Publications

Anna Clara Silva Campos, Thalita Macedo Araújo, Lauro Moraes, Renato Augusto Correa dos Santos, Gustavo Henrique Goldman, Diego Mauricio Riaño-Pachón, Juliana Velasco de Castro Oliveira, Fábio Márcio Squina, Ieso de Miranda Castro, Maria José Magalhães Trópia, Aureliano Claret da Cunha, Izinara C. Rosse, Rogelio Lopes Brandão (2023). Selected cachaça yeast strains share a genomic profile related to traits relevant to industrial fermentation processes.. Applied and environmental microbiology.

Leonardo T. Kimura, Ewerton R. Andrade, Ismael Nobre, Carlos A. Nobre, Bruno A. S. de Medeiros, Diego M. Riaño-Pachón, Felipe K. Shiraishi, Tereza C. M. B. Carvalho, Marcos A. Simplicio (2023). Amazon Biobank: a collaborative genetic database for bioeconomy development.. Functional & integrative genomics.

Katie Emelianova, Diego Mauricio Riaño-Pachón, Maria Fernanda Torres Jimenez (2023). Making sense of complexity: Advances in bioinformatics for plant biology. Applications in Plant Sciences.

Andrés Felipe Vásquez, Luis Alberto Gómez, Andrés González Barrios, Diego M. Riaño-Pachón (2022). Identification of Active Compounds against Melanoma Growth by Virtual Screening for Non-Classical Human DHFR Inhibitors.. International journal of molecular sciences.

Joni E. Lima, Luis H. D. Serezino, Melissa K. Alves, André L. Tagliaferro, Marielle Vitti, Silvana Creste, Diego Mauricio Riaño-Pachón, Renato V. Dos Santos, Antonio Figueira (2022). Root nitrate uptake in sugarcane (Saccharum spp.) is modulated by transcriptional and presumably posttranscriptional regulation of the NRT2.1/NRT3.1 transport system.. Molecular genetics and genomics : MGG.

Lauana Pereira de Oliveira, Bruno Viana Navarro, João Pedro de Jesus Pereira, Adriana Rios Lopes, Marina C. M. Martins, Diego Mauricio Riaño-Pachón, Marcos Silveira Buckeridge (2022). Bioinformatic analyses to uncover genes involved in trehalose metabolism in the polyploid sugarcane.. Scientific reports.

Sandra Milena Gonzalez Sayer, Ursula Oggenfuss, Ibonne García, Fabio Aristizabal, Daniel Croll, Diego Mauricio Riaño-Pachón (2022). High-quality genome assembly of Pseudocercospora ulei the main threat to natural rubber trees.. Genetics and molecular biology.

Beatriz Rodrigues Estevam, Diego Mauricio Riaño-Pachón (2022). CoCoView - A codon conservation viewer via sequence logos.. MethodsX.

Viviane Cristina Heinzen da Silva, Marina C. M. Martins, Maria Juliana Calderan-Rodrigues, Anthony Artins, Carolina Cassano Monte Bello, Saurabh Gupta, Tiago J. P. Sobreira, Diego Mauricio Riaño-Pachón, Valéria Mafra, Camila Caldana (2021). Shedding light on the dynamic role of the “Target of Rapamycin” kinase in the fast-growing C4 species Setaria viridis, a suitable model for biomass crops. Frontiers in plant science.

Jaqueline Raquel de Almeida, Diego Mauricio Riaño-Pachón, Livia Maria Franceschini, Isaneli Batista Dos Santos, Jessica Aparecida Ferrarezi, Pedro Avelino Maia de Andrade, Claudia Barros Monteiro-Vitorello, Carlos Alberto Labate, Maria Carolina Quecine (2021). Revealing the high variability on nonconserved core and mobile elements of Austropuccinia psidii and other rust mitochondrial genomes.. PloS one.

Amanda Fanelli, David M. Rancour, Michael Sullivan, Steven D. Karlen, John Ralph, Diego Mauricio Riaño-Pachón, Renato Vicentini, Tatiane da Franca Silva, André Ferraz, Ronald D. Hatfield, Elisson Romanel (2021). Overexpression of a Sugarcane BAHD Acyltransferase Alters Hydroxycinnamate Content in Maize Cell Wall.. Frontiers in plant science.

