Diego Mauricio Riano Pachon

  • Endereço para acessar este CV: http://lattes.cnpq.br/2580825196325707
  • Última atualização do currículo em 30/07/2018


I have a bachelor in Biology from the Universidad Nacional de Colombia (2001), a Doctorate in Plant Molecular Biology from the Universitaet Potsdam (2008), a Postdoc in Bioinformatics from the Max Planck Institute for Molecular Plant Physiology (2010), and a postdoc in applied bioinformatics for microalgae from the Institute of Chemistry, University of São Paulo (2018). Since May 2018 I am an Assistant Professor at the Center for Nuclear Energy in Agriculture (CENA/USP). My areas of expertise are biology, bioinformatics and computational and evolutionary biology. I am interested in the evolution of biological networks in general, and gene regulatory networks in particular; as well as in the evolution of gene families, molecular characterization of organisms, predicting the function of non-coding RNAs, genome assembly and annotation, machine learning, classification problems, identification and evolution of protein domains and the development of integrative databases for omics data. Recently, in my research group, we have been working mostly with data coming from Next Generation Sequencing technologies. We have dealt with 454, Illumina and PacBio datasets in order to reconstruct full genome sequences and call polymorphims from bacteria, green algae, angiosperms and fungi. We have also reconstructed complex transcriptomes from angiosperms and fungi, focused on organisms interactions and enzyme and biofuel production, in order to elucidate their molecular basis. Between January 2017 and April 2018 I was a postdoctoral guest researcher in the Laboratory of Regulatory Systems Biology lead by Prof. Dr. Flavia Vischi Winck at IQ/USP. From February 2013 and November 2016 I was a researcher at the Labóratorio Nacional de Ciência e Tecnologia do Bioetanol part of the Centro Nacional de Pesquisa em Energia e Materiais, Campinas, Brazil, leading the research group in Computational, Evolutionary and Systems Biology. Between August 2010 and December 2012 I was the leader of the research group "Computational and Evolutionary Biology" at the Universidad de Los Andes in Bogotá, Colombia, while serving as Assistant Professor in Computational Biology/Bioinformatics. (Texto informado pelo autor)


Identificação


Nome
Diego Mauricio Riano Pachon
Nome em citações bibliográficas
Riano-Pachon, DM;Riano-Pachon, Diego Mauricio;Riano-Pachon, Diego M;RIAÑO-PACHÓN, DIEGO MAURICIO;RIAÑO-PACHÓN, DIEGO M.;RIANO-PACHON, D. M.;RIAÑO-PACHÓN, DIEGO;RIANO-PACHON, DIEGO M.;RIAÑO-PACHÓN, D. M.;RIAÑO-PACHÓN, D.M.;Riaño, Diego;Riaño, D;RIAñO-PACHóN, DIEGO MAURICIO;RIAÑO PACHÓN, DIEGO M.;PACHÓN, DIEGO MAURICIO RIAÑO

Endereço


Endereço Profissional
Universidade de São Paulo, Centro de Energia Nuclear na Agricultura.
Avenida Centenário 303
São Dimas
13416000 - Piracicaba, SP - Brasil
Telefone: (19) 34294723


Formação acadêmica/titulação


2005 - 2008
Doutorado em Plant Molecular Biology.
University of Potsdam, UNI/Potsdam, Alemanha.
Título: Identification of trasncription factor genes in plants, Ano de obtenção: 2008.
Orientador: Prof. Dr. Bernd Mueller-Roeber.
Palavras-chave: plant molecular biology; evolution; gene families; viridiplantae; trasncription regulation; gene regulatory networks.
Grande área: Ciências Biológicas
Grande Área: Ciências Biológicas / Área: Biologia Geral / Subárea: Phylogenetics.
Grande Área: Ciências Biológicas / Área: Biologia Geral / Subárea: Computational biology.
1993 - 2001
Graduação em Biología.
Universidad Nacional de Colombia - Bogotá, UNAL/Bogotá, Colômbia.
Título: Diversidad genética y estructura de la población de Vibrio choierae en Colombia.
Orientador: Emilia María Valenzuela de Silva.


Pós-doutorado


2017 - 2018
Pós-Doutorado.
Universidade de São Paulo, USP, Brasil.
Grande área: Ciências Biológicas
Grande Área: Ciências Biológicas / Área: Bioquímica.
Grande Área: Ciências Biológicas / Área: Biologia Geral / Subárea: Molecular Physiology.
2010 - 2010
Pós-Doutorado.
Ohio State University, OSU, Estados Unidos.
Bolsista do(a): Human Frontier Science Program, HFSP, Estados Unidos.
Grande área: Ciências Biológicas
Grande Área: Ciências Biológicas / Área: Biologia Geral / Subárea: Bioinformatics.
Grande Área: Ciências Biológicas / Área: Biologia Geral / Subárea: Phylogenetics.
2008 - 2010
Pós-Doutorado.
Max-Planck-Institut für molekulare Pflanzenphysiologie, MPIMP, Alemanha.
Grande área: Ciências Biológicas
Grande Área: Ciências Biológicas / Área: Biologia Geral / Subárea: Genomics.
Grande Área: Ciências Biológicas / Área: Biologia Geral / Subárea: Phylogenetics.


Formação Complementar


2016 - 2016
Extensão universitária em PostGIS. (Carga horária: 32h).
Dextra Soluções em Informática S/C Ltda., DEXTRA, Brasil.


Atuação Profissional



Centro Nacional de Pesquisa em Energia e Materiais, CNPEM, Brasil.
Vínculo institucional

2013 - 2016
Vínculo: Formal labor contract, Enquadramento Funcional: Researcher, Carga horária: 40, Regime: Dedicação exclusiva.

Atividades

02/2013 - 11/2016
Pesquisa e desenvolvimento , Laboratório Nacional de Ciência e Tecnologia do Bioetanol, .


Universidad de los Andes Colombia, UNIANDES, Colômbia.
Vínculo institucional

2010 - 2012
Vínculo: , Enquadramento Funcional: Assistant Professor, Carga horária: 48, Regime: Dedicação exclusiva.
Outras informações
Group leader in Computational and Evolutionary Biology

Atividades

01/2012 - 12/2012
Direção e administração, Departamento of Biological Sciences, .

Cargo ou função
Coordinator of the Department Seminar, in charge of securing invited speakers, hosting them and publishing invitations.
08/2011 - 12/2012
Direção e administração, Departamento of Biological Sciences, .

Cargo ou função
Committee for managing sequencing facility, in charge of computational infraestructure.
08/2010 - 12/2012
Pesquisa e desenvolvimento , Departamento of Biological Sciences, Computational and Evolutionary Biology Group.

08/2010 - 12/2012
Ensino, Master in Biological Sciences, Nível: Pós-Graduação

Disciplinas ministradas
Bioinformatics
Computer programming for biological sciences
08/2010 - 12/2012
Ensino, Biology, Nível: Graduação

Disciplinas ministradas
Cell Biology
08/2010 - 12/2012
Conselhos, Comissões e Consultoria, Departamento of Biological Sciences, .

Cargo ou função
Leader committee for hiring a Professor in Computational Biology.

Max-Planck-Institut für molekulare Pflanzenphysiologie, MPIMP, Alemanha.
Vínculo institucional

2008 - 2010
Vínculo: Civil servant, Enquadramento Funcional: Postdoctoral fellow, Regime: Dedicação exclusiva.

Atividades

08/2008 - 07/2010
Pesquisa e desenvolvimento , Bioinformatics, .

08/2008 - 03/2009
Ensino, Molecular Plant Physiology, Nível: Pós-Graduação

Disciplinas ministradas
Non-coding RNAs
Molecular plant science: Genetics, molecular biology and evolution

University of Potsdam, UNI/Potsdam, Alemanha.
Vínculo institucional

2002 - 2008
Vínculo: , Enquadramento Funcional: Research Assistant, Regime: Dedicação exclusiva.
Outras informações
Research assistant in Bioinformatics

Atividades

01/2005 - 07/2008
Treinamentos ministrados , Biochemistry and Biology, Molecular Biology.

Treinamentos ministrados
Introduction to biological databases
09/2002 - 07/2008
Pesquisa e desenvolvimento , Biochemistry and Biology, Molecular Biology.


Universidad Nacional de Colombia - Bogotá, UNAL/Bogotá, Colômbia.
Vínculo institucional

2001 - 2002
Vínculo: Scholarship, Enquadramento Funcional: Young Researcher COLCIENCIAS, Carga horária: 40

Atividades

01/2001 - 07/2001
Pesquisa e desenvolvimento , Universidad Nacional de Colombia - Medellín, Instituto de Biotecnología.

01/2001 - 06/2001
Ensino, Mastría en Biotecnología, Nível: Pós-Graduação

Disciplinas ministradas
Introducción a la Bioinformática

Universidade de São Paulo, USP, Brasil.
Vínculo institucional

2018 - Atual
Vínculo: Civil servant, Enquadramento Funcional: Assistant Professor, Regime: Dedicação exclusiva.

Vínculo institucional

2017 - 2018
Vínculo: Volunteer, Enquadramento Funcional: Guest Researcher

Atividades

05/2018 - Atual
Pesquisa e desenvolvimento , Centro de Energia Nuclear na Agricultura, .

