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                        "title": "AMICI: high-performance sensitivity analysis for large ordinary differential equation models",
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                        "abstract": "Protein inference connects the peptide spectrum matches (PSMs) obtained from database search engines back to proteins, which are typically at the heart of most proteomics studies. Different search engines yield different PSMs and thus different protein lists. Analysis of results from one or multiple search engines is often hampered by different data exchange formats and lack of convenient and intuitive user interfaces. We present PIA, a flexible software suite for combining PSMs from different search engine runs and turning these into consistent results. PIA can be integrated into proteomics data analysis workflows in several ways. A user-friendly graphical user interface can be run either locally or (e.g., for larger core facilities) from a central server. For automated data processing, stand-alone tools are available. PIA implements several established protein inference algorithms and can combine results from different search engines seamlessly. On several benchmark data sets, we show that PIA can identify a larger number of proteins at the same protein FDR when compared to that using inference based on a single search engine. PIA supports the majority of established search engines and data in the mzIdentML standard format. It is implemented in Java and freely available at https://github.com/mpc-bioinformatics/pia.",
                        "date": "2015-07-02T00:00:00Z",
                        "citationCount": 57,
                        "authors": [
                            {
                                "name": "Uszkoreit J."
                            },
                            {
                                "name": "Maerkens A."
                            },
                            {
                                "name": "Perez-Riverol Y."
                            },
                            {
                                "name": "Meyer H.E."
                            },
                            {
                                "name": "Marcus K."
                            },
                            {
                                "name": "Stephan C."
                            },
                            {
                                "name": "Kohlbacher O."
                            },
                            {
                                "name": "Eisenacher M."
                            }
                        ],
                        "journal": "Journal of Proteome Research"
                    }
                },
                {
                    "doi": "10.1021/acs.jproteome.8b00723",
                    "pmid": "30474983",
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                    "metadata": {
                        "title": "Protein Inference Using PIA Workflows and PSI Standard File Formats",
                        "abstract": "Proteomics using LC-MS/MS has become one of the main methods to analyze the proteins in biological samples in high-throughput. But the existing mass-spectrometry instruments are still limited with respect to resolution and measurable mass ranges, which is one of the main reasons why shotgun proteomics is the major approach. Here proteins are digested, which leads to the identification and quantification of peptides instead. While often neglected, the important step of protein inference needs to be conducted to infer from the identified peptides to the actual proteins in the original sample. In this work, we highlight some of the previously published and newly added features of the tool PIA - Protein Inference Algorithms, which helps the user with the protein inference of measured samples. We also highlight the importance of the usage of PSI standard file formats, as PIA is the only current software supporting all available standards used for spectrum identification and protein inference. Additionally, we briefly describe the benefits of working with workflow environments for proteomics analyses and show the new features of the PIA nodes for the KNIME Analytics Platform. Finally, we benchmark PIA against a recently published data set for isoform detection. PIA is open source and available for download on GitHub (https://github.com/mpc-bioinformatics/pia) or directly via the community extensions inside the KNIME analytics platform.",
                        "date": "2019-02-01T00:00:00Z",
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                        "authors": [
                            {
                                "name": "Uszkoreit J."
                            },
                            {
                                "name": "Perez-Riverol Y."
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                            {
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                            },
                            {
                                "name": "Marcus K."
                            },
                            {
                                "name": "Eisenacher M."
                            }
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                        "journal": "Journal of Proteome Research"
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            "documentation": [
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                    "url": "http://ftp.mi.fu-berlin.de/pub/OpenMS/release-documentation/html/index.html",
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                    "metadata": {
                        "title": "OpenMS: A flexible open-source software platform for mass spectrometry data analysis",
                        "abstract": "© 2016 Nature America, Inc. All rights reserved.High-resolution mass spectrometry (MS) has become an important tool in the life sciences, contributing to the diagnosis and understanding of human diseases, elucidating biomolecular structural information and characterizing cellular signaling networks. However, the rapid growth in the volume and complexity of MS data makes transparent, accurate and reproducible analysis difficult. We present OpenMS 2.0 (http://www.openms.de), a robust, open-source, cross-platform software specifically designed for the flexible and reproducible analysis of high-throughput MS data. The extensible OpenMS software implements common mass spectrometric data processing tasks through a well-defined application programming interface in C++ and Python and through standardized open data formats. OpenMS additionally provides a set of 185 tools and ready-made workflows for common mass spectrometric data processing tasks, which enable users to perform complex quantitative mass spectrometric analyses with ease.",
                        "date": "2016-08-30T00:00:00Z",
                        "citationCount": 246,
                        "authors": [
                            {
                                "name": "Rost H.L."
                            },
                            {
                                "name": "Sachsenberg T."
                            },
                            {
                                "name": "Aiche S."
                            },
                            {
                                "name": "Bielow C."
                            },
                            {
                                "name": "Weisser H."
                            },
                            {
                                "name": "Aicheler F."
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                                "name": "Andreotti S."
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                                "name": "Ehrlich H.-C."
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                                "name": "Gutenbrunner P."
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                            {
                                "name": "Cottret L."
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                            {
                                "name": "Frainay C."
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                            {
                                "name": "Chazalviel M."
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                            {
                                "name": "Cabanettes F."
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                            {
                                "name": "Gloaguen Y."
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                            {
                                "name": "Camenen E."
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                            {
                                "name": "Merlet B."
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                            {
                                "name": "Heux S."
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                            {
                                "name": "Portais J.-C."
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                            {
                                "name": "Poupin N."
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                                "name": "Jourdan F."
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                        "title": "Bracken: Estimating species abundance in metagenomics data",
                        "abstract": "Metagenomic experiments attempt to characterize microbial communities using high-throughput DNA sequencing. Identification of the microorganisms in a sample provides information about the genetic profile, population structure, and role of microorganisms within an environment. Until recently, most metagenomics studies focused on high-level characterization at the level of phyla, or alternatively sequenced the 16S ribosomalRNAgene that is present in bacterial species. As the cost of sequencing has fallen, though, metagenomics experiments have increasingly used unbiased shotgun sequencing to capture all the organisms in a sample. This approach requires a method for estimating abundance directly from the raw read data. Here we describe a fast, accurate new method that computes the abundance at the species level using the reads collected in a metagenomics experiment. Bracken (Bayesian Reestimation of Abundance after Classification with KrakEN) uses the taxonomic assignments made by Kraken, a very fast read-level classifier, along with information about the genomes themselves to estimate abundance at the species level, the genus level, or above. We demonstrate that Bracken can produce accurate species- and genus-level abundance estimates even when a sample contains multiple near-identical species.",
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                            {
                                "name": "Lu J."
