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Article ; Online: The rise and fall of machine learning methods in biomedical research [version 2; referees

Hashem Koohy

F1000Research, Vol

2 approved]

2018 Volume 6

Abstract: In the era of explosion in biological data, machine learning techniques are becoming more popular in life sciences, including biology and medicine. This research note examines the rise and fall of the most commonly used machine learning techniques in ... ...

Abstract	In the era of explosion in biological data, machine learning techniques are becoming more popular in life sciences, including biology and medicine. This research note examines the rise and fall of the most commonly used machine learning techniques in life sciences over the past three decades.
Keywords	Bioinformatics ; Statistical Methodologies & Health Informatics ; Medicine ; R ; Science ; Q
Language	English
Publishing date	2018-01-01T00:00:00Z
Publisher	F1000 Research Ltd
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: In silico identification of vaccine targets for 2019-nCoV [version 2; peer review

Chloe H. Lee / Hashem Koohy

F1000Research, Vol

3 approved]

2020 Volume 9

Abstract: Background: The newly identified coronavirus known as 2019-nCoV has posed a serious global health threat. According to the latest report (18-February-2020), it has infected more than 72,000 people globally and led to deaths of more than 1,016 people in ... ...

Abstract	Background: The newly identified coronavirus known as 2019-nCoV has posed a serious global health threat. According to the latest report (18-February-2020), it has infected more than 72,000 people globally and led to deaths of more than 1,016 people in China. Methods: The 2019 novel coronavirus proteome was aligned to a curated database of viral immunogenic peptides. The immunogenicity of detected peptides and their binding potential to HLA alleles was predicted by immunogenicity predictive models and NetMHCpan 4.0. Results: We report in silico identification of a comprehensive list of immunogenic peptides that can be used as potential targets for 2019 novel coronavirus (2019-nCoV) vaccine development. First, we found 28 nCoV peptides identical to Severe acute respiratory syndrome-related coronavirus (SARS CoV) that have previously been characterized immunogenic by T cell assays. Second, we identified 48 nCoV peptides having a high degree of similarity with immunogenic peptides deposited in The Immune Epitope Database (IEDB). Lastly, we conducted a de novo search of 2019-nCoV 9-mer peptides that i) bind to common HLA alleles in Chinese and European population and ii) have T Cell Receptor (TCR) recognition potential by positional weight matrices and a recently developed immunogenicity algorithm, iPred, and identified in total 63 peptides with a high immunogenicity potential. Conclusions: Given the limited time and resources to develop vaccine and treatments for 2019-nCoV, our work provides a shortlist of candidates for experimental validation and thus can accelerate development pipeline.
Keywords	Medicine ; R ; Science ; Q
Language	English
Publishing date	2020-04-01T00:00:00Z
Publisher	F1000 Research Ltd
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: In silico identification of vaccine targets for 2019-nCoV [version 1; peer review

Chloe Hyun-Jung Lee / Hashem Koohy

F1000Research, Vol

2 approved]

2020 Volume 9

Abstract	Background: The newly identified coronavirus known as 2019-nCoV has posed a serious global health threat. According to the latest report (18-February-2020), it has infected more than 72,000 people globally and led to deaths of more than 1,016 people in China. Methods: The 2019 novel coronavirus proteome was aligned to a curated database of viral immunogenic peptides. The immunogenicity of detected peptides and their binding potential to HLA alleles was predicted by immunogenicity predictive models and NetMHCpan 4.0. Results: We report in silico identification of a comprehensive list of immunogenic peptides that can be used as potential targets for 2019 novel coronavirus (2019-nCoV) vaccine development. First, we found 28 nCoV peptides identical to Severe acute respiratory syndrome-related coronavirus (SARS CoV) that have previously been characterized immunogenic by T cell assays. Second, we identified 48 nCoV peptides having a high degree of similarity with immunogenic peptides deposited in The Immune Epitope Database (IEDB). Lastly, we conducted a de novo search of 2019-nCoV 9-mer peptides that i) bind to common HLA alleles in Chinese and European population and ii) have T Cell Receptor (TCR) recognition potential by positional weight matrices and a recently developed immunogenicity algorithm, iPred, and identified in total 63 peptides with a high immunogenicity potential. Conclusions: Given the limited time and resources to develop vaccine and treatments for 2019-nCoV, our work provides a shortlist of candidates for experimental validation and thus can accelerate development pipeline.
Keywords	Medicine ; R ; Science ; Q
Language	English
Publishing date	2020-02-01T00:00:00Z
Publisher	F1000 Research Ltd
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Dual RNA sequencing reveals dendritic cell reprogramming in response to typhoidal Salmonella invasion