01/2017 - 04/2018
Pesquisa e desenvolvimento , Instituto de Química, Departamento de Bioquímica.



Linhas de pesquisa


1.
Phylogenomics of Protists
2.
Eukaryotic transcription factors
3.
Genome sequence assembly
4.
Genome annotation
5.
Protein-ligand docking
6.
Transcriptomics
7.
Plant Transcription Factors
8.
Non coding RNA genes
9.
Genome annotation
10.
Gene regulatory networks
11.
Genomics databases
12.
Database development
13.
Phylogenetics
14.
Integrative omics database development

Objetivo: Nowadays biology suffers from what it is known as a data deluge, i.e., a wide variety of data type in large amounts. A part of the solution is the development of databases, structured arrangement of the data, with cross-references among the different data types. Such databases would ease the extraction/generation of new knowledge by revealing hidden relationships..
Palavras-chave: omics; databases; integrative databases; genomics.
15.
Genome annotation
16.
Next Generation Sequencing data analysis

Objetivo: Exploit NGS data to understand plant responses against biotic and abiotic stresses. Develop computational pipelines for the analysis of NGS data..
Grande área: Ciências Biológicas
Grande Área: Ciências Biológicas / Área: Biologia Geral / Subárea: Genomics.
Palavras-chave: computational pipeline; bioinformatics; computational biology; Next generation sequencing; genomics.
17.
Comparative Genomics
18.
Computational phosphoproteomics
19.
Computational proteomics
20.
Phylogenetics
21.
Bioinformatics
22.
Database and web page development
23.
Evolution of bacterial classification systems
24.
Computational biology
25.
Bioinformatics
26.
Database development
27.
Systems biology
28.
Evolutionary biology
29.
Genomics
30.
Applied bioinformatics to the study of microalgae
31.
Bioinformatics
32.
Computational Biology
33.
Evolutionary Biology
34.
Genomics
35.
Systems Biology
36.
Eukaryotic Gene Expression Regulation
37.
Integrative Bioinformatics


Projetos de pesquisa


2018 - Atual
Genomic Studies of Bioenergy Crops
Descrição: Study of the sugarcane pangenome and a comprehensive transcriptome for functional genomics studies. Evolutionary analyses of selected gene families related to the accumulation of sugar and fiber..
Situação: Em andamento; Natureza: Pesquisa.
2016 - 2017
Genome sequencing of Saccharomyces cerevisiae strain Barra Grande (BG-1)
Situação: Concluído; Natureza: Pesquisa.
Alunos envolvidos: Mestrado acadêmico: (1) .
Integrantes: Diego Mauricio Riano Pachon - Coordenador / OLIVEIRA, JULIANA VELASCO DE CASTRO - Integrante / Natalia Coutouné - Integrante.
2014 - 2018
Genomic analyses of the Xylanolytic yeast Kalmanozyma brasiliensis
Descrição: Brazil is responsible for 33% of the biethanol production in the world and dominates the technology for its production using hexoses and their dissacharides available in sugarcane. The use of pentoses present in lignocellulosic biomass, as in sugarcane bagasse, is a promising option for production of second generation bioethanol. However, industrial strains of Saccharomyces cerevisiae usually employed in the ethanolic fermentation process are naturally not able to ferment these sugars efficiently. The family Ustilaginaceae (Basidiomycota) has members with high biotechnological potential, including the yeasts of the genus Pseudozyma. Recently, our group isolated the strain Pseudozyma brasiliensis GHG001, producing a xylanase with high potential of xylan hydrolysis, as well as capacity of growth in xylose and xylan as unique carbon sources. Thus, this yeast is promising as source of genes and pathways for constructing recombinant S. cerevisiae. The aims of this work are (i) improvement of the genome annotation of P. brasiliensis GHG001, (ii) study comparative genomics of P. brasiliensis with other members of Ustilaginaceae, especially the gene families involved in biomass hydrolysis, pentose catabolism, oxidation-reduction and isomerization, including the genome of four Pseudozyma isolates already sequenced in our lab, (iii) the reconstruction of a draft of metabolic networks in P. brasiliensis, and (iv) in silico exploitation of interesting pathways using flux balance analysis..
Situação: Concluído; Natureza: Pesquisa.
Alunos envolvidos: Mestrado acadêmico: (1) .
Integrantes: Diego Mauricio Riano Pachon - Coordenador / GOLDMAN, GUSTAVO H. - Integrante / CORRÊA DOS SANTOS, RENATO AUGUSTO - Integrante.Financiador(es): Fundação de Amparo à Pesquisa do Estado de São Paulo - Bolsa.
Número de produções C, T & A: 4
2014 - 2017
Towards a genome sequence of sugarcane: Exploiting Illumina's TruSeq Synthetic Long Reads
Descrição: Here we used the new Illumina TruSeq Synthetic Long Read sequencing technology to survey the sugarcane genome (variety SP80-3280) using 9 libraries, each generating approx. 600Mbps, thus giving an estimated coverage between 4 and 5 of the monoploid genome. The generated long reads will undoubtedly aid in the genome assembly of this crop, and in identifying specific homologous/homeologous chromosome fragments..
Situação: Concluído; Natureza: Pesquisa.
2014 - Atual
Dual RNA-seq of semi-industrial fermentations with Saccharomyces cerevisiae CAT-1 and two bacterial isolates, frequently found contaminating industrial ethanolic fermentations.
Descrição: Ethanol has a great strategic importance for the brazilian energy sector due to its renewable nature and great capacity to generate employment and income. Furthermore, the use of ethanol has reduced brazilian dependence on fossil fuels. Currently, one of the main problems faced in ethanol production is the presence of contaminating microorganisms during the fermentation process. Their presence during fermentation can cause a reduction in efficiency of ethanol production, competition for essential nutrients and increase of toxic compounds levels that cause yeast flocculation. Even with these problems, most of the ethanol production process in Brazil are based on a complex interaction between the yeast S. cerevisiae and contaminating organisms. In this sense, this project aims to carry out DNA sequencing, assembly of genomes and complete annotation of two isolates of bacterial contaminants from different sugarcane mills in the state of São Paulo, belonging to the genus Lactobacillus and Acetobacter. Furthermore, it is also aims to peform the sequencing of CAT-1 S. cerevisiae transcripts and these contaminants in coexisting conditions, in fermentation trials conducted in semi-industrial reactors. We expect to better comprehend some of the interaction dynamics between these microrganisms..
Situação: Em andamento; Natureza: Pesquisa.
Alunos envolvidos: Doutorado: (1) .
Integrantes: Diego Mauricio Riano Pachon - Integrante / LABATE, CARLOS ALBERTO - Coordenador / Lucas Lopes - Integrante.Financiador(es): Conselho Nacional de Desenvolvimento Científico e Tecnológico - Bolsa / Fundação de Amparo à Pesquisa do Estado de São Paulo - Bolsa.
2013 - 2017
Sugarcane transcript catalogue
Descrição: Current technologies for nucleic acid sequencing together with the development of sophisticated and precise bioinformatics algorithms for assembly and annotations are paving the way towards a comprehensive knowledge of transcriptomes of commercial and social important species whose genome is not yet, or will not ever be, available. Sugarcane is a monocotyledonous C4 crop of the highest importance in the bioenergy field in Brazil. Nowadays there is an evident lack of functional genomics data and information for this crop. Overcoming this lack will facilitate improvement and breeding strategies. The use of new sequencing technologies must be accompanied by the development of a structured and integrative system to release and visualize the resulting data and information in such a way that new knowledge can be generated. In this project we proposed to generate data for the transcriptomes of three different sugarcane genotypes widely used in Brazil and integrated transcriptomes assemblies, annotation and expression levels in a publicly accessible database. This project will also provide information about the genetic variability of these sugarcane genotypes at the level of expressed loci, information that can directly be of use in breeding programs..
Situação: Concluído; Natureza: Pesquisa.
2011 - 2012
Identification of non-classical hDHFR inhibitors
Descrição: Identify new potential human dihydrofolate reductase (DHFR) inhibitors, aimed to the folate pathway involved in tetrahydrofolate (THF) synthesis, an important cofactor and antineoplastic drug target..
Situação: Concluído; Natureza: Pesquisa.
Alunos envolvidos: Mestrado acadêmico: (1) .
Integrantes: Diego Mauricio Riano Pachon - Coordenador / Luis Alberto Gómez - Integrante / María Luz Gunturiz - Integrante / Andrés Felipe Vasquez - Integrante.Número de orientações: 1
2011 - 2011
Identification of Lactobacillus spp with short reads from the 16S rRNA gene
Descrição: El 16s rRNA es utilizado para la identi acion bacteriana dada su tasa de variaci on entre especies, aunque no es su ciente para discriminar entre cepas. Algunas de las regiones variables de la subunidad ribosomal son m as informativas que otras por lo cual en este estudio se evalu o el potencial de identi caci on aportado por las diferentes regiones variables y combinaciones entre ellas..
Situação: Concluído; Natureza: Pesquisa.
Alunos envolvidos: Graduação: (1) .
Integrantes: Diego Mauricio Riano Pachon - Coordenador / Maria Consuelo Vargas - Integrante / Laura Natalia González Garcia - Integrante.
Número de produções C, T & A: 2 / Número de orientações: 1
2010 - 2012
Metanomics and metatranscriptomics of contamited solid in Cartagene Bay, Colombia
Descrição: The goal of this study is to describe the structure and composition of the microbial community in highly contaminated sediment samples in the Cartagena bay, an unexplored ecosystem model relevant to start the exploration to ultimately understand the microbial ecology of biodegradation. In order to achieve this, we implemented a careful sampling plan on which we are able to precisely assess the variability on the microbial community structures obtained out of in situ resampling and we applied advanced molecular biology methods to characterize the technical and subsampling variation. In addition we assessed the phylogenetic relationships of microbial communities thriving across a gradient of contamination in the sediments at the neotropical bay under study, by means of sequence analysis of taxonomically informative bacterial gene regions (V5--‐V6 hypervariable region of the 16S rRNA gene), obtained from environmental metagenomic DNA. In the realization of this study we coupled to the use of massive sequencing techniques (MiSeq--‐Illumina) and the development of bioinformatic analysis to infer the taxonomic structure. Even more, we have developed bioinformatics tools to precisely identify and annotate genes involved in the degradation of polycyclic aromatic hydrocarbons (PAH) from genomic, metagenomic and metatranscriptomic sequence reads. For this purpose, we took advantage of carefully curated databases collectively comprising a concept called microbial catabolome, a group of phylogenetically coherent catabolic gene families encoding enzymes crucial for aerobic/anaerobic aromatic/aliphatic degradation, and as such, for pollutant bioremediation in the environment..
Situação: Concluído; Natureza: Pesquisa.
Alunos envolvidos: Mestrado acadêmico: (1) .
Integrantes: Diego Mauricio Riano Pachon - Coordenador / Eric Juan Carlos Gálvez Bobadilla - Integrante / Howard Armando Junca Díaz - Integrante.
Número de produções C, T & A: 1 / Número de orientações: 1
2010 - 2012
Coffee Rust Genome Sequence Assembly and Annotation
Descrição: Hemileia vastatrix is a fungus belonging to the Phylum Basidiomycota and the causal agent of the coffee rust disease. It produces important economical losses on coffee crops worldwide. In this study, the genome of H. vastatrix was sequenced, assembled and annotated. The total size of the assembled genome was 339.48Mb close to the measurements obtained by flow cytometry, being a large genome when compared with other Basidiomycetes. The genome assembly was highly fragmented and showed some problems of over coverage and highly repetitive regions. However, large contigs were obtained and a reliable set of proteins (14445) could be predicted based on this assembly. Comparisons with other Basidiomycetes showed several gene blocks conserved and other blocks unique to H. vastatrix..
Situação: Concluído; Natureza: Pesquisa.
Alunos envolvidos: Mestrado acadêmico: (1) .
Integrantes: Diego Mauricio Riano Pachon - Coordenador / David Octavio Botero Rozo - Integrante / Silvia Restrepo Restrepo - Integrante / Marco Cristancho - Integrante.
Número de produções C, T & A: 3 / Número de orientações: 1
2005 - Atual
Eukaryotic Gene Regulatory Networks
Situação: Em andamento; Natureza: Pesquisa.
Alunos envolvidos: Graduação: (2) / Mestrado acadêmico: (2) / Doutorado: (1) .
Integrantes: Diego Mauricio Riano Pachon - Coordenador / DREYER, INGO - Integrante / GOMEZ-PORRAS, JUDITH LUCIA - Integrante / MUELLER-ROEBER, BERND - Integrante / RENSING, S. A. - Integrante / PEREZ-RODRIGUEZ, P. - Integrante / CORRÊA, LUIZ GUSTAVO GUEDES - Integrante / Flavia Vischi Winck - Integrante / Silvia Restrepo Restrepo - Integrante / Erich Grotewold - Integrante.
Número de produções C, T & A: 17 / Número de orientações: 3
2002 - 2005
Identification of orphan genes in the genome of Arabidopsis thaliana
Descrição: Expressed sequence tags (ESTs) represent a huge resource for the discovery of previously unknown genetic information and functional genome assignment. In this study we screened a collection of 178 292 ESTs from Arabidopsis thaliana by testing them against previously annotated genes of the Arabidopsis genome. We identified several hundreds of new transcripts that match the Arabidopsis genome at so far unassigned loci. The transcriptional activity of these loci was independently confirmed by comparison with the Salk Whole Genome Array Data. To a large extent, the newly identified transcriptionally active genomic regions do not encode 'classic' proteins, but instead generate non-coding RNAs and/or small peptide-coding RNAs of presently unknown biological function. More than 560 transcripts identified in this study are not represented by the Affymetrix GeneChip arrays currently widely used for expression profiling in A. thaliana. Our data strongly support the hypothesis that numerous previously unknown genes exist in the Arabidopsis genome..
Situação: Concluído; Natureza: Pesquisa.


