The bubble mechanism for methane transport from the shallow sea bed to the surface: A review and sensitivity study
I Leifer, RK Patro - Continental shelf research, 2002 - Elsevier
… The Laplace pressure is negligible for bubbles with r>15 μm (2σ/r=0.1 atm for r=15 μm).
In a system with no flux through the air–water interface (ie, HC=P A ), bubbles will outflow (invade…
In a system with no flux through the air–water interface (ie, HC=P A ), bubbles will outflow (invade…
Salmon provides fast and bias-aware quantification of transcript expression
We introduce Salmon, a lightweight method for quantifying transcript abundance from RNA–seq
reads. Salmon combines a new dual-phase parallel inference algorithm and feature-rich …
reads. Salmon combines a new dual-phase parallel inference algorithm and feature-rich …
RNA sequencing data: hitchhiker's guide to expression analysis
Gene expression is the fundamental level at which the results of various genetic and regulatory
programs are observable. The measurement of transcriptome-wide gene expression has …
programs are observable. The measurement of transcriptome-wide gene expression has …
TransRate: reference-free quality assessment of de novo transcriptome assemblies
TransRate is a tool for reference-free quality assessment of de novo transcriptome assemblies.
Using only the sequenced reads and the assembly as input, we show that multiple …
Using only the sequenced reads and the assembly as input, we show that multiple …
Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms
We introduce Sailfish, a computational method for quantifying the abundance of previously
annotated RNA isoforms from RNA-seq data. Because Sailfish entirely avoids mapping reads…
annotated RNA isoforms from RNA-seq data. Because Sailfish entirely avoids mapping reads…
A review of unsupervised band selection techniques: Land cover classification for hyperspectral earth observation data
A hyperspectral image (HSI) is a collection of several narrow-band images that span a wide
spectral range. Each band reflects the same scene, composed of various objects imaged at …
spectral range. Each band reflects the same scene, composed of various objects imaged at …
Global network alignment using multiscale spectral signatures
R Patro, C Kingsford - Bioinformatics, 2012 - academic.oup.com
Motivation: Protein interaction networks provide an important system-level view of biological
processes. One of the fundamental problems in biological network analysis is the global …
processes. One of the fundamental problems in biological network analysis is the global …
[HTML][HTML] Identification of alternative topological domains in chromatin
Chromosome conformation capture experiments have led to the discovery of dense, contiguous,
megabase-sized topological domains that are similar across cell types and conserved …
megabase-sized topological domains that are similar across cell types and conserved …
A general-purpose counting filter: Making every bit count
… r bits, which we call the remainder h1(x). The rank-and-selectbased quotient filter maintains
an array Q of 2q r-… Thus, the counter C for remainder x > 0 is encoded as a sequence of r-bit …
an array Q of 2q r-… Thus, the counter C for remainder x > 0 is encoded as a sequence of r-bit …
[HTML][HTML] Tximeta: Reference sequence checksums for provenance identification in RNA-seq
…, L Shepherd, M Morgan, R Patro - PLoS computational …, 2020 - journals.plos.org
… We provide a solution in the form of an R/Bioconductor package tximeta that performs
numerous annotation and metadata gathering tasks automatically on behalf of users during the …
numerous annotation and metadata gathering tasks automatically on behalf of users during the …