Diego Mauricio Riaño-Pachón, Hector Fabio Espitia-Navarro, John Jaime Riascos, Gabriel Rodrigues Alves Margarido (2021). Modern Approaches for Transcriptome Analyses in Plants.. Advances in experimental medicine and biology.

Tatiana Arias, Diego Mauricio Riaño-Pachón, Verónica S. Di Stilio (2021). Genomic and transcriptomic resources for candidate gene discovery in the Ranunculids.. Applications in plant sciences.

Aureliano C. Cunha, Renato A. Corrêa Dos Santos, Diego Mauricio Riaño-Pachón, Fábio M. Squina, Juliana V. C. Oliveira, Gustavo H. Goldman, Aline T. Souza, Lorena S. Gomes, Fernanda Godoy-Santos, Janaina A. Teixeira, Fábio Faria-Oliveira, Izinara C. Rosse, Ieso M. Castro, Cândida Lucas, Rogelio L. Brandão (2020). Draft genome sequence of Wickerhamomyces anomalus LBCM1105, isolated from cachaça fermentation.. Genetics and molecular biology.

Fernando Manuel Matias Hurtado, Maísa de Siqueira Pinto, Perla Novais de Oliveira, Diego Mauricio Riaño-Pachón, Laura Beatriz Inocente, Helaine Carrer (2019). Analysis of NAC Domain Transcription Factor Genes of Tectona grandis L.f. Involved in Secondary Cell Wall Deposition.. Genes.

Bruna S. Fernandes, Oscar Dias, Gisela Costa, Antonio A. Kaupert Neto, Tiago F. C. Resende, Juliana V. C. Oliveira, Diego Mauricio Riaño-Pachón, Marcelo Zaiat, José G. C. Pradella, Isabel Rocha (2019). Genome-wide sequencing and metabolic annotation of Pythium irregulare CBS 494.86: understanding Eicosapentaenoic acid production.. BMC biotechnology.

Juan Camilo Castro, Ivan Valdés, Laura Natalia Gonzalez-García, Giovanna Danies, Silvia Cañas, Flavia Vischi Winck, Carlos Eduardo Ñústez, Silvia Restrepo, Diego Mauricio Riaño-Pachón (2019). Gene regulatory networks on transfer entropy (GRNTE): a novel approach to reconstruct gene regulatory interactions applied to a case study for the plant pathogen Phytophthora infestans.. Theoretical biology & medical modelling.

Dyfed Lloyd Evans, Thandekile Thandiwe Hlongwane, Shailesh V. Joshi, Diego Mauricio Riaño-Pachón (2019). The sugarcane mitochondrial genome: assembly, phylogenetics and transcriptomics.. PeerJ.

Bruna Constante Fonseca, Diego Mauricio Riaño-Pachón, María-Eugenia Guazzaroni, Valeria Reginatto (2019). Genome sequence of the H2-producing Clostridium beijerinckii strain Br21 isolated from a sugarcane vinasse treatment plant.. Genetics and molecular biology.

Paula Fagundes de Gouvêa, Aline Vianna Bernardi, Luis Eduardo Gerolamo, Emerson de Souza Santos, Diego Mauricio Riaño-Pachón, Sergio Akira Uyemura, Taisa Magnani Dinamarco (2018). Transcriptome and secretome analysis of Aspergillus fumigatus in the presence of sugarcane bagasse.. BMC genomics.

Gustavo Pagotto Borin, Marcelo Falsarella Carazzolle, Renato Augusto Correa dos Santos, Diego Mauricio Riaño-Pachón, Juliana Velasco de Castro Oliveira (2018). Gene Co-expression Network Reveals Potential New Genes Related to Sugarcane Bagasse Degradation in Trichoderma reesei RUT-30.. Frontiers in bioengineering and biotechnology.

Fabiano Jares Contesini, Marcelo Vizoná Liberato, Marcelo Ventura Rubio, Felipe Calzado, Mariane Paludetti Zubieta, Diego Mauricio Riaño-Pachón, Fábio Márcio Squina, Fabricio Bracht, Munir S. Skaf, André Ricardo Damasio (2017). Structural and functional characterization of a highly secreted α-l-arabinofuranosidase (GH62) from Aspergillus nidulans grown on sugarcane bagasse.. Biochimica et biophysica acta. Proteins and proteomics.