Membro de corpo editorial


2015 - Atual
Periódico: BMC Genomics
2012 - Atual
Periódico: Frontiers in Plant Systems Biology


Revisor de periódico


2011 - Atual
Periódico: Nucleic Acids Research (Online)
2011 - Atual
Periódico: Revista Colombiana de Biotecnología
2011 - Atual
Periódico: Acta Biologica Colombiana
2010 - Atual
Periódico: Molecular Plant
2011 - Atual
Periódico: BMC Evolutionary Biology (Online)
2012 - Atual
Periódico: Plant Science (Limerick)
2011 - Atual
Periódico: Functional and Integrative Genomics
2015 - Atual
Periódico: Frontiers in Bioengineering and Biotechnology


Áreas de atuação


1.
Grande área: Ciências Biológicas / Área: Biologia Geral / Subárea: Computational biology.
2.
Grande área: Ciências Biológicas / Área: Biologia Geral / Subárea: Bioinformatics.
3.
Grande área: Ciências Biológicas / Área: Biologia Geral / Subárea: Systems Biology.
4.
Grande área: Ciências Biológicas / Área: Biologia Geral / Subárea: Phylogenetics.
5.
Grande área: Ciências Biológicas / Área: Biologia Geral / Subárea: Plant Molecular Biology.
6.
Grande área: Ciências Biológicas / Área: Biologia Geral / Subárea: Molecular Genetics and of Microorganisms.


Idiomas


Português
Compreende Bem, Fala Razoavelmente, Lê Razoavelmente, Escreve Pouco.
Espanhol
Compreende Bem, Fala Bem, Lê Bem, Escreve Bem.
Inglês
Compreende Bem, Fala Bem, Lê Bem, Escreve Bem.


Prêmios e títulos


2016
Prêmio Octavio Frias de Oliveira 2016 - Modalidade Pesquisa em Oncologia, Instituto do Câncer do Estado de São Paulo.
2008
PhD Thesis Summa cum laude Highest calification in the German University System, Universitaet Potsdam.
2001
Undergrad (Biology) thesis meritorious mention, Universidad Nacional de Colombia.
2001
Third place, Best Undergraduate Theses XI version. Category Health Sciences, Universidad Nacional de Colombia.


Produções



Produção bibliográfica
Citações

Web of Science
Total de trabalhos:56
Total de citações:3334
Fator H:17
Riano Pachon, Diego Mauricio  Data: 21/07/2018

SCOPUS
Total de trabalhos:47
Total de citações:3193
Riano-Pachon  Data: 28/05/2018

Outras
Total de trabalhos:48
Total de citações:4859
Diego M. Riano-Pachon  Data: 21/07/2018

Artigos completos publicados em periódicos

1.
DE GOUVÊA, PAULA FAGUNDES2018DE GOUVÊA, PAULA FAGUNDES ; BERNARDI, ALINE VIANNA ; GEROLAMO, LUIS EDUARDO ; DE SOUZA SANTOS, EMERSON ; RIAÑO-PACHÓN, DIEGO MAURICIO ; UYEMURA, SERGIO AKIRA ; DINAMARCO, TAISA MAGNANI . Transcriptome and secretome analysis of Aspergillus fumigatus in the presence of sugarcane bagasse. BMC GENOMICS, v. 19, p. 232, 2018.

2.
DOS REIS, THAILA FERNANDA2017DOS REIS, THAILA FERNANDA ; NITSCHE, BENJAMIN M. ; DE LIMA, POLLYNE BORBOREMA ALMEIDA ; DE ASSIS, LEANDRO JOSÉ ; MELLADO, LAURA ; HARRIS, STEVEN D. ; MEYER, VERA ; DOS SANTOS, RENATO A. CORRÊA ; RIAÑO-PACHÓN, DIEGO M. ; RIES, LAURE NICOLAS ANNICK ; GOLDMAN, GUSTAVO H. . The low affinity glucose transporter HxtB is also involved in glucose signalling and metabolism in Aspergillus nidulans. Scientific Reports, v. 7, p. 45073, 2017.

3.
COUTOUNÉ, NATALIA2017COUTOUNÉ, NATALIA ; MULATO, ALINE TIEPPO NOGUEIRA ; RIAÑO-PACHÓN, DIEGO MAURICIO ; OLIVEIRA, JULIANA VELASCO DE CASTRO . Draft Genome Sequence of Saccharomyces cerevisiae Barra Grande (BG-1), a Brazilian Industrial Bioethanol-Producing Strain. Genome Announcements, v. 5, p. e00111-17, 2017.