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                            {
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                {
                    "url": "https://pavlidislab.github.io/Gemma/",
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                        "General"
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                },
                {
                    "url": "https://gemma.msl.ubc.ca/resources/restapidocs/",
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                        "API documentation"
                    ],
                    "note": "Documentation for the Gemma REST API."
                }
            ],
            "publication": [
                {
                    "doi": "10.1093/bioinformatics/btp259",
                    "pmid": "19376825",
                    "pmcid": "PMC2687992",
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                        "Primary"
                    ],
                    "version": null,
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                    "metadata": {
                        "title": "Application and evaluation of automated semantic annotation of gene expression experiments",
                        "abstract": "Motivation: Many microarray datasets are available online with formalized standards describing the probe sequences and expression values. Unfortunately, the description, conditions and parameters of the experiments are less commonly formalized and often occur as natural language text. This hinders searching, high-throughput analysis, organization and integration of the datasets. Results: We use the lexical resources and software tools from the Unified Medical Language System (UMLS) to extract concepts from text. We then link the UMLS concepts to classes in open biomedical ontologies. The result is accessible and clear semantic annotations of gene expression experiments. We applied the method to 595 expression experiments from Gemma, a resource for re-use and meta-analysis of gene expression profiling data. We evaluated and corrected all stages of the annotation process. The majority of missed annotations were due to a lack of cross-references. The most error-prone stage was the extraction of concepts from phrases. Final review of the annotations in context of the experiments revealed 89% precision. A naive system, lacking the phrase to concept corrections is 68% precise. We have integrated this annotation pipeline into Gemma. © 2009 The Author(s).",
                        "date": "2009-06-09T00:00:00Z",
                        "citationCount": 9,
                        "authors": [
                            {
                                "name": "French L."
                            },
                            {
                                "name": "Lane S."
                            },
                            {
                                "name": "Law T."
                            },
                            {
                                "name": "Xu L."
                            },
                            {
                                "name": "Pavlidis P."
                            }
                        ],
                        "journal": "Bioinformatics"
                    }
                },
                {
                    "doi": "10.1093/database/baab006",
                    "pmid": "33599246",
                    "pmcid": "PMC7904053",
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                        "Primary"
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                    "version": null,
                    "note": null,
                    "metadata": {
                        "title": "Curation of over 10 000 transcriptomic studies to enable data reuse",
                        "abstract": "Vast amounts of transcriptomic data reside in public repositories, but effective reuse remains challenging. Issues include unstructured dataset metadata, inconsistent data processing and quality control, and inconsistent probe-gene mappings across microarray technologies. Thus, extensive curation and data reprocessing are necessary prior to any reuse. The Gemma bioinformatics system was created to help address these issues. Gemma consists of a database of curated transcriptomic datasets, analytical software, a web interface and web services. Here we present an update on Gemma's holdings, data processing and analysis pipelines, our curation guidelines, and software features. As of June 2020, Gemma contains 10 811 manually curated datasets (primarily human, mouse and rat), over 395 000 samples and hundreds of curated transcriptomic platforms (both microarray and RNA sequencing). Dataset topics were represented with 10 215 distinct terms from 12 ontologies, for a total of 54 316 topic annotations (mean topics/dataset = 5.2). While Gemma has broad coverage of conditions and tissues, it captures a large majority of available brain-related datasets, accounting for 34% of its holdings. Users can access the curated data and differential expression analyses through the Gemma website, RESTful service and an R package. Database URL: https://gemma.msl.ubc.ca/home.html",
                        "date": "2021-01-01T00:00:00Z",
                        "citationCount": 21,
                        "authors": [
                            {
                                "name": "Lim N."
                            },
                            {
                                "name": "Tesar S."
                            },
                            {
                                "name": "Belmadani M."
                            },
                            {
                                "name": "Poirier-Morency G."
                            },
                            {
                                "name": "Mancarci B.O."
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                            {
                                "name": "Sicherman J."
                            },
                            {
                                "name": "Jacobson M."
                            },
                            {
                                "name": "Leong J."
                            },
                            {
                                "name": "Tan P."
                            },
                            {
                                "name": "Pavlidis P."
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                        "journal": "Database"
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        {
            "name": "MetaPhlAn",
            "description": "Computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data.",
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                    "input": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_3494",
                                "term": "DNA sequence"
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                            "format": [
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                                    "uri": "http://edamontology.org/format_1930",
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                                    "term": "SAM"
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                                    "uri": "http://edamontology.org/format_3751",
                                    "term": "DSV"
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                    "note": null,
                    "cmd": "metaphlan <fastq_input> --input_type fastq -o <output>"
                },
                {
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                    "note": "Convert SGB-based profile to GTDB taxonomy",
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                    "uri": "http://edamontology.org/topic_3174",
                    "term": "Metagenomics"
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                {
                    "uri": "http://edamontology.org/topic_0194",
                    "term": "Phylogenomics"
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            ],
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                "Python"
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                    "url": "https://github.com/biobakery/MetaPhlAn",
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            ],
            "publication": [
                {
                    "doi": "10.1038/nmeth.2066",
                    "pmid": "22688413",
                    "pmcid": "PMC3443552",
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                    "version": null,
                    "note": null,
                    "metadata": {
                        "title": "Metagenomic microbial community profiling using unique clade-specific marker genes",
                        "abstract": "Metagenomic shotgun sequencing data can identify microbes populating a microbial community and their proportions, but existing taxonomic profiling methods are inefficient for increasingly large data sets. We present an approach that uses clade-specific marker genes to unambiguously assign reads to microbial clades more accurately and >50Ã-faster than current approaches. We validated our metagenomic phylogenetic analysis tool, MetaPhlAn, on terabases of short reads and provide the largest metagenomic profiling to date of the human gut. It can be accessed at http://huttenhower.sph.harvard.edu/ metaphlan/. © 2012 Nature America, Inc. All rights reserved.",
                        "date": "2012-08-01T00:00:00Z",
                        "citationCount": 1300,
                        "authors": [
                            {
                                "name": "Segata N."
