Publications

88 entries « 1 of 2 »

2016

Perla Lucía Ordóñez-Baquera Everardo González-Rodrígueza*, Gerardo Armando Aguado-Santacruz Quintín Rascón-Cruz Ana Conesa Verónica Moreno-Brito Raquel Echavarria Joel Dominguez-Viveros

Identification of miRNA from Bouteloua gracilis, a drought tolerant grass, by deep sequencing and their in silico analysis Journal Article

Computational Biology and Chemistry, 66 (2017), pp. 26-35, 2016.

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erla Lucía Ordóñez-Baquera Everardo González Rodríguez, Gerardo Armando Aguado Santacru Quintín Rascón Cruz Eduviges Burrola Barraza

Aislamiento de microRNAs a partir de células clorofílicas de Bouteloua gracilis y su caracterización in silico Journal Article

Rev Mex Cienc Pecu, 7 (3), pp. 263-274, 2016.

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De Panis DN* Padró J, Furió-Tarí Tarazona Milla Carmona PS Soto IM Dopazo Conesa Hasson P S H A* E*

Transcriptome modulation during host shift is driven by secondary metabolites in desert Drosophila. Journal Article

Mol Ecol. , 2016.

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Barroso I … Conesa A, Auffray Balling C R

Making sense of big data in health research: Towards an EU action plan Journal Article

Genome Medicine, (8), pp. 71, 2016.

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van der Kloet FM Sebastián-León P, Conesa Smilde AK Westerhuis JA. A

Separating common from distinctive variation Journal Article

BMC Bioinformatics, 17 (5), pp. 195, 2016.

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van der Kloet FM Sebastián-León P, Conesa Smilde AK Westerhuis JA A

Separating common from distinctive variation Journal Article

BMC Bioinformatics, 17 (Suppl 5:195), pp. 195, 2016, ISSN: 1471-2105.

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Furió-Tarí P Tarazona S, Gabaldón Enirght AJ Conesa T A

spongeScan: A web for detecting microRNA binding elements in lncRNA sequences Journal Article

Nucleid Acid Research, 2016.

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Conesa Ana; Madrigal, Pedro; Tarazona Sonia; Gomez-Cabrero David; Cervera Alejandra; McPherson Andrew; Wojciech Szcześniak Michał; Gaffney Daniel; Elo Laura Zhang Xuegong; Mortazavi Ali L ;

A Survey of Best Practices for RNA-seq Data Analysis. Genome Biology. 2016 Journal Article

Genome Biology, 17 (13), 2016.

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de la Jesús Ogando Manuel Tardáguila, Andrea Díaz-Alderete Alicia Usategui Vanessa Miranda-Ramos Dannys Jorge Martínez-Herrera Lorena Fuente María García-León María Moreno Sara Escudero Juan Cañete María Toribio Ildefonso Cases Alberto Pascual-Montano José Luis Pablos & Santos Mañes J C D L

Notch-regulated miR-223 targets the aryl hydrocarbon receptor pathway and increases cytokine production in macrophages from rheumatoid arthritis patients Journal Article

Scientific Reports, 6 (20223), 2016.

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2015

Turpin Sevilla MC García Solano J, Navarre Perez Guillermo Conesa Conesa- Zamora C M A P

Expression Profiling as Biomarkers in Colorectal Serrated Carcinoma Book

2015.

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Okonechnikov K Conesa A, Garcia-Alcalde F

Qualimap 2: advanced multi-sample quality control for high-throughput sequencing data Journal Article

Bioinformatics, 2015.

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Pablo Conesa-Zamora PhD; Jose Garcia-Solano, MD PhD; Maria Turpin PhD; Patrica Sebastián-León BSc; Daniel Torres-Moreno BSc; Eduardo Estrada BSc; Anne Tuomisto; Jamie Wilce BSc; Markus Mäkinen MD PhD; Miguel Perez-Guillermo MD PhD; Ana Conesa PhD. C J

Methylome profiling reveals functions and genes which are differentially methylated in serrated compared to conventional colorectal carcinoma Journal Article

Clin Epigenetics, 7 (1), pp. 101, 2015.