4.
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LANG, D.2010LANG, D. ; WEICHE, B. ; CORREA, L. G. G. ; RIANO-PACHON, D. M. ; MUELLER-ROEBER, B. ; RENSING, S. A. ; RESKI, R. ; TIMMERHAUS, G. ; RICHARDT, S. . Genome-Wide Phylogenetic Comparative Analysis of Plant Transcriptional Regulation: A Timeline of Loss, Gain, Expansion, and Correlation with Complexity. Genome Biology and Evolution, v. 2, p. 488-503, 2010.

41.
RIAÑO-PACHÓN, DIEGO2010RIAÑO-PACHÓN, DIEGO; KLEESSEN, SABRINA ; NEIGENFIND, JOST ; DUREK, PAWEL ; WEBER, ELKE ; ENGELSBERGER, WOLFGANG R ; WALTHER, DIRK ; SELBIG, JOACHIM ; SCHULZE, WALTRAUD X ; KERSTEN, BIRGIT . Proteome-wide survey of phosphorylation patterns affected by nuclear DNA polymorphisms in Arabidopsis thaliana. BMC Genomics, v. 11, p. 411, 2010.

42.
PEREZ-RODRIGUEZ, P.2009 PEREZ-RODRIGUEZ, P. ; RIANO-PACHON, D. M. ; CORREA, L. G. G. ; RENSING, S. A. ; KERSTEN, B. ; MUELLER-ROEBER, B. . PlnTFDB: updated content and new features of the plant transcription factor database. Nucleic Acids Research (Online), v. 38, p. D822-D827, 2009.

43.
RIANO-PACHON, D. M.2009RIANO-PACHON, D. M.; NAGEL, A. ; NEIGENFIND, J. ; WAGNER, R. ; BASEKOW, R. ; WEBER, E. ; MUELLER-ROEBER, B. ; DIEHL, S. ; KERSTEN, B. . GabiPD: the GABI primary database--a plant integrative 'omics' database. NUCLEIC ACIDS RESEARCH (ONLINE), v. 37, p. D954-D959, 2009.

44.
MUELLER-ROEBER, B.2009MUELLER-ROEBER, B. ; ARVIDSSON, S. ; BALAZADEH, S. ; CORRÊA, L.G.G. ; PÉREZ-RODRÍGUEZ, P. ; RIAÑO-PACHÓN, D.M. . Gene regulatory networks and transcription factor transcriptomics. New Biotechnology (Print), v. 25, p. S318, 2009.

45.
ARVIDSSON, SAMUEL2008ARVIDSSON, SAMUEL ; KWASNIEWSKI, MIROSLAW ; RIANO-PACHON, DIEGO M. ; MUELLER-ROEBER, BERND . QuantPrime - a flexible tool for reliable high-throughput primer design for quantitative PCR. BMC Bioinformatics, v. 9, p. 465, 2008.

46.
RIANO-PACHON, D. M.2008RIANO-PACHON, D. M.; CORREA, L. G. G. ; MUELLER-ROEBER, B. ; TREJOS-ESPINOSA, R. . Green Transcription Factors: A Chlamydomonas Overview. Genetics (Austin, Tex.), v. 179, p. 31-39, 2008.

47.
BALAZADEH, S.2008BALAZADEH, S. ; RIAÑO-PACHÓN, D. M. ; MUELLER-ROEBER, B. . Transcription factors regulating leaf senescence in. Plant Biology (Stuttgart), v. 10, p. 63-75, 2008.

48.
Corrêa, Luiz Gustavo Guedes2008Corrêa, Luiz Gustavo Guedes ; Riano-Pachon, DM ; Schrago, Carlos Guerra ; Vicentini dos Santos, Renato ; Mueller-Roeber, Bernd ; VINCENTZ, M. G. A. . The Role of bZIP Transcription Factors in Green Plant Evolution: Adaptive Features Emerging from Four Founder Genes. Plos One, v. 3, p. e2944, 2008.

49.
MERCHANT, S. S.2007MERCHANT, S. S. PROCHNIK, S. E. VALLON, O. HARRIS, E. H. KARPOWICZ, S. J. WITMAN, G. B. TERRY, A. SALAMOV, A. FRITZ-LAYLIN, L. K. MARECHAL-DROUARD, L. MARSHALL, W. F. QU, L.-H. NELSON, D. R. SANDERFOOT, A. A. SPALDING, M. H. KAPITONOV, V. V. REN, Q. FERRIS, P. LINDQUIST, E. SHAPIRO, H. LUCAS, S. M. GRIMWOOD, J. SCHMUTZ, J. CARDOL, P. CERUTTI, H. , et al.CHANFREAU, G. CHEN, C.-L. COGNAT, V. CROFT, M. T. DENT, R. DUTCHER, S. FERNANDEZ, E. FUKUZAWA, H. GONZALEZ-BALLESTER, D. GONZALEZ-HALPHEN, D. HALLMANN, A. HANIKENNE, M. HIPPLER, M. INWOOD, W. JABBARI, K. KALANON, M. KURAS, R. LEFEBVRE, P. A. LEMAIRE, S. D. LOBANOV, A. V. LOHR, M. MANUELL, A. MEIER, I. METS, L. MITTAG, M. MITTELMEIER, T. MORONEY, J. V. MOSELEY, J. NAPOLI, C. NEDELCU, A. M. NIYOGI, K. NOVOSELOV, S. V. PAULSEN, I. T. PAZOUR, G. PURTON, S. RAL, J.-P. RIANO-PACHON, D. M. RIEKHOF, W. RYMARQUIS, L. SCHRODA, M. STERN, D. UMEN, J. WILLOWS, R. WILSON, N. ZIMMER, S. L. ALLMER, J. BALK, J. BISOVA, K. CHEN, C.-J. ELIAS, M. GENDLER, K. HAUSER, C. LAMB, M. R. LEDFORD, H. LONG, J. C. MINAGAWA, J. PAGE, M. D. PAN, J. POOTAKHAM, W. ROJE, S. ROSE, A. STAHLBERG, E. TERAUCHI, A. M. YANG, P. BALL, S. BOWLER, C. DIECKMANN, C. L. GLADYSHEV, V. N. GREEN, P. JORGENSEN, R. MAYFIELD, S. MUELLER-ROEBER, B. RAJAMANI, S. SAYRE, R. T. BROKSTEIN, P. DUBCHAK, I. GOODSTEIN, D. HORNICK, L. HUANG, Y. W. JHAVERI, J. LUO, Y. MARTINEZ, D. NGAU, W. C. A. OTILLAR, B. POLIAKOV, A. PORTER, A. SZAJKOWSKI, L. WERNER, G. ZHOU, K. GRIGORIEV, I. V. ROKHSAR, D. S. GROSSMAN, A. R. ; The Chlamydomonas Genome Reveals the Evolution of Key Animal and Plant Functions. Science (New York, N.Y.: Online), v. 318, p. 245-250, 2007.

50.
GÓMEZ-PORRAS, JUDITH L2007GÓMEZ-PORRAS, JUDITH L ; RIAÑO-PACHÓN, DIEGO ; DREYER, INGO ; MAYER, JORGE E ; MUELLER-ROEBER, BERND . Genome-wide analysis of ABA-responsive elements ABRE and CE3 reveals divergent patterns in Arabidopsis and rice. BMC Genomics, v. 8, p. 260, 2007.

51.
RIAÑO-PACHÓN, DIEGO2007RIAÑO-PACHÓN, DIEGO; RUZICIC, SLOBODAN ; DREYER, INGO ; MUELLER-ROEBER, BERND . PlnTFDB: an integrative plant transcription factor database. BMC Bioinformatics, v. 8, p. 42, 2007.

52.
MONTOYA, J. D.2007MONTOYA, J. D. ; SUAREZ MORENO, Z. R. ; RIANO-PACHON, DIEGO M. ; MONTOYA, D. ; ARISTIZABAL GUTIERREZ, F. A. . Diseño de oligonucleótidos para el estudio de genes celulolíticos y solventogénicos en cepas colombianas de Clostridium sp. (Clostridiaceae). Acta Biologica Colombiana, v. 12S, p. 55-74, 2007.

53.
RIAÑO-PACHÓN, DIEGO MAURICIO2005RIAÑO-PACHÓN, DIEGO MAURICIO; DREYER, INGO ; MUELLER-ROEBER, BERND . Orphan transcripts in Arabidopsis thaliana: identification of several hundred previously unrecognized genes. Plant Journal (Print), v. 43, p. 205-212, 2005.

54.
RIAÑO-PACHÓN, DIEGO MAURICIO2003RIAÑO-PACHÓN, DIEGO MAURICIO; SILVA, E. M. V. ; ANAYA, J. R. M. ; AGUDELO, C. . Diversidad genética y estructura de la población de Vibrio choierae en Colombia. Revista Colombiana de Biotecnología, v. 5, p. 36-44, 2003.

Livros publicados/organizados ou edições
1.
WINCK, F. V. ; RIAÑO-PACHÓN, D.M. ; FRANCO, TELMA T. . Advances in Microalgae Biology and Sustainable Applications. 1. ed. Lausanne: Frontiers Media SA., 2016. v. 1. 152p .

