Additional file 4: of Peptimapper: proteogenomics workflow for the expert annotation of eukaryotic genomes

Additional file 1: of Evaluation of linear models and missing value imputation for the analysis of peptide-centric proteomics

Philip Berg (6468563)
Evan McConnell (3483155)
Leslie Hicks (2870870)
Sorina Popescu (6468506)
George Popescu (6468509)

March 2019

File containing the implementation of Progenesis LFQ workflow for UPS1 dataset. (PDF 206 kb

Additional file 4: of Systems-level organization of yeast methylotrophic lifestyle

Hannes Rußmayer (3588293)
Markus Buchetics (3588278)
Clemens Gruber (544217)
Minoska Valli (6800)
Karlheinz Grillitsch (3588290)
Gerda Modarres (3588263)
Raffaele Guerrasio (3588266)
Kristaps Klavins (1812859)
Stefan Neubauer (88474)
Hedda Drexler (1812856)
Matthias Steiger (1473007)
Christina Troyer (3588284)
Ali Al Chalabi (3588287)
Guido Krebiehl (252734)
Denise Sonntag (3588275)
Günther Zellnig (779345)
Günther Daum (469693)
Alexandra Graf (492269)
Friedrich Altmann (33138)
Gunda Koellensperger (1473001)
Stephan Hann (1472998)
Michael Sauer (6797)
Diethard Mattanovich (6803)
Brigitte Gasser (6799)

September 2015

Proteomic identification and quantification of methanol metabolic enzymes and control proteins in pe...

Additional file 4: of Harnessing single-cell genomics to improve the physiological fidelity of organoid-derived cell types

Benjamin Mead (5343608)
Jose Ordovas-Montanes (4805409)
Alexandra Braun (4862290)
Lauren Levy (5343611)
Prerna Bhargava (1572145)
Matthew Szucs (5343614)
Dustin Ammendolia (5343605)
Melanie MacMullan (5343617)
Xiaolei Yin (378829)
Travis Hughes (5343599)
Marc Wadsworth (5343602)
Rushdy Ahmad (443194)
Seth Rakoff-Nahoum (272894)
Steven Carr (5343596)
Robert Langer (166824)
James Collins (489526)
Alex Shalek (3424427)
Jeffrey Karp (1229817)

June 2018

Figure S2. Proteomic pipeline, sample-to-sample comparison, and insights from the in vitro PC proteo...

Additional file 5: of Peptimapper: proteogenomics workflow for the expert annotation of eukaryotic genomes

Laetitia Guillot (135890)
Ludovic Delage (220720)
Alain Viari (72589)
Yves Vandenbrouck (72588)
Emmanuelle Com (180558)
Andrés Ritter (3808825)
Régis Lavigne (613177)
Dominique Marie (257646)
Pierre Peterlongo (3282846)
Philippe Potin (216035)
Charles Pineau (515040)

January 2019

Bioinformatic tools distribution. A. Peptimapper dockerfile. B. Workflow labeled “Peptimapper” avail...

Additional file 6: of Peptimapper: proteogenomics workflow for the expert annotation of eukaryotic genomes

Laetitia Guillot (135890)
Ludovic Delage (220720)
Alain Viari (72589)
Yves Vandenbrouck (72588)
Emmanuelle Com (180558)
Andrés Ritter (3808825)
Régis Lavigne (613177)
Dominique Marie (257646)
Pierre Peterlongo (3282846)
Philippe Potin (216035)
Charles Pineau (515040)

January 2019

Study of additional clusters under investigation listed Table 3. RNA-sequencing and EST data have be...

Additional file 4: of Evolutionary hallmarks of the human proteome: chasing the age and coregulation of protein-coding genes

Katia Lopes (3512426)
Francisco Campos-Laborie (3430919)
Ricardo Vialle (3512423)
José Ortega (3512429)
Javier De Las Rivas (19407)

October 2016

TABLE (.XLS) including the data and IDs of the 17,437 human protein-coding genes included in each of...

