University of Ottawa

Contact Info:

Gareth Palidwor

501 Smyth Road

Ottawa, ON K1S0G9

http://www.ohri.ca/bioinformatics

Grants and Identifiers:

RRID: RRID:SCR_022466

Instrumentation:

Services Provided:

Computational - Bioinformatics

Computational - Biostatistics

Relevant Publications:

1.) Mottawea W, Yousuf B, Sultan S, Ahmed T, Yeo J, Hüttmann N, Li Y, Bouhlel NE, Hassan H, Zhang X, Minic Z, Hammami R (2024 Dec 19). Multi-level analysis of gut microbiome extracellular vesicles-host interaction reveals a connection to gut-brain axis signaling Microbiology Spectrum, 13(2), e01368-24. . PMCID: 11792502.

2.) Rehmani T, Dias AP, Applin BD, Salih M, Tuana BS (2024 Oct 4). SLMAP3 is essential for neurulation through mechanisms involving cytoskeletal elements, ABP, and PCP Life Science Alliance, 7(12), e202302545. . PMCID: 11452652.

3.) Dias AP, Rehmani T, Applin BD, Salih M, Tuana B (2024 Oct). SLMAP3 is crucial for organogenesis through mechanisms involving primary cilia formation. Open biology, 14(10), rsob240206. . PMID: 39417621.

4.) Yousuf B, Pasha R, Pineault N, Ramirez-Arcos S (2024 Jul 25). Modulation of Staphylococcus aureus gene expression during proliferation in platelet concentrates with focus on virulence and platelet functionality PLOS ONE, 19(7), e0307920. . PMCID: 11271859.

5.) Bergin CJ, Zouggar A, Mendes da Silva A, Fenouil T, Haebe JR, Masibag AN, Agrawal G, Shah MS, Sandouka T, Tiberi M, Auer RC, Ardolino M, Benoit YD (2024 Mar). The dopamine transporter antagonist vanoxerine inhibits G9a and suppresses cancer stem cell functions in colon tumors. Nature cancer, 5(3), 463-480. doi: 10.1038/s43018-024-00727-y. PMID: 38351181.

6.) Yeganeh B, Yeganeh A, Malone K, Beug ST, Jankov RP (2023 Oct 23). Suspension-Induced Stem Cell Transition: A Non-Transgenic Method to Generate Adult Stem Cells from Mouse and Human Somatic Cells Cells, 12(20), 2508. . PMCID: 10605402.

7.) Viñas JL, Spence M, Porter CJ, Douvris A, Gutsol A, Zimpelmann JA, Campbell PA, Burns KD (2021 Sep). micro-RNA-486-5p protects against kidney ischemic injury and modifies the apoptotic transcriptome in proximal tubules. Kidney international, 100(3), 597-612. . ID: 34181969.

8.) Alkailani M, Palidwor G, Poulin A, Mohan R, Pepin D, Vanderhyden B, Gibbings D (2021 Mar). A genome-wide strategy to identify causes and consequences of retrotransposon expression finds activation by BRCA1 in ovarian cancer. NAR cancer, 3(1), zcaa040. doi: 10.1093/narcan/zcaa040. ID: 33447827.

9.) Karimnezhad A, Palidwor GA, Thavorn K, Stewart DJ, Campbell PA, Lo B, Perkins TJ (2020 Oct 15). Accuracy and reproducibility of somatic point mutation calling in clinical-type targeted sequencing data. BMC medical genomics, 13(1), 156. doi: 10.1186/s12920-020-00803-z. ID: 33059707.

10.) Zagozewski J, Shahriary GM, Morrison LC, Saulnier O, Stromecki M, Fresnoza A, Palidwor G, Porter CJ, Forget A, Ayrault O, Hawkins C, Chan JA, Vladoiu MC, Sundaresan L, Arsenio J, Taylor MD, Ramaswamy V, Werbowetski-Ogilvie TE (2020 Jul 20). An OTX2-PAX3 signaling axis regulates Group 3 medulloblastoma cell fate. Nature communications, 11(1), 3627. doi: 10.1038/s41467-020-17357-4. ID: 32686664.

11.) Soleimani VD, Nguyen D, Ramachandran P, Palidwor GA, Porter CJ, Yin H, Perkins TJ, Rudnicki MA (2018 Aug 21). Cis-regulatory determinants of MyoD function. Nucleic acids research, 46(14), 7221-7235. . ID: 30016497.

12.) Chitiprolu M, Jagow C, Tremblay V, Bondy-Chorney E, Paris G, Savard A, Palidwor G, Barry FA, Zinman L, Keith J, Rogaeva E, Robertson J, Lavallée-Adam M, Woulfe J, Couture JF, Côté J, Gibbings D (2018 Jul 18). A complex of C9ORF72 and p62 uses arginine methylation to eliminate stress granules by autophagy. Nature communications, 9(1), 2794. doi: 10.1038/s41467-018-05273-7. ID: 30022074.

13.) Stromecki M, Tatari N, Morrison LC, Kaur R, Zagozewski J, Palidwor G, Ramaswamy V, Skowron P, Wölfl M, Milde T, Del Bigio MR, Taylor MD, Werbowetski-Ogilvie TE (2018 Apr). Characterization of a novel OTX2-driven stem cell program in Group 3 and Group 4 medulloblastoma. Molecular oncology, 12(4), 495-513. doi: 10.1002/1878-0261.12177. ID: 29377567.

14.) Rothberg JLM, Maganti HB, Jrade H, Porter CJ, Palidwor GA, Cafariello C, Battaion HL, Khan ST, Perkins TJ, Paulson RF, Ito CY, Stanford WL (2018). Mtf2-PRC2 control of canonical Wnt signaling is required for definitive erythropoiesis. Cell discovery, 4(), 21. doi: 10.1038/s41421-018-0022-5. ID: 29736258.

