[PDF][PDF] ComBat-seq: batch effect adjustment for RNA-seq count data
Y Zhang, G Parmigiani… - NAR genomics and …, 2020 - academic.oup.com
The benefit of integrating batches of genomic data to increase statistical power is often
hindered by batch effects, or unwanted variation in data caused by differences in technical …
hindered by batch effects, or unwanted variation in data caused by differences in technical …
Combating subclonal evolution of resistant cancer phenotypes
Metastatic breast cancer remains challenging to treat, and most patients ultimately progress
on therapy. This acquired drug resistance is largely due to drug-refractory sub-populations …
on therapy. This acquired drug resistance is largely due to drug-refractory sub-populations …
Fusion protein-driven IGF-IR/PI3K/AKT signals deregulate Hippo pathway promoting oncogenic cooperation of YAP1 and FUS-DDIT3 in myxoid liposarcoma
R Berthold, I Isfort, C Erkut, L Heinst, I Grünewald… - Oncogenesis, 2022 - nature.com
Myxoid liposarcoma (MLS) represents a common subtype of liposarcoma molecularly
characterized by a recurrent chromosomal translocation that generates a chimeric FUS …
characterized by a recurrent chromosomal translocation that generates a chimeric FUS …
SARS-CoV-2 early infection signature identified potential key infection mechanisms and drug targets
Y Li, A Duche, MR Sayer, D Roosan, FG Khalafalla… - BMC genomics, 2021 - Springer
Background The ongoing COVID-19 outbreak has caused devastating mortality and posed a
significant threat to public health worldwide. Despite the severity of this illness and 2.3 …
significant threat to public health worldwide. Despite the severity of this illness and 2.3 …
Alternative empirical Bayes models for adjusting for batch effects in genomic studies
Background Combining genomic data sets from multiple studies is advantageous to
increase statistical power in studies where logistical considerations restrict sample size or …
increase statistical power in studies where logistical considerations restrict sample size or …
pyComBat, a Python tool for batch effects correction in high-throughput molecular data using empirical Bayes methods
A Behdenna, M Colange, J Haziza, A Gema, G Appé… - BMC …, 2023 - Springer
Background Variability in datasets is not only the product of biological processes: they are
also the product of technical biases. ComBat and ComBat-Seq are among the most widely …
also the product of technical biases. ComBat and ComBat-Seq are among the most widely …
Biological significance of KRAS mutant allele expression in ovarian endometriosis
N Yachida, K Yoshihara, K Suda, H Nakaoka… - Cancer …, 2021 - Wiley Online Library
KRAS is the most frequently mutated in ovarian endometriosis. However, it is unclear
whether the KRAS mutant allele's mRNA is expressed and plays a biological role in ovarian …
whether the KRAS mutant allele's mRNA is expressed and plays a biological role in ovarian …
Pathway activity profiling of growth factor receptor network and stemness pathways differentiates metaplastic breast cancer histological subtypes
Background Gene expression profiling of rare cancers has proven challenging due to limited
access to patient materials and requirement of intact, non-degraded RNA for next …
access to patient materials and requirement of intact, non-degraded RNA for next …
Operationalizing healthcare big data in the electronic health records using a heatmap visualization technique
Background: The majority of the electronic health record (EHR) contains a wealth of
information, including unstructured notes. Healthcare professionals may be missing …
information, including unstructured notes. Healthcare professionals may be missing …
Evaluation of somatic mutations in solid metastatic pan-cancer patients
Simple Summary Cancer metastasis significantly contributes to cancer-related mortality. Our
retrospective cohort study aimed to evaluate the mutational landscape of seven solid …
retrospective cohort study aimed to evaluate the mutational landscape of seven solid …