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Morin-Adeline V Muellera K, Conesa Šlapeta A J

Comparative RNA-seq analysis of Tritrichomonas foetus PIG30/1 isolate from pigs reveals close association with Tritrichomonas foetus BP-4 isolate 'bovine genotype’ Journal Article

Vet Parasitol, 212 (3-4), pp. 111-7, 2015.

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Irmer H, Sonia Tarazona; Christoph Sasse; Patrick Olbermann; Jürgen Loeffler; Sven Krappmann; Ana Conesa; Gerhard Braus

RNAseq analysis of Aspergillus fumigatus in blood reveals a just wait and see resting stage behavior Journal Article

BMC Genomics, 16 (640), 2015.

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Tarazona S; Furio-Tari P; Turra D; Di Prieto A; Nueda Mª J, Ferrer Conesa A; A

Data quality aware analysis of differential expression in RNA-seq with NOISeq R/Bioc package Journal Article

Nucleic Acids Research , 43 (21), pp. e140, 2015.

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de la Fuente L Conesa A, Lloret Badenas Ríos A M L G

Genome-wide changes in histone H3 lysine 27 trimethylation associated with bud dormancy release in peach Journal Article

Tree Genetics & Genomes, 11:1-14 (3), pp. 1614-2942, 2015.

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van Atwood TK Bongcam-Rudloff E, Brazas ME Corpas Gaudet Lewitter Mulder Palagi PM Schneider MV Gelder CW; GOBLET Consortium M P F N

GOBLET: the Global Organisation for Bioinformatics Learning, Education and Training Journal Article

PLoS Comput Biol, 11(4):e1004143 , 2015.

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de Yáñez Y Grau E, Rodríguez-Cortez VC Hervás Vidal Noguera Hernández Segura Cañete Conesa Font Mora Castel D E R M V A A J V

Two independent epigenetic biomarkers predict survival in neuroblastoma Journal Article

Clin Epigenetics, 27 (7(1):16), 2015.

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2014

Garica-Solano J Alcaraz-Mateos E, Wilce Torres-Moreno Turpin-Sevilla MC Navarre Conesa Tuomisto Sirnio Makinen MJ Perez-Guillermo Conesa-Zamora J D C A A P M P

Methylation Microarray Analysis Identifies Differentially Methylated Genes in Serrated Compared to Conventional Colorectal Carcinomas Journal Article

Modern Pathology, (27), pp. 174A-174A, 2014.

BibTeX

MT Sevilla R Carbonell-Muñoz, Garcia-Solano Torres-Moreno Conesa Perez Guillermo Conesa-Zamora J D A M P

896: Differentially expressed functions and genes between serrated adenocarcinoma and sporadic colorectal carcinoma showing histological and molecular features of high level of microsatellite instability Journal Article

EUROPEAN JOURNAL OF CANCER, 50 (Suppplement 5), 2014.

BibTeX

Garica-Solano J Alcaraz-Mateos E, Wilce Torres-Moreno Turpin-Sevilla MC Navarre Conesa Tuomisto Sirnio Makinen MJ Perez-Guillermo Conesa-Zamora J D C A A P M P

Methylation Microarray Analysis Identifies Differentially Methylated Genes in Serrated Compared to Conventional Colorectal Carcinomas Journal Article

MODERN PATHOLOGY, 27 , pp. 174A-174A, 2014, ISBN: 08933952.

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Sebastian-Leon P Vidal E, Minguez Conesa Tarazona Amadoz Armero Salavert Vidal-Puig Montaner Dopazo P A S A C F A D J

Understanding disease mechanisms with models of signaling pathway activities Journal Article

BMC SYSTEMS BIOLOGY, 8 (121), 2014.

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Morin-Adeline V Lomas R, O'Meally Stack Conesa Slapet D C A* J*

Comparative transcriptomics reveal striking similarities between the bovine and feline Tritrichomonas foetus: consequences for in silico drug-target identification Journal Article

BMC GENOMICS, in rpess , 2014.

