHA, Arnaldo. Unravelling the Transcriptome Profile of the Swine
Respiratory Tract Mycoplasmas. Plos One, v. 9, p. e110327, 2014. PDF available
LIMA, PATRÍCIA DE SOUSA ; CASALETTI, LUCIANA ; BAILÃO, ALEXANDRE MELO ;
VASCONCELOS, ANA TEREZA RIBEIRO DE ; FERNANDES, GABRIEL DA ROCHA ; SOARES,
CÉLIA MARIA DE ALMEIDA. Transcriptional and Proteomic Responses to Carbon
Starvation in Paracoccidioides. PLoS Neglected Tropical Diseases (Online), v. 8, p.
e2855, 2014. PDF available
Biologie évolutionnaire
LEFÈVRE, CHRISTOPHER T.; TRUBITSYN, DENIS ; ABREU, FERNANDA ; KOLINKO,
SEBASTIAN; DE ALMEIDA, LUIZ GONZAGA PAULA ; DE VASCONCELOS, ANA TEREZA R. ;
LINS, ULYSSES ; SCHÜLER, DIRK ; GINET, NICOLAS ; PIGNOL, DAVID ; BAZYLINSKI, DENNIS
A.. Monophyletic Origin of Magnetotaxis and the First Magnetosomes. Environmental
Microbiology (Print), v. 1, p. n/a-n/a, 2013. PDF available
ALVES, JOÃO MP ; KLEIN, CECILIA C ; DA SILVA, FLÁVIA MAIA ; COSTA-MARTINS,
ANDRÉ G ; SERRANO, MYRNA G ; BUCK, GREGORY A ; Vasconcelos, Ana TR ; Sagot,
Marie-France ; TEIXEIRA, MARTA MG ; MOTTA, MARIA CRISTINA ; CAMARGO, ERNEY P .
Endosymbiosis in trypanosomatids: the genomic cooperation between bacterium
and host in the synthesis of essential amino acids is heavily influenced by multiple
horizontal gene transfers. BMC Evolutionary Biology (Online), v. 13, p. 190, 2013. PDF
available
Fernanda Abreua ; CANTAO, M. E. ; Nicolás, Marisa F ; BARCELLOS, F. G. ; Viviana
Morillo ; ALMEIDA, L. G. P. ; Fabrícia Ferreira do Nascimento ; Christopher T. Lefèvred ;
Dennis A. Bazylinskid ; VASCONCELOS, A. T. R. ; LINS, U. . Common ancestry of iron
oxide- and iron-sulfidebased biomineralization in magnetotactic bacteria. The ISME
Journal (Print), v. 35, p. 1-10, 2011. PDF available
PINEROGONZALEZ, J ; CARRILLOFARNES, O ; VASCONCELOS, A ; GONZALEZPEREZ, A ;
VASCONCELOS, A. T. R. . Conservation of key members in the course of the evolution
of the insulin signaling pathway. Biosystems, v. 95, p. 7-16, 2009. PDF available
Thompson, Cristiane C ; Vicente, Ana Carolina P ; Souza, Rangel C ; Vasconcelos,
Ana Tereza R ; Vesth, Tammi ; Alves, Nelson ; Ussery, David W ; Iida, Tetsuya ;
Thompson, Fabiano L . Genomic taxonomy of vibrios. BMC Evolutionary Biology
(Online), v. 9, p. 258, 2009. PDF available
de Mello Varani, Alessandro ; SOUZA, Rangel Celso ; Nakaya, Helder I. ; de Lima,
Wanessa Cristina ; Paula de Almeida, Luiz Gonzaga ; Kitajima, Elliot Watanabe ;
Chen, Jianchi ; Civerolo, Edwin ; Vasconcelos, Ana Tereza Ribeiro ; Van Sluys, MarieAnne . Origins of the Xylella fastidiosa Prophage-Like Regions and Their Impact in
Genome Differentiation. Plos One, v. 3, p. e4059, 2008. PDF available
Métagenomique
SOUZA, RENATA CAROLINI; HUNGRIA, Mariangela; CANTÃO, MAURÍCIO EGÍDIO;
Vasconcelos, Ana Tereza Ribeiro; NOGUEIRA, MARCO ANTONIO; VICENTE, VÂNIA