Paula Macedo Nobile, Alexandra Bottcher, Juliana L. S. Mayer, Michael S. Brito, Ivan A. Dos Anjos, Marcos Guimarães de Andrade Landell, Renato Vicentini, Silvana Creste, Diego Mauricio Riaño-Pachón, Paulo Mazzafera (2017). Identification, classification and transcriptional profiles of dirigent domain-containing proteins in sugarcane.. Molecular genetics and genomics : MGG.

Adriana Oliveira Manfiolli, Patrícia Alves de Castro, Thaila Fernanda Dos Reis, Stephen Dolan, Sean Doyle, Gary Jones, Diego Mauricio Riaño-Pachón, Mevlüt Ulaş, Luke M. Noble, Derek J. Mattern, Axel A. Brakhage, Vito Valiante, Rafael Silva-Rocha, Ozgur Bayram, Gustavo H. Goldman (2017). Aspergillus fumigatus protein phosphatase PpzA is involved in iron assimilation, secondary metabolite production, and virulence.. Cellular microbiology.

Renato Augusto Correa dos Santos, Gustavo Henrique Goldman, Diego Mauricio Riaño-Pachón (2017). ploidyNGS: visually exploring ploidy with Next Generation Sequencing data.. Bioinformatics (Oxford, England).

F. Mandelli, M. B. Couger, D. A. A. Paixão, C. B. Machado, C. M. Carnielli, J. A. Aricetti, I. Polikarpov, R. Prade, C. Caldana, A. F. Paes Leme, A. Z. Mercadante, Diego Mauricio Riaño-Pachón, Fábio Márcio Squina (2017). Thermal adaptation strategies of the extremophile bacterium Thermus filiformis based on multi-omics analysis.. Extremophiles : life under extreme conditions.

Gustavo Pagotto Borin, Camila Cristina Sanchez, Eliane Silva de Santana, Guilherme Keppe Zanini, Renato Augusto Correa dos Santos, Angélica de Oliveira Pontes, Aline Tieppo de Souza, Roberta Maria Menegaldo Tavares Soares Dal'Mas, Diego Mauricio Riaño-Pachón, Gustavo Henrique Goldman, Juliana Velasco de Castro Oliveira (2017). Comparative transcriptome analysis reveals different strategies for degradation of steam-exploded sugarcane bagasse by Aspergillus niger and Trichoderma reesei.. BMC genomics.

Lilian Pereira Silva, Patrícia Alves de Castro, Thaila Fernanda Dos Reis, Mario Henrique Paziani, Márcia Regina Von Zeska Kress, Diego Mauricio Riaño-Pachón, Daisuke Hagiwara, Laure N. A. Ries, Neil Andrew Brown, Gustavo H. Goldman (2017). Genome-wide transcriptome analysis of Aspergillus fumigatus exposed to osmotic stress reveals regulators of osmotic and cell wall stresses that are SakA(HOG1) and MpkC dependent.. Cellular microbiology.

Thaila Fernanda Dos Reis, Benjamin M. Nitsche, Pollyne Borborema Almeida de Lima, Leandro José de Assis, Laura Mellado, Steven D. Harris, Vera Meyer, Renato A. Corrêa Dos Santos, Diego Mauricio Riaño-Pachón, Laure Nicolas Annick Ries, Gustavo H. Goldman (2017). The low affinity glucose transporter HxtB is also involved in glucose signalling and metabolism in Aspergillus nidulans.. Scientific reports.

Natalia Coutouné, Aline Tieppo Nogueira Mulato, Diego Mauricio Riaño-Pachón, Juliana Velasco de Castro Oliveira (2017). Draft Genome Sequence of Saccharomyces cerevisiae Barra Grande (BG-1), a Brazilian Industrial Bioethanol-Producing Strain.. Genome announcements.

