Exploring the Alternative Proteome with OpenProt and Mass Spectrometry.

Proteogenomics has revealed the translation of unannotated open reading frames (ORFs) present in mRNAs and in noncoding RNAs (ncRNAs). OpenProt annotates all ORFs with a minimum of 30 codons in the transcriptome of several species and displays many functional features associated with the corresponding proteins. Two types of proteins are annotated: reference or canonical proteins which are proteins already annotated in UniProt, RefSeq, or Ensembl and noncanonical proteins.

OpenProt 2.0 builds a path to the functional characterization of alternative proteins.

The OpenProt proteogenomic resource (https://www.openprot.org/) provides users with a complete and freely accessible set of non-canonical or alternative open reading frames (AltORFs) within the transcriptome of various species, as well as functional annotations of the corresponding protein sequences not found in standard databases.

OpenCustomDB: Integration of Unannotated Open Reading Frames and Genetic Variants to Generate More Comprehensive Customized Protein Databases.

Proteomic diversity in biological samples can be characterized by mass spectrometry (MS)-based proteomics using customized protein databases generated from sets of transcripts previously detected by RNA-seq. This diversity has only been increased by the recent discovery that many translated alternative open reading frames rest unannotated at unsuspected locations of mRNAs and ncRNAs. These novel protein products, termed alternative proteins, have been left out of all previous custom database generation tools.

The impacts of implementing recovery innovations: a conceptual framework grounded in qualitative research.

Background: Implementing mental health recovery into services is a policy priority in Canada and globally. To that end, a 5 year study was undertaken with seven organisations providing mental health and housing services to people living with a mental health challenge to implement guidelines for the transformation of services and systems towards a recovery-orientation. Multi-stakeholder implementation teams were established and a facilitated process guided teams to choosing and planning for the implementation of one recovery innovation.

Newfound Coding Potential of Transcripts Unveils Missing Members of Human Protein Communities.

Recent proteogenomic approaches have led to the discovery that regions of the transcriptome previously annotated as non-coding regions [i.e., untranslated regions (UTRs), open reading frames overlapping annotated coding sequences in a different reading frame, and non-coding RNAs] frequently encode proteins, termed alternative proteins (altProts).

OpenVar: functional annotation of variants in non-canonical open reading frames.

Background: Recent technological advances have revealed thousands of functional open reading frames (ORF) that have eluded reference genome annotations. These overlooked ORFs are found throughout the genome, in any reading frame of transcripts, mature or non-coding, and can overlap annotated ORFs in a different reading frame. The exploration of these novel ORFs in genomic datasets and of their role in genetic traits is hindered by a lack of software.

Translating mental health recovery guidelines into recovery-oriented innovations: A strategy combining implementation teams and a facilitated planning process.

Recovery is the focus of mental health strategies internationally. However, little translation of recovery knowledge has occurred in mental health services. The purpose of this research is to bridge the gap between recovery guidelines and practice by developing a new implementation strategy involving the formation of implementation teams made up of different stakeholders (service users, service providers, managers, knowledge users) and facilitating a 12-meeting implementation planning process.

Identifying and understanding the contextual factors that shaped mid-implementation outcomes during the COVID-19 pandemic in organizations implementing mental health recovery innovations into services.

Background: Seven housing and health services organizations were guided through a process of translating Chapter Six of the Canadian Guidelines for Recovery-Oriented Practice into a recovery-oriented innovation and plan for its implementation. At the time of the COVID-19 outbreak and lockdown measures, six of the seven organizations had begun implementing their chosen innovation (peer workers, wellness recovery action planning facilitator training, staff training and a family support group). This mid-implementation study used the Consolidated Framework for Implementation Research (CFIR) to identify contextual factors that influenced organizations to continue or postpone implementation of recovery-oriented innovations in the early months of the COVID-19 pandemic.

Robust Physiological Metrics From Sparsely Sampled Networks.

Physiological and biochemical networks are highly complex, involving thousands of nodes as well as a hierarchical structure. True network structure is also rarely known. This presents major challenges for applying classical network theory to these networks.

The CFIR Card Game: a new approach for working with implementation teams to identify challenges and strategies.

Background: The Consolidated Framework for Implementation Research (CFIR) and the ERIC compilation of implementation strategies are key resources for identifying implementation barriers and strategies. However, their respective density and complexity make their application to implementation planning outside of academia challenging. We developed the CFIR Card Game as a way of working with multi-stakeholder implementation teams that were implementing mental health recovery into their services, to identify barriers and strategies to overcome them.

Modelling of pathogen-host systems using deeper ORF annotations and transcriptomics to inform proteomics analyses.

The Zika virus is a flavivirus that can cause fulminant outbreaks and lead to Guillain-Barré syndrome, microcephaly and fetal demise. Like other flaviviruses, the Zika virus is transmitted by mosquitoes and provokes neurological disorders. Despite its risk to public health, no antiviral nor vaccine are currently available.

Reconsidering proteomic diversity with functional investigation of small ORFs and alternative ORFs.

The discovery of functional yet non-annotated open reading frames (ORFs) throughout the genome of several species presents an unprecedented challenge in current genome annotation. These novel ORFs are shorter than annotated ones and many can be found on the same RNA, in opposition to current assumptions in annotation methodologies. Whilst the literature lacks consensus, these novel ORFs are commonly referred to as small ORFs (sORFs) or alternative ORFs (alt-ORFs).

OpenProt: a more comprehensive guide to explore eukaryotic coding potential and proteomes.

Advances in proteomics and sequencing have highlighted many non-annotated open reading frames (ORFs) in eukaryotic genomes. Genome annotations, cornerstones of today's research, mostly rely on protein prior knowledge and on ab initio prediction algorithms. Such algorithms notably enforce an arbitrary criterion of one coding sequence (CDS) per transcript, leading to a substantial underestimation of the coding potential of eukaryotes.