FinalOutput_Ovary

Validation of angiogenic ovarian cancer classification in our dataset and ten independent validation datasets.

Stefan Bentink (183842)
Benjamin Haibe-Kains (183845)
Thomas Risch (183849)
Jian-Bing Fan (28237)
Michelle S. Hirsch (183854)
Kristina Holton (183857)
Renee Rubio (15771)
Craig April (176343)
Jing Chen (4762)
Eliza Wickham-Garcia (183860)
Joyce Liu (183861)
Aedin Culhane (183862)
Ronny Drapkin (130800)
John Quackenbush (1213)
Ursula A. Matulonis (183863)

February 2012

Panels A, D and G display the gene expression of the 100 genes used to classify ovarian tumors in...

Four binary classifications of high grade ovarian serous cancer.

Stefan Bentink (183842)
Benjamin Haibe-Kains (183845)
Thomas Risch (183849)
Jian-Bing Fan (28237)
Michelle S. Hirsch (183854)
Kristina Holton (183857)
Renee Rubio (15771)
Craig April (176343)
Jing Chen (4762)
Eliza Wickham-Garcia (183860)
Joyce Liu (183861)
Aedin Culhane (183862)
Ronny Drapkin (130800)
John Quackenbush (1213)
Ursula A. Matulonis (183863)

February 2012

The ISIS algorithm identified four independent binary partition classifications (splits) of 129 o...

Comparison between 45 ovarian cancer (39 epithelial carcinoma and 6 borderline tissues) and 14 normal ovarian tissues.

Lin Wang (11986)
Miao-Jun Zhu (562073)
Ai-Min Ren (562074)
Hong-Fei Wu (562075)
Wu-Mei Han (562076)
Ruo-Ying Tan (562077)
Rui-Qin Tu (562078)

May 2014

A) The plot of miRNA assays used to profile compared samples: fold change (y-axis) against normal...

FinalOutput_Ovary

Beck, Andrew H.
Knoblauch, Nicholas W.
Hefti, Marco M.
Kaplan, Jennifer
Schnitt, Stuart J.
Culhane, Aedin C.
Schroeder, Markus S.
Quackenbush, John
Haibe-Kains, Benjamin

January 2013

FinalOutput_Ovary.RData contains the results from the traditional scaled data set in ovarian cancer,...

OvaryOutput_TradScaled

Beck, Andrew H.
Knoblauch, Nicholas W.
Hefti, Marco M.
Kaplan, Jennifer
Schnitt, Stuart J.
Culhane, Aedin C.
Schroeder, Markus S.
Quackenbush, John
Haibe-Kains, Benjamin

January 2013

OvaryOutput_TradScaled.RData contains the objects: allPs, allPs.adj, sumTable.BreastOutput_TradScale...

Ovary.Ps.OnPermutedData.RData

Beck, Andrew H.
Knoblauch, Nicholas W.
Hefti, Marco M.
Kaplan, Jennifer
Schnitt, Stuart J.
Culhane, Aedin C.
Schroeder, Markus S.
Quackenbush, John
Haibe-Kains, Benjamin

January 2013

ReadMe, Ovary.Ps.OnPermutedData.RData. Ovary.Ps.OnPermutedData.RData contains the results of perform...

BreastOutput_TradScaled

Andrew H. Beck (254596)
Nicholas W. Knoblauch (276487)
Marco M. Hefti (276488)
Jennifer Kaplan (276489)
Stuart J. Schnitt (276490)
Aedin C. Culhane (276491)
Markus S. Schroeder (276492)
John Quackenbush (1213)
Benjamin Haibe-Kains (183845)

October 2016

BreastOutput_TradScaled.RData is an R-workspace contains the objects: allPs, allPs.adj, sumTable. Th...

computeSAPS.Permute.PValue.R

Andrew H. Beck (254596)
Nicholas W. Knoblauch (276487)
Marco M. Hefti (276488)
Jennifer Kaplan (276489)
Stuart J. Schnitt (276490)
Aedin C. Culhane (276491)
Markus S. Schroeder (276492)
John Quackenbush (1213)
Benjamin Haibe-Kains (183845)

October 2016

computeSAPS.Permute.PValue.R – This script generates permutation-based p and q values for the SAPSsc...