Ronald P. de Vries, Robert Riley, Ad Wiebenga, Guillermo Aguilar-Osorio, Sotiris Amillis, Cristiane Akemi Uchima, Gregor Anderluh, Mojtaba Asadollahi, Marion Askin, Kerrie Barry, Evy Battaglia, Ozgur Bayram, Tiziano Benocci, Susanna A. Braus-Stromeyer, Camila Caldana, David Cánovas, Gustavo C. Cerqueira, Fusheng Chen, Wanping Chen, Cindy Choi, Alicia Clum, Renato Augusto Correa dos Santos, André Ricardo de Lima Damásio, George Diallinas, Tamás Emri, Erzsébet Fekete, Michel Flipphi, Susanne Freyberg, Antonia Gallo, Christos Gournas, Rob Habgood, Matthieu Hainaut, María Laura Harispe, Bernard Henrissat, Kristiina S. Hildén, Ryan Hope, Abeer Hossain, Eugenia Karabika, Levente Karaffa, Zsolt Karányi, Nada Kraševec, Alan Kuo, Harald Kusch, Kurt LaButti, Ellen L. Lagendijk, Alla Lapidus, Anthony Levasseur, Erika Lindquist, Anna Lipzen, Antonio F. Logrieco, Andrew MacCabe, Miia R. Mäkelä, Iran Malavazi, Petter Melin, Vera Meyer, Natalia Mielnichuk, Márton Miskei, Ákos P. Molnár, Giuseppina Mulé, Chew Yee Ngan, Margarita Orejas, Erzsébet Orosz, Jean Paul Ouedraogo, Karin M. Overkamp, Hee-Soo Park, Giancarlo Perrone, Francois Piumi, Peter J. Punt, Arthur F. J. Ram, Ana Ramón, Stefan Rauscher, Eric Record, Diego Mauricio Riaño-Pachón, Vincent Robert, Julian Röhrig, Roberto Ruller, Asaf Salamov, Nadhira S. Salih, Rob A. Samson, Erzsébet Sándor, Manuel Sanguinetti, Tabea Schütze, Kristina Sepčić, Ekaterina Shelest, Gavin Sherlock, Vicky Sophianopoulou, Fábio M. Squina, Hui Sun, Antonia Susca, Richard B. Todd, Adrian Tsang, Shiela E. Unkles, Nathalie van de Wiele, Diana van Rossen-Uffink, Juliana Velasco de Castro Oliveira, Tammi C. Vesth, Jaap Visser, Jae-Hyuk Yu, Miaomiao Zhou, Mikael R. Andersen, David B. Archer, Scott E. Baker, Isabelle Benoit, Axel A. Brakhage, Gerhard H. Braus, Reinhard Fischer, Jens C. Frisvad, Gustavo H. Goldman, Jos Houbraken, Berl Oakley, István Pócsi, Claudio Scazzocchio, Bernhard Seiboth, Patricia A. vanKuyk, Jennifer Wortman, Paul S. Dyer, Igor V. Grigoriev (2017). Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus.. Genome biology.

Bruno L. Mello, Anna M. Alessi, Diego Mauricio Riaño-Pachón, Eduardo R. deAzevedo, Francisco E. G. Guimarães, Melissa C. Espirito Santo, Simon McQueen-Mason, Neil C. Bruce, Igor Polikarpov (2017). Targeted metatranscriptomics of compost-derived consortia reveals a GH11 exerting an unusual exo-1,4-β-xylanase activity.. Biotechnology for biofuels.

Diego Mauricio Riaño-Pachón, Lucia Mattiello (2017). Draft genome sequencing of the sugarcane hybrid SP80-3280.. F1000Research.

Patrícia Alves de Castro, Thaila Fernanda Dos Reis, Stephen K. Dolan, Adriana Oliveira Manfiolli, Neil Andrew Brown, Gary W. Jones, Sean Doyle, Diego Mauricio Riaño-Pachón, Fábio Márcio Squina, Camila Caldana, Ashutosh Singh, Maurizio Del Poeta, Daisuke Hagiwara, Rafael Silva-Rocha, Gustavo H. Goldman (2016). The Aspergillus fumigatus SchA(SCH9) kinase modulates SakA(HOG1) MAP kinase activity and it is essential for virulence.. Molecular microbiology.

Neil Andrew Brown, Laure N. A. Ries, Thaila F. Reis, Ranjith Rajendran, Renato Augusto Correa dos Santos, Gordon Ramage, Diego Mauricio Riaño-Pachón, Gustavo H. Goldman (2016). RNAseq reveals hydrophobins that are involved in the adaptation of Aspergillus nidulans to lignocellulose.. Biotechnology for biofuels.