BibTeX

Sarah A. Munro Steve P. Lund, Scott Pine Hans Binder Djork-Arné Clevert Ana Conesa Joaquin Dopazo Mario Fasold Sepp Hochreiter Huixiao Hong Nederah Jafari David Kreil Paweł Łabaj Sheng Li Yang Liao Simon Lin Joseph Meehan Christopher Mason Javier Santoyo Robert Setterquist Leming Shi Wei Shi Gordon Smyth Nancy Stralis-Pavese Zhenqiang Su Weida Tong Charles Wang Jian Wang Joshua Xu Zhan Ye Yong Yang Ying Yu Marc Salit P P P E A K

Assessing technical performance in differential gene expression experiments with external Spike- in RNA control ratio mixtures Journal Article

NATURE COMMUNICATIONS, 5 (5125), 2014.

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Su Z Labaj PP, Li Thierry-Mieg Thierry-Mieg Shi Wang Schroth GP Setterquist RA Thompson JF Jones WD Xiao Xu Jensen RV Kelly Xu Conesa Furlanello Gao Hong Jafari Letovsky Liao Lu Oakeley EJ Peng Praul CA Santoyo-Lopez Scherer Shi Smyth GK Staedtler Sykacek Tan XX Thompson EA Vandesompele Wang MD Wang Wolfinger RD Zavadil Auerbach SS Bao Binder Blomquist Brilliant MH Bushel PR Cai Catalano JG S J D W C W W R J A C H H N S Y F Z J A T F P J J J W H T W

A comprenhensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Control Consortium Journal Article

Nat Biotechnol, 2014.

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María José Nueda, Sonia Tarazona ; Conesa, Ana

Next-maSigPro: updating maSigPro Bioconductor package for RNA-seq time series Journal Article

Oxford Journals, 2014.

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Larriba Eduardo; Jaime, Maria Carbonell-Caballero Jose; Conesa Ana; Dopazo Joaquin; Nislow Corey; Martin-Nieto Jose; Vicente Lopez-Llorca Luis D L A ;

Sequencing and functional analysis of the genome of a nematode egg-parasitic fungus, Pochonia chlamydosporia Journal Article

FUNGAL GENETICS AND BIOLOGY, 65 , pp. 69-80, 2014.

BibTeX

Ponzoni Ignacio; Nueda, Maria Jose; Tarazona Sonia; Goetz Stefan; Montaner David; Dussaut Julieta Sol; Dopazo Joaquin; Conesa Ana

Pathway network inference from gene expression data Journal Article

BMC SYSTEMS BIOLOGY, 8 , 2014.

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Hernandez de Diego Rafael; Boix-Chova, Noemi; Gomez-Cabrero David; Tegner Jesper; Abugessaisa Imad; Conesa Ana

STATegra EMS: an Experiment Management System for complex next-generation omics experiments Journal Article

BMC SYSTEMS BIOLOGY, 8 , 2014.

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Gomez-Cabrero David; Abugessaisa, Imad; Maier Dieter; Teschendorff Andrew; Merkenschlager Matthias; Gisel Andreas; Ballestar Esteban; Bongcam-Rudloff Erik; Conesa Ana; Tegner Jesper

Data integration in the era of omics: current and future challenges Journal Article

BMC SYSTEMS BIOLOGY, 8 , 2014.

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Conesa Ana; Mortazavi, Ali

The common ground of genomics and systems biology Journal Article

BMC SYSTEMS BIOLOGY, 8 , 2014.

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Desoignies N.; Carbonell, Moreau Conesa Dopazo Legreve J ; J -S ; A ; J ; A

Molecular interactions between sugar beet and Polymyxa betae during its life cycle Journal Article

ANNALS OF APPLIED BIOLOGY, 164 (2), pp. 244-256, 2014.

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2013

Galan, Amparo ; Diaz-Gimeno, Patricia ; Eugenia Poo, Maria ; Valbuena, Diana ; Sanchez, Eva ; Ruiz, Veronica ; Dopazo, Joaquin ; Montaner, David ; Conesa, Ana ; Simon, Carlos

Defining the Genomic Signature of Totipotency and Pluripotency during Early Human Development Journal Article

PLOS ONE, 8 (4), pp. e62135, 2013.

