RNA-Seq differential expression analysis: An extended review and a software tool
The correct identification of differentially expressed genes (DEGs) between specific
conditions is a key in the understanding phenotypic variation. High-throughput transcriptome …
conditions is a key in the understanding phenotypic variation. High-throughput transcriptome …
Challenges and best practices in omics benchmarking
TG Brooks, NF Lahens, A Mrčela, GR Grant - Nature Reviews Genetics, 2024 - nature.com
Technological advances enabling massively parallel measurement of biological features—
such as microarrays, high-throughput sequencing and mass spectrometry—have ushered in …
such as microarrays, high-throughput sequencing and mass spectrometry—have ushered in …
Differential analysis of RNA-seq incorporating quantification uncertainty
Abstract We describe sleuth (http://pachterlab. github. io/sleuth), a method for the differential
analysis of gene expression data that utilizes bootstrap** in conjunction with response …
analysis of gene expression data that utilizes bootstrap** in conjunction with response …
Alignment and map** methodology influence transcript abundance estimation
Background The accuracy of transcript quantification using RNA-seq data depends on many
factors, such as the choice of alignment or map** method and the quantification model …
factors, such as the choice of alignment or map** method and the quantification model …
RNA-viromics reveals diverse communities of soil RNA viruses with the potential to affect grassland ecosystems across multiple trophic levels
The distribution and diversity of RNA viruses in soil ecosystems are largely unknown,
despite their significant impact on public health, ecosystem functions, and food security …
despite their significant impact on public health, ecosystem functions, and food security …
Dosage analysis of the 7q11.23 Williams region identifies BAZ1B as a major human gene patterning the modern human face and underlying self-domestication
We undertook a functional dissection of chromatin remodeler BAZ1B in neural crest (NC)
stem cells (NCSCs) from a uniquely informative cohort of typical and atypical patients …
stem cells (NCSCs) from a uniquely informative cohort of typical and atypical patients …
pipeComp, a general framework for the evaluation of computational pipelines, reveals performant single cell RNA-seq preprocessing tools
Abstract We present pipeComp (https://github. com/plger/pipeComp), a flexible R framework
for pipeline comparison handling interactions between analysis steps and relying on multi …
for pipeline comparison handling interactions between analysis steps and relying on multi …
RNA sequencing data: hitchhiker's guide to expression analysis
K Van den Berge, KM Hembach… - Annual Review of …, 2019 - annualreviews.org
Gene expression is the fundamental level at which the results of various genetic and
regulatory programs are observable. The measurement of transcriptome-wide gene …
regulatory programs are observable. The measurement of transcriptome-wide gene …
YY1 haploinsufficiency causes an intellectual disability syndrome featuring transcriptional and chromatin dysfunction
Yin and yang 1 (YY1) is a well-known zinc-finger transcription factor with crucial roles in
normal development and malignancy. YY1 acts both as a repressor and as an activator of …
normal development and malignancy. YY1 acts both as a repressor and as an activator of …
Single cell-derived spheroids capture the self-renewing subpopulations of metastatic ovarian cancer
T Velletri, CE Villa, D Cilli, B Barzaghi… - Cell Death & …, 2022 - nature.com
Abstract High Grade Serous Ovarian cancer (HGSOC) is a major unmet need in oncology,
due to its precocious dissemination and the lack of meaningful human models for the …
due to its precocious dissemination and the lack of meaningful human models for the …