Flavia V. Winck, Diego Mauricio Riaño-Pachón, Telma T. Franco (2016). Editorial: Advances in Microalgae Biology and Sustainable Applications.. Frontiers in plant science.

Flavia V. Winck, David O. Páez Melo, Diego Mauricio Riaño-Pachón, Marina C. M. Martins, Camila Caldana, Andrés F. González Barrios (2016). Analysis of Sensitive CO2 Pathways and Genes Related to Carbon Uptake and Accumulation in Chlamydomonas reinhardtii through Genomic Scale Modeling and Experimental Validation.. Frontiers in plant science.

Lucia Mattiello, Diego Mauricio Riaño-Pachón, Marina Camara Mattos Martins, Larissa Prado da Cruz, Denis Bassi, Paulo Eduardo Ribeiro Marchiori, Rafael Vasconcelos Ribeiro, Mônica T. Veneziano Labate, Carlos Alberto Labate, Marcelo Menossi (2015). Physiological and transcriptional analyses of developmental stages along sugarcane leaf.. BMC plant biology.

Renato Augusto Correa dos Santos, Andresa Aparecida Berretta, Hernane da Silva Barud, Sidney José Lima Ribeiro, Laura Natalia Gonzalez-García, Tiago Domingues Zucchi, Gustavo H. Goldman, Diego Mauricio Riaño-Pachón (2015). Draft Genome Sequence of Komagataeibacter intermedius Strain AF2, a Producer of Cellulose, Isolated from Kombucha Tea.. Genome announcements.

Flavia V. Winck, Ana Carolina Prado Ribeiro, Romênia Ramos Domingues, Liu Yi Ling, Diego Mauricio Riaño-Pachón, César Rivera, Thaís Bianca Brandão, Adriele Ferreira Gouvea, Alan Roger Santos-Silva, Ricardo D. Coletta, Adriana F. Paes Leme (2015). Insights into immune responses in oral cancer through proteomic analysis of saliva and salivary extracellular vesicles.. Scientific reports.

Marçal Mariné, Neil Andrew Brown, Diego Mauricio Riaño-Pachón, Gustavo Henrique Goldman (2015). On and Under the Skin: Emerging Basidiomycetous Yeast Infections Caused by Trichosporon Species.. PLoS pathogens.

Juan Pablo Rosas-Morales, Ximena Perez Mancilla, Liliana López-Kleine, Dolly Montoya Castaño, Diego Mauricio Riaño-Pachón (2015). Draft genome sequences of clostridium strains native to Colombia with the potential to produce solvents.. Genome announcements.

Fernanda Mandelli, Brenda Oliveira Ramires, Matthew Brian Couger, Douglas A. A. Paixão, Cesar M. Camilo, Igor Polikarpov, Rolf Prade, Diego Mauricio Riaño-Pachón, Fábio M. Squina (2015). Draft Genome Sequence of the Thermophile Thermus filiformis ATCC 43280, Producer of Carotenoid-(Di)glucoside-Branched Fatty Acid (Di)esters and Source of Hyperthermostable Enzymes of Biotechnological Interest.. Genome announcements.

Renato Augusto Correa dos Santos, Andresa A. Berretta, Hernane da Silva Barud, Sidney José Lima Ribeiro, Laura Natalia Gonzalez-García, Tiago Domingues Zucchi, Gustavo H. Goldman, Diego Mauricio Riaño-Pachón (2014). Draft Genome Sequence of Komagataeibacter rhaeticus Strain AF1, a High Producer of Cellulose, Isolated from Kombucha Tea.. Genome announcements.

Juliana Velasco de Castro Oliveira, Thuanny A. Borges, Renato Augusto Correa dos Santos, Larissa F. D. Freitas, Carlos Augusto Rosa, Gustavo Henrique Goldman, Diego Mauricio Riaño-Pachón (2014). Pseudozyma brasiliensis sp. nov., a xylanolytic, ustilaginomycetous yeast species isolated from an insect pest of sugarcane roots.. International journal of systematic and evolutionary microbiology.

