ntLink: a toolkit for de novo genome assembly scaffolding and mapping using long reads

Authors: Coombe, Lauren, Warren, René L., Wong, Johnathan, Nikolic, Vladimir, Birol, Inanc

Source: Current Protocols, 3(4), e733 (2023)

Subject Terms: Quantitative Biology - Genomics

Access URL: http://arxiv.org/abs/2301.08785

GoldPolish-target: targeted long-read genome assembly polishing.

Authors: Zhang, Emily, Coombe, Lauren, Wong, Johnathan, Warren, René L., Birol, Inanç

Source: BMC Bioinformatics; 3/7/2025, Vol. 26 Issue 1, p1-13, 13p

Subject Terms: LIFE sciences, DROSOPHILA melanogaster, ERROR rates, NUCLEOTIDE sequencing, GENOMES

Progress towards drug discovery for Friedreich’s Ataxia: Identifying synthetic oligonucleotides that more potently activate expression of human frataxin protein

Authors: Shen, Xiulong, Wong, Johnathan, Prakash, Thahza P., Rigo, Frank, Li, Yanjie, Napierala, Marek, Corey, David R.

Source: In Bioorganic & Medicinal Chemistry 1 June 2020 28(11)

A peptide derived from TID1S rescues frataxin deficiency and mitochondrial defects in FRDA cellular models.

Authors: Yi Na Dong, Ngaba, Lucie Vanessa, An, Jacob, Adeshina, Miniat W., Warren, Nathan, Wong, Johnathan, Lynch, David R.

Source: Frontiers in Pharmacology; 2024, p1-12, 12p

Subject Terms: FRATAXIN, FRIEDREICH'S ataxia, PEPTIDES, RNA interference, SMALL interfering RNA, ANIMAL rescue, RECESSIVE genes, IRON clusters

Linear time complexity de novo long read genome assembly with GoldRush.

Authors: Wong, Johnathan, Coombe, Lauren, Nikolić, Vladimir, Zhang, Emily, Nip, Ka Ming, Sidhu, Puneet, Warren, René L., Birol, Inanç

Source: Nature Communications; 5/22/2023, Vol. 14 Issue 1, p1-9, 9p

Subject Terms: DATA structures, GENOMES, SEQUENCE alignment, CELL lines, NUCLEOTIDE sequencing

aaHash: recursive amino acid sequence hashing.

Authors: Wong, Johnathan¹ jowong@bcgsc.ca, Kazemi, Parham¹, Coombe, Lauren¹, Warren, René L¹, Birol, Inanç¹

Source: Bioinformatics Advances. 2023, Vol. 3 Issue 1, p1-5. 5p.

Subject Terms: *AMINO acid sequence, *BIOINFORMATICS, *BIOCHEMISTRY databases, *COMPUTATIONAL biology, *HASHING

Spruce giga‐genomes: structurally similar yet distinctive with differentially expanding gene families and rapidly evolving genes.

Authors: Gagalova, Kristina K., Warren, René L., Coombe, Lauren, Wong, Johnathan, Nip, Ka Ming, Yuen, Macaire Man Saint, Whitehill, Justin G. A., Celedon, Jose M., Ritland, Carol, Taylor, Greg A., Cheng, Dean, Plettner, Patrick, Hammond, S. Austin, Mohamadi, Hamid, Zhao, Yongjun, Moore, Richard A., Mungall, Andrew J., Boyle, Brian, Laroche, Jérôme, Cottrell, Joan

Source: Plant Journal; Sep2022, Vol. 111 Issue 5, p1469-1485, 17p

Subject Terms: SITKA spruce, GENETIC variation, WHITE spruce, CONIFEROUS forests, GENES, GENE families, GENOMES, SPRUCE

RResolver: efficient short-read repeat resolution within ABySS.

Authors: Nikolić, Vladimir, Afshinfard, Amirhossein, Chu, Justin, Wong, Johnathan, Coombe, Lauren, Nip, Ka Ming, Warren, René L., Birol, Inanç

Source: BMC Bioinformatics; 6/21/2022, Vol. 23 Issue 1, p1-15, 15p

Subject Terms: DE Bruijn graph, GRAPH connectivity, CHARTS, diagrams, etc., SHORT tandem repeat analysis, GENOMICS

Physlr: Next-Generation Physical Maps.