OvaryTradScaleRankDir

Beck, Andrew H.
Knoblauch, Nicholas W.
Hefti, Marco M.
Kaplan, Jennifer
Schnitt, Stuart J.
Culhane, Aedin C.
Schroeder, Markus S.
Quackenbush, John
Haibe-Kains, Benjamin

January 2013

OvaryTradScaleRankDircontains the ranked gene lists of concordance indices used to perform the GSEA ...

BreastOutput_SubScaled

Beck, Andrew H.
Knoblauch, Nicholas W.
Hefti, Marco M.
Kaplan, Jennifer
Schnitt, Stuart J.
Culhane, Aedin C.
Schroeder, Markus S.
Quackenbush, John
Haibe-Kains, Benjamin

January 2013

BreastOutput_SubScaled.RData is an R-workspace contains the objects: allPs, allPs.adj, sumTable. The...

Univariate and multivariate analyses of OS/RFS in patients with primary ovarian cancer in TCGA-OV.

Lianzhi Qin (4560334)
Ting Li (117885)
Yuhua Liu (37269)

November 2017

Univariate and multivariate analyses of OS/RFS in patients with primary ovarian cancer in TCGA-OV...

Forest plot of estimated DOR for quantitative analysis of circulating cell free DNA in the diagnosis of ovarian cancer.

Quan Zhou (492529)
Wei Li (7081)
Bingjie Leng (2814445)
Wenfei Zheng (2814439)
Ze He (549047)
Manzhen Zuo (2814442)
Aihua Chen (663136)

June 2016

Forest plot of estimated DOR for quantitative analysis of circulating cell free DNA in the diagno...

A novel algorithm for better distinction of primary mucinous ovarian carcinomas and mucinous carcinomas metastatic to the ovary

Simons, M.
Bolhuis, Thomas
Haan, A.F. de
Bruggink, Annette H.
Bulten, J.
Massuger, L.F.
Nagtegaal, I.D.

January 2019

Contains fulltext : 201898.pdf (publisher's version ) (Open Access

Analytical Code for "Cross-population analysis of high-grade serous ovarian cancer reveals only two robust subtypes"

Gregory Way
James Rudd
Casey Greene

October 2015

Analytical code to accompany the manuscript: "High-grade serous ovarian cancer subtypes are similar ...

Replication Data for: Performance of the MasSpec Pen for Rapid Diagnosis of Ovarian Cancer

Sans, Marta
Zhang, Jialing
Lin, John Q.
Feider, Clara L.
Giese, Noah
Breen, Michael
Sebastian, Katherine
Liu, Jinsong
Sood, Anil K.
S. Eberlin, Livia

Replication Data for: Performance of the MasSpec Pen for Rapid Diagnosis of Ovarian Cance

Validation of angiogenic ovarian cancer classification in our dataset and ten independent validation datasets.

Stefan Bentink (183842)
Benjamin Haibe-Kains (183845)
Thomas Risch (183849)
Jian-Bing Fan (28237)
Michelle S. Hirsch (183854)
Kristina Holton (183857)
Renee Rubio (15771)
Craig April (176343)
Jing Chen (4762)
Eliza Wickham-Garcia (183860)
Joyce Liu (183861)
Aedin Culhane (183862)
Ronny Drapkin (130800)
John Quackenbush (1213)
Ursula A. Matulonis (183863)

February 2012

Panels A, D and G display the gene expression of the 100 genes used to classify ovarian tumors in...

Four binary classifications of high grade ovarian serous cancer.

