Full Text Journal Articles by
Author Angel Pizarro

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htsget: a protocol for securely streaming genomic data.

Jerome Kelleher, Mike Lin, C H Albach, Ewan Birney, Robert Davies, Marina Gourtovaia, David Glazer, Cristina Y Gonzalez, David K Jackson, Aaron Kemp, John Marshall, Andrew Nowak, Alexander Senf, Jaime M Tovar-Corona, Alexander Vikhorev, Thomas M Keane, ,

Summary:Standardized interfaces for efficiently accessing high-throughput sequencing data are a fundamental requirement for large-scale genomic data sharing. We have developed htsget, a protocol for secure, efficient and reliable access to sequencing read and variation data. We demonstrate four independent client and server implementations, and the results of a comprehensive interoperability ... Read more >>

Bioinformatics (Bioinformatics (Oxford, England))
[2019, 35(1):119-121]

Cited: 1 time

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Absence of survival benefit of immediate lymph node dissection in melanoma.

Ángel Pizarro,

Med Clin (Barc) (Medicina Clinica)
[2019, 152(7):287-288]

Cited: 0 times

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Dermoscopy of Targetoid Hemosiderotic Hemangioma: A Morphological Study of 35 Cases.

Pedro Zaballos, Alex Llambrich, Luis Javier Del Pozo, Christian Landi, Angel Pizarro, Angel Vera, José Bañuls,

Targetoid hemosiderotic hemangioma is an uncommon, vascular, benign solitary lesion of lymphatic origin that can be misdiagnosed as other tumors including melanomas.To evaluate the dermoscopic features of a large series of targetoid hemosiderotic hemangiomas.Digital dermoscopic images of 35 histopathologically confirmed cases of targetoid hemosiderotic hemangiomas collected from 7 hospitals in ... Read more >>

Dermatology (Basel) (Dermatology (Basel, Switzerland))
[2015, 231(4):339-344]

Cited: 5 times

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Benchmark analysis of algorithms for determining and quantifying full-length mRNA splice forms from RNA-seq data.

Katharina E Hayer, Angel Pizarro, Nicholas F Lahens, John B Hogenesch, Gregory R Grant,

Because of the advantages of RNA sequencing (RNA-Seq) over microarrays, it is gaining widespread popularity for highly parallel gene expression analysis. For example, RNA-Seq is expected to be able to provide accurate identification and quantification of full-length splice forms. A number of informatics packages have been developed for this purpose, ... Read more >>

Bioinformatics (Bioinformatics (Oxford, England))
[2015, 31(24):3938-3945]

Cited: 34 times

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IVT-seq reveals extreme bias in RNA sequencing.

Nicholas F Lahens, Ibrahim Halil Kavakli, Ray Zhang, Katharina Hayer, Michael B Black, Hannah Dueck, Angel Pizarro, Junhyong Kim, Rafael Irizarry, Russell S Thomas, Gregory R Grant, John B Hogenesch,

RNA-seq is a powerful technique for identifying and quantifying transcription and splicing events, both known and novel. However, given its recent development and the proliferation of library construction methods, understanding the bias it introduces is incomplete but critical to realizing its value.We present a method, in vitro transcription sequencing (IVT-seq), ... Read more >>

Genome Biol. (Genome biology)
[2014, 15(6):R86]

Cited: 64 times

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IVT-seq reveals extreme bias in RNA-sequencing

Nicholas Lahens, Ibrahim Halil Kavakli, Ray Zhang, Katharina Hayer, Michael Black, Hannah Dueck, Angel Pizarro, Junhyong Kim, Rafael Irizarry, Russell Thomas, Gregory Grant, John Hogenesch,

Background RNA sequencing (RNA-seq) is a powerful technique for identifying and quantifying transcription and splicing events, both known and novel. However, given its recent development and the proliferation of library construction methods, understanding the bias it introduces is incomplete but critical to realizing its value. Results Here we present a ... Read more >>

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CircaDB: a database of mammalian circadian gene expression profiles.

Angel Pizarro, Katharina Hayer, Nicholas F Lahens, John B Hogenesch,

CircaDB (http://circadb.org) is a new database of circadian transcriptional profiles from time course expression experiments from mice and humans. Each transcript's expression was evaluated by three separate algorithms, JTK_Cycle, Lomb Scargle and DeLichtenberg. Users can query the gene annotations using simple and powerful full text search terms, restrict results to ... Read more >>

Nucleic Acids Res. (Nucleic acids research)
[2013, 41(Database issue):D1009-13]

Cited: 106 times

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The usefulness of dermoscopy for the recognition of basal cell carcinoma--seborrhoeic keratosis compound tumours.

