Additional file 1: of The genomic underpinnings of eukaryotic virus taxonomy: creating a sequence-based framework for family-level virus classification

Additional file 1: of Design and application of a novel two-amplicon approach for defining eukaryotic microbiota

Ana Popovic (1881349)
Celine Bourdon (2741548)
Pauline Wang (3567824)
David Guttman (3524483)
Wieger Voskuijl (2741554)
Michael Grigg (437179)
Robert Bandsma (2741539)
John Parkinson (4087)

December 2018

Table S1. Accuracy of taxonomic assignments of 18S and 28S rRNA variable genetic regions. Related to...

Additional file 3: of Lifespan of restriction-modification systems critically affects avoidance of their recognition sites in host genomes

Ivan Rusinov (3513974)
Anna Ershova (3513968)
Anna Karyagina (3513971)
Sergey Spirin (3513965)
Andrei Alexeevski (3513977)

December 2015

List of all analyzed genomic sequences of eukaryotic viruses. Tab-delimited table of viral genome se...

Additional file 3: Table S3. of A census of Îą-helical membrane proteins in double-stranded DNA viruses infecting bacteria and archaea

David Kristensen (3482000)
Usman Saeed (3482003)
Dmitrij Frishman (3652)
Eugene Koonin (8868)

November 2015

Virus categories. Description of virus categories and data shown in Figs.Â 5 and 6. (XLSX 49Â kb

Additional file 2: of The genomic underpinnings of eukaryotic virus taxonomy: creating a sequence-based framework for family-level virus classification

Pakorn Aiewsakun (3508907)
Peter Simmonds (191583)

February 2018

Table S2. Summary of the virus taxa analysed in this study. Listing of ICTV assigned taxa of the seq...

Additional file 3: of The genomic underpinnings of eukaryotic virus taxonomy: creating a sequence-based framework for family-level virus classification

Pakorn Aiewsakun (3508907)
Peter Simmonds (191583)

February 2018

Table S3. Summary of protein profile hidden Markov model databases. Complete list and description of...

Additional file 8: of The genomic underpinnings of eukaryotic virus taxonomy: creating a sequence-based framework for family-level virus classification

Pakorn Aiewsakun (3508907)
Peter Simmonds (191583)

February 2018

Table S8. Length thresholds used to identify (near) complete virus sequences in metagenomic datasets...

Additional file 11: of The genomic underpinnings of eukaryotic virus taxonomy: creating a sequence-based framework for family-level virus classification

Pakorn Aiewsakun (3508907)
Peter Simmonds (191583)

February 2018

Figures S13âS15. Phylogenetic trees of classified virus groups. Analysis of phylogeny relationship...

Additional file 6: of The genomic underpinnings of eukaryotic virus taxonomy: creating a sequence-based framework for family-level virus classification

Pakorn Aiewsakun (3508907)
Peter Simmonds (191583)

February 2018

Table S6. Cross-validation analysis. Scoring table for cross-validation analysis used to test specif...

Additional file 12: of The genomic underpinnings of eukaryotic virus taxonomy: creating a sequence-based framework for family-level virus classification

Pakorn Aiewsakun (3508907)
Peter Simmonds (191583)

February 2018

Figures S16–S19. Dendrograms of individual virus sequences of classified and metagenomic viruses in ...

Additional file 10: of The genomic underpinnings of eukaryotic virus taxonomy: creating a sequence-based framework for family-level virus classification

Pakorn Aiewsakun (3508907)
Peter Simmonds (191583)

February 2018

Figures S7–S12. Dendrograms of individual virus sequences of classified viruses in Baltimore groups ...

Additional file 13: of The genomic underpinnings of eukaryotic virus taxonomy: creating a sequence-based framework for family-level virus classification

Pakorn Aiewsakun (3508907)
Peter Simmonds (191583)

February 2018

Analysis of GRAViTy groupings that conflict with ITCV family assignments. Analysis of sequences whos...

Additional file 1: Table S1. of Transmission of viruses via our microbiomes

Melissa Ly (787775)
Marcus Jones (1784308)
Shira Abeles (3526082)
Tasha Santiago-Rodriguez (3419813)
Jonathan Gao (3539495)
Ivan Chan (3539498)
Chandrabali Ghose (61491)
David Pride (3419807)

December 2016

Study Subjects. Table S2. Viral homologues within and between households. Table S3. Primer sequences...