                            },
                            {
                                "name": "Waldron L."
                            },
                            {
                                "name": "Ballarini A."
                            },
                            {
                                "name": "Narasimhan V."
                            },
                            {
                                "name": "Jousson O."
                            },
                            {
                                "name": "Huttenhower C."
                            }
                        ],
                        "journal": "Nature Methods"
                    }
                }
            ],
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                    "url": "https://groups.google.com/forum/#!forum/metaphlan-users",
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        {
            "name": "samclip",
            "description": "Filter SAM file for soft and hard clipped alignments",
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        {
            "name": "NetPicoRNA",
            "description": "Neural network predictions of cleavage sites of picornaviral proteases.",
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            "biotoolsCURIE": "biotools:netpicorna",
            "version": [
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                    "operation": [
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                            "uri": "http://edamontology.org/operation_0422",
                            "term": "Protein cleavage site prediction"
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                    ],
                    "input": [
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                    "output": [
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                            "data": {
                                "uri": "http://edamontology.org/data_1277",
                                "term": "Protein features"
                            },
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                                    "uri": "http://edamontology.org/format_2330",
                                    "term": "Textual format"
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                            ]
                        },
                        {
                            "data": {
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                                "term": "Sequence report"
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                                    "term": "Binary format"
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                        }
                    ],
                    "note": "produces neural network predictions of cleavage sites of picornaviral proteases",
                    "cmd": null
                }
            ],
            "toolType": [
                "Web application"
            ],
            "topic": [
                {
                    "uri": "http://edamontology.org/topic_3510",
                    "term": "Protein sites, features and motifs"
                },
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                    "uri": "http://edamontology.org/topic_0160",
                    "term": "Sequence sites, features and motifs"
                }
            ],
            "operatingSystem": [
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            "link": [
                {
                    "url": "http://cbs.dtu.dk/services",
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                }
            ],
            "download": [],
            "documentation": [
                {
                    "url": "http://www.cbs.dtu.dk/services/NetPicoRNA/instructions.php",
                    "type": [
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            ],
            "publication": [
                {
                    "doi": "10.1002/pro.5560051107",
                    "pmid": "8931139",
                    "pmcid": "PMC2143287",
                    "type": [
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                    "version": null,
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                    "metadata": {
                        "title": "Cleavage site analysis in picornaviral polyproteins: Discovering cellular targets by neural networks",
                        "abstract": "Picornaviral proteinases are responsible for maturation cleavages of the viral polyprotein, but also catalyze the degradation of cellular targets. Using graphical visualization techniques and neural network algorithms, we have investigated the sequence specificity of the two proteinases 2A(pro) and 3C(pro). The cleavage of VP0 (giving rise to VP2 and VP4), which is carried out by a so-far unknown proteinase, was also examined. In combination with a novel surface exposure prediction algorithm, our neural network approach successfully distinguishes known cleavage sites from noncleavage sites and yields a more consistent definition of features common to these sites. The method is able to predict experimentally determined cleavage sites in cellular proteins. We present a list of mammalian and other proteins that are predicted to be possible targets for the vital proteinases. Whether these proteins are indeed cleaved awaits experimental verification. Additionally, we report several errors detected in the protein databases.",
                        "date": "1996-01-01T00:00:00Z",
                        "citationCount": 204,
                        "authors": [
                            {
                                "name": "Blom N."
                            },
                            {
                                "name": "Hansen J."
                            },
                            {
                                "name": "Blaas D."
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                            {
                                "name": "Brunak S."
                            }
                        ],
                        "journal": "Protein Science"
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                }
            ],
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                },
                {
                    "name": "Nikolaj Sorgenfrei Blom",
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        },
        {
            "name": "SLiM",
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                {
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                            "term": "DNA substitution modelling"
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                        {
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                            "term": "Sequence generation"
                        },
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                            "uri": "http://edamontology.org/operation_3946",
                            "term": "Ecological modelling"
                        }
                    ],
                    "input": [],
                    "output": [],
                    "note": "Run individual-based eco-evolutionary simulations with explicit genetics",
                    "cmd": null
                }
            ],
            "toolType": [
                "Command-line tool",
                "Desktop application"
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            "topic": [
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                    "uri": "http://edamontology.org/topic_0610",
                    "term": "Ecology"
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                {
                    "uri": "http://edamontology.org/topic_0602",
                    "term": "Molecular interactions, pathways and networks"
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                    "uri": "http://edamontology.org/topic_0199",
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            "link": [
                {
                    "url": "https://messerlab.org/slim/",
                    "type": [
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                    "note": "SLiM home page in the Messer Lab website"
                },
                {
                    "url": "https://github.com/MesserLab/SLiM",
                    "type": [
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                    "note": "GitHub repository for SLiM"
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                {
                    "url": "https://groups.google.com/g/slim-discuss",
                    "type": [
                        "Discussion forum"
                    ],
                    "note": "Discussion forum for SLiM questions"
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                {
                    "url": "https://groups.google.com/g/slim-announce",
                    "type": [
                        "Mailing list"
                    ],
                    "note": "Announcements mailing list"
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            ],
            "download": [
                {
                    "url": "http://benhaller.com/slim/SLiM.zip",
                    "type": "Source code",
                    "note": "A source archive for the command-line `slim` tool only.  Complete source code is on GitHub, but most platforms have an installer anyway; see the manual, chapter 2, for installation instructions.",
                    "version": null
                },
                {
                    "url": "https://github.com/MesserLab/SLiM/releases/latest",
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            ],
            "documentation": [
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                    "url": "http://benhaller.com/slim/SLiM_Manual.pdf",
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                },
                {
                    "url": "http://benhaller.com/slim/Eidos_Manual.pdf",
                    "type": [
                        "User manual"
                    ],
                    "note": "The manual for Eidos, the scripting language used by SLiM"
                },
                {
                    "url": "http://benhaller.com/slim/SLiMEidosRefSheets.zip",
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                    "note": "Quick reference sheets for SLiM and Eidos"
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                {
                    "doi": "10.1093/molbev/msy228",
                    "pmid": "30517680",
                    "pmcid": "PMC6389312",
                    "type": [
                        "Other"
                    ],
                    "version": null,
                    "note": "B.C. Haller, P.W. Messer. (2019). SLiM 3: Forward genetic simulations beyond the Wright–Fisher Model. Molecular Biology and Evolution 36(3), 632–637.",
                    "metadata": {
                        "title": "SLiM 3: Forward Genetic Simulations Beyond the Wright-Fisher Model",
                        "abstract": "With the desire to model population genetic processes under increasingly realistic scenarios, forward genetic simulations have become a critical part of the toolbox of modern evolutionary biology. The SLiM forward genetic simulation framework is one of the most powerful and widely used tools in this area. However, its foundation in the Wright-Fisher model has been found to pose an obstacle to implementing many types of models; it is difficult to adapt the Wright-Fisher model, with its many assumptions, to modeling ecologically realistic scenarios such as explicit space, overlapping generations, individual variation in reproduction, density-dependent population regulation, individual variation in dispersal or migration, local extinction and recolonization, mating between subpopulations, age structure, fitness-based survival and hard selection, emergent sex ratios, and so forth. In response to this need, we here introduce SLiM 3, which contains two key advancements aimed at abolishing these limitations. First, the new non-Wright-Fisher or \"nonWF\" model type provides a much more flexible foundation that allows the easy implementation of all of the above scenarios and many more. Second, SLiM 3 adds support for continuous space, including spatial interactions and spatial maps of environmental variables. We provide a conceptual overview of these new features, and present several example models to illustrate their use.",
                        "date": "2019-03-01T00:00:00Z",
                        "citationCount": 504,
                        "authors": [
                            {
                                "name": "Haller B.C."