Additional file 4: of Unsupervised statistical discovery of spaced motifs in prokaryotic genomes

Hao Tong (529793)
Paul Schliekelman (1849267)
Jan Mrรกzek (3620453)

January 2017

Table S4. List of the 30 genomes selected for detailed analysis. Description of data: The table cont...

Additional file 2: of Evaluation of linear models and missing value imputation for the analysis of peptide-centric proteomics

Philip Berg (6468563)
Evan McConnell (3483155)
Leslie Hicks (2870870)
Sorina Popescu (6468506)
George Popescu (6468509)

March 2019

File containing the implementation of Progenesis LFQ workflow for Chlamydomonas-yeast dataset. (PDF ...

Additional file 2: Figure S1. of Evaluating the effect of database inflation in proteogenomic search on sensitive and reliable peptide identification

Honglan Li (328866)
Yoon Joh (3601148)
Hyunwoo Kim (690467)
Eunok Paek (19302)
Sang-Won Lee (193873)
Kyu-Baek Hwang (5187)

December 2016

Workflow for generating a simulated proteogenomic database for yeast. (DOCX 743Â kb

Additional file 4: of Identification of new signalling peptides through a genome-wide survey of 250 fungal secretomes

Morgane Le Marquer (6244946)
HĂŠlĂ¨ne San Clemente (6244988)
Christophe Roux (17822)
Bruno Savelli (636402)
Nicolas Frei dit Frey (6244955)

January 2019

Figure S1. Scheme depicting the informatic pipeline used to identify KEX2 processed repeat proteins ...

Additional file 4: of The Listeria monocytogenes Core-Genome Sequence Typer (LmCGST): a bioinformatic pipeline for molecular characterization with next-generation sequence data

Arthur Pightling (3531110)
Nicholas Petronella (619646)
Franco Pagotto (619647)

October 2015

List of 1013 open-reading frames that comprise the high-confidence core genome with NCBI numbers for...

Peptimapper: proteogenomics workflow for the expert annotation of eukaryotic genomes

Laetitia Guillot
Ludovic Delage
Alain Viari
Yves Vandenbrouck
Emmanuelle Com
Andrés Ritter
Régis Lavigne
Dominique Marie
Pierre Peterlongo
Philippe Potin
Charles Pineau

January 2019

Abstract Background Accurate structural annotation of genomes is still a challenge, despite the prog...

Additional file 1: of Software-based analysis of bacteriophage genomes, physical ends, and packaging strategies

Bryan Merrill (3435632)
Andy Ward (3435635)
Julianne Grose (3435629)
Sandra Hope (2838263)

August 2016

Table of phages and large terminase proteins used in Phamerator database. (XLSX 15Â kb

Additional file 12: Figure S6. of A multi-omic analysis of human naĂŻve CD4+ T cells

Christopher Mitchell (3253833)
Derese Getnet (174411)
Min-Sik Kim (421554)
Srikanth Manda (3427979)
Praveen Kumar (8242)
Tai-Chung Huang (841150)
Sneha Pinto (3427976)
Raja Nirujogi (3427955)
Mio Iwasaki (2007559)
Patrick Shaw (2904647)
Xinyan Wu (314562)
Jun Zhong (236780)
Raghothama Chaerkady (156766)
Arivusudar Marimuthu (265325)
Babylakshmi Muthusamy (2131045)
Nandini Sahasrabuddhe (3427958)
Rajesh Raju (771787)
Caitlyn Bowman (3427973)
Ludmila Danilova (3427982)
Jevon Cutler (3427964)
Dhanashree Kelkar (1590292)
Charles Drake (3427961)
T. Prasad (3427985)
Luigi Marchionni (363972)
Peter Murakami (171557)
Alan Scott (3427967)
Leming Shi (22343)
Jean Thierry-Mieg (2989)
Danielle Thierry-Mieg (2990)
Rafael Irizarry (6337)
Leslie Cope (49815)
Yasushi Ishihama (44929)
Charles Wang (242565)
Harsha Gowda (1321746)
Akhilesh Pandey (14293)

November 2015

Proteogenomic pipeline. Custom protein databases that were used for searching tandem mass spectromet...

