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  1. Article: The R Language: An Engine for Bioinformatics and Data Science.

    Giorgi, Federico M / Ceraolo, Carmine / Mercatelli, Daniele

    Life (Basel, Switzerland)

    2022  Volume 12, Issue 5

    Abstract: The R programming language is approaching its 30th birthday, and in the last three decades it has achieved a prominent role in statistics, bioinformatics, and data science in general. It currently ranks among the top 10 most popular languages worldwide, ... ...

    Abstract The R programming language is approaching its 30th birthday, and in the last three decades it has achieved a prominent role in statistics, bioinformatics, and data science in general. It currently ranks among the top 10 most popular languages worldwide, and its community has produced tens of thousands of extensions and packages, with scopes ranging from machine learning to transcriptome data analysis. In this review, we provide an historical chronicle of how R became what it is today, describing all its current features and capabilities. We also illustrate the major tools of R, such as the current R editors and integrated development environments (IDEs), the R Shiny web server, the R methods for machine learning, and its relationship with other programming languages. We also discuss the role of R in science in general as a driver for reproducibility. Overall, we hope to provide both a complete snapshot of R today and a practical compendium of the major features and applications of this programming language.
    Language English
    Publishing date 2022-04-27
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2662250-6
    ISSN 2075-1729
    ISSN 2075-1729
    DOI 10.3390/life12050648
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Genomic variance of the 2019-nCoV coronavirus.

    Ceraolo, Carmine / Giorgi, Federico M

    Journal of medical virology

    2020  Volume 92, Issue 5, Page(s) 522–528

    Abstract: There is a rising global concern for the recently emerged novel coronavirus (2019-nCoV). Full genomic sequences have been released by the worldwide scientific community in the last few weeks to understand the evolutionary origin and molecular ... ...

    Abstract There is a rising global concern for the recently emerged novel coronavirus (2019-nCoV). Full genomic sequences have been released by the worldwide scientific community in the last few weeks to understand the evolutionary origin and molecular characteristics of this virus. Taking advantage of all the genomic information currently available, we constructed a phylogenetic tree including also representatives of other coronaviridae, such as Bat coronavirus (BCoV) and severe acute respiratory syndrome. We confirm high sequence similarity (>99%) between all sequenced 2019-nCoVs genomes available, with the closest BCoV sequence sharing 96.2% sequence identity, confirming the notion of a zoonotic origin of 2019-nCoV. Despite the low heterogeneity of the 2019-nCoV genomes, we could identify at least two hypervariable genomic hotspots, one of which is responsible for a Serine/Leucine variation in the viral ORF8-encoded protein. Finally, we perform a full proteomic comparison with other coronaviridae, identifying key aminoacidic differences to be considered for antiviral strategies deriving from previous anti-coronavirus approaches.
    MeSH term(s) Amino Acid Sequence ; Animals ; Base Sequence ; Betacoronavirus/classification ; Betacoronavirus/genetics ; COVID-19 ; Chiroptera/virology ; Coronavirus Infections/virology ; Genetic Variation ; Genome, Viral ; Humans ; Models, Genetic ; Phylogeny ; Pneumonia, Viral ; Proteome ; RNA, Viral/genetics ; SARS-CoV-2
    Chemical Substances Proteome ; RNA, Viral
    Keywords covid19
    Language English
    Publishing date 2020-02-19
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 752392-0
    ISSN 1096-9071 ; 0146-6615
    ISSN (online) 1096-9071
    ISSN 0146-6615
    DOI 10.1002/jmv.25700
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

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  3. Article ; Online: The R Language

    Federico M. Giorgi / Carmine Ceraolo / Daniele Mercatelli

    Life, Vol 12, Iss 648, p

    An Engine for Bioinformatics and Data Science

    2022  Volume 648

    Abstract: The R programming language is approaching its 30th birthday, and in the last three decades it has achieved a prominent role in statistics, bioinformatics, and data science in general. It currently ranks among the top 10 most popular languages worldwide, ... ...