Additional file 3: of Discovery and genome characterization of three new Jeilongviruses, a lineage of paramyxoviruses characterized by their unique membrane proteins

Bert Vanmechelen (4540189)
Magda Bletsa (5639471)
Lies Laenen (4540192)
Ana Lopes (356110)
Valentijn Vergote (400078)
Leen Beller (5639474)
Ward Deboutte (3858511)
Miša Korva (510982)
Tatjana Avšič Županc (5639477)
Joëlle Goüy de Bellocq (372546)
Sophie Gryseels (144917)
Herwig Leirs (40357)
Philippe Lemey (30422)
Bram Vrancken (546937)
Piet Maes (473809)

August 2018

Table S1. List of GenBank accession numbers of all viral sequences used, ordered by genus. A single ...

Additional file 1: of Phylogenetic and recombination analysis of the herpesvirus genus varicellovirus

Aaron Kolb (4605769)
Andrew Lewin (4605766)
Ralph Moeller Trane (4605760)
Gillian McLellan (4605757)
Curtis Brandt (4605763)

November 2017

Table S1. Accession numbers for the sequences used in the present study. The species, isolation host...

Additional file 6: Figure S2. of A robust and cost-effective approach to sequence and analyze complete genomes of small RNA viruses

Kiril Dimitrov (3811243)
Poonam Sharma (467670)
Jeremy Volkening (3914104)
Iryna Goraichuk (3811240)
Abdul Wajid (462803)
Shafqat Rehmani (3914101)
Asma Basharat (3914098)
Ismaila Shittu (3914107)
Tony Joannis (52866)
Patti Miller (3546770)
Claudio Afonso (41921)

April 2017

Phylogenetic analysis based on the complete genome coding sequence of Newcastle disease virus isolat...

Additional file 1: of Design and application of a novel two-amplicon approach for defining eukaryotic microbiota

Ana Popovic (1881349)
Celine Bourdon (2741548)
Pauline Wang (3567824)
David Guttman (3524483)
Wieger Voskuijl (2741554)
Michael Grigg (437179)
Robert Bandsma (2741539)
John Parkinson (4087)

December 2018

Table S1. Accuracy of taxonomic assignments of 18S and 28S rRNA variable genetic regions. Related to...

Additional file 3: of Lifespan of restriction-modification systems critically affects avoidance of their recognition sites in host genomes

Ivan Rusinov (3513974)
Anna Ershova (3513968)
Anna Karyagina (3513971)
Sergey Spirin (3513965)
Andrei Alexeevski (3513977)

December 2015

List of all analyzed genomic sequences of eukaryotic viruses. Tab-delimited table of viral genome se...

Additional file 3: Table S3. of A census of Îą-helical membrane proteins in double-stranded DNA viruses infecting bacteria and archaea

David Kristensen (3482000)
Usman Saeed (3482003)
Dmitrij Frishman (3652)
Eugene Koonin (8868)

November 2015

Virus categories. Description of virus categories and data shown in Figs.Â 5 and 6. (XLSX 49Â kb

Additional file 2: of The genomic underpinnings of eukaryotic virus taxonomy: creating a sequence-based framework for family-level virus classification

Pakorn Aiewsakun (3508907)
Peter Simmonds (191583)

February 2018

Table S2. Summary of the virus taxa analysed in this study. Listing of ICTV assigned taxa of the seq...

Additional file 3: of The genomic underpinnings of eukaryotic virus taxonomy: creating a sequence-based framework for family-level virus classification

Pakorn Aiewsakun (3508907)
Peter Simmonds (191583)

February 2018

Table S3. Summary of protein profile hidden Markov model databases. Complete list and description of...

Additional file 8: of The genomic underpinnings of eukaryotic virus taxonomy: creating a sequence-based framework for family-level virus classification

Pakorn Aiewsakun (3508907)
Peter Simmonds (191583)

February 2018

Table S8. Length thresholds used to identify (near) complete virus sequences in metagenomic datasets...

Additional file 11: of The genomic underpinnings of eukaryotic virus taxonomy: creating a sequence-based framework for family-level virus classification

Pakorn Aiewsakun (3508907)
Peter Simmonds (191583)

February 2018

Figures S13âS15. Phylogenetic trees of classified virus groups. Analysis of phylogeny relationship...

Additional file 6: of The genomic underpinnings of eukaryotic virus taxonomy: creating a sequence-based framework for family-level virus classification

Pakorn Aiewsakun (3508907)
Peter Simmonds (191583)

February 2018

Table S6. Cross-validation analysis. Scoring table for cross-validation analysis used to test specif...

Additional file 12: of The genomic underpinnings of eukaryotic virus taxonomy: creating a sequence-based framework for family-level virus classification

Pakorn Aiewsakun (3508907)
Peter Simmonds (191583)

February 2018

Figures S16–S19. Dendrograms of individual virus sequences of classified and metagenomic viruses in ...