APARECIDA. Metagenomic analysis reveals microbial functional redundancies and
specificities in a soil under different tillage and crop-management regimes. Applied
Soil Ecology (Print), v. 86, p. 106-112, 2015. PDF available
PACCHIONI, RALFO G. ; CARVALHO, FABÍOLA M. ; THOMPSON, CLAUDIA E. ;
FAUSTINO, ANDRÉ L. F. ; NICOLINI, FERNANDA ; PEREIRA, TATIANA S. ; SILVA, RITA C. B. ;
CANTÃO, MAURICIO E. ; GERBER, ALEXANDRA ; VASCONCELOS, ANA T. R. ; AGNEZLIMA, LUCYMARA F. . Taxonomic and functional profiles of soil samples from Atlantic
forest and Caatinga biomes in northeastern Brazil. MicrobiologyOpen, v. 1, p. n/an/a, 2014. PDF available
SOUZA, RENATA CAROLINI ; CANTÃO, MAURICIO EGÍDIO ; Vasconcelos, Ana Tereza
Ribeiro ; NOGUEIRA, MARCO ANTONIO ; HUNGRIA, Mariangela . Soil metagenomics
reveals differences under conventional and no-tillage with crop rotation or
succession. Applied Soil Ecology (Print), v. 72, p. 49-61, 2013. PDF available
THOMPSON, CLAUDIA ELIZABETH ; BEYS-DA-SILVA, WALTER ORLANDO ; SANTI, LUCÉLIA
; BERGER, MARKUS ; VAINSTEIN, MARILENE HENNING ; GUIMARÃES, JORGE ALMEIDA ;
Vasconcelos, Ana Tereza . A potential source for cellulolytic enzyme discovery and
environmental aspects revealed through metagenomics of Brazilian mangroves.
AMB Express, v. 3, p. 65, 2013. PDF available
Bruce, Thiago ; Meirelles, Pedro M. ; Garcia, Gizele ; Paranhos, Rodolfo ; Rezende,
Carlos E. ; de Moura, Rodrigo L. ; Filho, Ronaldo-Francini ; Coni, Ericka O. C. ;
Vasconcelos, Ana Tereza ; Amado Filho, Gilberto ; Hatay, Mark ; Schmieder, Robert ;
Edwards, Robert ; Dinsdale, Elizabeth ; Thompson, Fabiano L. . Abrolhos Bank Reef
Health Evaluated by Means of Water Quality, Microbial Diversity, Benthic Cover, and
Fish Biomass Data. Plos One, v. 7, p. e36687, 2012. PDF available.
Cardoso, Alexander M. ; Cavalcante, Janaína J. V. ; Vieira, Ricardo P. ; Lima, Joyce
L. ; Grieco, Maria Angela B. ; Clementino, Maysa M. ; Vasconcelos, Ana Tereza R. ;
Garcia, Eloi S. ; de Souza, Wanderley ; Albano, Rodolpho M. ; Martins, Orlando B. .
Gut Bacterial Communities in the Giant Land Snail Achatina fulica and Their
Modification by Sugarcane-Based Diet. Plos One, v. 7, p. e33440, 2012. PDF available
Trindade-Silva, Amaro E. ; Rua, Cintia ; Silva, Genivaldo G. Z. ; Dutilh, Bas E. ; Moreira,
Ana Paula B. ; Edwards, Robert A. ; Hajdu, Eduardo ; Lobo-Hajdu, Gisele ;
Vasconcelos, Ana Tereza ; Berlinck, Roberto G. S. ; Thompson, Fabiano L. . Taxonomic
and Functional Microbial Signatures of the Endemic Marine Sponge Arenosclera
brasiliensis. Plos One, v. 7, p. e39905, 2012. PDF available
HIGASHI, SUSAN ; BARRETO, ANDRÉ ; CANTÃO, MAURÍCIO ; Vasconcelos, Ana Tereza
R . Analysis of Composition-Based Metagenomic Classification. BMC Genomics, v. 13,
p. S1, 2012. PDF available
Alexander M. Cardoso ; Janaína J.V. Cavalcante ; CANTAO, M. E. ; THOMPSON, C. E.