                            },
                            {
                                "name": "Messer P.W."
                            }
                        ],
                        "journal": "Molecular Biology and Evolution"
                    }
                },
                {
                    "doi": "10.1093/molbev/msy237",
                    "pmid": "30590560",
                    "pmcid": "PMC6501880",
                    "type": [
                        "Usage"
                    ],
                    "version": null,
                    "note": "B.C. Haller, P.W. Messer. (2019). Evolutionary modeling in SLiM 3 for beginners. Molecular Biology and Evolution 36(5), 1101–1109.",
                    "metadata": {
                        "title": "Evolutionary Modeling in SLiM 3 for Beginners",
                        "abstract": "The SLiM forward genetic simulation framework has proved to be a powerful and flexible tool for population genetic modeling. However, as a complex piece of software with many features that allow simulating a diverse assortment of evolutionary models, its initial learning curve can be difficult. Here we provide a step-by-step demonstration of how to build a simple evolutionary model in SLiM 3, to help new users get started. We will begin with a panmictic neutral model, and build up to a model of the evolution of a polygenic quantitative trait under selection for an environmental phenotypic optimum.",
                        "date": "2019-05-01T00:00:00Z",
                        "citationCount": 12,
                        "authors": [
                            {
                                "name": "Haller B.C."
                            },
                            {
                                "name": "Messer P.W."
                            }
                        ],
                        "journal": "Molecular Biology and Evolution"
                    }
                },
                {
                    "doi": "10.1111/1755-0998.12968",
                    "pmid": "30565882",
                    "pmcid": "PMC6393187",
                    "type": [
                        "Method"
                    ],
                    "version": null,
                    "note": "B.C. Haller, J. Galloway, J. Kelleher, P.W. Messer, P.L. Ralph. (2019). Tree-sequence recording in SLiM opens new horizons for forward-time simulation of whole genomes. Molecular Ecology Resources 19(2), 552–566.",
                    "metadata": {
                        "title": "Tree-sequence recording in SLiM opens new horizons for forward-time simulation of whole genomes",
                        "abstract": "There is an increasing demand for evolutionary models to incorporate relatively realistic dynamics, ranging from selection at many genomic sites to complex demography, population structure, and ecological interactions. Such models can generally be implemented as individual-based forward simulations, but the large computational overhead of these models often makes simulation of whole chromosome sequences in large populations infeasible. This situation presents an important obstacle to the field that requires conceptual advances to overcome. The recently developed tree-sequence recording method (Kelleher, Thornton, Ashander, & Ralph, 2018), which stores the genealogical history of all genomes in the simulated population, could provide such an advance. This method has several benefits: (1) it allows neutral mutations to be omitted entirely from forward-time simulations and added later, thereby dramatically improving computational efficiency; (2) it allows neutral burn-in to be constructed extremely efficiently after the fact, using “recapitation”; (3) it allows direct examination and analysis of the genealogical trees along the genome; and (4) it provides a compact representation of a population's genealogy that can be analysed in Python using the msprime package. We have implemented the tree-sequence recording method in SLiM 3 (a free, open-source evolutionary simulation software package) and extended it to allow the recording of non-neutral mutations, greatly broadening the utility of this method. To demonstrate the versatility and performance of this approach, we showcase several practical applications that would have been beyond the reach of previously existing methods, opening up new horizons for the modelling and exploration of evolutionary processes.",
                        "date": "2019-03-01T00:00:00Z",
                        "citationCount": 109,
                        "authors": [
                            {
                                "name": "Haller B.C."
                            },
                            {
                                "name": "Galloway J."
                            },
                            {
                                "name": "Kelleher J."
                            },
                            {
                                "name": "Messer P.W."
                            },
                            {
                                "name": "Ralph P.L."
                            }
                        ],
                        "journal": "Molecular Ecology Resources"
                    }
                },
                {
                    "doi": "10.1086/723601",
                    "pmid": "37130229",
                    "pmcid": "PMC10793872",
                    "type": [
                        "Primary"
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                    "version": null,
                    "note": "B.C. Haller, P.W. Messer. (2023). SLiM 4: Multispecies eco-evolutionary modeling. The American Naturalist 201(5), E127–E139.",
                    "metadata": {
                        "title": "SLiM 4: Multispecies Eco-Evolutionary Modeling",
                        "abstract": "The SLiM software framework for genetically explicit forward simulation has been widely used in population genetics. However, it has been largely restricted to modeling only a single species, which has limited its broader utility in evolutionary biology. Indeed, to our knowledge no general-purpose, flexible modeling framework exists that provides support for simulating multiple species while also providing other key features, such as explicit genetics and continuous space. The lack of such software has limited our ability to model higher biological levels such as communities, eco-systems, coevolutionary and eco-evolutionary processes, and bio-diversity, which is crucial for many purposes, from extending our basic understanding of evolutionary ecology to informing conservation and management decisions. We here announce the release of SLiM 4, which fills this important gap by adding support for multiple species, including ecological interactions between species such as predation, parasitism, and mutualism, and illustrate its new features with examples.",
                        "date": "2023-05-01T00:00:00Z",
                        "citationCount": 79,
                        "authors": [
                            {
                                "name": "Haller B.C."