Additional file 4: Figure S2. of A viability-linked metagenomic analysis of cleanroom environments: eukarya, prokaryotes, and viruses

Thomas Weinmaier (124598)
Alexander Probst (3407996)
Myron Duc (3561614)
Doina Ciobanu (2648437)
Jan-Fang Cheng (48619)
Natalia Ivanova (8850)
Thomas Rattei (13991)
Parag Vaishampayan (783948)

December 2015

A PDF showing a heatmap of relative abundances. Heatmap of relative abundances of key enzymes, with ...

Additional file 1: of Evaluation of linear models and missing value imputation for the analysis of peptide-centric proteomics

Philip Berg (6468563)
Evan McConnell (3483155)
Leslie Hicks (2870870)
Sorina Popescu (6468506)
George Popescu (6468509)

March 2019

File containing the implementation of Progenesis LFQ workflow for UPS1 dataset. (PDF 206 kb

Additional file 4: of Systems-level organization of yeast methylotrophic lifestyle

Hannes Rußmayer (3588293)
Markus Buchetics (3588278)
Clemens Gruber (544217)
Minoska Valli (6800)
Karlheinz Grillitsch (3588290)
Gerda Modarres (3588263)
Raffaele Guerrasio (3588266)
Kristaps Klavins (1812859)
Stefan Neubauer (88474)
Hedda Drexler (1812856)
Matthias Steiger (1473007)
Christina Troyer (3588284)
Ali Al Chalabi (3588287)
Guido Krebiehl (252734)
Denise Sonntag (3588275)
Günther Zellnig (779345)
Günther Daum (469693)
Alexandra Graf (492269)
Friedrich Altmann (33138)
Gunda Koellensperger (1473001)
Stephan Hann (1472998)
Michael Sauer (6797)
Diethard Mattanovich (6803)
Brigitte Gasser (6799)

September 2015

Proteomic identification and quantification of methanol metabolic enzymes and control proteins in pe...

Additional file 4: of Harnessing single-cell genomics to improve the physiological fidelity of organoid-derived cell types

Benjamin Mead (5343608)
Jose Ordovas-Montanes (4805409)
Alexandra Braun (4862290)
Lauren Levy (5343611)
Prerna Bhargava (1572145)
Matthew Szucs (5343614)
Dustin Ammendolia (5343605)
Melanie MacMullan (5343617)
Xiaolei Yin (378829)
Travis Hughes (5343599)
Marc Wadsworth (5343602)
Rushdy Ahmad (443194)
Seth Rakoff-Nahoum (272894)
Steven Carr (5343596)
Robert Langer (166824)
James Collins (489526)
Alex Shalek (3424427)
Jeffrey Karp (1229817)

June 2018

Figure S2. Proteomic pipeline, sample-to-sample comparison, and insights from the in vitro PC proteo...

Additional file 5: of Peptimapper: proteogenomics workflow for the expert annotation of eukaryotic genomes

Laetitia Guillot (135890)
Ludovic Delage (220720)
Alain Viari (72589)
Yves Vandenbrouck (72588)
Emmanuelle Com (180558)
Andrés Ritter (3808825)
Régis Lavigne (613177)
Dominique Marie (257646)
Pierre Peterlongo (3282846)
Philippe Potin (216035)
Charles Pineau (515040)

January 2019

Bioinformatic tools distribution. A. Peptimapper dockerfile. B. Workflow labeled “Peptimapper” avail...

Additional file 6: of Peptimapper: proteogenomics workflow for the expert annotation of eukaryotic genomes

Laetitia Guillot (135890)
Ludovic Delage (220720)
Alain Viari (72589)
Yves Vandenbrouck (72588)
Emmanuelle Com (180558)
Andrés Ritter (3808825)
Régis Lavigne (613177)
Dominique Marie (257646)
Pierre Peterlongo (3282846)
Philippe Potin (216035)
Charles Pineau (515040)

January 2019

Study of additional clusters under investigation listed Table 3. RNA-sequencing and EST data have be...