Capítulos de livros publicados
1.
Cristancho, Marco ; Giraldo, William ; Botero, David ; Tabima, Javier ; Ortiz, Diana ; Peralta, Alejandro ; Gaitán, Álvaro ; RESTREPO, SILVIA ; Riaño, Diego . Application of Genome Studies of Coffee Rust. Advances in Intelligent Systems and Computing. 1ed.: Springer International Publishing, 2014, v. 232, p. 133-139.

2.
RIAÑO-PACHÓN, DIEGO MAURICIO; GONZALEZ ESTRADA, E. ; ALEXA, A. ; RAMIREZ, F. ; WINCK, F. V. ; PEREZ-RODRIGUEZ, P. . 1) Bases de bioinformática, 2) Herramientas bioinformáticas y 3) Análisis comparativo y evolución. In: Colegio de Postgraduados. (Org.). Bioinformática: Aplicaciones a la genómica y la proteómica. 1ed.Texcoco: Gómez Merino, Fernando,, 2010, v. , p. 1-.

Textos em jornais de notícias/revistas
1.
FOG, L. ; RIAÑO-PACHÓN, DIEGO MAURICIO . Planta completa la cadena de la evolución. El Espectador, 12 maio 2011.

2.
KERSTEN, BIRGIT ; NAGEL, A. ; RIAÑO-PACHÓN, DIEGO MAURICIO ; NEIGENFIND, JOST ; WEBER, ELKE ; WAGNER, R. ; DIEHL, S. . Die GABI-Primärdatenbank GabiPD - Komplete Integration von GABI-Daten aus Modell und Nutzp. GenomXPress, Germany, p. 17 - 19, 16 jan. 2008.

3.
MUELLER-ROEBER, BERND ; RIAÑO-PACHÓN, DIEGO MAURICIO ; RUZICIC, SLOBODAN ; SKIRYCZ, A. ; CALDANA, CAMILA ; WITT, I. ; ZANOR, M. I. . Pflanzliche Regulatorproteine. BioFORUM, Germany, p. 32 - 34, 02 jan. 2005.

Apresentações de Trabalho
1.
RIAÑO-PACHÓN, D.M.; Mattiello, L ; DA CRUZ, LARISSA PRADO . Surveying the sugarcane genome: Exploiting synthetic long reads. 2016. (Apresentação de Trabalho/Comunicação).

2.
CORRÊA DOS SANTOS, RENATO AUGUSTO ; GOLDMAN, G. H. ; RIAÑO-PACHÓN, D.M. . Phylogenomic analysis and comparative genomics of Ustilaginaceae (Basidiomycetes): Exploiting evolutionary information to uncover probable regulatory mechanisms of CAZyme expression. 2016. (Apresentação de Trabalho/Outra).

3.
LOPES, L. ; BONATELLI, M. L. ; Labate, CA ; RIAÑO-PACHÓN, D.M. . Genome sequencing of three bacterial isolates contaminating industrial ethanolic fermentations. 2016. (Apresentação de Trabalho/Outra).

4.
RIAÑO-PACHÓN, DIEGO MAURICIO. Exploring the sugarcane genome (SP80-3280) exploiting Illumina TruSeq synthetic long reads and strand-specific RNASeq. 2015. (Apresentação de Trabalho/Conferência ou palestra).

5.
RIAÑO-PACHÓN, DIEGO MAURICIO. Genomic Analyses of Colombian Clostridium Strains with Biotechnological Potential. 2015. (Apresentação de Trabalho/Conferência ou palestra).

6.
RIAÑO-PACHÓN, DIEGO MAURICIO. Exploring the sugarcane genome Exploiting Illumina TruSeq synthetic long reads and strand-specific RNASeq. 2015. (Apresentação de Trabalho/Conferência ou palestra).

7.
RIAÑO-PACHÓN, D. M.; Mattiello, L . Genomic studies of Sugarcane at CTBE. 2015. (Apresentação de Trabalho/Comunicação).

8.
GAITAN-CHAPARRO, S. L. ; RIAÑO-PACHÓN, DIEGO MAURICIO ; ROMERO, H. M. . Transcriptome Analalysis of the Oil Palm during its Interaction with Thielaviop. 2014. (Apresentação de Trabalho/Congresso).

9.
RIAÑO-PACHÓN, D. M.; BUITRAGO-FLOREZ, F. ; RESTREPO, SILVIA . Métodos computacionales para la identificación de genes reguladores en Stramenopiles. 2014. (Apresentação de Trabalho/Congresso).

10.
RIAÑO-PACHÓN, DIEGO MAURICIO. Exploring microbial diversity to further the bioethanol supply chain in Brazil. 2014. (Apresentação de Trabalho/Comunicação).

11.
Perlaza, L ; RIAÑO-PACHÓN, DIEGO MAURICIO ; Crawford, A. J. ; ARUNACHALAM, V. ; PEDRAZA, J. M. ; Bernal, A . DeEP: deconstructive evolutionary pipeline. 2013. (Apresentação de Trabalho/Congresso).

12.
RIAÑO-PACHÓN, DIEGO MAURICIO; Restrepo R, Silvia ; MUELLER-ROEBER, BERND ; BUITRAGO-FLOREZ, F. . Identification of transcription regulation associated proteins in plants and stramenopiles. 2012. (Apresentação de Trabalho/Congresso).

13.
URBINA-GOMEZ, D. A. ; MUELLER-ROEBER, BERND ; OMIDBAKHSHFARD, A. N. ; WINCK, F. V. ; Riano-Pachon, Diego Mauricio . An analysis pipeline for FAIRE-seq data. 2012. (Apresentação de Trabalho/Congresso).

14.
GALVEZ BOBADILLA, E. J. C. ; PIEPER, D. H. ; JUNCA DIAZ, H. A. ; Riano-Pachon, Diego Mauricio . Automated method for annotation of genes involved in the degradation of polycyclic aromatic hydrocarbons (PAH) from genomic, metagenomic and metatranscriptomic sequence reads. 2012. (Apresentação de Trabalho/Congresso).

15.
GONZALEZ GARCIA, L. N. G. ; VARGAS, M. C. ; Riano-Pachon, Diego Mauricio . Comparing the potential for identification of Lactobacillus spp of 16S rRNA variable regions. 2012. (Apresentação de Trabalho/Congresso).

16.
Botero Rozo, David Octavio ; GIRALDO, W. ; Cristancho, Marco ; Riano-Pachon, Diego Mauricio ; Restrepo R, Silvia . Data Mining of the Coffee Rust Genome. 2012. (Apresentação de Trabalho/Congresso).

17.
URBINA-GOMEZ, D. A. ; WINCK, FLAVIA V. ; MUELLER-ROEBER, BERND ; Riano-Pachon, Diego Mauricio . FAIRE-seq data analysis of Chlamydomonas reinhardtii under carbon deprivation. 2012. (Apresentação de Trabalho/Congresso).

18.
RIAÑO-PACHÓN, DIEGO MAURICIO. El genoma de Selaginella, entendiendo la evolución de las plantas vasculares. 2011. (Apresentação de Trabalho/Comunicação).

19.
BUITRAGO-FLOREZ, F. ; Restrepo R, Silvia ; Riano-Pachon, Diego Mauricio . Identification of transcription factor genes in Stramenopiles. 2011. (Apresentação de Trabalho/Congresso).

20.
BUITRAGO-FLOREZ, F. ; Riano-Pachon, Diego Mauricio ; Restrepo R, Silvia . Identification of transcription factors and their correlation with the high diversity of Stramenopiles. 2011. (Apresentação de Trabalho/Congresso).

21.
Isaza Agudelo, JP ; ALZATE RESTREPO, J. F. A. ; TRIANA CHAVEZ, O. ; Riano-Pachon, Diego Mauricio ; NIÑO GARCIA, J. P. ; GARCIA CHAVEZ, M . Secuenciación de un metagenoma de microorganismos aislados en condiciones termofílicas. 2011. (Apresentação de Trabalho/Congresso).

22.
Riano-Pachon, Diego Mauricio. Identi cation and Evolution of Transcription Factors in Plants. 2011. (Apresentação de Trabalho/Conferência ou palestra).

23.
Riano-Pachon, Diego Mauricio. Secuenciación y anotación del genoma de Selaginella: Entendiendo la evolución de las plantas vasculares. 2011. (Apresentação de Trabalho/Conferência ou palestra).

24.
KLEESSEN, SABRINA ; LOHSE, M. ; Riano-Pachon, Diego Mauricio ; Schweizer, Gunther ; KERSTEN, BIRGIT . Towards transcriptomic markers for drought tolerance in Barley. 2010. (Apresentação de Trabalho/Congresso).

25.
OMRANIAN, N. ; ARVIDSSON, SAMUEL ; Riano-Pachon, Diego Mauricio ; MUELLER-ROEBER, BERND . Towards a computational tool to uncover genes involved in signaling crosstalk in Arabidopsis thaliana. 2010. (Apresentação de Trabalho/Congresso).

