Cell fitness screens reveal a conflict between LINE-1 retrotransposition and DNA replication
- Daniel Ardeljan, Jared P Steranka, K. Burns
- BiologyNature Structural & Molecular Biology
- 1 January 2020
It is found that nontransformed cells undergo a TP53- dependent growth arrest and activate interferon signaling in response to LINE-1, revealing a retrotransposition–replication conflict that may be an important determinant of cancer growth.
Systematic Analysis of Splice-Site-Creating Mutations in Cancer
- R. Jayasinghe, Song Cao, L. Ding
- BiologyCell Reports
- 3 April 2018
Community Assessment of the Predictability of Cancer Protein and Phosphoprotein Levels from Genomics and Transcriptomics
- Pei Wang, D. Fenyö, Samuel H. Payne
- Biology
- 2020
Performance of the proposed proteogenomics methods was limited, suggesting that (phospho)proteomic cannot be replaced, at least yet, by genomic and transcriptomic profiling.
LINE-1 ORF2p expression is nearly imperceptible in human cancers
- Daniel Ardeljan, Xuya Wang, J. LaCava
- BiologyMobile DNA
- 22 August 2019
Mass spectrometry-based tumor proteome profiling studies wherein ORF2p eludes detection, and endogenous ORF1p-associated interactomes, affinity isolated from colorectal cancers, are reported, wherein these samples include primary tumors harboring hundreds of somatically acquired L1 insertions.
Crowdsourced Assessment of the of Predictability of Cancer Protein and Phosphoprotein Levels from Genomics and Transcriptomics.
- Mi Yang, F. Petralia, J. Saez-Rodriguez
- BiologyCell Systems
- 17 July 2020
DreamAI: algorithm for the imputation of proteomics data
- Weiping Ma, Sunkyu Kim, Pei Wang
- BiologybioRxiv
- 22 July 2020
The NCI-CPTAC Proteogenomics DREAM Challenge was carried out to develop effective imputation algorithms for labelled LC-MS/MS proteomics data through crowd learning and the final resulting algorithm, DreamAI, is based on an ensemble of six different imputation methods.
Discovery of Protein Modifications Using Differential Tandem Mass Spectrometry Proteomics.
- P. Cifani, Zhi Li, A. Kentsis
- Biology, ChemistryJournal of Proteome Research
- 22 March 2021
A spectral alignment method for the identification of protein modifications using high-resolution mass spectrometry proteomics, called SAMPEI for spectral alignment-based modified peptide identification, designed for the discovery of functional protein and peptide signaling modifications, without prior knowledge of their identities.
Distinct Features of Human Myeloid Cell Cytokine Response Profiles Identify Neutrophil Activation by Cytokines as a Prognostic Feature during Tuberculosis and Cancer
- J. Devlin, Erin E. Zwack, P. Loke
- Biology, MedicineJournal of Immunology
- 29 April 2020
By dissecting how different myeloid cells respond to cytokine activation, this study can delineate biological roles for myeloids cells in different cytokine environments during disease processes, especially during infection and tumor progression.
Diversity of Functionally Distinct Clonal Sets of Human Conventional Memory B Cells That Bind Staphylococcal Protein A
- Emily E Radke, Zhi Li, G. Silverman
- BiologyFrontiers in Immunology
- 28 April 2021
It is provided the first evidence that human memory responses are supplemented by B-cell clones, and circulating-antibodies, that bind to SpA determinants independent of the non-immune Fc- and Fab-binding sites.
Adenosine A2A receptor null chondrocyte transcriptome resembles that of human osteoarthritic chondrocytes
- C. Castro, C. Corciulo, B. Cronstein
- BiologyPurinergic Signalling Purinergic Signalling
- 11 May 2021
The molecular foundations for early-onset OA in A2AR null mice are identified, further establishing their role as models for human disease and the potential use of adenosine as a treatment for humans with OA.
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