Research data from the University of British Columbia Michael Smith Laboratories
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1 to 10 of 51 Results
Mar 6, 2024 - UBC Research Data Collection
Morin, Alexander; Chingpan Chu; Paul Pavlidis, 2024, "Identifying Reproducible Transcription Regulator Coexpression Patterns with Single Cell Transcriptomics", https://doi.org/10.5683/SP3/HJ1B24, Borealis, V1, UNF:6:MWyDnHubVD05w1kdJ5kRzw== [fileUNF]
This repository contains the summarized TR ranking information as described in: https://www.biorxiv.org/content/10.1101/2024.02.15.580581v2
Mar 6, 2023 - Dr. Paul Pavlidis
Morin, Alexander, 2022, "Characterizing the targets of transcription regulators by aggregating ChIP-seq and perturbation expression data sets", https://doi.org/10.5683/SP3/MAFGFL, Borealis, V2, UNF:6:NWNf4+NelyKPsz/pxyKZ2A== [fileUNF]
There is a growing collection of genomics data sets generated for identifying the gene targets under control of transcription regulators (TRs). TR ChIP-seq and RNA expression experiments that perturb TR activity are the most common strategies for mapping TRs to genes at a genomic...
Apr 13, 2021 - Dr. Paul Pavlidis
Chu, Eric Ching-Pan, 2021, "Experiment level curation identifies high confidence transcriptional regulatory interactions in neurodevelopment", https://doi.org/10.5683/SP2/XLLWRL, Borealis, V2, UNF:6:iXXMqIoqZ232Qn5IPlsGWg== [fileUNF]
The capacity to computationally reconstruct gene regulatory networks using large-scale biological data is currently limited by the absence of a high confidence set of one-to-one regulatory interactions. Given the lengthy history of using small scale experimental assays to investi...
Jun 19, 2020 - Dr. Leonard Foster
Foster, Leonard, 2020, "Attachments to paper Scott et al Molecular System Biology (2017)", https://doi.org/10.5683/SP2/NDW1WW, Borealis, V1
Attachments to paper Scott et al Molecular System Biology (2017)
Jun 19, 2020 - Dr. Leonard Foster
Foster, Leonard, 2020, "JProteomics2014", https://doi.org/10.5683/SP2/UVV4A0, Borealis, V1
Development of a computation framework for the analysis of protein correlation profiling and spatial proteomics experiments 2014
Jun 19, 2020 - Dr. Leonard Foster
Foster, Leonard, 2020, "finalList", https://doi.org/10.5683/SP2/V7OW8T, Borealis, V1
A tool that takes as input a non-redundant list of peptides identified in a project and compiles a non-redundant list of proteins identified. It will also subtract any peptides coming from a FASTA library of contaminants.
Jun 19, 2020 - Dr. Leonard Foster
Foster, Leonard, 2020, "transORF", https://doi.org/10.5683/SP2/5QDKLL, Borealis, V1
A tool that takes a FASTA nucleotide file and predicts all open reading frames in all six translation frames. The output is a FASTA amino acid file. This tool is useful for creating a protein library for database searching (where a good prediction is unavailable) if you don’t wan...
Jun 19, 2020 - Dr. Leonard Foster
Foster, Leonard, 2020, "PCP-SILAC", https://doi.org/10.5683/SP2/HFAA3V, Borealis, V1
PCP-SILAC, scripts, instructions and sample data for informatics treatment of PCP-SILAC data.
Dr. Leonard Foster(University of British Columbia)
Jun 19, 2020
Apr 4, 2020 - Dr. Joerg Gsponer
Nawar Malhis, 2019, "LIST-S2: pre-computed deleteriousness of all possible mutations in human (OX=9606) protein sequences", https://doi.org/10.5683/SP2/PM9TAB, Borealis, V4
LIST-S2 predicts the deleteriousness of amino acid mutations in protein sequences. Here we provide precomputed predictions of human protein sequences. Scores are in the range [0 .. 1], where lower scores indicate more benign and higher indicate deleteriousness. One can also visua...
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