15.) Chen Z, Chang WY, Etheridge A, Strickfaden H, Jin Z, Palidwor G, Cho JH, Wang K, Kwon SY, Doré C, Raymond A, Hotta A, Ellis J, Kandel RA, Dilworth FJ, Perkins TJ, Hendzel MJ, Galas DJ, Stanford WL (2017 Aug). Reprogramming progeria fibroblasts re-establishes a normal epigenetic landscape. Aging cell, 16(4), 870-887. doi: 10.1111/acel.12621. ID: 28597562.

16.) Ramachandran P, Palidwor GA, Perkins TJ (2015). BIDCHIPS: bias decomposition and removal from ChIP-seq data clarifies true binding signal and its functional correlates. Epigenetics & chromatin, 8(), 33. doi: 10.1186/s13072-015-0028-2. ID: 26388941.

17.) Soleimani VD, Palidwor GA, Ramachandran P, Perkins TJ, Rudnicki MA (2013 Aug). Chromatin tandem affinity purification sequencing. Nature protocols, 8(8), 1525-34. . ID: 23845964.

18.) Ramachandran P, Palidwor GA, Porter CJ, Perkins TJ (2013 Feb 15). MaSC: mappability-sensitive cross-correlation for estimating mean fragment length of single-end short-read sequencing data. Bioinformatics (Oxford, England), 29(4), 444-50. . ID: 23300135.

19.) Fournier D, Palidwor GA, Shcherbinin S, Szengel A, Schaefer MH, Perez-Iratxeta C, Andrade-Navarro MA (2013). Functional and genomic analyses of alpha-solenoid proteins. PloS one, 8(11), e79894. doi: 10.1371/journal.pone.0079894. ID: 24278209.

20.) Andrade-Navarro MA, Palidwor GA, Perez-Iratxeta C (2012 Sep 7). Peer2ref: a peer-reviewer finding web tool that uses author disambiguation. BioData mining, 5(1), 14. . ID: 22958760.

21.) Soleimani VD, Punch VG, Kawabe Y, Jones AE, Palidwor GA, Porter CJ, Cross JW, Carvajal JJ, Kockx CE, van IJcken WF, Perkins TJ, Rigby PW, Grosveld F, Rudnicki MA (2012 Jun 12). Transcriptional dominance of Pax7 in adult myogenesis is due to high-affinity recognition of homeodomain motifs. Developmental cell, 22(6), 1208-20. . ID: 22609161.

22.) Palidwor GA, Perkins TJ, Xia X (2010 Oct 27). A general model of codon bias due to GC mutational bias. PloS one, 5(10), e13431. doi: 10.1371/journal.pone.0013431. ID: 21048949.

23.) Palidwor GA, Andrade-Navarro MA (2010 Jan 25). MLTrends: Graphing MEDLINE term usage over time. Journal of biomedical discovery and collaboration, 5(), 1-6. . ID: 20333611.

24.) Scimè A, Desrosiers J, Trensz F, Palidwor GA, Caron AZ, Andrade-Navarro MA, Grenier G (2010 Jan). Transcriptional profiling of skeletal muscle reveals factors that are necessary to maintain satellite cell integrity during ageing. Mechanisms of ageing and development, 131(1), 9-20. . ID: 19913570.

25.) Sandie R, Palidwor GA, Huska MR, Porter CJ, Krzyzanowski PM, Muro EM, Perez-Iratxeta C, Andrade-Navarro MA (2009 Mar 10). Recent developments in StemBase: a tool to study gene expression in human and murine stem cells. BMC research notes, 2(), 39. . ID: 19284540.

26.) Palidwor GA, Shcherbinin S, Huska MR, Rasko T, Stelzl U, Arumughan A, Foulle R, Porras P, Sanchez-Pulido L, Wanker EE, Andrade-Navarro MA (2009 Mar). Detection of alpha-rod protein repeats using a neural network and application to huntingtin. PLoS computational biology, 5(3), e1000304. doi: 10.1371/journal.pcbi.1000304. ID: 19282972.

27.) Porter CJ, Palidwor GA, Sandie R, Krzyzanowski PM, Muro EM, Perez-Iratxeta C, Andrade-Navarro MA (2007). StemBase: a resource for the analysis of stem cell gene expression data. Methods in molecular biology (Clifton, N.J.), 407(), 137-48. doi: 10.1007/978-1-59745-536-7_11. ID: 18453254.

Description:

We are a Core Facility of the University of Ottawa and the Ottawa Hospital Research Institute. We provide advice on bioinformatics research design, conduct bioinformatics analysis, and provide support for grant proposals that involve bioinformatics (including conducting pilot studies, support/collaboration letters and methodological text) Our areas of expertise include: Analysis of high-throughput sequencing data; single cell (Chromium 10x), RNA-seq (including small RNA), ChIP-seq, ATAC-seq, Hi-C. Large scale analysis integrating multiple data types We have experience with many other types of bioinformatics, and/or can refer you to other local exports, depending on your needs. We can also help to arrange for the analysis of your biological samples with local core facilities such as StemCore, the Proteomics Resource Center, or the OHRI Mass Spectrometry Core Facility. We provide yearly training courses in RNA-seq analysis and Bioinformatics analysis using R as well as individual training and analysis support on request. We maintain a document containing a summary of our sequencing experiment recommendations for client use. Please contact us to discuss your project and how we might help you: gpalidwor@ohri.ca. Please note that our hourly rates will be increasing as of June 1, 2022: $85/hr: OHRI or uOttawa clients (from $80/hr) $120/hr: external academic clients (from $110/hr) $140/hr: industry clients (from $110/hr) All rates are in Canadian Dollars.