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Lilly CM, Kirk D, Pessach IM, Lotun G, Chen O, Lipsky A, Lieder I, Celniker G, Cucchi EW, Blum JM. Application of Machine Learning Models to Biomedical and Information System Signals From Critically Ill Adults. Chest 2024; 165:1139-1148. [PMID: 37923292 DOI: 10.1016/j.chest.2023.10.036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 10/19/2023] [Accepted: 10/21/2023] [Indexed: 11/07/2023] Open
Abstract
BACKGROUND Machine learning (ML)-derived notifications for impending episodes of hemodynamic instability and respiratory failure events are interesting because they can alert physicians in time to intervene before these complications occur. RESEARCH QUESTION Do ML alerts, telemedicine system (TS)-generated alerts, or biomedical monitors (BMs) have superior performance for predicting episodes of intubation or administration of vasopressors? STUDY DESIGN AND METHODS An ML algorithm was trained to predict intubation and vasopressor initiation events among critically ill adults. Its performance was compared with BM alarms and TS alerts. RESULTS ML notifications were substantially more accurate and precise, with 50-fold lower alarm burden than TS alerts for predicting vasopressor initiation and intubation events. ML notifications of internal validation cohorts demonstrated similar performance for independent academic medical center external validation and COVID-19 cohorts. Characteristics were also measured for a control group of recent patients that validated event detection methods and compared TS alert and BM alarm performance. The TS test characteristics were substantially better, with 10-fold less alarm burden than BM alarms. The accuracy of ML alerts (0.87-0.94) was in the range of other clinically actionable tests; the accuracy of TS (0.28-0.53) and BM (0.019-0.028) alerts were not. Overall test performance (F scores) for ML notifications were more than fivefold higher than for TS alerts, which were higher than those of BM alarms. INTERPRETATION ML-derived notifications for clinically actioned hemodynamic instability and respiratory failure events represent an advance because the magnitude of the differences of accuracy, precision, misclassification rate, and pre-event lead time is large enough to allow more proactive care and has markedly lower frequency and interruption of bedside physician work flows.
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Affiliation(s)
- Craig M Lilly
- Department of Medicine, UMass Memorial Medical Center, Worcester, MA; UMass Memorial Health, UMass Memorial Medical Center, Worcester, MA; Department of Anesthesiology and Surgery, University of Massachusetts, Worcester, MA; University of Massachusetts Chan Medical School, University of Massachusetts, Worcester, MA; Clinical and Population Health Research Program, University of Massachusetts, Worcester, MA; Graduate School of Biomedical Sciences, University of Massachusetts, Worcester, MA.
| | - David Kirk
- WakeMed Health & Hospitals, Raleigh/Cary, NC
| | - Itai M Pessach
- The Chaim Sheba Medical Center and Tel-Aviv University, Tel Hashomer, Israel; Clew Medical, Netanya, Israel
| | - Gurudev Lotun
- UMass Memorial Health, UMass Memorial Medical Center, Worcester, MA
| | | | - Ari Lipsky
- The Chaim Sheba Medical Center and Tel-Aviv University, Tel Hashomer, Israel; Department of Emergency Medicine, Rambam Health Care Campus, Haifa, Israel
| | | | | | - Eric W Cucchi
- UMass Memorial Health, UMass Memorial Medical Center, Worcester, MA
| | - James M Blum
- Department of Anesthesiology, University of Iowa, Iowa City, IA
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Jeddah D, Chen O, Lipsky AM, Forgacs A, Celniker G, Lilly CM, Pessach IM. Validation of an Automatic Tagging System for Identifying Respiratory and Hemodynamic Deterioration Events in the Intensive Care Unit. Healthc Inform Res 2021; 27:241-248. [PMID: 34384206 PMCID: PMC8369051 DOI: 10.4258/hir.2021.27.3.241] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 07/14/2021] [Indexed: 01/27/2023] Open
Abstract