Additional file 4: of Evolutionary hallmarks of the human proteome: chasing the age and coregulation of protein-coding genes

Katia Lopes (3512426)
Francisco Campos-Laborie (3430919)
Ricardo Vialle (3512423)
José Ortega (3512429)
Javier De Las Rivas (19407)

October 2016

TABLE (.XLS) including the data and IDs of the 17,437 human protein-coding genes included in each of...

Additional file 4: of Unsupervised statistical discovery of spaced motifs in prokaryotic genomes

Hao Tong (529793)
Paul Schliekelman (1849267)
Jan Mrรกzek (3620453)

January 2017

Table S4. List of the 30 genomes selected for detailed analysis. Description of data: The table cont...

Additional file 2: of Evaluation of linear models and missing value imputation for the analysis of peptide-centric proteomics

Philip Berg (6468563)
Evan McConnell (3483155)
Leslie Hicks (2870870)
Sorina Popescu (6468506)
George Popescu (6468509)

March 2019

File containing the implementation of Progenesis LFQ workflow for Chlamydomonas-yeast dataset. (PDF ...

Additional file 2: Figure S1. of Evaluating the effect of database inflation in proteogenomic search on sensitive and reliable peptide identification

Honglan Li (328866)
Yoon Joh (3601148)
Hyunwoo Kim (690467)
Eunok Paek (19302)
Sang-Won Lee (193873)
Kyu-Baek Hwang (5187)

December 2016

Workflow for generating a simulated proteogenomic database for yeast. (DOCX 743Â kb

Additional file 4: of Identification of new signalling peptides through a genome-wide survey of 250 fungal secretomes

Morgane Le Marquer (6244946)
HĂŠlĂ¨ne San Clemente (6244988)
Christophe Roux (17822)
Bruno Savelli (636402)
Nicolas Frei dit Frey (6244955)

January 2019

Figure S1. Scheme depicting the informatic pipeline used to identify KEX2 processed repeat proteins ...

Additional file 4: of The Listeria monocytogenes Core-Genome Sequence Typer (LmCGST): a bioinformatic pipeline for molecular characterization with next-generation sequence data

Arthur Pightling (3531110)
Nicholas Petronella (619646)
Franco Pagotto (619647)

October 2015

List of 1013 open-reading frames that comprise the high-confidence core genome with NCBI numbers for...

Peptimapper: proteogenomics workflow for the expert annotation of eukaryotic genomes

Laetitia Guillot
Ludovic Delage
Alain Viari
Yves Vandenbrouck
Emmanuelle Com
Andrés Ritter
Régis Lavigne
Dominique Marie
Pierre Peterlongo
Philippe Potin
Charles Pineau

January 2019

Abstract Background Accurate structural annotation of genomes is still a challenge, despite the prog...

Additional file 1: of Software-based analysis of bacteriophage genomes, physical ends, and packaging strategies

Bryan Merrill (3435632)
Andy Ward (3435635)
Julianne Grose (3435629)
Sandra Hope (2838263)

August 2016

Table of phages and large terminase proteins used in Phamerator database. (XLSX 15Â kb

Additional file 12: Figure S6. of A multi-omic analysis of human naĂŻve CD4+ T cells