Anna Aulicino / Agne Antanaviciute / Joe Frost / Ana Sousa Geros / Esther Mellado / Moustafa Attar / Marta Jagielowicz / Philip Hublitz / Julia Sinz / Lorena Preciado-Llanes / Giorgio Napolitani / Rory Bowden / Hashem Koohy / Hal Drakesmith / Alison Simmons

Communications Biology, Vol 5, Iss 1, Pp 1-

2022 Volume 17

Abstract: Aulicino, Antanaviciute et al investigate the transcriptional response to invasive Salmonella strains in dendritic cells (DCs). They show that S. Typhi mount a response against nitrosative stress pathways and propose a role of iron uptake and transport ... ...

Abstract	Aulicino, Antanaviciute et al investigate the transcriptional response to invasive Salmonella strains in dendritic cells (DCs). They show that S. Typhi mount a response against nitrosative stress pathways and propose a role of iron uptake and transport in preventing infection, which the pathogen can bypass. In parallel, they find that invasive Salmonella employs several mechanisms targeting more classic aspects of immunity to impair DC function.
Keywords	Biology (General) ; QH301-705.5
Language	English
Publishing date	2022-02-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Potential CD8+ T Cell Cross-Reactivity Against SARS-CoV-2 Conferred by Other Coronavirus Strains

Chloe H. Lee / Mariana Pereira Pinho / Paul R. Buckley / Isaac B. Woodhouse / Graham Ogg / Alison Simmons / Giorgio Napolitani / Hashem Koohy

Frontiers in Immunology, Vol

2020 Volume 11

Abstract: While individuals infected with coronavirus disease 2019 (COVID-19) manifested a broad range in susceptibility and severity to the disease, the pre-existing immune memory to related pathogens cross-reactive against SARS-CoV-2 can influence the disease ... ...

Abstract	While individuals infected with coronavirus disease 2019 (COVID-19) manifested a broad range in susceptibility and severity to the disease, the pre-existing immune memory to related pathogens cross-reactive against SARS-CoV-2 can influence the disease outcome in COVID-19. Here, we investigated the potential extent of T cell cross-reactivity against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that can be conferred by other coronaviruses and influenza virus, and generated an in silico map of public and private CD8+ T cell epitopes between coronaviruses. We observed 794 predicted SARS-CoV-2 epitopes of which 52% were private and 48% were public. Ninety-nine percent of the public epitopes were shared with SARS-CoV and 5.4% were shared with either one of four common coronaviruses, 229E, HKU1, NL63, and OC43. Moreover, to assess the potential risk of self-reactivity and/or diminished T cell response for peptides identical or highly similar to the host, we identified predicted epitopes with high sequence similarity with human proteome. Lastly, we compared predicted epitopes from coronaviruses with epitopes from influenza virus deposited in IEDB, and found only a small number of peptides with limited potential for cross-reactivity between the two virus families. We believe our comprehensive in silico profile of private and public epitopes across coronaviruses would facilitate design of vaccines, and provide insights into the presence of pre-existing coronavirus-specific memory CD8+ T cells that may influence immune responses against SARS-CoV-2.
Keywords	cross-reactivity ; antigen presentation ; predict immunogenicity ; epitopes ; CD8+ T cell recognition ; COVID-19 ; Immunologic diseases. Allergy ; RC581-607 ; covid19
Subject code	610
Language	English
Publishing date	2020-11-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Book ; Online: Table_3_Potential CD8+ T Cell Cross-Reactivity Against SARS-CoV-2 Conferred by Other Coronavirus Strains.xlsx