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Conesa-Zamora, Pablo ; Garcia-Solano, Jose ; Garcia-Garcia, Francisco ; del Carmen Turpin, Maria ; Trujillo-Santos, Javier ; Torres-Moreno, Daniel ; Oviedo-Ramirez, Isabel ; Carbonell-Munoz, Rosa ; Munoz-Delgado, Encarnacion ; Rodriguez-Braun, Edith ; Conesa, Ana ; Perez-Guillermo, Miguel

Expression profiling shows differential molecular pathways and provides potential new diagnostic biomarkers for colorectal serrated adenocarcinoma Journal Article

INTERNATIONAL JOURNAL OF CANCER, 132 (2), pp. 297-307, 2013, (1 Citations).

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2012

Yanez, Yania ; Grau, Elena ; Canete, Adela ; Conesa, Ana ; Gonzalez Neira, Ana ; Castel, Victoria

METHYLATION STATUS IN NEUROBLASTOMA AND ITS PROGNOSTIC VALUE Journal Article

PEDIATRIC BLOOD & CANCER, 59 (6), pp. 1053-1054, 2012.

BibTeX

Fernandez, Paula ; Soria, Marcelo ; Blesa, David ; DiRienzo, Julio ; Moschen, Sebastian ; Rivarola, Maximo ; Jose Clavijo, Bernardo ; Gonzalez, Sergio ; Peluffo, Lucila ; Principi, Dario ; Dosio, Guillermo ; Aguirrezabal, Luis ; Garcia-Garcia, Francisco ; Conesa, Ana ; Hopp, Esteban ; Dopazo, Joaquin ; Amelia Heinz, Ruth ; Paniego, Norma

Development, Characterization and Experimental Validation of a Cultivated Sunflower (Helianthus annuus L.) Gene Expression Oligonucleotide Microarray Journal Article

PLOS ONE, 7 (10), pp. e45899, 2012, (1 Citations).

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Garcia-Alcalde, Fernando ; Okonechnikov, Konstantin ; Carbonell, Jose ; Cruz, Luis M; Goetz, Stefan ; Tarazona, Sonia ; Dopazo, Joaquin ; Meyer, Thomas F; Conesa, Ana

Qualimap: evaluating next-generation sequencing alignment data Journal Article

BIOINFORMATICS, 28 (20), pp. 2678-2679, 2012, (3 Citations).

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Agusti, Javier ; Gimeno, Jacinta ; Merelo, Paz ; Serrano, Ramon ; Cercos, Manuel ; Conesa, Ana ; Talon, Manuel ; Tadeo, Francisco R

Early gene expression events in the laminar abscission zone of abscission-promoted citrus leaves after a cycle of water stress/rehydration: involvement of CitbHLH1 Journal Article

JOURNAL OF EXPERIMENTAL BOTANY, 63 (17), pp. 6079-6091, 2012.

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Rizza, Serena ; Conesa, Ana ; Juarez, Jose ; Catara, Antonino ; Navarro, Luis ; Duran-Vila, Nuria ; Ancillo, Gema

Microarray analysis of Etrog citron (Citrus medica L.) reveals changes in chloroplast, cell wall, peroxidase and symporter activities in response to viroid infection Journal Article

MOLECULAR PLANT PATHOLOGY, 13 (8), pp. 852-864, 2012, (2 Citations).

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Nueda, Maria J; Ferrer, Alberto ; Conesa, Ana

ARSyN: a method for the identification and removal of systematic noise in multifactorial time course microarray experiments Journal Article

BIOSTATISTICS, 13 (3), pp. 553-566, 2012.

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Jaime, Maria D L A; Vicente Lopez-Llorca, Luis ; Conesa, Ana ; Lee, Anna Y; Proctor, Michael ; Heisler, Lawrence E; Gebbia, Marinella ; Giaever, Guri ; Westwood, Timothy J; Nislow, Corey

Identification of yeast genes that confer resistance to chitosan oligosaccharide (COS) using chemogenomics Journal Article

BMC GENOMICS, 13 , pp. 267, 2012.