; Roberto B. Flatschart ; Arnaldo Glogauerb ; Sandra M.N. Scapin ; Youssef B. Sade ;
BELTRAO, P. J. ; Alexandra L. Gerber ; Orlando B. Martins ; GARCIA, E. S. ; Wanderley
de Souza ; VASCONCELOS, A. T. R. . Metagenomic Analysis of the Microbiota from
the Crop of an Invasive Snail Reveals a Rich Reservoir of Novel Genes. Plos One, v. 7,
p. e48505, 2012. PDF available
Parasitologie
AZEVEDO-MARTINS, A. C. ; MACHADO, A. C. L. ; KLEIN, C. C. ; CIAPINA, L. ;
GONZAGA, L. ; VASCONCELOS, A. T. R. ; SAGOT, M. F. ; DE SOUZA, W. ; EINICKERLAMAS, M. ; GALINA, A. ; MOTTA, M. C. M. . Mitochondrial respiration and genomic
analysis provide insight into the influence of the symbiotic bacterium on host
trypanosomatid oxygen consumption. Parasitology (London. Print), v. 1, p. 1-11, 2014.
PDF available
DE ANDRADE ROSA, IVONE ; CARUSO, MARJOLLY BRIGIDO ; RODRIGUES, SILAS PESSINI
; GERALDO, REINALDO BARROS ; KIST, LUIZA WILGES ; BOGO, MAURICIO REIS ;
GONZAGA, LUIZ ; DE VASCONCELOS, ANA TEREZA R ; MORGADO-DÍAZ, JOSE ANDRES
; ZINGALI, RUSSOLINA BENEDETA ; BENCHIMOL, MARLENE . New insights on the Golgi
complex of Tritrichomonas foetus. Parasitology (London. Print), v. sn, p. 1-13, 2013.
PDF available.
Expression génétique
FERREIRA GOLBERT, DAIANE CRISTINA ; Correa-de-Santana, Eliane ; RIBEIRO-ALVES,
MARCELO ; DE VASCONCELOS, ANA TEREZA RIBEIRO ; Savino, Wilson . ITGA6 gene
silencing by RNA interference modulates the expression of a large number of cell
migration-related genes in human thymic epithelial cells. BMC Genomics, v. 14, p. S3,
2013. PDF available
Gonzalez Perez, Abel ; Espinosa Angarica, Vladimir ; Collado-Vides, Julio ;
VASCONCELOS, A. T. R. . From sequence to dynamics: the effects of transcription
factor and polymerase concentration changes on activated and repressed
promoters. BMC Molecular Biology, v. 10, p. 92, 2009. PDF available
Métabolisme
ORTEGA, I.; SOARES FELIPE, M. S.; VASCONCELOS, A. T. R.; LOPES BEZERRA, L. M.; DA
SILVA DANTAS, A.. Peroxide sensing and signaling in the Sporothrix schenckii complex:
an in silico analysis to uncover putative mechanisms regulating the Hog1 and AP-1
like signaling pathways. Medical Mycology (Oxford. Print), v. 53, p. 51-59, 2015. PDF
available
KLEIN, CECILIA C. ; ALVES, JOÃO M. P. ; SERRANO, MYRNA G. ; BUCK, GREGORY A. ;
Vasconcelos, Ana Tereza R. ; Sagot, Marie-France ; TEIXEIRA, MARTA M. G. ;
CAMARGO, ERNEY P. ; MOTTA, MARIA CRISTINA M. . Biosynthesis of Vitamins and
Cofactors in Bacterium-Harbouring Trypanosomatids Depends on the Symbiotic
Association as Revealed by Genomic Analyses. Plos One, v. 8, p. e79786, 2013. PDF
available
KLEIN, C. C. ; COTTRET, L. ; KIELBASSA, J. ; CHARLES, H. ; GAUTIER, C. ; Vasconcelos,
Ana Tereza R ; LACROIX, V. ; SAGOT, M. . Exploration of the core metabolism of
symbiotic bacteria. BMC Genomics, v. 13, p. 438, 2012. PDF available
Bases de données
Golbert, D. C. F. ; SANTANA-VAN-VLIET, E. ; MUNDSTEIN, A. S. ; CALFO, V. ; SAVINO, W.