Authors: Afshinfard, Amirhossein^1,2, aafshinfard@bcgsc.ca, Jackman, Shaun D.¹, sjackman@gmail.com, Wong, Johnathan¹, jowong@bcgsc.ca, Coombe, Lauren¹, lcoombe@bcgsc.ca, Chu, Justin¹, justinchu1989@gmail.com, Nikolic, Vladimir^1,2, vnikolic@bcgsc.ca, Dilek, Gokce¹, gokcedilek99@gmail.com, Malkoç, Yaman¹, yamanmalkoc14@gmail.com, Warren, René L.¹, rwarren@bcgsc.ca, Birol, Inanc^1,3, ibirol@bcgsc.ca

Source: DNA (2673-8856); Jun2022, Vol. 2 Issue 2, p116-130, 15p

ntEdit+Sealer: Efficient Targeted Error Resolution and Automated Finishing of Long‐Read Genome Assemblies.

Authors: Li, Janet X., Coombe, Lauren, Wong, Johnathan, Birol, Inanç, Warren, René L.

Source: Current Protocols; May2022, Vol. 2 Issue 5, p1-13, 13p

LongStitch: high-quality genome assembly correction and scaffolding using long reads.

Authors: Coombe, Lauren, Li, Janet X., Lo, Theodora, Wong, Johnathan, Nikolic, Vladimir, Warren, René L., Birol, Inanc

Source: BMC Bioinformatics; 10/30/2021, Vol. 22 Issue 1, p1-13, 13p

Subject Terms: GENOMES, RICE, CAENORHABDITIS elegans, NUCLEOTIDE sequencing, GENOMICS

ONTbarcoder and MinION barcodes aid biodiversity discovery and identification by everyone, for everyone.

Authors: Srivathsan, Amrita, Lee, Leshon, Katoh, Kazutaka, Hartop, Emily, Kutty, Sujatha Narayanan, Wong, Johnathan, Yeo, Darren, Meier, Rudolf

Source: BMC Biology; 9/29/2021, Vol. 19 Issue 1, p1-21, 21p

Subject Terms: BAR codes, GRAPHICAL user interfaces, BIODIVERSITY monitoring, BIODIVERSITY, SOFTWARE compatibility, ENVIRONMENTAL degradation, CAPITAL costs

Reviews & Products: MICROSOFT Windows (Operating system)

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Recurrent tumor-specific regulation of alternative polyadenylation of cancerrelated genes.

Authors: Zhuyi Xue, Warren, René L., Gibb, Ewan A., MacMillan, Daniel, Wong, Johnathan, Chiu, Readman, Austin Hammond, S., Chen Yang, Nip, Ka Ming, Ennis, Catherine A., Hahn, Abigail, Reynolds, Sheila, Birol, Inanc

Source: BMC Genomics; 7/13/2018, Vol. 19 Issue 1, p1-12, 12p, 4 Graphs

Virtual Screening in Search of Allosteric Modulators of Nav1.1 Channels

Authors: Wong, Johnathan, Ali, Syed R., Wadsworth, Paul, Singh, Aditya K., Liu, Zhiqing, Chen, Haiying, Zhou, Jia, Laezza, Fernanda

Source: In Biophysical Journal 3 February 2017 112(3) Supplement 1:242a-242a

ntHash2: recursive spaced seed hashing for nucleotide sequences.

Authors: Kazemi, Parham^1,2 (AUTHOR) pkazemi@bcgsc.ca, Wong, Johnathan¹ (AUTHOR), Nikolić, Vladimir¹ (AUTHOR), Mohamadi, Hamid³ (AUTHOR), Warren, René L¹ (AUTHOR), Birol, Inanç^1,4 (AUTHOR) pkazemi@bcgsc.ca

Source: Bioinformatics. 10/15/2022, Vol. 38 Issue 20, p4812-4813. 2p.

Subject Terms: *PROTEIN-protein interactions, *GENOMICS, *SEEDS, *SEQUENCE analysis

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