    Abstract The R programming language is approaching its 30th birthday, and in the last three decades it has achieved a prominent role in statistics, bioinformatics, and data science in general. It currently ranks among the top 10 most popular languages worldwide, and its community has produced tens of thousands of extensions and packages, with scopes ranging from machine learning to transcriptome data analysis. In this review, we provide an historical chronicle of how R became what it is today, describing all its current features and capabilities. We also illustrate the major tools of R, such as the current R editors and integrated development environments (IDEs), the R Shiny web server, the R methods for machine learning, and its relationship with other programming languages. We also discuss the role of R in science in general as a driver for reproducibility. Overall, we hope to provide both a complete snapshot of R today and a practical compendium of the major features and applications of this programming language.
    Keywords R ; statistics ; bioinformatics ; programming ; CRAN ; data science ; Science ; Q
    Subject code 004
    Language English
    Publishing date 2022-04-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: Genomic variance of the 2019-nCoV coronavirus

    Ceraolo, Carmine / Giorgi, Federico M.

    bioRxiv

    Keywords covid19
    Language English
    Publishing date 2020-02-05
    Publisher Cold Spring Harbor Laboratory
    Document type Article ; Online
    DOI 10.1101/2020.02.02.931162
    Database COVID19

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  5. Article: Genomic variance of the 2019-nCoV coronavirus

    Ceraolo, Carmine / Giorgi, Federico M

    J Med Virol

    Abstract: There is a rising global concern for the recently emerged novel coronavirus (2019-nCoV). Full genomic sequences have been released by the worldwide scientific community in the last few weeks to understand the evolutionary origin and molecular ... ...

    Abstract There is a rising global concern for the recently emerged novel coronavirus (2019-nCoV). Full genomic sequences have been released by the worldwide scientific community in the last few weeks to understand the evolutionary origin and molecular characteristics of this virus. Taking advantage of all the genomic information currently available, we constructed a phylogenetic tree including also representatives of other coronaviridae, such as Bat coronavirus (BCoV) and severe acute respiratory syndrome. We confirm high sequence similarity (>99%) between all sequenced 2019-nCoVs genomes available, with the closest BCoV sequence sharing 96.2% sequence identity, confirming the notion of a zoonotic origin of 2019-nCoV. Despite the low heterogeneity of the 2019-nCoV genomes, we could identify at least two hypervariable genomic hotspots, one of which is responsible for a Serine/Leucine variation in the viral ORF8-encoded protein. Finally, we perform a full proteomic comparison with other coronaviridae, identifying key aminoacidic differences to be considered for antiviral strategies deriving from previous anti-coronavirus approaches.
    Keywords covid19
    Publisher WHO
    Document type Article
    Note WHO #Covidence: #10412
    Database COVID19

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  6. Article ; Online: Phylogenomic analysis of the 2019-nCoV coronavirus

    Ceraolo, Carmine / Giorgi, Federico M

    bioRxiv

    Abstract: There is rising global concern for the recently emerged novel Coronavirus (2019-nCov). Full genomic sequences have been released by the worldwide scientific community in the last few weeks in order to understand the evolutionary origin and molecular ... ...

    Abstract There is rising global concern for the recently emerged novel Coronavirus (2019-nCov). Full genomic sequences have been released by the worldwide scientific community in the last few weeks in order to understand the evolutionary origin and molecular characteristics of this virus. Taking advantage of all the genomic information currently available, we constructed a phylogenetic tree including also representatives of other coronaviridae, such as Bat coronavirus (BCoV) and SARS. We confirm high sequence similarity (>99%) between all sequenced 2019-nCoVs genomes available, with the closest BCoV sequence sharing 96.2% sequence identity, confirming the notion of a zoonotic origin of 2019-nCoV. Despite the low heterogeneity of the 2019-nCoV genomes, we could identify at least two hyper-variable genomic hotspots, one of which is responsible for a Serine/Leucine variation in the viral ORF8-encoded protein. Finally, we perform a full proteomic comparison with other coronaviridae, identifying key aminoacidic differences to be considered for antiviral strategies deriving from previous anti-coronavirus approaches.
    Keywords covid19
    Publisher BioRxiv; MedRxiv; WHO
    Document type Article ; Online
    Note WHO #Covidence: #931162
    DOI 10.1101/2020.02.02.931162
    Database COVID19

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  7. Article: Master Regulator Analysis of the SARS-CoV-2/Human Interactome.

    Guzzi, Pietro H / Mercatelli, Daniele / Ceraolo, Carmine / Giorgi, Federico M

    Journal of clinical medicine

    2020  Volume 9, Issue 4

    Abstract: The recent epidemic outbreak of a novel human coronavirus called SARS-CoV-2 causing the respiratory tract disease COVID-19 has reached worldwide resonance and a global effort is being undertaken to characterize the molecular features and evolutionary ... ...