Objectives Predictive models for critical events in the intensive care unit (ICU) might help providers anticipate patient deterioration. At the heart of predictive model development lies the ability to accurately label significant events, thereby facilitating the use of machine learning and similar strategies. We conducted this study to establish the validity of an automated system for tagging respiratory and hemodynamic deterioration by comparing automatic tags to tagging by expert reviewers. Methods This retrospective cohort study included 72,650 unique patient stays collected from Electronic Medical Records of the University of Massachusetts’ eICU. An enriched subgroup of stays was manually tagged by expert reviewers. The tags generated by the reviewers were compared to those generated by an automated system. Results The automated system was able to rapidly and efficiently tag the complete database utilizing available clinical data. The overall agreement rate between the automated system and the clinicians for respiratory and hemodynamic deterioration tags was 89.4% and 87.1%, respectively. The automatic system did not add substantial variability beyond that seen among the reviewers. Conclusions We demonstrated that a simple rule-based tagging system could provide a rapid and accurate tool for mass tagging of a compound database. These types of tagging systems may replace human reviewers and save considerable resources when trying to create a validated, labeled database used to train artificial intelligence algorithms. The ability to harness the power of artificial intelligence depends on efficient clinical validation of targeted conditions; hence, these systems and the methodology used to validate them are crucial.
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Affiliation(s)
- Danielle Jeddah
- The Chaim Sheba Medical Center, Tel-Hashomer and the Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel.,Clew Medical Ltd., Netanya, Israel
| | | | - Ari M Lipsky
- Clew Medical Ltd., Netanya, Israel.,Department of Emergency Medicine, Rambam Health Care Campus, Haifa, Israel
| | | | | | - Craig M Lilly
- Departments of Medicine, Anesthesiology and Surgery, University of Massachusetts Medical School, Worcester, MA, USA.,Clinical and Population Health Research Program, Graduate School of Biomedical Sciences, University of Massachusetts Medical School, Worcester, MA, USA.,UMass Memorial Health Care, UMass Memorial Medical Center, Worcester, MA, USA
| | - Itai M Pessach
- The Chaim Sheba Medical Center, Tel-Hashomer and the Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
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3
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Barbezange C, Jones L, Blanc H, Isakov O, Celniker G, Enouf V, Shomron N, Vignuzzi M, van der Werf S. Seasonal Genetic Drift of Human Influenza A Virus Quasispecies Revealed by Deep Sequencing. Front Microbiol 2018; 9:2596. [PMID: 30429836 PMCID: PMC6220372 DOI: 10.3389/fmicb.2018.02596] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 10/11/2018] [Indexed: 01/06/2023] Open
Abstract
After a pandemic wave in 2009 following their introduction in the human population, the H1N1pdm09 viruses replaced the previously circulating, pre-pandemic H1N1 virus and, along with H3N2 viruses, are now responsible for the seasonal influenza type A epidemics. So far, the evolutionary potential of influenza viruses has been mainly documented by consensus sequencing data. However, like other RNA viruses, influenza A viruses exist as a population of diverse, albeit related, viruses, or quasispecies. Interest in this quasispecies nature has increased with the development of next generation sequencing (NGS) technologies that allow a more in-depth study of the genetic variability. NGS deep sequencing methodologies were applied to determine the whole genome genetic heterogeneity of the three categories of influenza A viruses that circulated in humans between 2007 and 2012 in France, directly from clinical respiratory specimens. Mutation frequencies and single nucleotide polymorphisms were used for comparisons to address the level of natural intrinsic heterogeneity of influenza A viruses. Clear differences in single nucleotide polymorphism profiles between seasons for a given subtype also revealed the constant genetic drift that human influenza A virus quasispecies undergo.
