{"entity": "journal", "iuid": "1bef6fe554514f808e043f191dc82c4e", "timestamp": "2026-08-08T15:40:36.120Z", "links": {"self": {"href": "https://publications.scilifelab.se/journal/Computational%20and%20Structural%20Biotechnology%20Journal.json"}, "display": {"href": "https://publications.scilifelab.se/journal/Computational%20and%20Structural%20Biotechnology%20Journal"}}, "title": "Computational and Structural Biotechnology Journal", "issn": "2001-0370", "issn-l": "2001-0370", "publications_count": 3, "publications": [{"entity": "publication", "iuid": "ca23b1230056405c893bae33407679c4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ca23b1230056405c893bae33407679c4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ca23b1230056405c893bae33407679c4"}}, "title": "Designing custom CRISPR libraries for hypothesis-driven drug target discovery.", "authors": [{"family": "Iyer", "given": "Vaishnavi Srinivasan", "initials": "VS"}, {"family": "Jiang", "given": "Long", "initials": "L", "orcid": "0000-0002-8720-8992", "researcher": {"href": "https://publications.scilifelab.se/researcher/1d46414099a14d3ba156b86e18ff9a97.json"}}, {"family": "Shen", "given": "Yunbing", "initials": "Y"}, {"family": "Boddul", "given": "Sanjaykumar V", "initials": "SV"}, {"family": "Panda", "given": "Sudeepta Kumar", "initials": "SK"}, {"family": "Kasza", "given": "Zsolt", "initials": "Z"}, {"family": "Schmierer", "given": "Bernhard", "initials": "B", "orcid": "0000-0002-9082-7022", "researcher": {"href": "https://publications.scilifelab.se/researcher/d3ee96f9eb454850be6db3318b28479f.json"}}, {"family": "Wermeling", "given": "Fredrik", "initials": "F", "orcid": "0000-0001-9633-677X", "researcher": {"href": "https://publications.scilifelab.se/researcher/a34df8186ba24df3b14fe9743cf546b4.json"}}], "type": "journal article", "published": "2020-08-18", "journal": {"title": "Computational and Structural Biotechnology Journal", "issn": "2001-0370", "volume": "18", "issue": null, "pages": "2237-2246", "issn-l": "2001-0370"}, "abstract": "Over the last decade Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) has been developed into a potent molecular biology tool used to rapidly modify genes or their expression in a multitude of ways. In parallel, CRISPR-based screening approaches have been developed as powerful discovery platforms for dissecting the genetic basis of cellular behavior, as well as for drug target discovery. CRISPR screens can be designed in numerous ways. Here, we give a brief background to CRISPR screens and discuss the pros and cons of different design approaches, including unbiased genome-wide screens that target all known genes, as well as hypothesis-driven custom screens in which selected subsets of genes are targeted (Fig. 1). We provide several suggestions for how a custom screen can be designed, which could broadly serve as inspiration for any experiment that includes candidate gene selection. Finally, we discuss how results from CRISPR screens could be translated into drug development, as well as future trends we foresee in the rapidly evolving CRISPR screen field.", "doi": "10.1016/j.csbj.2020.08.009", "pmid": "32952937", "labels": {"CRISPR Functional Genomics": "Collaborative", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S2001-0370(20)30362-7"}, {"db": "pmc", "key": "PMC7479249"}], "notes": [], "created": "2020-11-10T16:34:04.296Z", "modified": "2024-01-16T13:48:41.924Z"}, {"entity": "publication", "iuid": "a3e86d61c33c4ce1847b11a113c5be8e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a3e86d61c33c4ce1847b11a113c5be8e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a3e86d61c33c4ce1847b11a113c5be8e"}}, "title": "Optimizing cultivation of Cordyceps militaris for fast growth and cordycepin overproduction using rational design of synthetic media.", "authors": [{"family": "Raethong", "given": "Nachon", "initials": "N"}, {"family": "Wang", "given": "Hao", "initials": "H"}, {"family": "Nielsen", "given": "Jens", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a596e289be4438a8a2653b1f25fea8b.json"}}, {"family": "Vongsangnak", "given": "Wanwipa", "initials": "W"}], "type": "journal article", "published": "2019-11-26", "journal": {"volume": "18", "issn": "2001-0370", "issue": null, "pages": "1-8", "title": "Computational and Structural Biotechnology