26.
Riano-Pachon, Diego Mauricio; DUREK, PAWEL ; KLEESSEN, SABRINA ; NEIGENFIND, JOST ; ENGELSBERGER, WOLFGANG R ; WALTHER, DIRK ; SELBIG, JOACHIM ; SCHULZE, WALTRAUD X ; KERSTEN, BIRGIT . Protein phosphorylation patterns affected by nuclear DNA polyorphisms in a genome-wide scale in Arabidopsis. 2009. (Apresentação de Trabalho/Congresso).

27.
MUELLER-ROEBER, BERND ; ARVIDSSON, S. ; BALAZADEH, S. ; CORRÊA, LUIZ GUSTAVO GUEDES ; Riano-Pachon, Diego Mauricio . Gene regulatory networks and transcription factor transcriptomics. 2009. (Apresentação de Trabalho/Congresso).

28.
Riano-Pachon, Diego Mauricio; NAGEL, A. ; WAGNER, R. ; BASEKOW, R. ; NEIGENFIND, JOST ; WEBER, ELKE ; KLEESSEN, SABRINA ; KERSTEN, BIRGIT . GabiPD: The Gabi Primary Database - a plant integrative 'omics' database -- update. 2009. (Apresentação de Trabalho/Congresso).

29.
ARVIDSSON, S. ; KWASNIEWSKI, MIROSLAW ; Riano-Pachon, Diego Mauricio ; MUELLER-ROEBER, BERND . QuantPrime - a flexible tool for reliable highthroughput primer design for quantitative PCR.. 2009. (Apresentação de Trabalho/Congresso).

30.
Riano-Pachon, Diego Mauricio. Identi cación de factores de transcripción en plantas - un enfoque computacional. 2009. (Apresentação de Trabalho/Conferência ou palestra).

31.
Riano-Pachon, Diego Mauricio. GabiPD y PlnTFDB: Integrando datos de genómica funcional (-ómicas) en plantas.. 2009. (Apresentação de Trabalho/Conferência ou palestra).

32.
WINCK, FLAVIA V. ; KWASNIEWSKI, MIROSLAW ; Riano-Pachon, Diego Mauricio ; MUELLER-ROEBER, BERND . Towards Chlamydomonas nuclear proteomics: Optimizing the isolation of nuclei and aggregating information. 2008. (Apresentação de Trabalho/Congresso).

33.
Riano-Pachon, Diego Mauricio; NAGEL, A. ; NEIGENFIND, JOST ; WAGNER, R. ; WEBER, ELKE ; DIEHL, S. ; KERSTEN, BIRGIT . GabiPD: Gabi Primary Database - A plant integrative 'omics' database. 2008. (Apresentação de Trabalho/Congresso).

34.
CORRÊA, LUIZ GUSTAVO GUEDES ; Riano-Pachon, Diego Mauricio ; SCHRAGO, CARLOS GUERRA ; VICENTINI DOS SANTOS, RENATO ; MUELLER-ROEBER, BERND ; VINCENTZ, MICHEL . Green evolutionary history of bZIP transcription factors. 2007. (Apresentação de Trabalho/Congresso).

35.
CORRÊA, LUIZ GUSTAVO GUEDES ; VICENTINI DOS SANTOS, RENATO ; Riano-Pachon, Diego Mauricio ; MUELLER-ROEBER, BERND ; VINCENTZ, MICHEL . From Chlamydomonas to Arabidopsis: a bZIP history. 2007. (Apresentação de Trabalho/Congresso).

36.
Riano-Pachon, Diego Mauricio; DREYER, INGO ; RUZICIC, SLOBODAN ; MUELLER-ROEBER, BERND . Plant Transcription Factors at Uni-Potsdam.de. 2006. (Apresentação de Trabalho/Congresso).

37.
CORRÊA, LUIZ GUSTAVO GUEDES ; BALAZADEH, S. ; Riano-Pachon, Diego Mauricio ; MUELLER-ROEBER, BERND . Functional analysis of transcription factors that play important roles in leaf development and/or physiology at sink-to-source transition and the onset of senescence. 2006. (Apresentação de Trabalho/Congresso).

38.
CALDANA, CAMILA ; MUELLER-ROEBER, BERND ; Riano-Pachon, Diego Mauricio ; RUZICIC, SLOBODAN . Transcription factor networks in the initial phase of salt stress in rice. 2006. (Apresentação de Trabalho/Congresso).

39.
Riano-Pachon, Diego Mauricio; DREYER, INGO ; MUELLER-ROEBER, BERND . Are biological networks scale-free graphs. 2006. (Apresentação de Trabalho/Simpósio).

40.
RUZICIC, SLOBODAN ; CALDANA, CAMILA ; SOLTANINAJAFABADI, M. ; Riano-Pachon, Diego Mauricio ; MUELLER-ROEBER, BERND . Comparative expression pro ling of different rice varieties during initial phase of abiotic stress. 2005. (Apresentação de Trabalho/Congresso).

41.
CALDANA, CAMILA ; RUZICIC, SLOBODAN ; Riano-Pachon, Diego Mauricio ; MUELLER-ROEBER, BERND . Genomewide identi cation of transcription factors involved in the initial phase of salt stress in rice. 2005. (Apresentação de Trabalho/Congresso).

42.
GOMEZ-PORRAS, JUDITH LUCIA ; Riano-Pachon, Diego Mauricio ; DREYER, INGO ; MUELLER-ROEBER, BERND . Analysis of Non-coding Regions in Arabidopsis thaliana. 2004. (Apresentação de Trabalho/Congresso).


Produção técnica
Programas de computador sem registro
1.
CORRÊA DOS SANTOS, RENATO AUGUSTO ; GOLDMAN, GUSTAVO H. ; RIAÑO-PACHÓN, D.M. . ploidyNGS: Visually exploring ploidy with Next Generation Sequencing data. 2016.

2.
ARVIDSSON, S. ; KWASNIEWSKI, M. ; RIAÑO-PACHÓN, DIEGO M. ; MUELLER-ROEBER, B. . QuantPrime - a flexible primer design tool for high-throughput qPCR. 2008.

3.
RIANO-PACHON, D. M.; PEREZ-RODRIGUEZ, P. ; DREYER, INGO ; RUZICIC, SLOBODAN ; KERSTEN, BIRGIT ; MUELLER-ROEBER, BERND . PlnTFDB: A Plant Transcription Factor Database. 2007.

Redes sociais, websites e blogs
1.
RIAÑO-PACHÓN, D.M.. Grupo de Biologia Computacional, Evolutiva e de Sistemas. 2012; Tema: Research group home page. (Site).

2.
RIAÑO-PACHÓN, DIEGO MAURICIO. http://eterno-bucle.blogspot.com.br/. 2005; Tema: Science. (Blog).


Demais tipos de produção técnica
1.
RIAÑO-PACHÓN, D.M.; Mattiello, L ; DA CRUZ, LARISSA PRADO . Surveying the complex polyploid sugarcane genome sequence using synthetic long reads. 2016. (Relatório de pesquisa).

2.
Restrepo R, Silvia ; Reyes, A ; RIAÑO-PACHÓN, DIEGO MAURICIO . Taller ensamblaje y anotación de genomas y metagenomas usando Galaxy. 2015. (Curso de curta duração ministrado/Extensão).

3.
Riano-Pachon, Diego Mauricio. Flujos de Trabajo de Bioinformatica en la Nube: Análisis de secuencias al alcance de todos. 2014. (Curso de curta duração ministrado/Extensão).

4.
Riano-Pachon, Diego Mauricio. Desarrollo de flujos de trabajo en Galaxy - Ensamblaje y anotación de Genomas. 2014. (Desenvolvimento de material didático ou instrucional - Hands-on Workshop).

5.
RIAÑO-PACHÓN, DIEGO MAURICIO; Restrepo R, Silvia ; ANZOLA, J. M. ; ALZATE RESTREPO, J. F. A. . Bioinformática Básica. 2011. (Curso de curta duração ministrado/Extensão).

6.
RIAÑO-PACHÓN, DIEGO MAURICIO; RAMIREZ, F. ; ALEXA, A. ; PEREZ-RODRIGUEZ, P. ; GONZALEZ ESTRADA, E. ; WINCK, FLAVIA V. . Curso internacional sobre bioinformática: Applicaciones a la genómica y proteómica. 2009. (Curso de curta duração ministrado/Extensão).



Bancas



Participação em bancas de trabalhos de conclusão
Mestrado
1.
PEREIRA, G. A. G.; VICENTINI DOS SANTOS, RENATO; RIAÑO-PACHÓN, D.M.. Participação em banca de FELIPE ALONSO MARTINS. APLICAÇÃO DE FERRAMENTAS DE BIOLOGIA DE SISTEMAS EM LEVEDURA INDUSTRIAL PARA PRODUÇÃO DE BIOETANOL DE SEGUNDA GERAÇÃO. 2015. Dissertação (Mestrado em Genética e Biologia Molecular) - Universidade Estadual de Campinas.

Teses de doutorado
1.
RIAÑO-PACHÓN, DIEGO MAURICIO; LABATE, CARLOS ALBERTO; Margarido, G. R. A.; MARINO, C. L.; Missiaggia, Alexandre A.. Participação em banca de Ana Paula Chiaverini Pinto. Perfil transcricional da xilogênese em Eucalyptus grandis. 2017. Tese (Doutorado em Agronomia (Genética e Melhoramento de Plantas)) - Universidade de São Paulo.