; DE VASCONCELOS, A. T. R. . Laminin-database v.2.0: an update on laminins in health
and neuromuscular disorders. Nucleic Acids Research, v. 42, p. D426-9, 2013. PDF
available
Varani, Alessandro M. ; Monteiro-Vitorello, Claudia B. ; Almeida, Luiz G.P. de ; Souza,
Rangel C. ; Cunha, Oberdan L. ; Lima, Wanessa C. ; Civerolo, Edwin ; Sluys, MarieAnne Van ; VASCONCELOS, A. T. R. . Xylella fastidiosa comparative genomic
database is an information resource to explore the annotation, genomic features,
and biology of different strains. Genetics and Molecular Biology (Impresso), v. 1, p.
01-0, 2012. PDF available.
Rangel Souza ; Guadalupe del Rosario Quispe Saji ; Maiana O C Costa ; Diogo S
Netto ; LIMA, N. C. B. ; KLEIN, C. C. ; de Vasconcelos, A. T. R. ; Nicolás, Marisa F .
AtlasT4SS: A curated database for type IV secretion systems. BMC Microbiology
(Online), v. 12, p. 172, 2012. PDF available
Golbert, D. C. F. ; Linhares-Lacerda, L. ; ALMEIDA, L. G. P. ; Correa-de-Santana, E. ;
OLIVEIRA, A. R. ; MUNDSTEIN, A. S. ; SAVINO, W. ; VASCONCELOS, A. T. R. . Laminin
database: a tool to retrieve high-throughput and curated data for studies on
laminins. Nucleic Acids Research, v. 193, p. 1-4, 2011. PDF available
Almeida, L. G. ; Sakabe, N. J. ; deOliveira, A. R. ; SILVA, M. C. C. ; MUNDSTEIN, A. S. ;
Cohen, T. ; Chen, Y.-T. ; Chua, R. ; Gurung, S. ; Gnjatic, S. ; Jungbluth, A. A. ;
Caballero, O. L. ; Bairoch, A. ; Kiesler, E. ; White, S. L. ; Simpson, A. J. G. ; Old, L. J. ;
Camargo, A. A. ; VASCONCELOS, A. T. R. . CTdatabase: a knowledge-base of highthroughput and curated data on cancer-testis antigens. Nucleic Acids Research, v.
37, p. D816-D819, 2009. PDF available
Bernardes, Juliana S ; Fernandez, Jorge H ; Vasconcelos, Ana Tereza R . Structural
descriptor database: a new tool for sequence based functional site prediction. BMC
Bioinformatics, v. 9, p. 492, 2008. PDF available
GONZALEZ, A. ; ESPINOSA, V. ; VASCONCELOS, A. T. R. ; COLLADO-VIDES, J. .
Tractor_DB (version 2.0): a database of regulatory interactions in. Nucleic Acids
Research, v. 35, p. D132-D136., 2007. PDF available
GONZALEZ, A. ; ESPINOSA, V. ; VASCONCELOS, A. T. R. ; PEREZ-RUEDA, E. ; COLLADOVIDES, J. . TRACTOR_DB: a Database of Regulatory Networks in GammaProteobacterial Genomes. Nucleic Acids Research, Inglaterra, v. 33, p. D98-D102,
2005. PDF available
de Vasconcelos, A. T. R. . MamMiBase: a mitochondrial genome database for
mammalian phylogenetic studies. Bioinformatics (Oxford), v. 21, p. 2566-2567, 2005.