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Affiliation(s)
- Cyril Barbezange
- Viral Populations and Pathogenesis, Department of Virology, Institut Pasteur, Paris, France
- Molecular Genetics of RNA Viruses, Department of Virology, Institut Pasteur, Paris, France
- UMR 3569, Centre National de la Recherche Scientifique, Paris, France
- Cellule Pasteur, Université Paris Diderot–Université Sorbonne Paris Cité, Paris, France
| | - Louis Jones
- Molecular Genetics of RNA Viruses, Department of Virology, Institut Pasteur, Paris, France
- UMR 3569, Centre National de la Recherche Scientifique, Paris, France
- Cellule Pasteur, Université Paris Diderot–Université Sorbonne Paris Cité, Paris, France
- Bioinformatics and Biostatistics HUB, The Center of Bioinformatics, Biostatistics and Integrative Biology, Institut Pasteur, Paris, France
| | - Hervé Blanc
- Viral Populations and Pathogenesis, Department of Virology, Institut Pasteur, Paris, France
- UMR 3569, Centre National de la Recherche Scientifique, Paris, France
| | - Ofer Isakov
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Gershon Celniker
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Vincent Enouf
- Molecular Genetics of RNA Viruses, Department of Virology, Institut Pasteur, Paris, France
- UMR 3569, Centre National de la Recherche Scientifique, Paris, France
- Cellule Pasteur, Université Paris Diderot–Université Sorbonne Paris Cité, Paris, France
| | - Noam Shomron
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Marco Vignuzzi
- Viral Populations and Pathogenesis, Department of Virology, Institut Pasteur, Paris, France
- UMR 3569, Centre National de la Recherche Scientifique, Paris, France
| | - Sylvie van der Werf
- Molecular Genetics of RNA Viruses, Department of Virology, Institut Pasteur, Paris, France
- UMR 3569, Centre National de la Recherche Scientifique, Paris, France
- Cellule Pasteur, Université Paris Diderot–Université Sorbonne Paris Cité, Paris, France
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Yahalom V, Pillar N, Zhao Y, Modan S, Fang M, Yosephi L, Asher O, Shinar E, Celniker G, Resnik-Wolf H, Brantz Y, Hauschner H, Rosenberg N, Cheng L, Shomron N, Pras E. SMYD1 is the underlying gene for the AnWj-negative blood group phenotype. Eur J Haematol 2018; 101:496-501. [PMID: 29956848 DOI: 10.1111/ejh.13133] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 06/22/2018] [Accepted: 06/24/2018] [Indexed: 11/30/2022]
Abstract
BACKGROUND AnWj is a high-incidence blood group antigen associated with three clinical disorders: lymphoid malignancies, immunologic disorders, and autoimmune hemolytic anemia. The aim of this study was to determine the genetic basis of an inherited AnWj-negative phenotype. METHODS We identified a consanguineous family with two AnWj-negative siblings and 4 additional AnWj-negative individuals without known familial relationship to the index family. We performed exome sequencing in search for rare homozygous variants shared by the two AnWj-negative siblings of the index family and searched for these variants in the four non-related AnWj-negative individuals. RESULTS Exome sequencing revealed seven candidate genes that showed complete segregation in the index family and for which the two AnWj-negative siblings were homozygous. However, the four additional non-related AnWj-negative subjects were homozygous for only one of these variants, rs114851602 (R320Q) in the SMYD1 gene. Considering the frequency of the minor allele, the chance of randomly finding 4 consecutive such individuals is 2.56 × 10-18 . CONCLUSION We present genetic and statistical evidence that the R320Q substitution in SMYD1 underlies an inherited form of the AnWj-negative blood group phenotype. The mechanism by which the mutation leads to this phenotype remains to be determined.