Mohammad Amin Omidbakhshfard, Flavia Vischi Winck, Samuel Arvidsson, Diego Mauricio Riaño-Pachón, Bernd Mueller-Roeber (2014). A step-by-step protocol for formaldehyde-assisted isolation of regulatory elements from Arabidopsis thaliana.. Journal of integrative plant biology.

Francisco Javier Buitrago Flórez, Silvia Restrepo, Diego Mauricio Riaño-Pachón (2014). Identification of transcription factor genes and their correlation with the high diversity of stramenopiles.. PloS one.

Marco A. Cristancho, David Octavio Botero-Rozo, William Giraldo, Javier Tabima, Diego Mauricio Riaño-Pachón, Carolina Escobar, Yomara Rozo, Luis F. Rivera, Andrés Durán, Silvia Restrepo, Tamar Eilam, Yehoshua Anikster, Alvaro L. Gaitán (2014). Annotation of a hybrid partial genome of the coffee rust (Hemileia vastatrix) contributes to the gene repertoire catalog of the Pucciniales.. Frontiers in plant science.

Juliana Velasco de Castro Oliveira, Renato Augusto Correa dos Santos, Thuanny A. Borges, Diego Mauricio Riaño-Pachón, Gustavo Henrique Goldman (2013). Draft Genome Sequence of Pseudozyma brasiliensis sp. nov. Strain GHG001, a High Producer of Endo-1,4-Xylanase Isolated from an Insect Pest of Sugarcane.. Genome announcements.

Liliana López-Kleine, Andrés Pinzón, Diego Chaves, Silvia Restrepo, Diego Mauricio Riaño-Pachón (2013). Chromosome 10 in the tomato plant carries clusters of genes responsible for field resistance/defence to Phytophthora infestans.. Genomics.

Flavia Vischi Winck, Samuel Arvidsson, Diego Mauricio Riaño-Pachón, Sabrina Hempel, Aneta Koseska, Zoran Nikoloski, David Alejandro Urbina Gomez, Jens Rupprecht, Bernd Mueller-Roeber (2013). Genome-wide identification of regulatory elements and reconstruction of gene regulatory networks of the green alga Chlamydomonas reinhardtii under carbon deprivation.. PloS one.

Flavia V. Winck, Diego Mauricio Riaño-Pachón, Frederik Sommer, Jens Rupprecht, Bernd Mueller-Roeber (2012). The nuclear proteome of the green alga Chlamydomonas reinhardtii.. Proteomics.

Judith Lucia Gomez-Porras, Diego Mauricio Riaño-Pachón, Begoña Benito, Rosario Haro, Kamil Sklodowski, Alonso Rodríguez-Navarro, Ingo Dreyer (2012). Phylogenetic analysis of k(+) transporters in bryophytes, lycophytes, and flowering plants indicates a specialization of vascular plants.. Frontiers in plant science.

Ingo Dreyer, Judith Lucia Gomez-Porras, Diego Mauricio Riaño-Pachón, Rainer Hedrich, Dietmar Geiger (2012). Molecular Evolution of Slow and Quick Anion Channels (SLACs and QUACs/ALMTs).. Frontiers in plant science.

Johannes Rohrmann, Takayuki Tohge, Rob Alba, Sonia Osorio, Camila Caldana, Ryan McQuinn, Samuel Arvidsson, Margaretha J. van der Merwe, Diego Mauricio Riaño-Pachón, Bernd Mueller-Roeber, Zhangjun Fei, Adriano Nunes Nesi, James J. Giovannoni, Alisdair R. Fernie (2011). Combined transcription factor profiling, microarray analysis and metabolite profiling reveals the transcriptional control of metabolic shifts occurring during tomato fruit development.. The Plant journal : for cell and molecular biology.