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Lin, C J; Irmer, H; Tarazona, S; Olbermann, P; Krappmann, S; Conesa, A; Braus, G

Regulatory proteins in the opportunistic human pathogen Aspergillus fumigatus Journal Article

MYCOSES, 55 , pp. 135-136, 2012.

BibTeX

Oppert, Brenda ; Dowd, Scot E; Bouffard, Pascal ; Li, Lewyn ; Conesa, Ana ; Lorenzen, Marce D; Toutges, Michelle ; Marshall, Jeremy ; Huestis, Diana L; Fabrick, Jeff ; Oppert, Cris ; Jurat-Fuentes, Juan Luis

Transcriptome Profiling of the Intoxication Response of Tenebrio molitor Larvae to Bacillus thuringiensis Cry3Aa Protoxin Journal Article

PLOS ONE, 7 (4), pp. e34624, 2012, (7 Citations).

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Perez-Quintero, Alvaro L; Sablok, Gaurav ; Tatarinova, Tatiana V; Conesa, Ana ; Kuo, Jimmy ; Lopez, Camilo

Mining of miRNAs and potential targets from gene oriented clusters of transcripts sequences of the anti-malarial plant, Artemisia annua Journal Article

BIOTECHNOLOGY LETTERS, 34 (4), pp. 737-745, 2012, (1 Citations).

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Tarazona, Sonia ; Prado-Lopez, Sonia ; Dopazo, Joaquin ; Ferrer, Alberto ; Conesa, Ana

Variable selection for multifactorial genomic data Journal Article

CHEMOMETRICS AND INTELLIGENT LABORATORY SYSTEMS, 110 (1), pp. 113-122, 2012, (1 Citations).

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Carcel-Trullols, Jaime ; Aguilar-Gallardo, Cristobal ; Garcia-Alcalde, Fernando ; Pardo-Cea, Miguel Angel ; Dopazo, Joaquin ; Conesa, Ana ; Simon, Carlos

Transdifferentiation of MALME-3M and MCF-7 Cells toward Adipocyte-like Cells is Dependent on Clathrin-mediated Endocytosis. Journal Article

SpringerPlus, 1 , pp. 44-44, 2012.

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Leida, Carmen ; Conesa, Ana ; Llacer, Gerardo ; Luisa Badenes, Maria ; Rios, Gabino

Histone modifications and expression of DAM6 gene in peach are modulated during bud dormancy release in a cultivar-dependent manner Journal Article

NEW PHYTOLOGIST, 193 (1), pp. 67-80, 2012, (16 Citations).

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2011

Yung, Sun ; Ledran, Maria ; Moreno-Gimeno, Inmaculada ; Conesa, Ana ; Montaner, David ; Dopazo, Joaquin ; Dimmick, Ian ; Slater, Nicholas J; Marenah, Lamin ; Real, Pedro J; Paraskevopoulou, Iliana ; Bisbal, Viviana ; Burks, Deborah ; Santibanez-Koref, Mauro ; Moreno, Ruben ; Mountford, Joanne ; Menendez, Pablo ; Armstrong, Lyle ; Lako, Majlinda

Large-scale transcriptional profiling and functional assays reveal important roles for Rho-GTPase signalling and SCL during haematopoietic differentiation of human embryonic stem cells Journal Article

HUMAN MOLECULAR GENETICS, 20 (24), pp. 4932-4946, 2011, (7 Citations).

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Tarazona, Sonia ; Garcia-Alcalde, Fernando ; Dopazo, Joaquin ; Ferrer, Alberto ; Conesa, Ana

Differential expression in RNA-seq: A matter of depth Journal Article

GENOME RESEARCH, 21 (12), pp. 2213-2223, 2011, (74 Citations).

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Khalaf, Abeer A; Gmitter Frederick G., Jr. ; Conesa, Ana ; Dopazo, Joaquin ; Moore, Gloria A

Fortunella margarita Transcriptional Reprogramming Triggered by Xanthomonas citri subsp citri Journal Article

BMC PLANT BIOLOGY, 11 , pp. 159, 2011, (3 Citations).

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88 entries « 1 of 2 »