ORCID Profile
0000-0003-3202-7008
Current Organisations
University of Manchester
,
University of British Columbia
,
University of Melbourne
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Publisher: IMPERIAL COLLEGE PRESS
Date: 10-2008
Publisher: Cold Spring Harbor Laboratory
Date: 05-01-2011
Abstract: The main way of analyzing biological sequences is by comparing and aligning them to each other. It remains difficult, however, to compare modern multi-billionbase DNA data sets. The difficulty is caused by the nonuniform (oligo)nucleotide composition of these sequences, rather than their size per se. To solve this problem, we modified the standard seed-and-extend approach (e.g., BLAST) to use adaptive seeds. Adaptive seeds are matches that are chosen based on their rareness, instead of using fixed-length matches. This method guarantees that the number of matches, and thus the running time, increases linearly, instead of quadratically, with sequence length. LAST, our open source implementation of adaptive seeds, enables fast and sensitive comparison of large sequences with arbitrarily nonuniform composition.
Publisher: ACM
Date: 13-03-2005
Publisher: Springer Science and Business Media LLC
Date: 20-11-2009
Publisher: Cold Spring Harbor Laboratory
Date: 19-04-2018
DOI: 10.1101/304683
Abstract: Adult tissue repair and regeneration require the activation of resident stem rogenitor cells that can self-renew and generate differentiated progeny. The regenerative capacity of skeletal muscle relies on muscle satellite cells (MuSCs) and their interplay with different cell types within the niche. Yet, our understanding of the cells that compose the skeletal muscle tissue is limited and molecular definitions of the principal cell types are lacking. Using a combined approach of single-cell RNA-sequencing and mass cytometry, we precisely mapped the different cell types in adult skeletal muscle tissue and highlighted previously overlooked populations. We identified known functional populations, characterized their gene signatures, and determined key markers. Among the ten main cell populations present in skeletal muscle, we found an unexpected complexity in the interstitial compartment and identified two new cell populations. One express the transcription factor Scleraxis and generate tenocyte-like cells. The second express smooth muscle and mesenchymal cell markers (SMMCs). While distinct from MuSCs, SMMCs are endowed with myogenic potential and promote MuSC engraftment following transplantation. Our high-dimensional single-cell atlas uncovers principles of an adult tissue composition and can be exploited to reveal unknown cellular sub-fractions that contribute to tissue regeneration.
Publisher: Wiley
Date: 03-11-2006
DOI: 10.1002/ASI.20515
Publisher: Oxford University Press (OUP)
Date: 27-01-2010
DOI: 10.1093/NAR/GKQ010
Publisher: Association for Computing Machinery (ACM)
Date: 12-2005
Publisher: Oxford University Press (OUP)
Date: 13-12-2011
DOI: 10.1093/BIOINFORMATICS/BTR689
Abstract: Motivation: The growth of next-generation sequencing means that more effective and efficient archiving methods are needed to store the generated data for public dissemination and in anticipation of more mature analytical methods later. This article examines methods for compressing the quality score component of the data to partly address this problem. Results: We compare several compression policies for quality scores, in terms of both compression effectiveness and overall efficiency. The policies employ lossy and lossless transformations with one of several coding schemes. Experiments show that both lossy and lossless transformations are useful, and that simple coding methods, which consume less computing resources, are highly competitive, especially when random access to reads is needed. Availability and implementation: Our C++ implementation, released under the Lesser General Public License, is available for download at www.cb.k.u-tokyo.ac.jp/asailab/members/rwan. Contact: rwan@cuhk.edu.hk Supplementary information: Supplementary data are available at Bioinformatics online.
Publisher: Springer Berlin Heidelberg
Date: 2009
Publisher: Oxford University Press (OUP)
Date: 12-01-2013
DOI: 10.1093/BIOINFORMATICS/BTT011
Abstract: Summary: Insertional mutagenesis from virus infection is an important pathogenic risk for the development of cancer. Despite the advent of high-throughput sequencing, discovery of viral integration sites and expressed viral fusion events are still limited. Here, we present ViralFusionSeq (VFS), which combines soft-clipping information, read-pair analysis and targeted de novo assembly to discover and annotate viral–human fusions. VFS was used in an RNA-Seq experiment, simulated DNA-Seq experiment and re-analysis of published DNA-Seq datasets. Our experiments demonstrated that VFS is both sensitive and highly accurate. Availability: VFS is distributed under GPL version 3 at hkbic.cuhk.edu.hk/software/viralfusionseq Contact: tf.chan@cuhk.edu.hk Supplementary information: Supplementary data are available at Bioinformatics Online
Publisher: IEEE
Date: 12-2010
Publisher: IEEE
Date: 12-2010
Location: United Kingdom of Great Britain and Northern Ireland
No related grants have been discovered for Raymond Wan.