Jo Ann Banks, Tomoaki Nishiyama, Mitsuyasu Hasebe, John L. Bowman, Michael Gribskov, Claude dePamphilis, Victor A. Albert, Naoki Aono, Tsuyoshi Aoyama, Barbara A. Ambrose, Neil W. Ashton, Michael J. Axtell, Elizabeth Barker, Michael S. Barker, Jeffrey L. Bennetzen, Nicholas D. Bonawitz, Clint Chapple, Chaoyang Cheng, Luiz Gustavo Guedes Correa, Michael Dacre, Jeremy DeBarry, Ingo Dreyer, Marek Elias, Eric M. Engstrom, Mark Estelle, Liang Feng, Cédric Finet, Sandra K. Floyd, Wolf B. Frommer, Tomomichi Fujita, Lydia Gramzow, Michael Gutensohn, Jesper Harholt, Mitsuru Hattori, Alexander Heyl, Tadayoshi Hirai, Yuji Hiwatashi, Masaki Ishikawa, Mineko Iwata, Kenneth G. Karol, Barbara Koehler, Uener Kolukisaoglu, Minoru Kubo, Tetsuya Kurata, Sylvie Lalonde, Kejie Li, Ying Li, Amy Litt, Eric Lyons, Gerard Manning, Takeshi Maruyama, Todd P. Michael, Koji Mikami, Saori Miyazaki, Shin-ichi Morinaga, Takashi Murata, Bernd Mueller-Roeber, David R. Nelson, Mari Obara, Yasuko Oguri, Richard G. Olmstead, Naoko Onodera, Bent Larsen Petersen, Birgit Pils, Michael Prigge, Stefan A. Rensing, Diego Mauricio Riaño-Pachón, Alison W. Roberts, Yoshikatsu Sato, Henrik Vibe Scheller, Burkhard Schulz, Christian Schulz, Eugene V. Shakirov, Nakako Shibagaki, Naoki Shinohara, Dorothy E. Shippen, Iben Sørensen, Ryo Sotooka, Nagisa Sugimoto, Mamoru Sugita, Naomi Sumikawa, Milos Tanurdzic, Günter Theissen, Peter Ulvskov, Sachiko Wakazuki, Jing-Ke Weng, William W. G. T. Willats, Daniel Wipf, Paul G. Wolf, Lixing Yang, Andreas D. Zimmer, Qihui Zhu, Therese Mitros, Uffe Hellsten, Dominique Loqué, Robert Otillar, Asaf Salamov, Jeremy Schmutz, Harris Shapiro, Erika Lindquist, Susan Lucas, Daniel Rokhsar, Igor V. Grigoriev (2011). The Selaginella genome identifies genetic changes associated with the evolution of vascular plants.. Science (New York, N.Y.).

Diego Mauricio Riaño-Pachón, Sabrina Kleessen, Jost Neigenfind, Pawel Durek, Elke Weber, Wolfgang R. Engelsberger, Dirk Walther, Joachim Selbig, Waltraud X. Schulze, Birgit Kersten (2010). Proteome-wide survey of phosphorylation patterns affected by nuclear DNA polymorphisms in Arabidopsis thaliana.. BMC genomics.

Daniel Lang, Benjamin Weiche, Gerrit Timmerhaus, Sandra Richardt, Diego Mauricio Riaño-Pachón, Luiz G. G. Corrêa, Ralf Reski, Bernd Mueller-Roeber, Stefan A. Rensing (2010). Genome-wide phylogenetic comparative analysis of plant transcriptional regulation: a timeline of loss, gain, expansion, and correlation with complexity.. Genome biology and evolution.

Paulino Pérez-Rodríguez, Diego Mauricio Riaño-Pachón, Luiz Gustavo Guedes Correa, Stefan A. Rensing, Birgit Kersten, Bernd Mueller-Roeber (2010). PlnTFDB: updated content and new features of the plant transcription factor database.. Nucleic acids research.

Diego Mauricio Riaño-Pachón, Axel Nagel, Jost Neigenfind, Robert Wagner, Rico Basekow, Elke Weber, Bernd Mueller-Roeber, Svenja Diehl, Birgit Kersten (2009). GabiPD: the GABI primary database--a plant integrative 'omics' database.. Nucleic acids research.

Samuel Arvidsson, Miroslaw Kwasniewski, Diego Mauricio Riaño-Pachón, Bernd Mueller-Roeber (2008). QuantPrime--a flexible tool for reliable high-throughput primer design for quantitative PCR.. BMC bioinformatics.

S. Balazadeh, Diego Mauricio Riaño-Pachón, B. Mueller-Roeber (2008). Transcription factors regulating leaf senescence in Arabidopsis thaliana.. Plant biology (Stuttgart, Germany).