Chloe H. Lee / Mariana Pereira Pinho / Paul R. Buckley / Isaac B. Woodhouse / Graham Ogg / Alison Simmons / Giorgio Napolitani / Hashem Koohy

2020

Abstract	While individuals infected with coronavirus disease 2019 (COVID-19) manifested a broad range in susceptibility and severity to the disease, the pre-existing immune memory to related pathogens cross-reactive against SARS-CoV-2 can influence the disease outcome in COVID-19. Here, we investigated the potential extent of T cell cross-reactivity against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that can be conferred by other coronaviruses and influenza virus, and generated an in silico map of public and private CD8+ T cell epitopes between coronaviruses. We observed 794 predicted SARS-CoV-2 epitopes of which 52% were private and 48% were public. Ninety-nine percent of the public epitopes were shared with SARS-CoV and 5.4% were shared with either one of four common coronaviruses, 229E, HKU1, NL63, and OC43. Moreover, to assess the potential risk of self-reactivity and/or diminished T cell response for peptides identical or highly similar to the host, we identified predicted epitopes with high sequence similarity with human proteome. Lastly, we compared predicted epitopes from coronaviruses with epitopes from influenza virus deposited in IEDB, and found only a small number of peptides with limited potential for cross-reactivity between the two virus families. We believe our comprehensive in silico profile of private and public epitopes across coronaviruses would facilitate design of vaccines, and provide insights into the presence of pre-existing coronavirus-specific memory CD8+ T cells that may influence immune responses against SARS-CoV-2.
Keywords	Immunology ; Applied Immunology (incl. Antibody Engineering ; Xenotransplantation and T-cell Therapies) ; Autoimmunity ; Cellular Immunology ; Humoural Immunology and Immunochemistry ; Immunogenetics (incl. Genetic Immunology) ; Innate Immunity ; Transplantation Immunology ; Tumour Immunology ; Immunology not elsewhere classified ; Genetic Immunology ; Animal Immunology ; Veterinary Immunology ; cross-reactivity ; antigen presentation ; predict immunogenicity ; epitopes ; CD8+ T cell recognition ; COVID-19 ; SARS-CoV-2 ; covid19
Subject code	610
Publishing date	2020-11-05T05:28:57Z
Publishing country	uk
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Book ; Online: Table_4_Potential CD8+ T Cell Cross-Reactivity Against SARS-CoV-2 Conferred by Other Coronavirus Strains.csv

Chloe H. Lee / Mariana Pereira Pinho / Paul R. Buckley / Isaac B. Woodhouse / Graham Ogg / Alison Simmons / Giorgio Napolitani / Hashem Koohy

2020

Abstract	While individuals infected with coronavirus disease 2019 (COVID-19) manifested a broad range in susceptibility and severity to the disease, the pre-existing immune memory to related pathogens cross-reactive against SARS-CoV-2 can influence the disease outcome in COVID-19. Here, we investigated the potential extent of T cell cross-reactivity against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that can be conferred by other coronaviruses and influenza virus, and generated an in silico map of public and private CD8+ T cell epitopes between coronaviruses. We observed 794 predicted SARS-CoV-2 epitopes of which 52% were private and 48% were public. Ninety-nine percent of the public epitopes were shared with SARS-CoV and 5.4% were shared with either one of four common coronaviruses, 229E, HKU1, NL63, and OC43. Moreover, to assess the potential risk of self-reactivity and/or diminished T cell response for peptides identical or highly similar to the host, we identified predicted epitopes with high sequence similarity with human proteome. Lastly, we compared predicted epitopes from coronaviruses with epitopes from influenza virus deposited in IEDB, and found only a small number of peptides with limited potential for cross-reactivity between the two virus families. We believe our comprehensive in silico profile of private and public epitopes across coronaviruses would facilitate design of vaccines, and provide insights into the presence of pre-existing coronavirus-specific memory CD8+ T cells that may influence immune responses against SARS-CoV-2.
Keywords	Immunology ; Applied Immunology (incl. Antibody Engineering ; Xenotransplantation and T-cell Therapies) ; Autoimmunity ; Cellular Immunology ; Humoural Immunology and Immunochemistry ; Immunogenetics (incl. Genetic Immunology) ; Innate Immunity ; Transplantation Immunology ; Tumour Immunology ; Immunology not elsewhere classified ; Genetic Immunology ; Animal Immunology ; Veterinary Immunology ; cross-reactivity ; antigen presentation ; predict immunogenicity ; epitopes ; CD8+ T cell recognition ; COVID-19 ; SARS-CoV-2 ; covid19
Subject code	610
Publishing date	2020-11-05T05:28:58Z
Publishing country	uk
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Book ; Online: DataSheet_1_Potential CD8+ T Cell Cross-Reactivity Against SARS-CoV-2 Conferred by Other Coronavirus Strains.pdf