                            },
                            {
                                "name": "Messer P.W."
                            }
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                        "journal": "American Naturalist"
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                    "input": [
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                },
                {
                    "url": "https://github.com/524D/compareMS2",
                    "type": [
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            ],
            "publication": [
                {
                    "doi": "10.1002/rcm.6162",
                    "pmid": "22368051",
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                    "type": [
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                    "version": "1.0",
                    "note": null,
                    "metadata": {
                        "title": "Molecular phylogenetics by direct comparison of tandem mass spectra",
                        "abstract": "Rationale: Molecular phylogenetics is the study of evolution and relatedness of organisms or genes. Mass spectrometry is used routinely for bacterial identification and has also been used for phylogenetic analysis, for instance from bone material. Unfortunately, only a small fraction of the acquired tandem mass spectra allow direct interpretation. Methods: We describe a new algorithm and software for molecular phylogenetics using pairwise comparisons of tandem mass spectra from enzymatically digested proteins. The spectra need not be annotated and all acquired data is used in the analysis. To demonstrate the method, we analyzed tryptic digests of sera from four great apes and two other primates. Results: The distribution of spectra dot products for thousands of tandem mass spectra collected from two samples provides a measure on the fraction of shared peptides between the two samples. When inverted, this becomes a distance metric. By pairwise comparison between species and averaging over four individuals per species, it was possible to reconstruct the unique correct phylogenetic tree for the great apes and other primates. Conclusions: The new method described here has several attractive features compared with existing methods, among them simplicity, the unbiased use of all acquired data rather than a small subset of spectra, and the potential use of heavily degraded proteins or proteins with a priori unknown modifications. © 2012 John Wiley & Sons, Ltd.",
                        "date": "2012-04-15T00:00:00Z",
                        "citationCount": 30,
                        "authors": [
                            {
                                "name": "Palmblad M."
                            },
                            {
                                "name": "Deelder A.M."
                            }
                        ],
                        "journal": "Rapid Communications in Mass Spectrometry"
                    }
                },
                {
                    "doi": "10.1021/acs.jproteome.2c00457",
                    "pmid": "36173614",
                    "pmcid": "PMC9903320",
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                    ],
                    "version": "2.0",
                    "note": null,
                    "metadata": {
                        "title": "compareMS2 2.0: An Improved Software for Comparing Tandem Mass Spectrometry Datasets",
                        "abstract": "It has long been known that biological species can be identified from mass spectrometry data alone. Ten years ago, we described a method and software tool, compareMS2, for calculating a distance between sets of tandem mass spectra, as routinely collected in proteomics. This method has seen use in species identification and mixture characterization in food and feed products, as well as other applications. Here, we present the first major update of this software, including a new metric, a graphical user interface and additional functionality. The data have been deposited to ProteomeXchange with dataset identifier PXD034932.",
                        "date": "2023-02-03T00:00:00Z",
                        "citationCount": 7,
                        "authors": [
                            {
                                "name": "Marissen R."
                            },
                            {
                                "name": "Varunjikar M.S."
                            },
                            {
                                "name": "Laros J.F.J."
                            },
                            {
                                "name": "Rasinger J.D."
                            },
                            {
                                "name": "Neely B.A."
                            },
                            {
                                "name": "Palmblad M."
                            }
                        ],
                        "journal": "Journal of Proteome Research"
                    }
                },
                {
                    "doi": "10.1021/acs.jproteome.1c00528",
                    "pmid": "34523928",
                    "pmcid": "PMC8491155",
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                    "metadata": {
                        "title": "Rewinding the Molecular Clock: Looking at Pioneering Molecular Phylogenetics Experiments in the Light of Proteomics",
                        "abstract": "Science is full of overlooked and undervalued research waiting to be rediscovered. Proteomics is no exception. In this perspective, we follow the ripples from a 1960 study of Zuckerkandl, Jones, and Pauling comparing tryptic peptides across animal species. This pioneering work directly led to the molecular clock hypothesis and the ensuing explosion in molecular phylogenetics. In the decades following, proteins continued to provide essential clues on evolutionary history. While technology has continued to improve, contemporary proteomics has strayed from this larger biological context, rarely comparing species or asking how protein structure, function, and interactions have evolved. Here we recombine proteomics with molecular phylogenetics, highlighting the value of framing proteomic results in a larger biological context and how almost forgotten research, though technologically surpassed, can still generate new ideas and illuminate our work from a different perspective. Though it is infeasible to read all research published on a large topic, looking up older papers can be surprisingly rewarding when rediscovering a \"gem\"at the end of a long citation chain, aided by digital collections and perpetually helpful librarians. Proper literature study reduces unnecessary repetition and allows research to be more insightful and impactful by truly standing on the shoulders of giants. All data was uploaded to MassIVE (https://massive.ucsd.edu/) as dataset MSV000087993.",
                        "date": "2021-10-01T00:00:00Z",
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                        "authors": [
                            {
                                "name": "Neely B.A."
                            },
                            {
                                "name": "Palmblad M."
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                        "title": "PLAZA 4.0: An integrative resource for functional, evolutionary and comparative plant genomics",
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                            {
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                                "name": "Vancaester E."
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                            {
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                        "title": "MuDoGeR: Multi-Domain Genome recovery from metagenomes made easy",
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                                "name": "Rocha U."
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                                "name": "CoelhoKasmanas J."
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                                "name": "Kallies R."