Luiz Gustavo Guedes Correa, Diego Mauricio Riaño-Pachón, Carlos Guerra Schrago, Renato Vicentini dos Santos, Bernd Mueller-Roeber, Michel Vincentz (2008). The role of bZIP transcription factors in green plant evolution: adaptive features emerging from four founder genes.. PloS one.

Diego Mauricio Riaño-Pachón, Luiz Gustavo Guedes Correa, Raúl Trejos-Espinosa, Bernd Mueller-Roeber (2008). Green transcription factors: a chlamydomonas overview.. Genetics.

Sabeeha S. Merchant, Simon E. Prochnik, Olivier Vallon, Elizabeth H. Harris, Steven J. Karpowicz, George B. Witman, Astrid Terry, Asaf Salamov, Lillian K. Fritz-Laylin, Laurence Maréchal-Drouard, Wallace F. Marshall, Liang-Hu Qu, David R. Nelson, Anton A. Sanderfoot, Martin H. Spalding, Vladimir V. Kapitonov, Qinghu Ren, Patrick Ferris, Erika Lindquist, Harris Shapiro, Susan M. Lucas, Jane Grimwood, Jeremy Schmutz, Pierre Cardol, Heriberto Cerutti, Guillaume Chanfreau, Chun-Long Chen, Valérie Cognat, Martin T. Croft, Rachel Dent, Susan Dutcher, Emilio Fernández, Hideya Fukuzawa, David González-Ballester, Diego González-Halphen, Armin Hallmann, Marc Hanikenne, Michael Hippler, William Inwood, Kamel Jabbari, Ming Kalanon, Richard Kuras, Paul A. Lefebvre, Stéphane D. Lemaire, Alexey V. Lobanov, Martin Lohr, Andrea Manuell, Iris Meier, Laurens Mets, Maria Mittag, Telsa Mittelmeier, James V. Moroney, Jeffrey Moseley, Carolyn Napoli, Aurora M. Nedelcu, Krishna Niyogi, Sergey V. Novoselov, Ian T. Paulsen, Greg Pazour, Saul Purton, Jean-Philippe Ral, Diego Mauricio Riaño-Pachón, Wayne Riekhof, Linda Rymarquis, Michael Schroda, David Stern, James Umen, Robert Willows, Nedra Wilson, Sara Lana Zimmer, Jens Allmer, Janneke Balk, Katerina Bisova, Chong-Jian Chen, Marek Elias, Karla Gendler, Charles Hauser, Mary Rose Lamb, Heidi Ledford, Joanne C. Long, Jun Minagawa, M. Dudley Page, Junmin Pan, Wirulda Pootakham, Sanja Roje, Annkatrin Rose, Eric Stahlberg, Aimee M. Terauchi, Pinfen Yang, Steven Ball, Chris Bowler, Carol L. Dieckmann, Vadim N. Gladyshev, Pamela Green, Richard Jorgensen, Stephen Mayfield, Bernd Mueller-Roeber, Sathish Rajamani, Richard T. Sayre, Peter Brokstein, Inna Dubchak, David Goodstein, Leila Hornick, Y. Wayne Huang, Jinal Jhaveri, Yigong Luo, Diego Martínez, Wing Chi Abby Ngau, Bobby Otillar, Alexander Poliakov, Aaron Porter, Lukasz Szajkowski, Gregory Werner, Kemin Zhou, Igor V. Grigoriev, Daniel S. Rokhsar, Arthur R. Grossman (2007). The Chlamydomonas genome reveals the evolution of key animal and plant functions.. Science (New York, N.Y.).

Judith L. Gómez-Porras, Diego Mauricio Riaño-Pachón, Ingo Dreyer, Jorge E. Mayer, Bernd Mueller-Roeber (2007). Genome-wide analysis of ABA-responsive elements ABRE and CE3 reveals divergent patterns in Arabidopsis and rice.. BMC genomics.

Diego Mauricio Riaño-Pachón, Slobodan Ruzicic, Ingo Dreyer, Bernd Mueller-Roeber (2007). PlnTFDB: an integrative plant transcription factor database.. BMC bioinformatics.

Diego Mauricio Riaño-Pachón, Ingo Dreyer, Bernd Mueller-Roeber (2005). Orphan transcripts in Arabidopsis thaliana: identification of several hundred previously unrecognized genes.. The Plant journal : for cell and molecular biology.