Chloe H. Lee / Mariana Pereira Pinho / Paul R. Buckley / Isaac B. Woodhouse / Graham Ogg / Alison Simmons / Giorgio Napolitani / Hashem Koohy

2020

Abstract	While individuals infected with coronavirus disease 2019 (COVID-19) manifested a broad range in susceptibility and severity to the disease, the pre-existing immune memory to related pathogens cross-reactive against SARS-CoV-2 can influence the disease outcome in COVID-19. Here, we investigated the potential extent of T cell cross-reactivity against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that can be conferred by other coronaviruses and influenza virus, and generated an in silico map of public and private CD8+ T cell epitopes between coronaviruses. We observed 794 predicted SARS-CoV-2 epitopes of which 52% were private and 48% were public. Ninety-nine percent of the public epitopes were shared with SARS-CoV and 5.4% were shared with either one of four common coronaviruses, 229E, HKU1, NL63, and OC43. Moreover, to assess the potential risk of self-reactivity and/or diminished T cell response for peptides identical or highly similar to the host, we identified predicted epitopes with high sequence similarity with human proteome. Lastly, we compared predicted epitopes from coronaviruses with epitopes from influenza virus deposited in IEDB, and found only a small number of peptides with limited potential for cross-reactivity between the two virus families. We believe our comprehensive in silico profile of private and public epitopes across coronaviruses would facilitate design of vaccines, and provide insights into the presence of pre-existing coronavirus-specific memory CD8+ T cells that may influence immune responses against SARS-CoV-2.
Keywords	Immunology ; Applied Immunology (incl. Antibody Engineering ; Xenotransplantation and T-cell Therapies) ; Autoimmunity ; Cellular Immunology ; Humoural Immunology and Immunochemistry ; Immunogenetics (incl. Genetic Immunology) ; Innate Immunity ; Transplantation Immunology ; Tumour Immunology ; Immunology not elsewhere classified ; Genetic Immunology ; Animal Immunology ; Veterinary Immunology ; cross-reactivity ; antigen presentation ; predict immunogenicity ; epitopes ; CD8+ T cell recognition ; COVID-19 ; SARS-CoV-2 ; covid19
Subject code	610
Publishing date	2020-11-05T05:28:57Z
Publishing country	uk
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Book ; Online: Table_1_Potential CD8+ T Cell Cross-Reactivity Against SARS-CoV-2 Conferred by Other Coronavirus Strains.csv

Chloe H. Lee / Mariana Pereira Pinho / Paul R. Buckley / Isaac B. Woodhouse / Graham Ogg / Alison Simmons / Giorgio Napolitani / Hashem Koohy