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Affiliation(s)
- Vered Yahalom
- Magen David Adom (MDA) National Blood Services, Tel Hashomer, Ramat Gan, Israel
| | - Nir Pillar
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Yingying Zhao
- School of Medicine, Health Science Centre, Shenzhen University, Shenzhen, China
| | - Shirley Modan
- Magen David Adom (MDA) National Blood Services, Tel Hashomer, Ramat Gan, Israel
| | - Mingyan Fang
- BGI-Shenzhen, Shenzhen, China.,The Division of Clinical Immunology, Department of Laboratory Medicine, Karolinska Institutet at Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - Lydia Yosephi
- Magen David Adom (MDA) National Blood Services, Tel Hashomer, Ramat Gan, Israel
| | - Orna Asher
- Magen David Adom (MDA) National Blood Services, Tel Hashomer, Ramat Gan, Israel
| | - Eilat Shinar
- Magen David Adom (MDA) National Blood Services, Tel Hashomer, Ramat Gan, Israel
| | - Gershon Celniker
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Haike Resnik-Wolf
- The Danek Gertner Institute of Human Genetics, Chaim Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel
| | - Yael Brantz
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel.,The Danek Gertner Institute of Human Genetics, Chaim Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel
| | - Hagit Hauschner
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel.,The Amalia Biron Research Institute of Thrombosis and Hemostasis, Chaim Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel
| | - Nurit Rosenberg
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel.,The Amalia Biron Research Institute of Thrombosis and Hemostasis, Chaim Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel
| | - Le Cheng
- BGI-Shenzhen, Shenzhen, China.,The Division of Clinical Immunology, Department of Laboratory Medicine, Karolinska Institutet at Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - Noam Shomron
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Elon Pras
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel.,The Danek Gertner Institute of Human Genetics, Chaim Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel
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Pras E, Kristal D, Shoshany N, Volodarsky D, Vulih I, Celniker G, Isakov O, Shomron N, Pras E. Rare genetic variants in Tunisian Jewish patients suffering from age-related macular degeneration. J Med Genet 2015; 52:484-92. [PMID: 25986072 DOI: 10.1136/jmedgenet-2015-103130] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 04/21/2015] [Indexed: 11/03/2022]
Abstract
PURPOSE To explore the molecular basis of familial, early onset, age-related macular degeneration (AMD) with diverse phenotypes, using whole exome sequencing (WES). METHODS We performed WES on four patients (two sibs from two families) manifesting early-onset AMD and searched for disease-causing genetic variants in previously identified macular degeneration related genes. Validation studies of the variants included bioinformatics tools, segregation analysis of mutations within the families and mutation screening in an AMD cohort of patients. RESULTS The index patients were in their 50s when diagnosed and displayed a wide variety of clinical AMD presentations: from limited drusen in the posterior pole to multiple basal-laminar drusen extending peripherally. Severe visual impairment due to extensive geographic atrophy and/or choroidal-neovascularisation was common by the age of 75 years. Approximately, 400 000 genomic variants for each DNA sample were included in the downstream bioinformatics analysis, which ended in the discovery of two novel variants; in one family a single bp deletion was identified in the Hemicentin (HMCN1) gene (c.4162delC), whereas in the other, a missense variant (p.V412M) in the Complement Factor-I (CFI) gene was found. Screening for these variants in a cohort of patients with AMD identified another family with the CFI variant. CONCLUSIONS This report uses WES to uncover rare genetic variants in AMD. A null-variant in HMCN1 has been identified in one AMD family, and a missense variant in CFI was discovered in two other families. These variants confirm the genetic complexity and significance of rare genetic variants in the pathogenesis of AMD.