PDF available
Cancer
Pedro A. Galante Raphael B. Parmigiani3 Qi Zhao Caballero, O. L. Jorge E. De
Souza1 Fabio C.P. Navarro Alexandra L. Gerber Nicolás, Marisa F Anna Christina M.
Salim Ana Paula M. Silva1 Lee Edsall Sylvie Devalle ALMEIDA, L. G. P. Zhen Ye
Samantha Kuan Daniel G. Pinheiro SILVA, I. T. Renato G. Pedigoni Rodrigo G. M. A.
de Sousa Thiago Y. K. Oliveira Marcelo G. de Paula Lucila Ohno-Machado Ewen F.
Kirkness Samuel Levy Wilson A. da Silva Jr , et al. ; Distinct patterns of somatic
alterations in a lymphoblastoid and a tumor genome derived from the same
individual. Nucleic Acids Research, v. 35, p. 1-13, 2011. PDF available
Zhao, Qi ; Kirkness, Ewen F ; Caballero, Otavia L ; Galante, Pedro A ; Parmigiani,
Raphael B ; Edshall, Lee ; Kuan, Samantha ; Ye, Zhen ; Levy, Samuel ; Vasconcelos,
Ana Tereza R ; Ren, Bing ; de Souza, Sandro J ; Camargo, Anamaria A ; Simpson,
Andrew JG ; Strausberg, Robert L . Systematic detection of putative tumor suppressor
genes through the combined use of exome and transcriptome sequencing.
Genome Biology (London. Print), v. 11, p. R114, 2010. PDF available
Freire, Pablo ; Vilela, Marco ; Deus, Helena ; Kim, Yong-Wan ; Koul, Dimpy ; Colman,
Howard ; Aldape, Kenneth D. ; Bogler, Oliver ; Yung, W. K. Alfred ; Coombes, Kevin ;
Mills, Gordon B. ; Vasconcelos, Ana T. ; VASCONCELOS, A. T. R. ; Almeida, Jonas S. .
Exploratory Analysis of the Copy Number Alterations in Glioblastoma Multiforme. Plos
One, v. 3, p. e4076, 2008. PDF available
Modellisation moléculaire
Fonsêca, Marbella Maria ; ZAHA, Arnaldo ; Caffarena, Ernesto R. ; Vasconcelos, Ana
Tereza Ribeiro. Structure-based functional inference of hypothetical proteins from
Mycoplasma hyopneumoniae. Journal of Molecular Modeling, v. 17, p. 1-9, 2011. PDF
available
Diversité génétique
Ramos P.L. ; Cristiane C Thompson ; VASCONCELOS, A. T. R. ; Fabiano L. Thompson . A
MLSA-based online scheme for rapid identification of Stenotrophomonas isolates.
Memórias do Instituto Oswaldo Cruz (Online), v. online, p. online, 2011. PDF available
BARRETO, K. S. ; TORRES, A. R. ; BARRETO, M. R. ; VASCONCELOS, A. T. R. ; ASTOLFOFILHO, Spartaco ; HUNGRIA, Mariangela . Diversity in antifungal activity of strains of
Chromobacterium violaceum from the Brazilian Amazon.. Journal of Industrial
Microbiology and Biotechnology, v. 1, p. 10.1007/s10295, 2008. PDF available
THOMPSON, F. ; Bruno Gomez-Gil ; VASCONCELOS, A. T. R. ; Tomoo Sawabe .
Multilocus sequence analysis reveals that Vibrio harveyi and V. campbellii form
distinct species.. Applied and Environmental Microbiology (Online), v. 13, p. 42794285, 2007. PDF available
Hungria, M. ; Astolfi-Filho, S. ; Chueire, L.M.O. ; Nicolas, M.F. ; Santos, E.B.P. ; Bulbol,
M.R. ; Souza-Filho, A. ; Nogueira Assuncao, E. ; Germano, M.G. ; Vasconcelos, A.T.R. .
