2017
Authors
Cavadas, B; Ferreira, J; Camacho, R; Fonseca, NA; Pereira, L;
Publication
11th International Conference on Practical Applications of Computational Biology & Bioinformatics, PACBB 2017, Porto, Portugal, 21-23 June, 2017
Abstract
The huge amount of genomic and transcriptomic data obtained to characterize human diversity can also be exploited to indirectly gather information on the human microbiome. Here we present the pipeline QmihR designed to identify and quantify the abundance of known microbiome communities and to search for new/rare pathogenic species in RNA-seq datasets. We applied QmihR to 36 RNA-seq tumor tissue samples from Ukrainian gastric carcinoma patients available in TCGA, in order to characterize their microbiome and check for efficiency of the pipeline. The microbes present in the samples were in accordance to published data in other European datasets, and the independent BLAST evaluation of microbiome-aligned reads confirmed that the assigned species presented the highest BLAST match-hits. QmihR is available at GitHub (https://github.com/ Pereira-lab/QmihR). © Springer International Publishing AG 2017.
2017
Authors
Petryszak, R; Fonseca, NA; Füllgrabe, A; Huerta, L; Keays, M; Tang, YA; Brazma, A;
Publication
Bioinformatics
Abstract
Motivation: The exponential growth of publicly available RNA-sequencing (RNA-Seq) data poses an increasing challenge to researchers wishing to discover, analyse and store such data, particularly those based in institutions with limited computational resources. EMBL-EBI is in an ideal position to address these challenges and to allow the scientific community easy access to not just raw, but also processed RNA-Seq data. We present a Web service to access the results of a systematically and continually updated standardized alignment as well as gene and exon expression quantification of all public bulk (and in the near future also single-cell) RNA-Seq runs in 264 species in European Nucleotide Archive, using Representational State Transfer. Results: The RNASeq-er API (Application Programming Interface) enables ontology-powered search for and retrieval of CRAM, bigwig and bedGraph files, gene and exon expression quantification matrices (Fragments Per Kilobase Of Exon Per Million Fragments Mapped, Transcripts Per Million, raw counts) as well as sample attributes annotated with ontology terms. To date over 270 00 RNA-Seq runs in nearly 10 000 studies (1PB of raw FASTQ data) in 264 species in ENA have been processed and made available via the API.
2017
Authors
Schwarzer, W; Abdennur, N; Goloborodko, A; Pekowska, A; Fudenberg, G; Loe Mie, Y; Fonseca, NA; Huber, W; Haering, CH; Mirny, L; Spitz, F;
Publication
Nature
Abstract
Imaging and chromosome conformation capture studies have revealed several layers of chromosome organization, including segregation into megabase-sized active and inactive compartments, and partitioning into sub-megabase domains (TADs). It remains unclear, however, how these layers of organization form, interact with one another and influence genome function. Here we show that deletion of the cohesin-loading factor Nipbl in mouse liver leads to a marked reorganization of chromosomal folding. TADs and associated Hi-C peaks vanish globally, even in the absence of transcriptional changes. By contrast, compartmental segregation is preserved and even reinforced. Strikingly, the disappearance of TADs unmasks a finer compartment structure that accurately reflects the underlying epigenetic landscape. These observations demonstrate that the three-dimensional organization of the genome results from the interplay of two independent mechanisms: cohesin-independent segregation of the genome into fine-scale compartments, defined by chromatin state; and cohesin-dependent formation of TADs, possibly by loop extrusion, which helps to guide distant enhancers to their target genes.
2017
Authors
Rheinbay, E; Nielsen, MM; Abascal, F; Tiao, G; Hornshøj, H; Hess, JM; Pedersen, RI; Feuerbach, L; Sabarinathan, R; Madsen, T; Kim, J; Mularoni, L; Shuai, S; Lanzós, A; Herrmann, C; Maruvka, YE; Shen, C; Amin, SB; Bertl, J; Dhingra, P; Diamanti, K; Gonzalez-Perez, A; Guo, Q; Haradhvala, NJ; Isaev, K; Juul, M; Komorowski, J; Kumar, S; Lee, D; Lochovsky, L; Liu, EM; Pich, O; Tamborero, D; Umer, HM; Uusküla-Reimand, L; Wadelius, C; Wadi, L; Zhang, J; Boroevich, KA; Carlevaro-Fita, J; Chakravarty, D; Chan, CW; Fonseca, NA; Hamilton, MP; Hong, C; Kahles, A; Kim, Y; Lehmann, K; Johnson, TA; Kahraman, A; Park, K; Saksena, G; Sieverling, L; Sinnott-Armstrong, NA; Campbell, PJ; Hobolth, A; Kellis, M; Lawrence, MS; Raphael, B; Rubin, MA; Sander, C; Stein, L; Stuart, J; Tsunoda, T; Wheeler, DA; Johnson, R; Reimand, J; Gerstein, MB; Khurana, E; López-Bigas, N; Martincorena, I; Pedersen, JS; Getz, G;
Publication
Abstract
2017
Authors
Calabrese, C; Davidson, NR; Fonseca, NA; He, Y; Kahles, A; Lehmann, K; Liu, F; Shiraishi, Y; Soulette, CM; Urban, L; Demircioglu, D; Greger, L; Li, S; Liu, D; Perry, MD; Xiang, L; Zhang, F; Zhang, J; Bailey, P; Erkek, S; Hoadley, KA; Hou, Y; Kilpinen, H; Korbel, JO; Marin, MG; Markowski, J; Nandi, T; Pan-Hammarström, Q; Pedamallu, CS; Siebert, R; Stark, SG; Su, H; Tan, P; Waszak, SM; Yung, C; Zhu, S; Awadalla, P; Creighton, CJ; Meyerson, M; Ouellette, BF; Wu, K; Yang, H; Brazma, A; Brooks, AN; Göke, J; Rätsch, G; Schwarz, RF; Stegle, O; Zhang, Z;
Publication
Abstract
2017
Authors
Demircioglu, D; Kindermans, M; Nandi, T; Cukuroglu, E; Calabrese, C; Fonseca, NA; Kahles, A; Lehmann, K; Stegle, O; Brazma, A; Brooks, AN; Rätsch, G; Tan, P; Göke, J;
Publication
Abstract
The access to the final selection minute is only available to applicants.
Please check the confirmation e-mail of your application to obtain the access code.