Additional file 10: of The genomic underpinnings of eukaryotic virus taxonomy: creating a sequence-based framework for family-level virus classification

Pakorn Aiewsakun (3508907)
Peter Simmonds (191583)

February 2018

Figures S7–S12. Dendrograms of individual virus sequences of classified viruses in Baltimore groups ...

Additional file 13: of The genomic underpinnings of eukaryotic virus taxonomy: creating a sequence-based framework for family-level virus classification

Pakorn Aiewsakun (3508907)
Peter Simmonds (191583)

February 2018

Analysis of GRAViTy groupings that conflict with ITCV family assignments. Analysis of sequences whos...

Additional file 1: Table S1. of Transmission of viruses via our microbiomes

Melissa Ly (787775)
Marcus Jones (1784308)
Shira Abeles (3526082)
Tasha Santiago-Rodriguez (3419813)
Jonathan Gao (3539495)
Ivan Chan (3539498)
Chandrabali Ghose (61491)
David Pride (3419807)

December 2016

Study Subjects. Table S2. Viral homologues within and between households. Table S3. Primer sequences...

Additional file 3: of Discovery and genome characterization of three new Jeilongviruses, a lineage of paramyxoviruses characterized by their unique membrane proteins

Bert Vanmechelen (4540189)
Magda Bletsa (5639471)
Lies Laenen (4540192)
Ana Lopes (356110)
Valentijn Vergote (400078)
Leen Beller (5639474)
Ward Deboutte (3858511)
Miša Korva (510982)
Tatjana Avšič Županc (5639477)
Joëlle Goüy de Bellocq (372546)
Sophie Gryseels (144917)
Herwig Leirs (40357)
Philippe Lemey (30422)
Bram Vrancken (546937)
Piet Maes (473809)

August 2018

Table S1. List of GenBank accession numbers of all viral sequences used, ordered by genus. A single ...

Additional file 1: of Phylogenetic and recombination analysis of the herpesvirus genus varicellovirus

Aaron Kolb (4605769)
Andrew Lewin (4605766)
Ralph Moeller Trane (4605760)
Gillian McLellan (4605757)
Curtis Brandt (4605763)

November 2017

Table S1. Accession numbers for the sequences used in the present study. The species, isolation host...

Additional file 6: Figure S2. of A robust and cost-effective approach to sequence and analyze complete genomes of small RNA viruses

Kiril Dimitrov (3811243)
Poonam Sharma (467670)
Jeremy Volkening (3914104)
Iryna Goraichuk (3811240)
Abdul Wajid (462803)
Shafqat Rehmani (3914101)
Asma Basharat (3914098)
Ismaila Shittu (3914107)
Tony Joannis (52866)
Patti Miller (3546770)
Claudio Afonso (41921)

April 2017

Phylogenetic analysis based on the complete genome coding sequence of Newcastle disease virus isolat...

Additional file 1: of Design and application of a novel two-amplicon approach for defining eukaryotic microbiota

Ana Popovic (1881349)
Celine Bourdon (2741548)
Pauline Wang (3567824)
David Guttman (3524483)
Wieger Voskuijl (2741554)
Michael Grigg (437179)
Robert Bandsma (2741539)
John Parkinson (4087)

December 2018

Table S1. Accuracy of taxonomic assignments of 18S and 28S rRNA variable genetic regions. Related to...

Additional file 3: of Lifespan of restriction-modification systems critically affects avoidance of their recognition sites in host genomes

Ivan Rusinov (3513974)
Anna Ershova (3513968)
Anna Karyagina (3513971)
Sergey Spirin (3513965)
Andrei Alexeevski (3513977)

December 2015

List of all analyzed genomic sequences of eukaryotic viruses. Tab-delimited table of viral genome se...

Additional file 3: Table S3. of A census of Îą-helical membrane proteins in double-stranded DNA viruses infecting bacteria and archaea

David Kristensen (3482000)
Usman Saeed (3482003)
Dmitrij Frishman (3652)
Eugene Koonin (8868)

November 2015

Virus categories. Description of virus categories and data shown in Figs.Â 5 and 6. (XLSX 49Â kb

Additional file 1: of The genomic underpinnings of eukaryotic virus taxonomy: creating a sequence-based framework for family-level virus classification

Abstract

Extracted data

Additional file 1: of The genomic underpinnings of eukaryotic virus taxonomy: creating a sequence-based framework for family-level virus classification

Abstract

Extracted data

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