Genetic characterization of Chromobacterium isolates from black water
environments in the Brazilian Amazon. Letters in Applied Microbiology, v. 41, p. 17-23,
2005. PDF available
Logiciels et outils
Correa, Miria C ; Deus, Helena F ; Vasconcelos, Ana T ; Hayashi, Yuki ; Ajani, Jaffer A ;
Patnana, Srikrishna V ; Almeida, Jonas S . AGUIA: autonomous graphical user
interface assembly for clinical trials semantic data services. BMC Medical Informatics
and Decision Making (Online), v. 10, p. 65, 2010. PDF available
Veiga, Diogo F T ; Deus, Helena F ; Akdemir, Caner ; Vasconcelos, Ana Tereza R ;
Almeida, Jonas S . DASMiner: discovering and integrating data from DAS sources.
BMC Systems Biology, v. 3, p. 109, 2009. PDF available
TSUNODA, Denise Fukumi ; LOPES, Heitor Silvério ; VASCONCELOS, A. T. R. . Webbased Tools for Biological Data Analysis. Encyclopedia of Information Science And
Technology, Estados Unidos da América, p. 3068-3073, 2005. No PDF available
ALMEIDA, Luiz Gonzaga Paula ; PAIXÃO, Roger Ferreira Cury ; SOUZA, Rangel Celso ;
COSTA, Gisele Cavalcante da ; ALMEIDA, Darcy Fontoura de ; VASCONCELOS, A. T.
R.. A New Set of Bioinformatics Tools for Genome Projects. Genetics and Molecular
Research, v. 3, n.1, p. 26-52, 2004. PDF available
ALMEIDA, L. G. P. ; VASCONCELOS, A. T. R. . A System for Automated Bacterial
(genome) Integrated Annotation--SABIA. Bioinformatics, Inglaterra, v. 20, p. 28322833, 2004. PDF available
VASCONCELOS, A. T. R. ; GUIA, M. H. ; GONZALEZ, A. ; ESPINOSA, V. ; COLLADO-VIDES,
J. Complementing computationally predicted regulatory sites in Tractor_DB using a
pattern matching approach.. In Silico Biology (Online), v. 5, p. 0020, 2004. PDF
available
Modellistion computationnelle et mathématique Souza-e-Silva, Hallan ; Savino, Wilson ; Feijóo, Raúl A. ; Vasconcelos, Ana Tereza
Ribeiro. A Cellular Automata-Based Mathematical Model for Thymocyte
Development. Plos One, v. 4, p. e8233, 2009. PDF available
Veiga, Diogo FT ; Vicente, Fábio FR ; Nicolás, Marisa F ; Vasconcelos, Ana Tereza R .
Predicting transcriptional regulatory interactions with artificial neural networks
applied to E. coli multidrug resistance efflux pumps. BMC Microbiology (Online), v. 8,
p. 101, 2008. PDF available
Espinosa Angarica, Vladimir ; Gonzalez Perez, Abel ; Vasconcelos, Ana T ; ColladoVides, Julio ; Contreras-Moreira, Bruno ; VASCONCELOS, A. T. R. . Prediction of TF
target sites based on atomistic models of protein-DNA complexes. BMC
Bioinformatics, v. 9, p. 436, 2008. PDF available
Biologie des systèmes
VILELA, M. A. ; CHOU, I. ; VINGA, S. ; VASCONCELOS, A. T. R. ; Eberhard O. Voit ;
ALMEIDA, J. S. . Parameter optimization in S-system models. BMC Systems Biology, v.
2, p. 1752-0509-2-35, 2008. PDF available
VILELA, M. A. M. ; BORGES, Carlos Cristiano ; VINGA, S. ; VASCONCELOS, A. T. R. ;
Santos Helena ; Eberhard O. Voit ; ALMEIDA, J. S. . Automated Smoother for the
Numerical Decoupling of Dynamics Models. BMC Bioinformatics, v. 8, p. 1-8, 2007.
PDF available