Pedro Zaballos, José Bañuls, Horacio Cabo, Alex Llambrich, Elisabeth Salsench, Susana Puig, Angel Pizarro, Josep Malvehy,

Australas. J. Dermatol. (The Australasian journal of dermatology)
[2013, 54(3):208-212]

Cited: 3 times

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The mzIdentML data standard for mass spectrometry-based proteomics results.

Andrew R Jones, Martin Eisenacher, Gerhard Mayer, Oliver Kohlbacher, Jennifer Siepen, Simon J Hubbard, Julian N Selley, Brian C Searle, James Shofstahl, Sean L Seymour, Randall Julian, Pierre-Alain Binz, Eric W Deutsch, Henning Hermjakob, Florian Reisinger, Johannes Griss, Juan Antonio Vizcaíno, Matthew Chambers, Angel Pizarro, David Creasy,

We report the release of mzIdentML, an exchange standard for peptide and protein identification data, designed by the Proteomics Standards Initiative. The format was developed by the Proteomics Standards Initiative in collaboration with instrument and software vendors, and the developers of the major open-source projects in proteomics. Software implementations have ... Read more >>

Mol. Cell Proteomics (Molecular & cellular proteomics : MCP)
[2012, 11(7):M111.014381]

Cited: 79 times

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Comparative analysis of RNA-Seq alignment algorithms and the RNA-Seq unified mapper (RUM).

Gregory R Grant, Michael H Farkas, Angel D Pizarro, Nicholas F Lahens, Jonathan Schug, Brian P Brunk, Christian J Stoeckert, John B Hogenesch, Eric A Pierce,

A critical task in high-throughput sequencing is aligning millions of short reads to a reference genome. Alignment is especially complicated for RNA sequencing (RNA-Seq) because of RNA splicing. A number of RNA-Seq algorithms are available, and claim to align reads with high accuracy and efficiency while detecting splice junctions. RNA-Seq ... Read more >>

Bioinformatics (Bioinformatics (Oxford, England))
[2011, 27(18):2518-2528]

Cited: 178 times

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Genetic polymorphisms in DNA repair and oxidative stress pathways associated with malignant melanoma susceptibility.

Maider Ibarrola-Villava, Maria Peña-Chilet, Lara P Fernandez, Jose A Aviles, Matias Mayor, Manuel Martin-Gonzalez, Cristina Gomez-Fernandez, Beatriz Casado, Pablo Lazaro, Ana Lluch, Javier Benitez, Rafael Lozoya, Enrique Boldo, Angel Pizarro, Conrado Martinez-Cadenas, Gloria Ribas,

BACKGROUND: Base excision repair (BER) and nucleotide excision repair (NER) pathways eliminate a wide variety of DNA damage, including UV photoproducts. The ability of each individual to repair DNA damage following different causes might explain at least in part the variability in cancer susceptibility. Moreover, inflammatory response to UV exposure ... Read more >>

Eur. J. Cancer (European journal of cancer (Oxford, England : 1990))
[2011, 47(17):2618-2625]

Cited: 28 times

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Dermoscopic findings and histological correlation of the acral volar pigmented maculae in Laugier-Hunziker syndrome.

Elena Sendagorta, Marta Feito, Paloma Ramírez, María Gonzalez-Beato, Toshiaki Saida, Angel Pizarro,

Laugier-Hunziker syndrome (LHS) is an acquired, benign, macular hyperpigmentation of the lips and oral mucosa, often associated with pigmentation of the nails. Volar acral maculae on the palms and fingertips of patients affected by LHS are a typical feature of this rare entity. Dermoscopic examination of these maculae has been ... Read more >>

J. Dermatol. (The Journal of dermatology)
[2010, 37(11):980-984]

Cited: 6 times

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A customized pigmentation SNP array identifies a novel SNP associated with melanoma predisposition in the SLC45A2 gene.

Maider Ibarrola-Villava, Lara P Fernandez, Santos Alonso, M Dolores Boyano, Maria Peña-Chilet, Guillermo Pita, Jose A Aviles, Matias Mayor, Cristina Gomez-Fernandez, Beatriz Casado, Manuel Martin-Gonzalez, Neskuts Izagirre, Concepcion De la Rua, Aintzane Asumendi, Gorka Perez-Yarza, Yoana Arroyo-Berdugo, Enrique Boldo, Rafael Lozoya, Arantxa Torrijos-Aguilar, Ana Pitarch, Gerard Pitarch, Jose M Sanchez-Motilla, Francisca Valcuende-Cavero, Gloria Tomas-Cabedo, Gemma Perez-Pastor, Jose L Diaz-Perez, Jesus Gardeazabal, Iñigo Martinez de Lizarduy, Ana Sanchez-Diez, Carlos Valdes, Angel Pizarro, Mariano Casado, Gregorio Carretero, Rafael Botella-Estrada, Eduardo Nagore, Pablo Lazaro, Ana Lluch, Javier Benitez, Conrado Martinez-Cadenas, Gloria Ribas,

As the incidence of Malignant Melanoma (MM) reflects an interaction between skin colour and UV exposure, variations in genes implicated in pigmentation and tanning response to UV may be associated with susceptibility to MM. In this study, 363 SNPs in 65 gene regions belonging to the pigmentation pathway have been ... Read more >>

PLoS ONE (PloS one)
[2011, 6(4):e19271]

Cited: 13 times

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Letter: Umbilical basal cell carcinoma in a 21-year-old man: Report of an exceptional case and dermatoscopic evaluation.