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Affiliation(s)
- Eran Pras
- The Matlow's Ophthalmo-Genetics Laboratory, Department of Ophthalmology, Assaf-Harofeh Medical Center, Zerifin, Israel Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Dana Kristal
- Department of Ophthalmology, Edith-Wolfson Medical Center, Holon, Israel
| | - Nadav Shoshany
- The Matlow's Ophthalmo-Genetics Laboratory, Department of Ophthalmology, Assaf-Harofeh Medical Center, Zerifin, Israel
| | | | - Inna Vulih
- Dyn Labs, Assaf-Harofeh Medical Center, Zerifin, Israel
| | - Gershon Celniker
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel Functional Genomics Laboratory, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ofer Isakov
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel Functional Genomics Laboratory, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Noam Shomron
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel Functional Genomics Laboratory, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Elon Pras
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel Danek Gartener Institute of Human Genetics, Sheba Medical Center, Tel Aviv University, Tel Aviv, Israel
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6
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Isakov O, Bordería AV, Golan D, Hamenahem A, Celniker G, Yoffe L, Blanc H, Vignuzzi M, Shomron N. Deep sequencing analysis of viral infection and evolution allows rapid and detailed characterization of viral mutant spectrum. ACTA ACUST UNITED AC 2015; 31:2141-50. [PMID: 25701575 PMCID: PMC4481840 DOI: 10.1093/bioinformatics/btv101] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Accepted: 02/11/2015] [Indexed: 12/22/2022]
Abstract
Motivation: The study of RNA virus populations is a challenging task. Each population of RNA virus is composed of a collection of different, yet related genomes often referred to as mutant spectra or quasispecies. Virologists using deep sequencing technologies face major obstacles when studying virus population dynamics, both experimentally and in natural settings due to the relatively high error rates of these technologies and the lack of high performance pipelines. In order to overcome these hurdles we developed a computational pipeline, termed ViVan (Viral Variance Analysis). ViVan is a complete pipeline facilitating the identification, characterization and comparison of sequence variance in deep sequenced virus populations. Results: Applying ViVan on deep sequenced data obtained from samples that were previously characterized by more classical approaches, we uncovered novel and potentially crucial aspects of virus populations. With our experimental work, we illustrate how ViVan can be used for studies ranging from the more practical, detection of resistant mutations and effects of antiviral treatments, to the more theoretical temporal characterization of the population in evolutionary studies. Availability and implementation: Freely available on the web at http://www.vivanbioinfo.org Contact: nshomron@post.tau.ac.il Supplementary information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Ofer Isakov
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel, Institut Pasteur, Viral Populations and Pathogenesis, CNRS URA 3015, Paris, France and Department of Statistics and Operations Research, Tel Aviv University, Tel Aviv 69978, Israel
| | - Antonio V Bordería
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel, Institut Pasteur, Viral Populations and Pathogenesis, CNRS URA 3015, Paris, France and Department of Statistics and Operations Research, Tel Aviv University, Tel Aviv 69978, Israel
| | - David Golan
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel, Institut Pasteur, Viral Populations and Pathogenesis, CNRS URA 3015, Paris, France and Department of Statistics and Operations Research, Tel Aviv University, Tel Aviv 69978, Israel
| | - Amir Hamenahem
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel, Institut Pasteur, Viral Populations and Pathogenesis, CNRS URA 3015, Paris, France and Department of Statistics and Operations Research, Tel Aviv University, Tel Aviv 69978, Israel
| | - Gershon Celniker
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel, Institut Pasteur, Viral Populations and Pathogenesis, CNRS URA 3015, Paris, France and Department of Statistics and Operations Research, Tel Aviv University, Tel Aviv 69978, Israel
| | - Liron Yoffe
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel, Institut Pasteur, Viral Populations and Pathogenesis, CNRS URA 3015, Paris, France and Department of Statistics and Operations Research, Tel Aviv University, Tel Aviv 69978, Israel
| | - Hervé Blanc
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel, Institut Pasteur, Viral Populations and Pathogenesis, CNRS URA 3015, Paris, France and Department of Statistics and Operations Research, Tel Aviv University, Tel Aviv 69978, Israel
| | - Marco Vignuzzi
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel, Institut Pasteur, Viral Populations and Pathogenesis, CNRS URA 3015, Paris, France and Department of Statistics and Operations Research, Tel Aviv University, Tel Aviv 69978, Israel
| | - Noam Shomron
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel, Institut Pasteur, Viral Populations and Pathogenesis, CNRS URA 3015, Paris, France and Department of Statistics and Operations Research, Tel Aviv University, Tel Aviv 69978, Israel
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Isakov O, Lev D, Blumkin L, Celniker G, Leshinsky-Silver E, Shomron N. Crowdfunding effort identifies the causative mutation in a patient with nystagmus, microcephaly, dystonia and hypomyelination. J Genet Genomics 2015; 42:79-81. [PMID: 25697102 DOI: 10.1016/j.jgg.2014.12.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2014] [Revised: 12/26/2014] [Accepted: 12/30/2014] [Indexed: 10/24/2022]
Affiliation(s)
- Ofer Isakov
- Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Dorit Lev
- Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel; Metabolic-Neurogenetic Clinic, Wolfson Medical Center, Holon 58100, Israel; Institute of Medical Genetics, Wolfson Medical Center, Holon 58100, Israel
| | - Lubov Blumkin
- Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel; Metabolic-Neurogenetic Clinic, Wolfson Medical Center, Holon 58100, Israel; Pediatric Neurology Unit, Wolfson Medical Center, Holon 58100, Israel
| | - Gershon Celniker
- Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Esther Leshinsky-Silver
- Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel; Metabolic-Neurogenetic Clinic, Wolfson Medical Center, Holon 58100, Israel; Molecular Genetic Laboratory, Wolfson Medical Center, Holon 58100, Israel
| | - Noam Shomron
- Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel.
