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

Additional file 3: of Mining, analyzing, and integrating viral signals from metagenomic data

Tingting Zheng (400620)
Jun Li (6494)
Yueqiong Ni (691206)
Kang Kang (120256)
Maria-Anna Misiakou (6486560)
Lejla Imamovic (180270)
Billy Chow (6486563)
Anne Rode (6486566)
Peter Bytzer (5752637)
Morten Sommer (3453896)
Gianni Panagiotou (87405)

March 2019

Table S3. The number of putative metagenomic phage contigs and non-phage contigs in metagenomic asse...

Additional file 4: of Genome-wide diversity in temporal and regional populations of the betabaculovirus Erinnyis ello granulovirus (ErelGV)

A. Brito (2906399)
F. Melo (3527822)
D. Ardisson-Araújo (5783990)
W. Sihler (5783960)
M. Souza (5783963)
B. Ribeiro (5783969)

November 2018

Showing a phylogram of Betabaculovirus and ErelGV isolates. The phylogeny was inferred using concate...

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 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 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 1: 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 S1. Viruses used in this study and their associated information. Listing of classified virus s...

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 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 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 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 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 3: of Metagenomic analysis of viruses associated with maize lethal necrosis in Kenya

Mwathi Wamaitha (5269673)
Deepti Nigam (5269685)
Solomon Maina (803966)
Francesca Stomeo (679105)
Anne Wangai (5269676)
Joyce Njuguna (3179466)
Timothy Holton (5269682)
Bramwel Wanjala (5269679)
Mark Wamalwa (679106)
Tanui Lucas (5269670)
Appolinaire Djikeng (41915)
Hernan Garcia-Ruiz (711430)

May 2018

Figure S2. Size and frequency of de novo-assembled representative contigs with high similarity to kn...

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 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 2: of Generation and comparative genomics of synthetic dengue viruses

Eli Goz (769957)
Yael Tsalenchuck (5185529)
Rony Benaroya (5185523)
Zohar Zafrir (589604)
Shimshi Atar (769956)
Tahel Altman (5185532)
Justin Julander (5185526)
Tamir Tuller (123492)

May 2018

List ofÂ the accession numbers of the DENV-1/DENV-2/DENV-3/DENV-4/ZIKV genomes analyzed. (XLSX 72 kb

Additional file 3: of Mining, analyzing, and integrating viral signals from metagenomic data

Tingting Zheng (400620)
Jun Li (6494)
Yueqiong Ni (691206)
Kang Kang (120256)
Maria-Anna Misiakou (6486560)
Lejla Imamovic (180270)
Billy Chow (6486563)
Anne Rode (6486566)
Peter Bytzer (5752637)
Morten Sommer (3453896)
Gianni Panagiotou (87405)

March 2019

Table S3. The number of putative metagenomic phage contigs and non-phage contigs in metagenomic asse...

Additional file 4: of Genome-wide diversity in temporal and regional populations of the betabaculovirus Erinnyis ello granulovirus (ErelGV)

A. Brito (2906399)
F. Melo (3527822)
D. Ardisson-Araújo (5783990)
W. Sihler (5783960)
M. Souza (5783963)
B. Ribeiro (5783969)

November 2018

Showing a phylogram of Betabaculovirus and ErelGV isolates. The phylogeny was inferred using concate...

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 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 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 1: 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 S1. Viruses used in this study and their associated information. Listing of classified virus s...

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 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 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 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 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 3: of Metagenomic analysis of viruses associated with maize lethal necrosis in Kenya

Mwathi Wamaitha (5269673)
Deepti Nigam (5269685)
Solomon Maina (803966)
Francesca Stomeo (679105)
Anne Wangai (5269676)
Joyce Njuguna (3179466)
Timothy Holton (5269682)
Bramwel Wanjala (5269679)
Mark Wamalwa (679106)
Tanui Lucas (5269670)
Appolinaire Djikeng (41915)
Hernan Garcia-Ruiz (711430)

May 2018

Figure S2. Size and frequency of de novo-assembled representative contigs with high similarity to kn...

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 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 2: of Generation and comparative genomics of synthetic dengue viruses

Eli Goz (769957)
Yael Tsalenchuck (5185529)
Rony Benaroya (5185523)
Zohar Zafrir (589604)
Shimshi Atar (769956)
Tahel Altman (5185532)
Justin Julander (5185526)
Tamir Tuller (123492)

May 2018

List ofÂ the accession numbers of the DENV-1/DENV-2/DENV-3/DENV-4/ZIKV genomes analyzed. (XLSX 72 kb

Additional file 3: of Mining, analyzing, and integrating viral signals from metagenomic data

Tingting Zheng (400620)
Jun Li (6494)
Yueqiong Ni (691206)
Kang Kang (120256)
Maria-Anna Misiakou (6486560)
Lejla Imamovic (180270)
Billy Chow (6486563)
Anne Rode (6486566)
Peter Bytzer (5752637)
Morten Sommer (3453896)
Gianni Panagiotou (87405)

March 2019

Table S3. The number of putative metagenomic phage contigs and non-phage contigs in metagenomic asse...

Additional file 4: of Genome-wide diversity in temporal and regional populations of the betabaculovirus Erinnyis ello granulovirus (ErelGV)

A. Brito (2906399)
F. Melo (3527822)
D. Ardisson-Araújo (5783990)
W. Sihler (5783960)
M. Souza (5783963)
B. Ribeiro (5783969)

November 2018

Showing a phylogram of Betabaculovirus and ErelGV isolates. The phylogeny was inferred using concate...

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

Abstract

Extracted data

Additional file 12: 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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