2.
RIAÑO-PACHÓN, DIEGO MAURICIO; VITORELLO, C. B. M.; CAMARGO, L. E. A.; CERESINI, P. C.; OLIVEIRA, G. C. X.. Participação em banca de Juliana Benevenuto. Molecular variability among Brazilian strains of the sugarcane smut pathogen and the genetic basis of host specialization in smut fungi. 2017. Tese (Doutorado em Agronomia (Genética e Melhoramento de Plantas)) - Universidade de São Paulo.

3.
Labate, CA; VITORELLO, C. B. M.; CAMARGO, L. E. A.; González, ER; RIAÑO-PACHÓN, DIEGO MAURICIO. Participação em banca de Andressa Peres Bini. Estudo molecular do desenvolvimento de Puccinia psiddi Winter in vitro e no processo de infecção em Eucalyptus grandis. 2016. Tese (Doutorado em Agronomia (Genética e Melhoramento de Plantas)) - Universidade de São Paulo.

4.
SOUZA, G. M.; ARAUJO, L. V.; DIGIAMPIETRI, L. A.; BRANDAO, M. M.; RIAÑO-PACHÓN, D.M.. Participação em banca de Milton Y. Nishiyama Jr. Desenvolvimento da Plataforma CaneRegNet para Anotação Funcional e Análises do Transcriptoma da Cana-de-açúcar. 2015. Tese (Doutorado em Bioinformática) - Universidade de São Paulo.

5.
VINCENTZ, M. G. A.; Garcia, A. F.; Margarido, G. R. A.; Reis, S. F.; RIAÑO-PACHÓN, DIEGO MAURICIO. Participação em banca de MARIANE DE MENDONÇA VILELA. UNDERSTANDING POLYPLOID GENOMES: INSIGHTS ON THE ORGANIZATION AND EVOLUTION OF SUGARCANE GENOME. 2015. Tese (Doutorado em Genética e Biologia Molecular) - Universidade Estadual de Campinas.




Eventos



Participação em eventos, congressos, exposições e feiras
1.
Brazilian BioEnergy Science and Technology Conference. IDENTIFYING POTENTIAL NEW GENES RELATED TO LIGNOCELLULOSE DEGRADATION USING TRANSCRIPTOME AND GENE CO-EXPRESSION NETWORK ANALYSIS IN TRICHODERMA REESEI RUT-C30. 2017. (Congresso).

2.
Brazilian BioEnergy Science and Technology Conference. Identification, phylogeny, and expression analysis of putative coding p-hydroxycinnamates genes from Saccharum spp.. 2017. (Congresso).

3.
Brazilian BioEnergy Science and Technology Conference. UNDERSTANDING THE METABOLISM OF HEMICELLULOSIC SUGARS FROM OMICS OF THE YEAST-LIKE FUNGUS KALMANOZYMA BRASILIENSIS GHG001 AND THE COMPARATIVE GENOMICS WITH USTILAGINACEAE (BASIDIOMYCETES). 2017. (Congresso).

4.
IV Congresso Colombiano de Biologia Computacional y Bioinformática y VII Conferencia Iberoamericana de Bioinformática. Identifying key genes for pentose metabolism in the ustilaginaceous yeast Kalmanozyma brasiliensis and development of ploidyNGS and TCDB-HMM. 2017. (Congresso).

5.
Meeting of the International Society for History, Philosophy and Social Studies of Biology. 2017. (Encontro).

6.
9th Tripartite Meeting: OSU-Rutgers-USP. Surveying the sugarcane genome: Exploiting synthetic long reads. 2016. (Congresso).

7.
Genetica 2016. Surveying the sugarcane genome: Exploiting synthetic long reads. 2016. (Congresso).

8.
Genetics 2016. Phylogenomic analysis and comparative genomics of Ustilaginaceae (Basidiomycetes): Exploiting evolutionary information to uncover probable regulatory mechanisms of CAZyme expression. 2016. (Congresso).

9.
Genetics 2016. Genome sequencing of three bacterial isolates contaminating industrial ethanolic fermentations. 2016. (Congresso).

10.
1º Encontro Nacional de Química Biotecnológica e Agroindustrial. Exploring the sugarcane genome (SP80-3280) exploiting Illumina TruSeq synthetic long reads and strand-specific RNASeq. 2015. (Congresso).

11.
28o congresso Brasileiro de Microbiologia. Genomic Analyses of Colombian Clostridium Strains with Biotechnological Potential.. 2015. (Congresso).

12.
3er Congreso Colombiano de Biología Computacional y Bioinformática. Exploring the sugarcane genome Exploiting Illumina TruSeq synthetic long reads and strand-specific RNASeq. 2015. (Congresso).

13.
FAPESP- British Council Workshop on. Surveying the sugarcane genome: Exploiting synthetic long reads. 2015. (Congresso).

14.
Plant and Animal Genome XXII. Transcriptome Analalysis of the Oil Palm during its Interaction with Thielaviopsis paradoxa. 2014. (Congresso).

15.
XXII Congreso Latinoamericano de Microbiología. Omics: Exploring the microbial world. 2014. (Congresso).

16.
XXII Congreso Latinoamericano de Microbiología. Métodos computacionales para la identificación de genes reguladores en Stramenopiles. 2014. (Congresso).

17.
Segundo Congreso Colombiano de Biología Computacional y Bioinformática. Sequencing and annotation of the transcriptome of oil palm during the interaction with Thielaviopsis paradoxa. 2013. (Congresso).

18.
Segundo Congreso Colombiano de Biología Computacional y Bioinformática. Application of Genome Studies of Coffee Rust. 2013. (Congresso).

19.
Segundo Congreso Colombiano de Biología Computacional y Bioinformática. Novedosa aproximación al análisis de datos de SAGE para la estimación de genes implicados en el tizón tardío de la papa criolla. 2013. (Congresso).

20.
20th Annual International Conference on Intelligent Systems for Molecular Biology. Automated method for annotation of genes involved in the degradation of polycyclic aromatic hydrocarbons (PAH) from genomic, metagenomic and metatranscriptomic sequence reads.. 2012. (Congresso).

21.
ISCB-LATAM 2012. Identification of transcription regulation associated proteins in plants and stramenopiles. 2012. (Congresso).

22.
19th Annual International Conference on Intelligent Systems for Molecular Biology and 10th European Conference on Computational Biology. Identification of transcription factors and their correlation with the high diversity of Stramenopiles. 2011. (Congresso).

23.
Primer Congreso Colombiano de Biología Computacional. Identification of transcription factor genes in Stramenopiles. 2011. (Congresso).

24.
Seminario del Departamento de Ciencias Biológicas.El genoma de Selaginella, entendiendo la evolución de las plantas vasculares. 2011. (Seminário).

25.
9th European Conference on Computational Biology. Towards a computational tool to uncover genes involved in signaling crosstalk in Arabidopsis thaliana. 2010. (Congresso).

26.
German Conference on Bioinformatics. Towards transcriptomic markers for drought tolerance in Barley. 2010. (Congresso).

27.
17th Annual International Conference on Intelligent Systems for Molecular Biology and 8th European Conference on Computational Biology. GabiPD: The Gabi Primary Database - a plant integrative 'omics' database -- update. 2009. (Congresso).

28.
4th international qPCR Symposium & Industrial Exhibition & Application Workshop. QuantPrime - a fl exible tool for reliable highthroughput primer design for quantitative PCR. 2009. (Congresso).

29.
Seminario Instituto de Biotecnología, Universidad Nacional de Colombia.GabiPD y PlnTFDB: Integrando datos de genómica funcional (-ómicas) en plantas.. 2009. (Seminário).

30.
Seminario Instituto de Genética, Universidad Nacional de Colombia.Identi cación de factores de transcripción en plantas -- un enfoque computacional.. 2009. (Seminário).

31.
7th European Conference on Computational Biology. GabiPD: Gabi Primary Database - A plant integrative 'omics' database. 2008. (Congresso).

32.
European Bioalpine Convention: Bridging Public and Private Research On Bioinformatics and Proteomics. Towards Chlamydomonas nuclear proteomics: Optimizing the isolation of nuclei and aggregating information. 2008. (Congresso).

33.
18th International Conference on Arabidopsis Research. From Chlamydomonas to Arabidopsis: a bZIP history. 2007. (Congresso).

34.
German Conference on Bioinformatics. Green evolutionary history of bZIP transcription factors. 2007. (Congresso).

35.
14th Annual International Conference on Intelligent Systems for Molecular Biology. Plant Transcription Factors at Uni-Potsdam.de. 2006. (Congresso).

36.
8th International Congress of Plant Molecular Biology. Functional analysis of transcription factors that play important roles in leaf development and/or physiology at sink-to-source transition and the onset of senescence. 2006. (Congresso).

37.
Workshop on Molecular Interactions.Are biological networks scale-free graphs. 2006. (Simpósio).

38.
16th International Conference on Arabidopsis Research. Genomewide identi cation of transcription factors involved in the initial phase of salt stress in rice. 2005. (Congresso).

39.
5th International Rice Genetics Symposium and 3rd International Rice Functional Genomics Symposium. Comparative expression pro ling of different rice varieties during initial phase of abiotic stress. 2005. (Congresso).

