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Items: 1 to 20 of 56


Host and microbiome multi-omics integration: applications and methodologies.

Wang Q, Wang K, Wu W, Giannoulatou E, Ho JWK, Li L.

Biophys Rev. 2019 Jan 9. doi: 10.1007/s12551-018-0491-7. [Epub ahead of print] Review.


Identification of active signaling pathways by integrating gene expression and protein interaction data.

Kabir MH, Patrick R, Ho JWK, O'Connor MD.

BMC Syst Biol. 2018 Dec 31;12(Suppl 9):120. doi: 10.1186/s12918-018-0655-x.


C3: An R package for cross-species compendium-based cell-type identification.

Kabir MH, Djordjevic D, O'Connor MD, Ho JWK.

Comput Biol Chem. 2018 Dec;77:187-192. doi: 10.1016/j.compbiolchem.2018.10.003. Epub 2018 Oct 9.


Identification of clinically actionable variants from genome sequencing of families with congenital heart disease.

Alankarage D, Ip E, Szot JO, Munro J, Blue GM, Harrison K, Cuny H, Enriquez A, Troup M, Humphreys DT, Wilson M, Harvey RP, Sholler GF, Graham RM, Ho JWK, Kirk EP, Pachter N, Chapman G, Winlaw DS, Giannoulatou E, Dunwoodie SL.

Genet Med. 2018 Oct 8. doi: 10.1038/s41436-018-0296-x. [Epub ahead of print]


A Screening Approach to Identify Clinically Actionable Variants Causing Congenital Heart Disease in Exome Data.

Szot JO, Cuny H, Blue GM, Humphreys DT, Ip E, Harrison K, Sholler GF, Giannoulatou E, Leo P, Duncan EL, Sparrow DB, Ho JWK, Graham RM, Pachter N, Chapman G, Winlaw DS, Dunwoodie SL.

Circ Genom Precis Med. 2018 Mar;11(3):e001978. doi: 10.1161/CIRCGEN.117.001978.


Biologically active constituents of the secretome of human W8B2+ cardiac stem cells.

Nie S, Wang X, Sivakumaran P, Chong MMW, Liu X, Karnezis T, Bandara N, Takov K, Nowell CJ, Wilcox S, Shambrook M, Hill AF, Harris NC, Newcomb AE, Strappe P, Shayan R, Hernández D, Clarke J, Hanssen E, Davidson SM, Dusting GJ, Pébay A, Ho JWK, Williamson N, Lim SY.

Sci Rep. 2018 Jan 25;8(1):1579. doi: 10.1038/s41598-018-19855-4.


Discovery of cell-type specific DNA motif grammar in cis-regulatory elements using random Forest.

Wang X, Lin P, Ho JWK.

BMC Genomics. 2018 Jan 19;19(Suppl 1):929. doi: 10.1186/s12864-017-4340-z.


Identification of satellite cells from anole lizard skeletal muscle and demonstration of expanded musculoskeletal potential.

Palade J, Djordjevic D, Hutchins ED, George RM, Cornelius JA, Rawls A, Ho JWK, Kusumi K, Wilson-Rawls J.

Dev Biol. 2018 Jan 15;433(2):344-356. doi: 10.1016/j.ydbio.2017.08.037. Epub 2017 Dec 25.


Light-focusing human micro-lenses generated from pluripotent stem cells model lens development and drug-induced cataract in vitro.

Murphy P, Kabir MH, Srivastava T, Mason ME, Dewi CU, Lim S, Yang A, Djordjevic D, Killingsworth MC, Ho JWK, Harman DG, O'Connor MD.

Development. 2018 Jan 9;145(1). pii: dev155838. doi: 10.1242/dev.155838.


iSyTE 2.0: a database for expression-based gene discovery in the eye.

Kakrana A, Yang A, Anand D, Djordjevic D, Ramachandruni D, Singh A, Huang H, Ho JWK, Lachke SA.