Paloma Ramirez, Elena Sendagorta, Marta Feito, Maria Gonzalez-Beato, Matias Mayor, Angel Pizarro,

We report an exceptional case of umbilical basal cell carcinoma (BCC) in a 21-year-old man, whose correct diagnosis was suggested by dermoscopy during initial complete body mole mapping. Although BCC is a common skin tumor, only 7 cases of BCC arising within the umbilicus have been reported previously. To the ... Read more >>

Dermatol. Online J. (Dermatology online journal)
[2011, 17(1):16]

Cited: 3 times

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mzML--a community standard for mass spectrometry data.

Lennart Martens, Matthew Chambers, Marc Sturm, Darren Kessner, Fredrik Levander, Jim Shofstahl, Wilfred H Tang, Andreas Römpp, Steffen Neumann, Angel D Pizarro, Luisa Montecchi-Palazzi, Natalie Tasman, Mike Coleman, Florian Reisinger, Puneet Souda, Henning Hermjakob, Pierre-Alain Binz, Eric W Deutsch,

Mass spectrometry is a fundamental tool for discovery and analysis in the life sciences. With the rapid advances in mass spectrometry technology and methods, it has become imperative to provide a standard output format for mass spectrometry data that will facilitate data sharing and analysis. Initially, the efforts to develop ... Read more >>

Mol. Cell Proteomics (Molecular & cellular proteomics : MCP)
[2011, 10(1):R110.000133]

Cited: 156 times

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Elective affinities--bioinformatic analysis of proteomic mass spectrometry data.

Xuanwen Li, Angel Pizarro, Tilo Grosser,

Shotgun proteomic strategies based on the identification of proteolytic peptides by tandem mass spectrometry and sequence database searches have emerged as useful approaches for qualitative and quantitative measurement of proteins in large scale studies. Coincidentally, the automated analysis of the resulting mass spectrometry data has become increasingly challenging. Important steps ... Read more >>

Arch. Physiol. Biochem. (Archives of physiology and biochemistry)
[2009, 115(5):311-319]

Cited: 2 times

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The Gene Wiki: community intelligence applied to human gene annotation.

Jon W Huss, Pierre Lindenbaum, Michael Martone, Donabel Roberts, Angel Pizarro, Faramarz Valafar, John B Hogenesch, Andrew I Su,

Annotating the function of all human genes is a critical, yet formidable, challenge. Current gene annotation efforts focus on centralized curation resources, but it is increasingly clear that this approach does not scale with the rapid growth of the biomedical literature. The Gene Wiki utilizes an alternative and complementary model ... Read more >>

Nucleic Acids Res. (Nucleic acids research)
[2010, 38(Database issue):D633-9]

Cited: 48 times

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Dermatoscopic characteristics of acrochordon-like basal cell carcinomas in Gorlin-Goltz syndrome.

Marta Feito-Rodríguez, Elena Sendagorta-Cudós, Marta Moratinos-Martínez, María José González-Beato, Raúl de Lucas-Laguna, Angel Pizarro,

BACKGROUND: Gorlin-Goltz syndrome (GGS) is an autosomal-dominant disease characterized by the early onset of multiple basal cell carcinomas (BCCs), among other findings. Clinically, the BCCs may appear as soft pedunculated neoplasms that can be mistaken for true acrochordons. OBJECTIVE: We sought to describe the dermatoscopic characteristics of small acrochordon-like or ... Read more >>

J. Am. Acad. Dermatol. (Journal of the American Academy of Dermatology)
[2009, 60(5):857-861]

Cited: 5 times

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Diffuse melanosis and ascites due to metastatic malignant melanoma.

Elena Sendagorta, Angel Pizarro, Marta Feito, Matias Mayor, Paloma Ramírez, Uxua Floristan, Rosa Feltes,

We present a female patient who developed mucosal and skin hyperpigmentation due to metastatic malignant melanoma. Diffuse cutaneous melanosis is a rare entity that complicates a small percentage of metastatic melanomas, confering a fatal prognosis. We discuss briefly the current evidence on pathogenesis of melanosis arising from metastatic melanoma. ... Read more >>

ScientificWorldJournal (TheScientificWorldJournal)
[2008, 8:556-557]

Cited: 1 time

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Five years of progress in the Standardization of Proteomics Data 4th Annual Spring Workshop of the HUPO-Proteomics Standards Initiative April 23-25, 2007 Ecole Nationale Supérieure (ENS), Lyon, France.