    Abstract The recent epidemic outbreak of a novel human coronavirus called SARS-CoV-2 causing the respiratory tract disease COVID-19 has reached worldwide resonance and a global effort is being undertaken to characterize the molecular features and evolutionary origins of this virus. In this paper, we set out to shed light on the SARS-CoV-2/host receptor recognition, a crucial factor for successful virus infection. Based on the current knowledge of the interactome between SARS-CoV-2 and host cell proteins, we performed Master Regulator Analysis to detect which parts of the human interactome are most affected by the infection. We detected, amongst others, affected apoptotic and mitochondrial mechanisms, and a downregulation of the ACE2 protein receptor, notions that can be used to develop specific therapies against this new virus.
    Keywords covid19
    Language English
    Publishing date 2020-04-01
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2662592-1
    ISSN 2077-0383
    ISSN 2077-0383
    DOI 10.3390/jcm9040982
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Master Regulator Analysis of the SARS-CoV-2/Human Interactome

    Pietro H. Guzzi / Daniele Mercatelli / Carmine Ceraolo / Federico M. Giorgi

    Journal of Clinical Medicine, Vol 9, Iss 982, p

    2020  Volume 982

    Abstract: The recent epidemic outbreak of a novel human coronavirus called SARS-CoV-2 causing the respiratory tract disease COVID-19 has reached worldwide resonance and a global effort is being undertaken to characterize the molecular features and evolutionary ... ...

    Abstract The recent epidemic outbreak of a novel human coronavirus called SARS-CoV-2 causing the respiratory tract disease COVID-19 has reached worldwide resonance and a global effort is being undertaken to characterize the molecular features and evolutionary origins of this virus. In this paper, we set out to shed light on the SARS-CoV-2/host receptor recognition, a crucial factor for successful virus infection. Based on the current knowledge of the interactome between SARS-CoV-2 and host cell proteins, we performed Master Regulator Analysis to detect which parts of the human interactome are most affected by the infection. We detected, amongst others, affected apoptotic and mitochondrial mechanisms, and a downregulation of the ACE2 protein receptor, notions that can be used to develop specific therapies against this new virus.
    Keywords coronavirus ; bioinformatics ; gene network analysis ; COVID-19 ; SARS-CoV-2 ; Medicine ; R ; covid19
    Language English
    Publishing date 2020-04-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  9. Article ; Online: Master Regulator Analysis of the SARS-CoV-2/Human interactome

    Guzzi, Pietro Hiram / Mercatelli, Daniele / Ceraolo, Carmine / Giorgi, Federico M.

    bioRxiv

    Abstract: the recent epidemic outbreak of a novel human coronavirus called SARS-CoV-2 and causing the respiratory tract disease COVID-19 has reached worldwide resonance and a global effort is being undertaken to characterize the molecular features and evolutionary ...

    Abstract the recent epidemic outbreak of a novel human coronavirus called SARS-CoV-2 and causing the respiratory tract disease COVID-19 has reached worldwide resonance and a global effort is being undertaken to characterize the molecular features and evolutionary origins of this virus. In this paper, we set out to shed light on the SARS-CoV-2/host receptor recognition, a crucial factor for successful virus infection. Based on the current knowledge of the interactome between SARS-CoV-2 and host cell proteins, we performed Master Regulator Analysis to detect which parts of the human interactome are most affected by the infection. We detected, amongst others, affected apoptotic and mitochondrial mechanisms, and a downregulation of the ACE2 protein receptor, notions that can be used to develop specific therapies against this new virus.
    Keywords covid19
    Publisher BioRxiv; WHO
    Document type Article ; Online
    DOI 10.1101/2020.03.15.992925
    Database COVID19

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    Inter-library loan at ZB MED

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  10. Article ; Online: Master Regulator Analysis of the SARS-CoV-2/Human interactome

    Guzzi, Pietro Hiram / Mercatelli, Daniele / Ceraolo, Carmine / Giorgi, Federico M.

    bioRxiv

    Abstract: The recent epidemic outbreak of a novel human coronavirus called SARS-CoV-2 and causing the respiratory tract disease COVID-19 has reached worldwide resonance and a global effort is being undertaken to characterize the molecular features and evolutionary ...

    Abstract The recent epidemic outbreak of a novel human coronavirus called SARS-CoV-2 and causing the respiratory tract disease COVID-19 has reached worldwide resonance and a global effort is being undertaken to characterize the molecular features and evolutionary origins of this virus. In this paper, we set out to shed light on the SARS-CoV-2/host receptor recognition, a crucial factor for successful virus infection. Based on the current knowledge of the interactome between SARS-CoV-2 and host cell proteins, we performed Master Regulator Analysis to detect which parts of the human interactome are most affected by the infection. We detected, amongst others, affected apoptotic and mitochondrial mechanisms, and a downregulation of the ACE2 protein receptor, notions that can be used to develop specific therapies against this new virus.
    Keywords covid19
    Language English
    Publishing date 2020-03-17
    Publisher Cold Spring Harbor Laboratory
    Document type Article ; Online
    DOI 10.1101/2020.03.15.992925
    Database COVID19

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