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                    "term": "Protein folds and structural domains"
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                    "term": "Protein secondary structure"
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                    "term": "Protein folding, stability and design"
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                    "metadata": {
                        "title": "The PSIPRED protein structure prediction server",
                        "abstract": "The PSIPRED protein structure prediction server allows users to submit a protein sequence, perform a prediction of their choice and receive the results of the prediction both textually via e-mail and graphically via the web. The user may select one of three prediction methods to apply to their sequence: PSIPRED, a highly accurate secondary structure prediction method; MEMSAT 2, a new version of a widely used transmembrane topology prediction method; or GenTHREADER, a sequence profile based fold recognition method. Availability: Freely available to non-commercial users at http://globin.bio.warwick.ac.uk/psipred/.",
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                        "authors": [
                            {
                                "name": "McGuffin L.J."
                            },
                            {
                                "name": "Bryson K."
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                            {
                                "name": "Jones D.T."
                            }
                        ],
                        "journal": "Bioinformatics"
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                },
                {
                    "doi": "10.1006/jmbi.1999.3091",
                    "pmid": "10493868",
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                    "metadata": {
                        "title": "Protein secondary structure prediction based on position-specific scoring matrices",
                        "abstract": "A two-stage neural network has been used to predict protein secondary structure based on the position specific scoring matrices generated by PSI-BLAST. Despite the simplicity and convenience of the approach used, the results are found to be superior to those produced by other methods, including the popular PHD method according to our own benchmarking results and the results from the recent Critical Assessment of Techniques for Protein Structure Prediction experiment (CASP3), where the method was evaluated by stringent blind testing. Using a new testing set based on a set of 187 unique folds, and three-way cross-validation based on structural similarity criteria rather than sequence similarity criteria used previously (no similar folds were present in both the testing and training sets) the method presented here (PSIPRED) achieved an average Q3 score of between 76.5% to 78.3% depending on the precise definition of observed secondary structure used, which is the highest published score for any method to date. Given the success of the method in CASP3, it is reasonable to be confident that the evaluation presented here gives a fair indication of the performance of the method in general.",
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                    "pmid": "23748958",
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                    "type": [],
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                    "note": null,
                    "metadata": {
                        "title": "Scalable web services for the PSIPRED Protein Analysis Workbench.",
                        "abstract": "Here, we present the new UCL Bioinformatics Group's PSIPRED Protein Analysis Workbench. The Workbench unites all of our previously available analysis methods into a single web-based framework. The new web portal provides a greatly streamlined user interface with a number of new features to allow users to better explore their results. We offer a number of additional services to enable computationally scalable execution of our prediction methods; these include SOAP and XML-RPC web server access and new HADOOP packages. All software and services are available via the UCL Bioinformatics Group website at http://bioinf.cs.ucl.ac.uk/.",
                        "date": "2013-01-01T00:00:00Z",
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                        "authors": [
                            {
                                "name": "Buchan D.W."
                            },
                            {
                                "name": "Minneci F."
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                            {
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                            },
                            {
                                "name": "Bryson K."
                            },
                            {
                                "name": "Jones D.T."
                            }
                        ],
                        "journal": "Nucleic acids research"
                    }
                }
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                    "name": "psipred team",
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            "name": "neXtProt",
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                            "term": "Protein sequence analysis"
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                    "term": "Proteins"
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                    "uri": "http://edamontology.org/topic_0601",
                    "term": "Protein modifications"
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                    "term": "Protein variants"
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                    "url": "https://twitter.com/nextprot_news",
                    "type": [
                        "Social media"
                    ],
                    "note": "neXtProt release news, publications, presentations, tips and more. DM us with feedback!"
                },
                {
                    "url": "https://www.expasy.org/resources/nextprot",
                    "type": [
                        "Software catalogue"
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                    "note": "neXtProt entry in Expasy"
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                    "doi": "10.1093/nar/gkz995",
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                    "metadata": {
                        "title": "The neXtProt knowledgebase in 2020: Data, tools and usability improvements",
                        "abstract": "The neXtProt knowledgebase (https://www.nextprot.org) is an integrative resource providing both data on human protein and the tools to explore these. In order to provide comprehensive and up-to-date data, we evaluate and add new data sets. We describe the incorporation of three new data sets that provide expression, function, protein-protein binary interaction, post-translational modifications (PTM) and variant information. New SPARQL query examples illustrating uses of the new data were added. neXtProt has continued to develop tools for proteomics. We have improved the peptide uniqueness checker and have implemented a new protein digestion tool. Together, these tools make it possible to determine which proteases can be used to identify trypsin-resistant proteins by mass spectrometry. In terms of usability, we have finished revamping our web interface and completely rewritten our API. Our SPARQL endpoint now supports federated queries. All the neXtProt data are available via our user interface, API, SPARQL endpoint and FTP site, including the new PEFF 1.0 format files. Finally, the data on our FTP site is now CC BY 4.0 to promote its reuse.",
                        "date": "2020-01-01T00:00:00Z",
                        "citationCount": 155,
                        "authors": [
                            {
                                "name": "Zahn-Zabal M."
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                            {
                                "name": "Michel P.-A."
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                            {
                                "name": "Gateau A."
                            },
                            {
                                "name": "Nikitin F."
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                            {
                                "name": "Schaeffer M."
                            },
                            {
                                "name": "Audot E."
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                            {
                                "name": "Gaudet P."
                            },
                            {
                                "name": "Duek P.D."
                            },
                            {
                                "name": "Teixeira D."
                            },
                            {
                                "name": "De Laval V.R."
                            },
                            {
                                "name": "Samarasinghe K."
                            },
                            {
                                "name": "Bairoch A."
                            },
                            {
                                "name": "Lane L."
                            }
                        ],
                        "journal": "Nucleic Acids Research"
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                    "doi": "10.1093/nar/gkr1179",
                    "pmid": "22139911",
                    "pmcid": "PMC3245017",
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                        "Primary"
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                    "version": null,
                    "note": null,
                    "metadata": {
                        "title": "NeXtProt: A knowledge platform for human proteins",
                        "abstract": "neXtProt (http://www.nextprot.org/) is a new human protein-centric knowledge platform. Developed at the Swiss Institute of Bioinformatics (SIB), it aims to help researchers answer questions relevant to human proteins. To achieve this goal, neXtProt is built on a corpus containing both curated knowledge originating from the UniProtKB/Swiss-Prot knowledgebase and carefully selected and filtered high-throughput data pertinent to human proteins. This article presents an overview of the database and the data integration process. We also lay out the key future directions of neXtProt that we consider the necessary steps to make neXtProt the one-stop-shop for all research projects focusing on human proteins. © The Author(s) 2011.",
                        "date": "2012-01-01T00:00:00Z",
                        "citationCount": 168,
                        "authors": [
                            {
                                "name": "Lane L."
