UBC Michael Smith Laboratories

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1 to 10 of 50 Results

Characterizing the targets of transcription regulators by aggregating ChIP-seq and perturbation expression data sets 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...
Experiment level curation identifies high confidence transcriptional regulatory interactions in neurodevelopment 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...
Attachments to paper Scott et al Molecular System Biology (2017) 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)
JProteomics2014 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
finalList 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.
transORF 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...
PCP-SILAC 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
LIST-S2: pre-computed deleteriousness of all possible mutations in human (OX=9606) protein sequences 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...
Multi-model functionalization of disease-associated PTEN missense mutations identifies multiple molecular mechanisms underlying protein dysfunction Mar 4, 2020 - Dr. Paul Pavlidis Kathryn L. Post; Manuel Belmadani; Payel Ganguly; Fabian Meili; Riki Dingwall; Troy A. McDiarmid; Warren M. Meyers; Caitlin Herrington; Barry P. Young; Daniel B. Callaghan; Sanja Rogic; Matthew Edwards; Ana Niciforovic; Alessandro Cau; Catharine H. Rankin; Timothy P. O’Connor; Shernaz X. Bamji; Christopher J. Loewen; Douglas W. Allan; Paul Pavlidis; Kurt Haas, 2020, "Multi-model functionalization of disease-associated PTEN missense mutations identifies multiple molecular mechanisms underlying protein dysfunction", https://doi.org/10.5683/SP2/DQOKPB, Borealis, V1 Supporting data for "Multi-model functionalization of disease-associated PTEN missense mutations identifies multiple molecular mechanisms underlying protein dysfunction"

Characterizing the targets of transcription regulators by aggregating ChIP-seq and perturbation expression data sets

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...

Experiment level curation identifies high confidence transcriptional regulatory interactions in neurodevelopment

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...

Attachments to paper Scott et al Molecular System Biology (2017)

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)

JProteomics2014

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

finalList

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.

transORF

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...

PCP-SILAC

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

LIST-S2: pre-computed deleteriousness of all possible mutations in human (OX=9606) protein sequences

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...

Multi-model functionalization of disease-associated PTEN missense mutations identifies multiple molecular mechanisms underlying protein dysfunction

Mar 4, 2020 - Dr. Paul Pavlidis

Kathryn L. Post; Manuel Belmadani; Payel Ganguly; Fabian Meili; Riki Dingwall; Troy A. McDiarmid; Warren M. Meyers; Caitlin Herrington; Barry P. Young; Daniel B. Callaghan; Sanja Rogic; Matthew Edwards; Ana Niciforovic; Alessandro Cau; Catharine H. Rankin; Timothy P. O’Connor; Shernaz X. Bamji; Christopher J. Loewen; Douglas W. Allan; Paul Pavlidis; Kurt Haas, 2020, "Multi-model functionalization of disease-associated PTEN missense mutations identifies multiple molecular mechanisms underlying protein dysfunction", https://doi.org/10.5683/SP2/DQOKPB, Borealis, V1

Supporting data for "Multi-model functionalization of disease-associated PTEN missense mutations identifies multiple molecular mechanisms underlying protein dysfunction"

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