Search Results - "Ochoa, Idoia"

Moss enables high sensitivity single-nucleotide variant calling from multiple bulk DNA tumor samples by Zhang, Chuanyi, El-Kebir, Mohammed, Ochoa, Idoia

“…Intra-tumor heterogeneity renders the identification of somatic single-nucleotide variants (SNVs) a challenging problem. In particular, low-frequency SNVs are…”
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SPRING: a next-generation compressor for FASTQ data by Chandak, Shubham, Tatwawadi, Kedar, Ochoa, Idoia, Hernaez, Mikel, Weissman, Tsachy

“…Abstract Motivation High-Throughput Sequencing technologies produce huge amounts of data in the form of short genomic reads, associated quality values and read…”
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iDoComp: a compression scheme for assembled genomes by Ochoa, Idoia, Hernaez, Mikel, Weissman, Tsachy

“…With the release of the latest next-generation sequencing (NGS) machine, the HiSeq X by Illumina, the cost of sequencing a Human has dropped to a mere $4000…”
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Phertilizer: Growing a clonal tree from ultra-low coverage single-cell DNA sequencing of tumors by Weber, Leah L, Zhang, Chuanyi, Ochoa, Idoia, El-Kebir, Mohammed

“…Emerging ultra-low coverage single-cell DNA sequencing (scDNA-seq) technologies have enabled high resolution evolutionary studies of copy number aberrations…”
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MassComp, a lossless compressor for mass spectrometry data by Yang, Ruochen, Chen, Xi, Ochoa, Idoia

“…Mass Spectrometry (MS) is a widely used technique in biology research, and has become key in proteomics and metabolomics analyses. As a result, the amount of…”
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Genomic Data Compression by Hernaez, Mikel, Pavlichin, Dmitri, Weissman, Tsachy, Ochoa, Idoia

“…Recently, there has been growing interest in genome sequencing, driven by advances in sequencing technology, in terms of both efficiency and affordability…”
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Single-cell transcriptional profile of CD34+ hematopoietic progenitor cells from del(5q) myelodysplastic syndromes and impact of lenalidomide by Serrano, Guillermo, Berastegui, Nerea, Díaz-Mazkiaran, Aintzane, García-Olloqui, Paula, Rodriguez-Res, Carmen, Huerga-Dominguez, Sofia, Ainciburu, Marina, Vilas-Zornoza, Amaia, Martin-Uriz, Patxi San, Aguirre-Ruiz, Paula, Ullate-Agote, Asier, Ariceta, Beñat, Lamo-Espinosa, Jose-Maria, Acha, Pamela, Calvete, Oriol, Jimenez, Tamara, Molero, Antonieta, Montoro, Maria Julia, Díez-Campelo, Maria, Valcarcel, David, Solé, Francisco, Alfonso-Pierola, Ana, Ochoa, Idoia, Prósper, Felipe, Ezponda, Teresa, Hernaez, Mikel

“…While myelodysplastic syndromes with del(5q) (del(5q) MDS) comprises a well-defined hematological subgroup, the molecular basis underlying its origin remains…”
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Application of Graph Models to the Identification of Transcriptomic Oncometabolic Pathways in Human Hepatocellular Carcinoma by Barace, Sergio, Santamaría, Eva, Infante, Stefany, Arcelus, Sara, De La Fuente, Jesus, Goñi, Enrique, Tamayo, Ibon, Ochoa, Idoia, Sogbe, Miguel, Sangro, Bruno, Hernaez, Mikel, Avila, Matias A, Argemi, Josepmaria

“…Whole-tissue transcriptomic analyses have been helpful to characterize molecular subtypes of hepatocellular carcinoma (HCC). Metabolic subtypes of human HCC…”
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SimiC enables the inference of complex gene regulatory dynamics across cell phenotypes by Peng, Jianhao, Serrano, Guillermo, Traniello, Ian M., Calleja-Cervantes, Maria E., Chembazhi, Ullas V., Bangru, Sushant, Ezponda, Teresa, Rodriguez-Madoz, Juan Roberto, Kalsotra, Auinash, Prosper, Felipe, Ochoa, Idoia, Hernaez, Mikel

“…Single-cell RNA-Sequencing has the potential to provide deep biological insights by revealing complex regulatory interactions across diverse cell phenotypes at…”
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DeepZip: Lossless Data Compression Using Recurrent Neural Networks by Goyal, Mohit, Tatwawadi, Kedar, Chandak, Shubham, Ochoa, Idoia

“…Sequential data is being generated at an unprecedented pace in various forms, including text and genomic data. This creates the need for efficient compression…”
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VEF: a variant filtering tool based on ensemble methods by Zhang, Chuanyi, Ochoa, Idoia

“…Abstract Motivation Variants identified by current genomic analysis pipelines contain many incorrectly called variants. These can be potentially eliminated by…”
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GPress: a framework for querying general feature format (GFF) files and expression files in a compressed form by Meng, Qingxi, Ochoa, Idoia, Hernaez, Mikel

“…Sequencing data are often summarized at different annotation levels for further analysis, generally using the general feature format (GFF) or its descendants,…”
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FaStore: a space-saving solution for raw sequencing data by Roguski, Łukasz, Ochoa, Idoia, Hernaez, Mikel, Deorowicz, Sebastian

“…Abstract Motivation The affordability of DNA sequencing has led to the generation of unprecedented volumes of raw sequencing data. These data must be stored,…”
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mspack: efficient lossless and lossy mass spectrometry data compression by Hanau, Felix, Röst, Hannes, Ochoa, Idoia

“…Abstract Motivation Mass spectrometry (MS) data, used for proteomics and metabolomics analyses, have seen considerable growth in the last years. Aiming at…”
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METHCOMP: a special purpose compression platform for DNA methylation data by Peng, Jianhao, Milenkovic, Olgica, Ochoa, Idoia

“…Abstract Motivation DNA methylation is one of the most important epigenetic mechanisms in cells that exhibits a significant role in controlling gene…”
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Effect of lossy compression of quality scores on variant calling by Ochoa, Idoia, Hernaez, Mikel, Goldfeder, Rachel, Weissman, Tsachy, Ashley, Euan

“…Abstract Recent advancements in sequencing technology have led to a drastic reduction in genome sequencing costs. This development has generated an…”
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Denoising of Aligned Genomic Data by Fischer-Hwang, Irena, Ochoa, Idoia, Weissman, Tsachy, Hernaez, Mikel

“…Noise in genomic sequencing data is known to have effects on various stages of genomic data analysis pipelines. Variant identification is an important step of…”
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Unsupervised ensemble learning for genome sequencing by Pagès-Zamora, Alba, Ochoa, Idoia, Cavero, Gonzalo Ruiz, Villalvilla-Ornat, Pol

“…•The variant calling step in next generation sequencing technologies is formulated as a classification problem.•An unsupervised ensemble classification method…”
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JIND: joint integration and discrimination for automated single-cell annotation by Goyal, Mohit, Serrano, Guillermo, Argemi, Josepmaria, Shomorony, Ilan, Hernaez, Mikel, Ochoa, Idoia

“…Abstract Motivation An important step in the transcriptomic analysis of individual cells involves manually determining the cellular identities. To ease this…”
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QVZ: lossy compression of quality values by Malysa, Greg, Hernaez, Mikel, Ochoa, Idoia, Rao, Milind, Ganesan, Karthik, Weissman, Tsachy

“…Recent advancements in sequencing technology have led to a drastic reduction in the cost of sequencing a genome. This has generated an unprecedented amount of…”
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