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Celniker G, Nimrod G, Ashkenazy H, Glaser F, Martz E, Mayrose I, Pupko T, Ben-Tal N. ConSurf: Using Evolutionary Data to Raise Testable Hypotheses about Protein Function. Isr J Chem 2013. [DOI: 10.1002/ijch.201200096] [Citation(s) in RCA: 369] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Celniker G, Nimrod G, Ashkenazy H, Glaser F, Martz E, Mayrose I, Pupko T, Ben-Tal N, Hanson RM, Prilusky J, Renjian Z, Nakane T, Sussman JL. Cover Picture: ConSurf: Using Evolutionary Data to Raise Testable Hypotheses about Protein Function / JSmol and the Next-Generation Web-Based Representation of 3D Molecular Structure as Applied to Proteopedia(Isr. J. Chem. 3-4/2013). Isr J Chem 2013. [DOI: 10.1002/ijch.201390002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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10
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Shazman S, Celniker G, Haber O, Glaser F, Mandel-Gutfreund Y. Patch Finder Plus (PFplus): a web server for extracting and displaying positive electrostatic patches on protein surfaces. Nucleic Acids Res 2007; 35:W526-30. [PMID: 17537808 PMCID: PMC1933175 DOI: 10.1093/nar/gkm401] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Positively charged electrostatic patches on protein surfaces are usually indicative of nucleic acid binding interfaces. Interestingly, many proteins which are not involved in nucleic acid binding possess large positive patches on their surface as well. In some cases, the positive patches on the protein are related to other functional properties of the protein family. PatchFinderPlus (PFplus) http://pfp.technion.ac.il is a web-based tool for extracting and displaying continuous electrostatic positive patches on protein surfaces. The input required for PFplus is either a four letter PDB code or a protein coordinate file in PDB format, provided by the user. PFplus computes the continuum electrostatics potential and extracts the largest positive patch for each protein chain in the PDB file. The server provides an output file in PDB format including a list of the patch residues. In addition, the largest positive patch is displayed on the server by a graphical viewer (Jmol), using a simple color coding.
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Affiliation(s)
- Shula Shazman
- Department of Biology and The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering, Technion - Israel Institute of Technology Haifa 32000, Israel
| | - Gershon Celniker
- Department of Biology and The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering, Technion - Israel Institute of Technology Haifa 32000, Israel
| | - Omer Haber
- Department of Biology and The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering, Technion - Israel Institute of Technology Haifa 32000, Israel
| | - Fabian Glaser
- Department of Biology and The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering, Technion - Israel Institute of Technology Haifa 32000, Israel
| | - Yael Mandel-Gutfreund
- Department of Biology and The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering, Technion - Israel Institute of Technology Haifa 32000, Israel
- *To whom correspondence should be addressed. 972 4 8293958972 4 8225153
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