Nucleic Acids Res. 2018 Jan 4;46(D1):D875-D885. doi: 10.1093/nar/gkx837.


Impact of sequencing depth and read length on single cell RNA sequencing data of T cells.

Rizzetto S, Eltahla AA, Lin P, Bull R, Lloyd AR, Ho JWK, Venturi V, Luciani F.

Sci Rep. 2017 Oct 6;7(1):12781. doi: 10.1038/s41598-017-12989-x.


An Embryonic and Induced Pluripotent Stem Cell Model for Ovarian Granulosa Cell Development and Steroidogenesis.

Lipskind S, Lindsey JS, Gerami-Naini B, Eaton JL, O'Connell D, Kiezun A, Ho JWK, Ng N, Parasar P, Ng M, Nickerson M, Demirci U, Maas R, Anchan RM.

Reprod Sci. 2018 May;25(5):712-726. doi: 10.1177/1933719117725814. Epub 2017 Aug 31.


Scalability and Validation of Big Data Bioinformatics Software.

Yang A, Troup M, Ho JWK.

Comput Struct Biotechnol J. 2017 Jul 20;15:379-386. doi: 10.1016/j.csbj.2017.07.002. eCollection 2017. Review.


NAD Deficiency, Congenital Malformations, and Niacin Supplementation.

Shi H, Enriquez A, Rapadas M, Martin EMMA, Wang R, Moreau J, Lim CK, Szot JO, Ip E, Hughes JN, Sugimoto K, Humphreys DT, McInerney-Leo AM, Leo PJ, Maghzal GJ, Halliday J, Smith J, Colley A, Mark PR, Collins F, Sillence DO, Winlaw DS, Ho JWK, Guillemin GJ, Brown MA, Kikuchi K, Thomas PQ, Stocker R, Giannoulatou E, Chapman G, Duncan EL, Sparrow DB, Dunwoodie SL.

N Engl J Med. 2017 Aug 10;377(6):544-552. doi: 10.1056/NEJMoa1616361.


Modelling, inference and big data in biophysics.

Ho JWK, Grant GH.

Biophys Rev. 2017 Aug;9(4):297-298. doi: 10.1007/s12551-017-0282-6. Epub 2017 Jul 30.


CIDR: Ultrafast and accurate clustering through imputation for single-cell RNA-seq data.

Lin P, Troup M, Ho JW.

Genome Biol. 2017 Mar 28;18(1):59. doi: 10.1186/s13059-017-1188-0.


Integrative analysis identifies co-dependent gene expression regulation of BRG1 and CHD7 at distal regulatory sites in embryonic stem cells.

Yang P, Oldfield A, Kim T, Yang A, Yang JYH, Ho JWK.

Bioinformatics. 2017 Jul 1;33(13):1916-1920. doi: 10.1093/bioinformatics/btx092.


PBrowse: a web-based platform for real-time collaborative exploration of genomic data.

Szot PS, Yang A, Wang X, Parsania C, Röhm U, Wong KH, Ho JWK.

Nucleic Acids Res. 2017 May 19;45(9):e67. doi: 10.1093/nar/gkw1358.


Falco: a quick and flexible single-cell RNA-seq processing framework on the cloud.

Yang A, Troup M, Lin P, Ho JW.

Bioinformatics. 2017 Mar 1;33(5):767-769. doi: 10.1093/bioinformatics/btw732.


Male-lineage transmission of an acquired metabolic phenotype induced by grand-paternal obesity.

Cropley JE, Eaton SA, Aiken A, Young PE, Giannoulatou E, Ho JWK, Buckland ME, Keam SP, Hutvagner G, Humphreys DT, Langley KG, Henstridge DC, Martin DIK, Febbraio MA, Suter CM.

Mol Metab. 2016 Jun 23;5(8):699-708. doi: 10.1016/j.molmet.2016.06.008. eCollection 2016 Aug.

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