Explanipedia

Alternative splicing of synaptotagmin 7 regulates oligomerization and short-term synaptic plasticity Open

Nikunj Mehta, Daniel L. Larson, Raghava Jagadeesh Salaka, Mitch Wozney, Smrithika Subramani , et al. · 2025

Synaptic plasticity is crucial for learning and memory. The presynaptic calcium sensor synaptotagmin 7 (syt7) regulates aspects of short-term plasticity (STP), but the underlying mechanisms remain unclear. Here, we show that alternative sp…

Evidence of a Three-State Mechanism in DNA Hairpin Folding Open

Brendan Cullinane, Kunihiko Ishii, Simi Kaur, Tahei Tahara, Randall H. Goldsmith · 2025

Chemistry Physics Biology

DNA hairpins are a model system for biomolecule folding as well as key structures in biology and nanotechnology. However, limitations in traditional solution-phase spectroscopy shorten the window of observable kinetics and cannot account f…

Evidence of a Three-State Mechanism in DNA Hairpins Folding Open

Brendan Cullinane, Kunihiko Ishii, Simi Kaur, Tahei Tahara, Randall H. Goldsmith · 2025

Chemistry Physics Computer science

DNA hairpins are a model system for biomolecule folding as well as key structures in biology and nanotechnology. However, limitations in traditional solution-phase spectroscopy shorten the window of observable kinetics and cannot account f…

Aggregation in Aqueous Solutions of 2-(Tetrafluoro(trifluoromethyl)-λ6-sulfanyl-ethan-1-ol (CF3SF4-ethanol)): A Comparison with Aqueous Trifluoroethanol and Hexafluoroisopropanol Using Molecular Dynamics Simulations and Dynamic Light Scattering Experiments Open

Samadrita Biswas, Simi Kaur, Christopher A. Myers, Alan Chen, John T. Welch · 2023

Chemistry

2-Tetrafluoro(trifluoromethyl)-λ6-sulfanylethan-1-ol (CF3SF4-ethanol) combines the polar hydrophobicity of tetrafluoro(trifluoromethyl)-λ6-sulfanyl (CF3SF4) group with the polarity of simple alcohols. The properties of aqueous solutions of…

Enhanced Protein Isoform Characterization Through Long-Read Proteogenomics - Workflow Results Open

Rachel Miller, Ben T. Jordan, Madison Mehlferber, Erin D. Jeffery, Christina Chatzipantsiou , et al. · 2022

Computer science Chemistry Biology

The detection of physiologically relevant protein isoforms encoded by the human genome is critical to biomedicine. Mass spectrometry (MS)-based proteomics is the preeminent method for protein detection, but isoform-resolved proteomic ana…

Enhanced Protein Isoform Characterization Through Long-Read Proteogenomics - Workflow Results Open

Rachel Miller, Ben T. Jordan, Madison Mehlferber, Erin D. Jeffery, Christina Chatzipantsiou , et al. · 2022

Computer science Chemistry Biology

The detection of physiologically relevant protein isoforms encoded by the human genome is critical to biomedicine. Mass spectrometry (MS)-based proteomics is the preeminent method for protein detection, but isoform-resolved proteomic ana…

Enhanced Protein Isoform Characterization Through Long-Read Proteogenomics - Workflow Results Open

Rachel Miller, Ben T. Jordan, Madison Mehlferber, Erin D. Jeffery, Christina Chatzipantsiou , et al. · 2022

Computer science Chemistry Biology

The detection of physiologically relevant protein isoforms encoded by the human genome is critical to biomedicine. Mass spectrometry (MS)-based proteomics is the preeminent method for protein detection, but isoform-resolved proteomic ana…

Additional file 4 of Enhanced protein isoform characterization through long-read proteogenomics Open

Rachel Miller, Ben T. Jordan, Madison Mehlferber, Erin D. Jeffery, Christina Chatzipantsiou , et al. · 2022

Computer science Biology

Additional file 4: Table S2. Number of isoforms for each transcript and protein isoform classifications between SQANTI and SQANTI Protein (FSM = full-splice_match; ISM = incomplete-splice_match; NIC = novel_in_catalog; NNC = novel_not_in_c…

Additional file 8 of Enhanced protein isoform characterization through long-read proteogenomics Open

Rachel Miller, Ben T. Jordan, Madison Mehlferber, Erin D. Jeffery, Christina Chatzipantsiou , et al. · 2022

Computer science Chemistry Biology

Additional file 8: Table S6. Search parameters for all MetaMorpheus proteomics searches.

Additional file 7 of Enhanced protein isoform characterization through long-read proteogenomics Open

Rachel Miller, Ben T. Jordan, Madison Mehlferber, Erin D. Jeffery, Christina Chatzipantsiou , et al. · 2022

Computer science Biology

Additional file 7: Table S5. Protein groups (list of the PB accessions) which contain a rescued or resolved isoform.

Additional file 6 of Enhanced protein isoform characterization through long-read proteogenomics Open

Rachel Miller, Ben T. Jordan, Madison Mehlferber, Erin D. Jeffery, Christina Chatzipantsiou , et al. · 2022

Biology Computer science Physics

Additional file 6: Table S4. Detailed information for all high confidence novel peptide identifications such as: their annotated spectra, novel peptide classification and isoform track image.

Additional file 3 of Enhanced protein isoform characterization through long-read proteogenomics Open

Rachel Miller, Ben T. Jordan, Madison Mehlferber, Erin D. Jeffery, Christina Chatzipantsiou , et al. · 2022

Computer science Chemistry Biology

Additional file 3: Table S1. Detailed breakdown of protein classifications based on SQANTI Protein. Provides information on the key protein elements which differ from the GENCODE reference.

Additional file 5 of Enhanced protein isoform characterization through long-read proteogenomics Open

Rachel Miller, Ben T. Jordan, Madison Mehlferber, Erin D. Jeffery, Christina Chatzipantsiou , et al. · 2022

Computer science Biology Physics

Additional file 5: Table S3. Summary of MetaMorpheus search results on the gene, peptide and protein levels at 1% FDR for the PacBio-Hybrid, GENCODE and UniProt databases.

TEST DATA for Enhanced protein isoform characterization through long-read proteogenomics Open

Rachel Miller, Ben T. Jordan, Madison Mehlferber, Erin D. Jeffery, Christina Chatzipantsiou , et al. · 2021

Computer science Biology Physics

Test data for The detection of physiologically relevant protein isoforms encoded by the human genome is critical to biomedicine. Mass spectrometry (MS)-based proteomics is the preeminent method for protein detection, but isoform-resolved p…

TEST DATA for Enhanced protein isoform characterization through long-read proteogenomics Open

Rachel Miller, Ben T. Jordan, Madison Mehlferber, Erin D. Jeffery, Christina Chatzipantsiou , et al. · 2021

Computer science Chemistry Biology

Test data for The detection of physiologically relevant protein isoforms encoded by the human genome is critical to biomedicine. Mass spectrometry (MS)-based proteomics is the preeminent method for protein detection, but isoform-resolved p…

Long read proteogenomics codeathon Open