                            },
                            {
                                "name": "Argoud-Puy G."
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                            {
                                "name": "Britan A."
                            },
                            {
                                "name": "Cusin I."
                            },
                            {
                                "name": "Duek P.D."
                            },
                            {
                                "name": "Evalet O."
                            },
                            {
                                "name": "Gateau A."
                            },
                            {
                                "name": "Gaudet P."
                            },
                            {
                                "name": "Gleizes A."
                            },
                            {
                                "name": "Masselot A."
                            },
                            {
                                "name": "Zwahlen C."
                            },
                            {
                                "name": "Bairoch A."
                            }
                        ],
                        "journal": "Nucleic Acids Research"
                    }
                }
            ],
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                {
                    "name": "SIB Swiss Institute of Bioinformatics",
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                    "name": "Pascale Gaudet",
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        {
            "name": "csdR",
            "description": "Differential gene coexpression analysis based on the Conserved, Specific, and Differentiated (CSD) method",
            "homepage": "https://almaaslab.github.io/csdR/",
            "biotoolsID": "csdr",
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            "topic": [
                {
                    "uri": "http://edamontology.org/topic_0204",
                    "term": "Gene regulation"
                },
                {
                    "uri": "http://edamontology.org/topic_0085",
                    "term": "Functional genomics"
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                "Windows"
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            "link": [
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                    "url": "https://www.bioconductor.org/packages/release/bioc/html/csdR.html",
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                },
                {
                    "url": "https://github.com/AlmaasLab/csdR",
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            "publication": [
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                    "doi": "10.1186/s12859-022-04605-1",
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                    "type": [
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                    "version": null,
                    "note": null,
                    "metadata": {
                        "title": "csdR, an R package for differential co-expression analysis",
                        "abstract": "Background: Differential co-expression network analysis has become an important tool to gain understanding of biological phenotypes and diseases. The CSD algorithm is a method to generate differential co-expression networks by comparing gene co-expressions from two different conditions. Each of the gene pairs is assigned conserved (C), specific (S) and differentiated (D) scores based on the co-expression of the gene pair between the two conditions. The result of the procedure is a network where the nodes are genes and the links are the gene pairs with the highest C-, S-, and D-scores. However, the existing CSD-implementations suffer from poor computational performance, difficult user procedures and lack of documentation. Results: We created the R-package csdR aimed at reaching good performance together with ease of use, sufficient documentation, and with the ability to play well with other tools for data analysis. csdR was benchmarked on a realistic dataset with 20,645 genes. After verifying that the chosen number of iterations gave sufficient robustness, we tested the performance against the two existing CSD implementations. csdR was superior in performance to one of the implementations, whereas the other did not run. Our implementation can utilize multiple processing cores. However, we were unable to achieve more than ∼ 2.7 parallel speedup with saturation reached at about 10 cores. Conclusion: The results suggest that csdR is a useful tool for differential co-expression analysis and is able to generate robust results within a workday on datasets of realistic sizes when run on a workstation or compute server.",
                        "date": "2022-12-01T00:00:00Z",
                        "citationCount": 3,
                        "authors": [
                            {
                                "name": "Pettersen J.P."
                            },
                            {
                                "name": "Almaas E."
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                        ],
                        "journal": "BMC Bioinformatics"
                    }
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        {
            "name": "WeSA",
            "description": "WeSA, (weighted socioaffinity), is a statistical score which can rank results from protein experiments of the bait-prey type, e.g. affinity purification, immunoprecipitation or proximity labelling.\n\nYou can enter lists of interacting proteins according to the results of your experiment. Input your raw data before any filtering is done.\n\nAs a result you will get a re-ordered list of scores which allows one to understand which interactions are more likely than others based on what previous experiments can add to your data.",
            "homepage": "https://wesa.russelllab.org/",
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                    "uri": "http://edamontology.org/topic_0121",
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                },
                {
                    "uri": "http://edamontology.org/topic_3957",
                    "term": "Protein interaction experiment"
                }
            ],
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                "Mac",
                "Linux",
                "Windows"
            ],
            "language": [
                "Python"
            ],
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            "cost": "Free of charge",
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            ],
            "download": [],
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                {
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                        "User manual"
                    ],
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                }
            ],
            "publication": [
                {
                    "doi": "10.1093/nar/gkae423",
                    "pmid": "38795065",
                    "pmcid": "PMC11223876",
                    "type": [],
                    "version": null,
                    "note": null,
                    "metadata": {
                        "title": "WeSA: A web server for improving analysis of affinity proteomics data",
                        "abstract": "Protein-protein interaction experiments still yield many false positive interactions. The socioaffinity metric can distinguish true protein-protein interactions from noise based on available data. Here, we present WeSA (Weighted SocioAffinity), which considers large datasets of interaction proteomics data (IntAct, BioGRID, the BioPlex) to score human protein interactions and, in a statistically robust way, flag those (even from a single experiment) that are likely to be false positives. ROC analysis (using CORUM-PDB positives and Negatome negatives) shows that WeSA improves over other measures of interaction confidence. WeSA shows consistently good results over all datasets (up to: AUC = 0.93 and at best threshold: TPR = 0.84, FPR = 0.11, Precision = 0.98). WeSA is freely available without login (wesa.russelllab.org). Users can submit their own data or look for organized information on human protein interactions using the web server. Users can either retrieve available information for a list of proteins of interest or calculate scores for new experiments. The server outputs either pre-computed or updated WeSA scores for the input enriched with information from databases. The summary is presented as a table and a network-based visualization allowing the user to remove those nodes/edges that the method considers spurious.",
                        "date": "2024-07-05T00:00:00Z",
                        "citationCount": 1,
                        "authors": [
                            {
                                "name": "Shtetinska M.M."
                            },
                            {
                                "name": "Gonzalez-Sanchez J.-C."
                            },
                            {
                                "name": "Beyer T."
                            },
                            {
                                "name": "Boldt K."
                            },
                            {
                                "name": "Ueffing M."
                            },
                            {
                                "name": "Russell R.B."