40.
12th Annual International Conference on Intelligent Systems for Molecular Biology and 4th European Conference on Computational Biology. Analysis of Non-coding Regions in Arabidopsis thaliana. 2004. (Congresso).


Organização de eventos, congressos, exposições e feiras
1.
Mattiello, L ; CALDANA, CAMILA ; MARTINS, M. C. M. ; FRANCO, H. C. J. ; RIAÑO-PACHÓN, D.M. . III Workshop on Sugarcane Physiology for Agronomic Applications. 2014. (Outro).

2.
CASTILLO, J. F. ; Cristancho, Marco ; PINZON, A. ; ISAZA, G. ; Riano-Pachon, Diego M . Segundo Congreso Colombiano de Biología Computacional y Bioinformática. 2013. (Congresso).

3.
Riano-Pachon, Diego Mauricio; BARRETO, E. ; Restrepo R, Silvia . Primer Congreso Colombiano de Biología Computacional. 2011. (Congresso).



Orientações



Orientações e supervisões em andamento
Tese de doutorado
1.
Lucas Lopes. Dual RNA-seq of semi-industrial fermentations with Saccharomyces cerevisiae CAT-1 and two bacterial isolates, frequently found contaminating industrial ethanolic fermentations.. Início: 2015. Tese (Doutorado em BIOENERGIA USP, UNICAMP E UNESP) - Universidade de São Paulo, Fundação de Amparo à Pesquisa do Estado de São Paulo. (Coorientador).

2.
Sandra Liliana Gaitán. Molecular mechanisms of Thielaviospis tolerance in Elaeis guinensis (Palm oil) using RNASeq. Início: 2013. Tese (Doutorado em Doctorado en Biotecnología) - Universidad Nacional de Colombia - Bogotá. (Orientador).

3.
Ximena Carolina Pérez Mancilla. ESTRATEGIA DE MODIFICACIÓN METABÓLICA BASADA EN EL TRANSCRIPTOMA DE Clostridium IBUN 158B PARA LA PRODUCCIÓN DE 1,3-PROPANODIOL A PARTIR DE GLICEROL. Início: 2012. Tese (Doutorado em Doctorado en Biotecnología) - Universidad Nacional de Colombia - Bogotá, Departamento Administrativo de Ciencia Tecnología e Innovación. (Coorientador).


Orientações e supervisões concluídas
Dissertação de mestrado
1.
Renato Augusto Corrêa dos Santos. Análise genômica da levedura xilanolítica Pseudozyma brasiliensis. 2018. Dissertação (Mestrado em Genética e Biologia Molecular) - Universidade Estadual de Campinas, Fundação de Amparo à Pesquisa do Estado de São Paulo. Coorientador: Diego Mauricio Riano Pachon.

2.
Laura Natalia González García. Assembly and Annotation of the Phytophthora genome: Looking for host specificity. 2015. Dissertação (Mestrado em Bioinformática) - Universidad de los Andes Colombia, . Coorientador: Diego Mauricio Riano Pachon.

3.
Juan Camilo Castro. Decision making in host-pathogen interactions: Exploring Phytophthora infestans regulatory network. 2014. Dissertação (Mestrado em Master in Biological Sciences) - Universidad de los Andes Colombia, . Coorientador: Diego Mauricio Riano Pachon.

4.
David Alejandro Urbina Gomez. An analysis pipeline for FAIRE-seq data. 2012. Dissertação (Mestrado em Master in Biological Sciences) - Universidad de los Andes Colombia, . Orientador: Diego Mauricio Riano Pachon.

5.
David Octavio Botero Rozo. TOWARDS A DRAFT OF THE COFFEE RUST GENOME SEQUENCE. 2012. Dissertação (Mestrado em Master in Biological Sciences) - Universidad de los Andes Colombia, . Coorientador: Diego Mauricio Riano Pachon.

6.
ANDRÉS FELIPE VÁSQUEZ J.. IDENTIFICATION OF NEW POTENTIAL NON-CLASSICAL LIPOPHILIC DIHYDROFOLATE REDUCTASE INHIBITORS WITH POTENTIAL ANTITUMORAL ACTIVITY ON MELANOMA CELL LINES A375 AND B16. 2012. Dissertação (Mestrado em Master in Biological Sciences) - Universidad de los Andes Colombia, . Orientador: Diego Mauricio Riano Pachon.

7.
Eric Juan Carlos Galvez Bobadilla. Assessment of Microbial Composition andDegradation Functions in PAH Contaminated Neotropical Caribbean MarineSediments (Cartagena Bay, Colombia) as Determined by Functional Metagenomicsand Metatranscriptomics. 2012. Dissertação (Mestrado em Master in Biological Sciences) - Universidad de los Andes Colombia, . Coorientador: Diego Mauricio Riano Pachon.

8.
Francisco Buitrago Florez. Identification of transcription factor genes and their correlation with the high diversity of Stramenopiles. 2011. Dissertação (Mestrado em Master in Biological Sciences) - Universidad de los Andes Colombia, Universidad de los Andes. Orientador: Diego Mauricio Riano Pachon.

Tese de doutorado
1.
Ana Catalina Lara. GENETIC STRUCTURE AND CRUDE OIL ASSOCIATED TRANSCRIPTOMIC PROFILE OF ENVIRONMENTAL AND CLINICAL STRAINS OF Pseudomonas aeruginosa. 2018. Tese (Doutorado em PhD in Biological Sciences) - Universidad de los Andes Colombia, Departamento Administrativo de Ciencia Tecnología e Innovación. Coorientador: Diego Mauricio Riano Pachon.

Trabalho de conclusão de curso de graduação
1.
Laura Natalia Gonzalez Garcia. Comparaci on entre el potencial de las regiones variables del 16S rRNA para la identi caci on de Lactobacillus spp. 2011. Trabalho de Conclusão de Curso. (Graduação em Microbiology) - Universidad de los Andes Colombia. Orientador: Diego Mauricio Riano Pachon.

2.
David Alejandro Urbina gomez. An alisis de datos de FAIRE-seq: Chlamydomonas reinhardtii en condiciones de baja disponibilidad de carbono. 2011. Trabalho de Conclusão de Curso. (Graduação em Microbiology) - Universidad de los Andes Colombia. Orientador: Diego Mauricio Riano Pachon.

3.
Juan David Enciso. Evolutionary history of the kingdom Protista using a phylogenomical approach. 2011. Trabalho de Conclusão de Curso. (Graduação em Biology) - Universidad de los Andes Colombia. Orientador: Diego Mauricio Riano Pachon.



Educação e Popularização de C & T



Livros e capítulos
1.
RIAÑO-PACHÓN, DIEGO MAURICIO; GONZALEZ ESTRADA, E. ; ALEXA, A. ; RAMIREZ, F. ; WINCK, F. V. ; PEREZ-RODRIGUEZ, P. . 1) Bases de bioinformática, 2) Herramientas bioinformáticas y 3) Análisis comparativo y evolución. In: Colegio de Postgraduados. (Org.). Bioinformática: Aplicaciones a la genómica y la proteómica. 1ed.Texcoco: Gómez Merino, Fernando,, 2010, v. , p. 1-.


Textos em jornais de notícias/revistas
1.
FOG, L. ; RIAÑO-PACHÓN, DIEGO MAURICIO . Planta completa la cadena de la evolución. El Espectador, 12 maio 2011.

2.
MUELLER-ROEBER, BERND ; RIAÑO-PACHÓN, DIEGO MAURICIO ; RUZICIC, SLOBODAN ; SKIRYCZ, A. ; CALDANA, CAMILA ; WITT, I. ; ZANOR, M. I. . Pflanzliche Regulatorproteine. BioFORUM, Germany, p. 32 - 34, 02 jan. 2005.

3.
KERSTEN, BIRGIT ; NAGEL, A. ; RIAÑO-PACHÓN, DIEGO MAURICIO ; NEIGENFIND, JOST ; WEBER, ELKE ; WAGNER, R. ; DIEHL, S. . Die GABI-Primärdatenbank GabiPD - Komplete Integration von GABI-Daten aus Modell und Nutzp. GenomXPress, Germany, p. 17 - 19, 16 jan. 2008.


Cursos de curta duração ministrados
1.
RIAÑO-PACHÓN, DIEGO MAURICIO; Restrepo R, Silvia ; ANZOLA, J. M. ; ALZATE RESTREPO, J. F. A. . Bioinformática Básica. 2011. (Curso de curta duração ministrado/Extensão).

2.
RIAÑO-PACHÓN, DIEGO MAURICIO; RAMIREZ, F. ; ALEXA, A. ; PEREZ-RODRIGUEZ, P. ; GONZALEZ ESTRADA, E. ; WINCK, FLAVIA V. . Curso internacional sobre bioinformática: Applicaciones a la genómica y proteómica. 2009. (Curso de curta duração ministrado/Extensão).


Organização de eventos, congressos, exposições e feiras
1.
Mattiello, L ; CALDANA, CAMILA ; MARTINS, M. C. M. ; FRANCO, H. C. J. ; RIAÑO-PACHÓN, D.M. . III Workshop on Sugarcane Physiology for Agronomic Applications. 2014. (Outro).




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