Sandra Orchard, Luisa Montechi-Palazzi, Eric W Deutsch, Pierre-Alain Binz, Andrew R Jones, Norman Paton, Angel Pizarro, David M Creasy, Jérôme Wojcik, Henning Hermjakob,

Over the last five years, the Human Proteome Organisation Proteomics Standards Initiative (HUPO PSI) has produced and released community-accepted XML interchange formats in the fields of mass spectrometry, molecular interactions and gel electrophoresis, have led the field in the discussion of the minimum information with which such data should be ... Read more >>

Proteomics (Proteomics)
[2007, 7(19):3436-3440]

Cited: 24 times

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EBP, a program for protein identification using multiple tandem mass spectrometry datasets.

Thomas S Price, Margaret B Lucitt, Weichen Wu, David J Austin, Angel Pizarro, Anastasia K Yocum, Ian A Blair, Garret A FitzGerald, Tilo Grosser,

MS/MS combined with database search methods can identify the proteins present in complex mixtures. High throughput methods that infer probable peptide sequences from enzymatically digested protein samples create a challenge in how best to aggregate the evidence for candidate proteins. Typically the results of multiple technical and/or biological replicate experiments ... Read more >>

Mol. Cell Proteomics (Molecular & cellular proteomics : MCP)
[2007, 6(3):527-536]

Cited: 33 times

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The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics.

Andrew R Jones, Michael Miller, Ruedi Aebersold, Rolf Apweiler, Catherine A Ball, Alvis Brazma, James Degreef, Nigel Hardy, Henning Hermjakob, Simon J Hubbard, Peter Hussey, Mark Igra, Helen Jenkins, Randall K Julian, Kent Laursen, Stephen G Oliver, Norman W Paton, Susanna-Assunta Sansone, Ugis Sarkans, Christian J Stoeckert, Chris F Taylor, Patricia L Whetzel, Joseph A White, Paul Spellman, Angel Pizarro,

The Functional Genomics Experiment data model (FuGE) has been developed to facilitate convergence of data standards for high-throughput, comprehensive analyses in biology. FuGE models the components of an experimental activity that are common across different technologies, including protocols, samples and data. FuGE provides a foundation for describing entire laboratory workflows ... Read more >>

Nat. Biotechnol. (Nature biotechnology)
[2007, 25(10):1127-1133]

Cited: 56 times

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Proteomics and Beyond: a report on the 3rd Annual Spring Workshop of the HUPO-PSI 21-23 April 2006, San Francisco, CA, USA.

Sandra Orchard, Rolf Apweiler, Robert Barkovich, Dawn Field, John S Garavelli, David Horn, Andy Jones, Philip Jones, Randall Julian, Ruth McNally, Jason Nerothin, Norman Paton, Angel Pizarro, Sean Seymour, Chris Taylor, Stefan Wiemann, Henning Hermjakob,

The theme of the third annual Spring workshop of the HUPO-PSI was "proteomics and beyond" and its underlying goal was to reach beyond the boundaries of the proteomics community to interact with groups working on the similar issues of developing interchange standards and minimal reporting requirements. Significant developments in many ... Read more >>

Proteomics (Proteomics)
[2006, 6(16):4439-4443]

Cited: 6 times

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Entering the implementation era: a report on the HUPO-PSI Fall workshop 25-27 September 2006, Washington DC, USA.

Sandra Orchard, Chris F Taylor, Phil Jones, Luisa Montechi-Palazzo, Pierre-Alain Binz, Andrew R Jones, Angel Pizarro, Randall K Julian, Henning Hermjakob,

Since its conception in April 2002, the Human Proteome Organisation Proteomics Standards Initiative has contributed to the development of community standards for proteomics in a collaborative and very dynamic manner, resulting in the publication and increasing adoption of a number of interchange formats and controlled vocabularies. Repositories supporting these formats ... Read more >>

Proteomics (Proteomics)
[2007, 7(3):337-339]

Cited: 9 times

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FuGE: Functional Genomics Experiment Object Model.

Andrew R Jones, Angel Pizarro, Paul Spellman, Michael Miller, ,

This is an interim report on the Functional Genomics Experiment (FuGE) Object Model. FuGE is a framework for creating data standards for high-throughput biological experiments, developed by a consortium of researchers from academia and industry. FuGE supports rich annotation of samples, protocols, instruments, and software, as well as providing extension ... Read more >>

OMICS (Omics : a journal of integrative biology)
[2006, 10(2):179-184]

Cited: 13 times

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