<i>GenomicTools</i>: a computational platform for developing high-throughput analytics in genomics

Tsirigos, Aristotelis; Haiminen, Niina; Bilal, Erhan; Utro, Filippo

doi:10.1093/bioinformatics/btr646

Cited by 42 publications

(28 citation statements)

References 7 publications

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“…MACS version 2.0.10 57 was used to perform peak calling for both broad and narrow peaks. The files with the aligned reads were converted to wig format using GenomicTools 58 and then to bigwig format using the corresponding UCSC tool (wigToBigWig, UCSC Browser binary utilities) in order to visualize the tracks. Snapshots were prepared using the Integrative Genomics Viewer (IGV).…”

Section: Methodsmentioning

confidence: 99%

The ubiquitin ligase Huwe1 regulates the maintenance and lymphoid commitment of hematopoietic stem cells

et al. 2016

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Hematopoietic stem cells (HSCs) are dormant in the bone marrow and can be activated in response to diverse stresses to replenish all blood cell types. Here we identify the ubiquitin ligase Huwe1 as a crucial regulator of HSC functions via its post-translational control of N-myc. We found Huwe1 to be essential for HSC self-renewal, quiescence and lymphoid fate specification. Using a novel fluorescent fusion allele (MycnM), we observed that N-myc expression was restricted to the most immature, multipotent stem and progenitor populations. N-myc was upregulated in response to stress or upon loss of Huwe1, leading to increased proliferation and stem cell exhaustion. Mycn depletion reversed most of these phenotypes in vivo, suggesting that the attenuation of N-myc by Huwe1 is essential to reestablish homeostasis following stress.

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Section: Methodsmentioning

confidence: 99%

The ubiquitin ligase Huwe1 regulates the maintenance and lymphoid commitment of hematopoietic stem cells

et al. 2016

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“…All computations, including correction for multiple hypothesis testing using the false discovery rate (FDR) were performed with the permutation test tool (permutation_test -kmin 5 -S n -p 1000 -f -a) included in the GenomicTools open-source package. 66 …”

Section: Bioinformatics and Data Miningmentioning

confidence: 99%

JNK1 stress signaling is hyper-activated in high breast density and the tumor stroma: Connecting fibrosis, inflammation, and stemness for cancer prevention

Lisanti

Tsirigos

Pavlides³

et al. 2013

Cell Cycle

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“…With the developing of high-throughput sequencing technology, recent advances have been achieved with leading a multiple abundant sequencing data for RNA-Seq analyses [13], which provided the high speed and efficient tools to monitor transcriptomic changes [14,15]. This technology could also efficiently generate the functional genomic data and protein annotation for non-model organisms [16,17].…”

Section: Introductionmentioning

confidence: 99%

De novo assembly and characterization of stress transcriptome and regulatory networks under temperature, salt and hormone stresses in Lilium lancifolium

Wang

Yang

et al. 2014

Mol Biol Rep

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Plants have continually confrontation with different abiotic stresses, including salt, low temperature, drought or hormone stress. The plants acclimate to the environmental stresses relating with the falls of the molecular mesh including the stress signal receiver, signal transcriptional regulation and the expression of functional and structure genes. Using the RNA-seq, we carried out a transcriptional analysis under cold treatment for investigating a profound comprehension of the signal network and molecular metabolisms reaction included in abiotic stress reaction for Lilium lancifolium. Our study identified 18,722 unigenes had demonstrated the resemblance to the known exact proteins in the Swiss-Prot protein database and classified them by Gene ontology into three primary kinds: cellular component, biological process, and molecular function, and then 15,898 unigenes aligned to existing sequences in the KEGG databases. Based on the transcriptome results of cold stress, more stress-related genes were identified and analyzed of their expressions in other abiotic stress treatments as 37 °C, ABA, JA and Na. Meanwhile, bioinformatics qRT-PCR analyses of stress genes as LlDREB1, LlAP2, LlNAC1, LlHOT, LlR2R3-MYB and LlCDPK revealed that novel candidate genes encoding ethylene responsive transporters and serine/threonine receptor-like kinases, which contributed to speculate the signal regulation pathway during the abiotic stresses; engineering genes could also boost the tolerance to stress, as protected and maintained the function and structure of cellular components. Our research conjectured the abiotic stress signal transduction pathway and identified the expected key ingredients regulating the stress tolerance in Lilium lancifolium, which would enable the in-depth molecular exploration of stress-tolerance mechanisms in lily.

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GenomicTools: a computational platform for developing high-throughput analytics in genomics

Abstract: The GenomicTools platform (version 2.0.0) was implemented in C++. The source code, documentation, user manual, example datasets and scripts are available online at http://code.google.com/p/ibm-cbc-genomic-tools.

Cited by 42 publications

References 7 publications

The ubiquitin ligase Huwe1 regulates the maintenance and lymphoid commitment of hematopoietic stem cells

The ubiquitin ligase Huwe1 regulates the maintenance and lymphoid commitment of hematopoietic stem cells

JNK1 stress signaling is hyper-activated in high breast density and the tumor stroma: Connecting fibrosis, inflammation, and stemness for cancer prevention

De novo assembly and characterization of stress transcriptome and regulatory networks under temperature, salt and hormone stresses in Lilium lancifolium

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