Journal", "issn-l": "2001-0370"}, "abstract": "Cordyceps militaris is an entomopathogenic fungus which is often used in Asia as a traditional medicine developed from age-old wisdom. Presently, cordycepin from C. militaris is a great interest in medicinal applications. However, cellular growth of C. militaris and the association with cordycepin production remain poorly understood. To explore the metabolism of C. militaris as potential cell factories in medical and biotechnology applications, this study developed a high-quality genome-scale metabolic model of C. militaris, iNR1329, based on its genomic content and physiological data. The model included a total of 1329 genes, 1821 biochemical reactions, and 1171 metabolites among 4 different cellular compartments. Its in silico growth simulation results agreed well with experimental data on different carbon sources. iNR1329 was further used for optimizing the growth and cordycepin overproduction using a novel approach, POPCORN, for rational design of synthetic media. In addition to the high-quality GEM iNR1329, the presented POPCORN approach was successfully used to rationally design an optimal synthetic medium with C:N ratio of 8:1 for enhancing 3.5-fold increase in cordycepin production. This study thus provides a novel insight into C. militaris physiology and highlights a potential GEM-driven method for synthetic media design and metabolic engineering application. The iNR1329 and the POPCORN approach are available at the GitHub repository: https://github.com/sysbiomics/Cordyceps_militaris-GEM.", "doi": "10.1016/j.csbj.2019.11.003", "pmid": "31890138", "labels": {"Systems Biology": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S2001-0370(19)30354-X"}, {"db": "pmc", "key": "PMC6926140"}], "notes": [], "created": "2020-01-07T14:44:59.925Z", "modified": "2021-07-05T13:05:37.721Z"}, {"entity": "publication", "iuid": "dc6cbf271f4f4b0797348492fd6ae0bd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dc6cbf271f4f4b0797348492fd6ae0bd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dc6cbf271f4f4b0797348492fd6ae0bd"}}, "title": "Copper Chaperone Atox1 Interacts with Cell Cycle Proteins.", "authors": [{"family": "Matson Dzebo", "given": "Maria", "initials": "M"}, {"family": "Blockhuys", "given": "St\u00e9phanie", "initials": "S"}, {"family": "Valenzuela", "given": "Sebastian", "initials": "S"}, {"family": "Celauro", "given": "Emanuele", "initials": "E"}, {"family": "Esbj\u00f6rner", "given": "Elin K", "initials": "EK"}, {"family": "Wittung-Stafshede", "given": "Pernilla", "initials": "P", "orcid": "0000-0003-1058-1964", "researcher": {"href": "https://publications.scilifelab.se/researcher/9016aa00d62f439fb15532a1f4ba814e.json"}}], "type": "journal article", "published": "2018-10-31", "journal": {"title": "Computational and Structural Biotechnology Journal", "issn": "2001-0370", "volume": "16", "issue": null, "pages": "443-449", "issn-l": "2001-0370"}, "abstract": "The anaphase-promoting complex (APC) is involved in several processes in the cell cycle, most prominently it facilitates the separation of the sister chromatids during mitosis, before cell division. Because of the key role in the cell cycle, APC is suggested as a putative target for anticancer agents. We here show that the copper chaperone Atox1, known for shuttling copper in the cytoplasm from Ctr1 to ATP7A/B in the secretory pathway, interacts with several APC subunits. Atox1 interactions with APC subunits were discovered by mass spectrometry of co-immunoprecipitated samples and further confirmed using proximity ligation assays in HEK293T cells. Upon comparing wild-type cells with those in which the Atox1 gene had been knocked out, we found that in the absence of Atox1 protein, cells have prolonged G 2/M phases and a slower proliferation rate. Thus, in addition to copper transport for loading of copper-dependent enzymes, Atox1 may modulate the cell cycle by interacting with APC subunits.", "doi": "10.1016/j.csbj.2018.10.018", "pmid": "30455854", "labels": {"Glycoproteomics and MS Proteomics": "Service"}, "xrefs": [{"db": "pii", "key": "S2001-0370(18)30138-7"}, {"db": "pmc", "key": "PMC6231052"}], "notes": [], "created": "2020-01-30T15:59:55.307Z", "modified": "2024-01-16T13:46:32.131Z"}], "created": "2020-01-07T14:44:59.939Z", "modified": "2020-11-27T13:14:08.595Z"}