2020

Abstract	While individuals infected with coronavirus disease 2019 (COVID-19) manifested a broad range in susceptibility and severity to the disease, the pre-existing immune memory to related pathogens cross-reactive against SARS-CoV-2 can influence the disease outcome in COVID-19. Here, we investigated the potential extent of T cell cross-reactivity against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that can be conferred by other coronaviruses and influenza virus, and generated an in silico map of public and private CD8+ T cell epitopes between coronaviruses. We observed 794 predicted SARS-CoV-2 epitopes of which 52% were private and 48% were public. Ninety-nine percent of the public epitopes were shared with SARS-CoV and 5.4% were shared with either one of four common coronaviruses, 229E, HKU1, NL63, and OC43. Moreover, to assess the potential risk of self-reactivity and/or diminished T cell response for peptides identical or highly similar to the host, we identified predicted epitopes with high sequence similarity with human proteome. Lastly, we compared predicted epitopes from coronaviruses with epitopes from influenza virus deposited in IEDB, and found only a small number of peptides with limited potential for cross-reactivity between the two virus families. We believe our comprehensive in silico profile of private and public epitopes across coronaviruses would facilitate design of vaccines, and provide insights into the presence of pre-existing coronavirus-specific memory CD8+ T cells that may influence immune responses against SARS-CoV-2.
Keywords	Immunology ; Applied Immunology (incl. Antibody Engineering ; Xenotransplantation and T-cell Therapies) ; Autoimmunity ; Cellular Immunology ; Humoural Immunology and Immunochemistry ; Immunogenetics (incl. Genetic Immunology) ; Innate Immunity ; Transplantation Immunology ; Tumour Immunology ; Immunology not elsewhere classified ; Genetic Immunology ; Animal Immunology ; Veterinary Immunology ; cross-reactivity ; antigen presentation ; predict immunogenicity ; epitopes ; CD8+ T cell recognition ; COVID-19 ; SARS-CoV-2 ; covid19
Subject code	610
Publishing date	2020-11-05T05:28:57Z
Publishing country	uk
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Book ; Online: Table_2_Potential CD8+ T Cell Cross-Reactivity Against SARS-CoV-2 Conferred by Other Coronavirus Strains.csv

Chloe H. Lee / Mariana Pereira Pinho / Paul R. Buckley / Isaac B. Woodhouse / Graham Ogg / Alison Simmons / Giorgio Napolitani / Hashem Koohy

2020

Abstract	While individuals infected with coronavirus disease 2019 (COVID-19) manifested a broad range in susceptibility and severity to the disease, the pre-existing immune memory to related pathogens cross-reactive against SARS-CoV-2 can influence the disease outcome in COVID-19. Here, we investigated the potential extent of T cell cross-reactivity against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that can be conferred by other coronaviruses and influenza virus, and generated an in silico map of public and private CD8+ T cell epitopes between coronaviruses. We observed 794 predicted SARS-CoV-2 epitopes of which 52% were private and 48% were public. Ninety-nine percent of the public epitopes were shared with SARS-CoV and 5.4% were shared with either one of four common coronaviruses, 229E, HKU1, NL63, and OC43. Moreover, to assess the potential risk of self-reactivity and/or diminished T cell response for peptides identical or highly similar to the host, we identified predicted epitopes with high sequence similarity with human proteome. Lastly, we compared predicted epitopes from coronaviruses with epitopes from influenza virus deposited in IEDB, and found only a small number of peptides with limited potential for cross-reactivity between the two virus families. We believe our comprehensive in silico profile of private and public epitopes across coronaviruses would facilitate design of vaccines, and provide insights into the presence of pre-existing coronavirus-specific memory CD8+ T cells that may influence immune responses against SARS-CoV-2.
Keywords	Immunology ; Applied Immunology (incl. Antibody Engineering ; Xenotransplantation and T-cell Therapies) ; Autoimmunity ; Cellular Immunology ; Humoural Immunology and Immunochemistry ; Immunogenetics (incl. Genetic Immunology) ; Innate Immunity ; Transplantation Immunology ; Tumour Immunology ; Immunology not elsewhere classified ; Genetic Immunology ; Animal Immunology ; Veterinary Immunology ; cross-reactivity ; antigen presentation ; predict immunogenicity ; epitopes ; CD8+ T cell recognition ; COVID-19 ; SARS-CoV-2 ; covid19
Subject code	610
Publishing date	2020-11-05T05:28:57Z
Publishing country	uk
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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