                            }
                        ],
                        "journal": "Nucleic Acids Research"
                    }
                }
            ],
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        {
            "name": "ChemFH",
            "description": "An integrated online platform developed for the screening and prediction of potential frequent drug hitters, thus improving the efficiency of drug R&D in colloidal aggregate, firefly luciferase reporter enzyme inhibition, fluorescence, chemical reactivity, and promiscuity. ChemFH: an integrated tool for screening frequent false positives in chemical biology and drug discovery.",
            "homepage": "https://chemfh.scbdd.com/",
            "biotoolsID": "chemfh",
            "biotoolsCURIE": "biotools:chemfh",
            "version": [
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                {
                    "operation": [
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                            "uri": "http://edamontology.org/operation_3938",
                            "term": "Virtual screening"
                        }
                    ],
                    "input": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_2301",
                                "term": "SMILES string"
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                    ],
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                        "title": "Gene coexpression analysis in Arabidopsis thaliana based on public microarray data",
                        "abstract": "Coexpressed genes tend to participate in related biological processes. Gene coexpression analysis allows the discovery of functional gene partners or the assignment of biological roles to genes of unknown function. In this protocol, we describe the steps necessary to create a gene coexpression tree for Arabidopsis thaliana, using publicly available Affymetrix CEL microarray data. Because the computational analysis described here is highly dependent on sample quality, we detail an automatic quality control approach. For complete details on the use and execution of this protocol, please refer to Zogopoulos et al. (2021).",
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                        "title": "Approaches in Gene Coexpression Analysis in Eukaryotes",
                        "abstract": "Gene coexpression analysis constitutes a widely used practice for gene partner identification and gene function prediction, consisting of many intricate procedures. The analysis begins with the collection of primary transcriptomic data and their preprocessing, continues with the calculation of the similarity between genes based on their expression values in the selected sample dataset and results in the construction and visualisation of a gene coexpression network (GCN) and its evaluation using biological term enrichment analysis. As gene coexpression analysis has been studied ex-tensively, we present most parts of the methodology in a clear manner and the reasoning behind the selection of some of the techniques. In this review, we offer a comprehensive and comprehensi-ble account of the steps required for performing a complete gene coexpression analysis in eukary-otic organisms. We comment on the use of RNA‐Seq vs. microarrays, as well as the best practices for GCN construction. Furthermore, we recount the most popular webtools and standalone applications performing gene coexpression analysis, with details on their methods, features and outputs.",
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                        "title": "Arabidopsis Co-expression Tool (ACT): Web server tools for microarray-based gene expression analysis",
                        "abstract": "The Arabidopsis Co-expression Tool, ACT, ranks the genes across a large microarray dataset according to how closely their expression follows the expression of a query gene. A database stores pre-calculated co-expression results for ∼21 800 genes based on data from over 300 arrays. These results can be corroborated by calculation of co-expression results for user-defined sub-sets of arrays or experiments from the NASC/GARNet array dataset. Clique Finder (CF) identifies groups of genes which are consistently co-expressed with each other across a user-defined co-expression list. The parameters can be altered easily to adjust cluster size and the output examined for optimal inclusion of genes with known biological roles. Alternatively, a Scatter Plot tool displays the correlation coefficients for all genes against two user-selected queries on a scatter plot which can be useful for visual identification of clusters of genes with similar r-values. User-input groups of genes can be highlighted on the scatter plots. Inclusion of genes with known biology in sets of genes identified using CF and Scatter Plot tools allows inferences to be made about the roles of the other genes in the set and both tools can therefore be used to generate short lists of genes for further characterization. ACT is freely available at www.Arabidopsis.leeds.ac.uk/ACT. © The Author 2006. Published by Oxford University Press. All rights reserved.",
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                                "name": "Manfield I.W."
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                                "name": "Jen C.-H."
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                                "name": "Michalopoulos I."
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                        "title": "The Arabidopsis co-expression tool (ACT): A WWW-based tool and database for microarray-based gene expression analysis",
                        "abstract": "We present a new WWW-based tool for plant gene analysis, the Arabidopsis Co-Expression Tool (ACT), based on a large Arabidopsis thaliana microarray data set obtained from the Nottingham Arabidopsis Stock Centre. The co-expression analysis tool allows users to identify genes whose expression patterns are correlated across selected experiments or the complete data set. Results are accompanied by estimates of the statistical significance of the correlation relationships, expressed as probability (P) and expectation (E) values. Additionally, highly ranked genes on a correlation list can be examined using the novel CLIQUE FINDER tool to determine the sets of genes most likely to be regulated in a similar manner. In combination, these tools offer three levels of analysis: creation of correlation lists of co-expressed genes, refinement of these lists using two-dimensional scatter plots, and dissection into cliques of co-regulated genes. We illustrate the applications of the software by analysing genes encoding functionally related proteins, as well as pathways involved in plant responses to environmental stimuli. These analyses demonstrate novel biological relationships underlying the observed gene co-expression patterns. To demonstrate the ability of the software to develop testable hypotheses on gene function within a defined biological process we have used the example of cell wall biosynthesis genes. The resource is freely available at http://www.arabidopsis.leeds.ac.uk/ACT/. © 2006 The Authors.",
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                        "title": "Arabidopsis Coexpression Tool: a tool for gene coexpression analysis in Arabidopsis thaliana",
                        "abstract": "Gene coexpression analysis refers to the discovery of sets of genes which exhibit similar expression patterns across multiple transcriptomic data sets, such as microarray experiment data of public repositories. Arabidopsis Coexpression Tool (ACT), a gene coexpression analysis web tool for Arabidopsis thaliana, identifies genes which are correlated to a driver gene. Primary microarray data from ATH1 Affymetrix platform were processed with Single-Channel Array Normalization algorithm and combined to produce a coexpression tree which contains ∼21,000 A. thaliana genes. ACT was developed to present subclades of coexpressed genes, as well as to perform gene set enrichment analysis, being unique in revealing enriched transcription factors targeting coexpressed genes. ACT offers a simple and user-friendly interface producing working hypotheses which can be experimentally verified for the discovery of gene partnership, pathway membership, and transcriptional regulation. ACT analyses have been successful in identifying not only genes with coordinated ubiquitous expressions but also genes with tissue-specific expressions.",
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                                "name": "Zogopoulos V.L."
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                                "name": "Saxami G."
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