Christopher Mitchell (3253833)
Derese Getnet (174411)
Min-Sik Kim (421554)
Srikanth Manda (3427979)
Praveen Kumar (8242)
Tai-Chung Huang (841150)
Sneha Pinto (3427976)
Raja Nirujogi (3427955)
Mio Iwasaki (2007559)
Patrick Shaw (2904647)
Xinyan Wu (314562)
Jun Zhong (236780)
Raghothama Chaerkady (156766)
Arivusudar Marimuthu (265325)
Babylakshmi Muthusamy (2131045)
Nandini Sahasrabuddhe (3427958)
Rajesh Raju (771787)
Caitlyn Bowman (3427973)
Ludmila Danilova (3427982)
Jevon Cutler (3427964)
Dhanashree Kelkar (1590292)
Charles Drake (3427961)
T. Prasad (3427985)
Luigi Marchionni (363972)
Peter Murakami (171557)
Alan Scott (3427967)
Leming Shi (22343)
Jean Thierry-Mieg (2989)
Danielle Thierry-Mieg (2990)
Rafael Irizarry (6337)
Leslie Cope (49815)
Yasushi Ishihama (44929)
Charles Wang (242565)
Harsha Gowda (1321746)
Akhilesh Pandey (14293)

November 2015

Proteogenomic pipeline. Custom protein databases that were used for searching tandem mass spectromet...

Additional file 4: Figure S2. of A viability-linked metagenomic analysis of cleanroom environments: eukarya, prokaryotes, and viruses

Thomas Weinmaier (124598)
Alexander Probst (3407996)
Myron Duc (3561614)
Doina Ciobanu (2648437)
Jan-Fang Cheng (48619)
Natalia Ivanova (8850)
Thomas Rattei (13991)
Parag Vaishampayan (783948)

December 2015

A PDF showing a heatmap of relative abundances. Heatmap of relative abundances of key enzymes, with ...

Additional file 1: of Evaluation of linear models and missing value imputation for the analysis of peptide-centric proteomics

Philip Berg (6468563)
Evan McConnell (3483155)
Leslie Hicks (2870870)
Sorina Popescu (6468506)
George Popescu (6468509)

March 2019

File containing the implementation of Progenesis LFQ workflow for UPS1 dataset. (PDF 206 kb

Additional file 4: of Systems-level organization of yeast methylotrophic lifestyle

Hannes Rußmayer (3588293)
Markus Buchetics (3588278)
Clemens Gruber (544217)
Minoska Valli (6800)
Karlheinz Grillitsch (3588290)
Gerda Modarres (3588263)
Raffaele Guerrasio (3588266)
Kristaps Klavins (1812859)
Stefan Neubauer (88474)
Hedda Drexler (1812856)
Matthias Steiger (1473007)
Christina Troyer (3588284)
Ali Al Chalabi (3588287)
Guido Krebiehl (252734)
Denise Sonntag (3588275)
Günther Zellnig (779345)
Günther Daum (469693)
Alexandra Graf (492269)
Friedrich Altmann (33138)
Gunda Koellensperger (1473001)
Stephan Hann (1472998)
Michael Sauer (6797)
Diethard Mattanovich (6803)
Brigitte Gasser (6799)

September 2015

Proteomic identification and quantification of methanol metabolic enzymes and control proteins in pe...

Additional file 4: of Harnessing single-cell genomics to improve the physiological fidelity of organoid-derived cell types

Benjamin Mead (5343608)
Jose Ordovas-Montanes (4805409)
Alexandra Braun (4862290)
Lauren Levy (5343611)
Prerna Bhargava (1572145)
Matthew Szucs (5343614)
Dustin Ammendolia (5343605)
Melanie MacMullan (5343617)
Xiaolei Yin (378829)
Travis Hughes (5343599)
Marc Wadsworth (5343602)
Rushdy Ahmad (443194)
Seth Rakoff-Nahoum (272894)
Steven Carr (5343596)
Robert Langer (166824)
James Collins (489526)
Alex Shalek (3424427)
Jeffrey Karp (1229817)

June 2018

Figure S2. Proteomic pipeline, sample-to-sample comparison, and insights from the in vitro PC proteo...

Additional file 4: of Peptimapper: proteogenomics workflow for the expert annotation of eukaryotic genomes

Abstract

Extracted data

Additional file 4: of Peptimapper: proteogenomics workflow for the expert annotation of eukaryotic genomes

Abstract

Extracted data

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