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BioBloom tools: fast, accurate and memory-efficient host species sequence screening using bloom filters

Justin Chu, Sara Sadeghi, Anthony Raymond, Shaun D. Jackman, Ka Ming Nip, Richard Mar, Hamid Mohamadi, Yaron S. Butterfield, A. Gordon Robertson, Inanç Birol
2014 Computer applications in the biosciences : CABIOS  
We present BioBloom Tools, a Bloom filter-based sequence-screening tool that is faster than BWA, Bowtie 2 (popular alignment algorithms) and FACS (a membership query algorithm).  ...  Large datasets can be screened for sequences from a specific organism, quickly and with low memory requirements, by a data structure that supports time-and memory-efficient set membership queries.  ...  ACKNOWLEDGEMENTS The authors thank Genome Canada, British Columbia Cancer Foundation, and Genome British Columbia for their support, and Irene Li, Rene Warren and Karen Mungall for useful discussions.  ... 
doi:10.1093/bioinformatics/btu558 pmid:25143290 pmcid:PMC4816029 fatcat:iama6ruvnbbkppu4hbzuxfftsq

FastqPuri: high-performance preprocessing of RNA-seq data

Paula Pérez-Rubio, Claudio Lottaz, Julia C. Engelmann
2019 BMC Bioinformatics  
We here present FastqPuri, a light-weight and highly efficient preprocessing tool for fastq data.  ...  FastqPuri is most flexible in filtering undesired biological sequences by offering two approaches to optimize speed and memory usage dependent on the total size of the potential contaminating sequences  ...  Acknowledgements We thank Maria Attenberger and Phu Tran for proof-reading the user manual and testing the software.  ... 
doi:10.1186/s12859-019-2799-0 pmid:31053060 pmcid:PMC6500068 fatcat:glikf6suxnc3laevkccfbdhz54

The Integrated Genomic Landscape of Thymic Epithelial Tumors

Milan Radovich, Curtis R. Pickering, Ina Felau, Gavin Ha, Hailei Zhang, Heejoon Jo, Katherine A. Hoadley, Pavana Anur, Jiexin Zhang, Mike McLellan, Reanne Bowlby, Thomas Matthew (+176 others)
2018 Cancer Cell  
Using multi-platform omics analyses on 117 TETs, we define four subtypes of these tumors defined by genomic hallmarks and an association with survival and World Health Organization histological subtype  ...  We further observe enrichment of mutations in HRAS, NRAS, and TP53.  ...  ., and Birol, I. (2014). BioBloom tools: fast, accurate and memory-efficient host species sequence screening using bloom filters. Bioinformatics 30, 3402-3404.  ... 
doi:10.1016/j.ccell.2018.01.003 pmid:29438696 pmcid:PMC5994906 fatcat:5khwqh4jsjdyhilaclblvv7a7q

Comprehensive and Integrative Genomic Characterization of Hepatocellular Carcinoma

Adrian Ally, Miruna Balasundaram, Rebecca Carlsen, Eric Chuah, Amanda Clarke, Noreen Dhalla, Robert A. Holt, Steven J.M. Jones, Darlene Lee, Yussanne Ma, Marco A. Marra, Michael Mayo (+226 others)
2017 Cell  
DNA sequencing and mutation analysis identified significantly mutated genes, including LZTR1, EEF1A1, SF3B1, and SMARCA4.  ...  We analyzed 363 hepatocellular carcinoma (HCC) cases by whole-exome sequencing and DNA copy number analyses, and we analyzed 196 HCC cases by DNA methylation, RNA, miRNA, and proteomic expression also.  ...  BioBloom tools: fast, accurate and memory-efficient host species sequence screening using bloom filters.Bioinformatics 30, 3402-3404. Chung, J.H., Larsen, A.R., Chen, E., and Bunz, F. (2014).  ... 
doi:10.1016/j.cell.2017.05.046 pmid:28622513 pmcid:PMC5680778 fatcat:drfldh7h3vhb5mq3zcrqcthc3a

Interleukin-6 trans-signaling is a candidate mechanism to drive progression of human DCCs during periods of clinical latency [article]

Melanie Werner-Klein, Ana Grujovic, Christoph Irlbeck, Milan Obradovic, Martin Hoffmann, Huiqin Koerkel-Qu, Xin Lu, Steffie Treitschke, Caecilia Koestler, Catherine Botteron, Kathrin Weidele, Christian Werno (+18 others)
2020 bioRxiv   pre-print
Surprisingly, and similar to mammary epithelial cells, DCCs lacked membranous IL6 receptor expression and mechanistic dissection revealed IL6 trans-signaling to regulate a stem-like state of mammary epithelial  ...  Although thousands of breast cancer cells disseminate and home to bone marrow until primary surgery, usually less than a handful will succeed in establishing manifest metastases months to years later.  ...  BioBloom tools: fast, accurate and memory-efficient host species sequence 714 screening using bloom filters. Bioinformatics 30, 3402-3404 (2014). 715 89. Dobin, A. et al.  ... 
doi:10.1101/2020.05.28.121145 fatcat:4nf75xdkxnhufjatgg3rcezs2i