Stefan Bentink (183842)
Benjamin Haibe-Kains (183845)
Thomas Risch (183849)
Jian-Bing Fan (28237)
Michelle S. Hirsch (183854)
Kristina Holton (183857)
Renee Rubio (15771)
Craig April (176343)
Jing Chen (4762)
Eliza Wickham-Garcia (183860)
Joyce Liu (183861)
Aedin Culhane (183862)
Ronny Drapkin (130800)
John Quackenbush (1213)
Ursula A. Matulonis (183863)

February 2012

The ISIS algorithm identified four independent binary partition classifications (splits) of 129 o...

Comparison between 45 ovarian cancer (39 epithelial carcinoma and 6 borderline tissues) and 14 normal ovarian tissues.

Lin Wang (11986)
Miao-Jun Zhu (562073)
Ai-Min Ren (562074)
Hong-Fei Wu (562075)
Wu-Mei Han (562076)
Ruo-Ying Tan (562077)
Rui-Qin Tu (562078)

May 2014

A) The plot of miRNA assays used to profile compared samples: fold change (y-axis) against normal...

FinalOutput_Ovary

Beck, Andrew H.
Knoblauch, Nicholas W.
Hefti, Marco M.
Kaplan, Jennifer
Schnitt, Stuart J.
Culhane, Aedin C.
Schroeder, Markus S.
Quackenbush, John
Haibe-Kains, Benjamin

January 2013

FinalOutput_Ovary.RData contains the results from the traditional scaled data set in ovarian cancer,...

OvaryOutput_TradScaled

Beck, Andrew H.
Knoblauch, Nicholas W.
Hefti, Marco M.
Kaplan, Jennifer
Schnitt, Stuart J.
Culhane, Aedin C.
Schroeder, Markus S.
Quackenbush, John
Haibe-Kains, Benjamin

January 2013

OvaryOutput_TradScaled.RData contains the objects: allPs, allPs.adj, sumTable.BreastOutput_TradScale...

Ovary.Ps.OnPermutedData.RData

Beck, Andrew H.
Knoblauch, Nicholas W.
Hefti, Marco M.
Kaplan, Jennifer
Schnitt, Stuart J.
Culhane, Aedin C.
Schroeder, Markus S.
Quackenbush, John
Haibe-Kains, Benjamin

January 2013

ReadMe, Ovary.Ps.OnPermutedData.RData. Ovary.Ps.OnPermutedData.RData contains the results of perform...

BreastOutput_TradScaled

Andrew H. Beck (254596)
Nicholas W. Knoblauch (276487)
Marco M. Hefti (276488)
Jennifer Kaplan (276489)
Stuart J. Schnitt (276490)
Aedin C. Culhane (276491)
Markus S. Schroeder (276492)
John Quackenbush (1213)
Benjamin Haibe-Kains (183845)

October 2016

BreastOutput_TradScaled.RData is an R-workspace contains the objects: allPs, allPs.adj, sumTable. Th...

computeSAPS.Permute.PValue.R

Andrew H. Beck (254596)
Nicholas W. Knoblauch (276487)
Marco M. Hefti (276488)
Jennifer Kaplan (276489)
Stuart J. Schnitt (276490)
Aedin C. Culhane (276491)
Markus S. Schroeder (276492)
John Quackenbush (1213)
Benjamin Haibe-Kains (183845)

October 2016

computeSAPS.Permute.PValue.R – This script generates permutation-based p and q values for the SAPSsc...

OvaryTradScaleRankDir

Beck, Andrew H.
Knoblauch, Nicholas W.
Hefti, Marco M.
Kaplan, Jennifer
Schnitt, Stuart J.
Culhane, Aedin C.
Schroeder, Markus S.
Quackenbush, John
Haibe-Kains, Benjamin

January 2013

OvaryTradScaleRankDircontains the ranked gene lists of concordance indices used to perform the GSEA ...

BreastOutput_SubScaled

Beck, Andrew H.
Knoblauch, Nicholas W.
Hefti, Marco M.
Kaplan, Jennifer
Schnitt, Stuart J.
Culhane, Aedin C.
Schroeder, Markus S.
Quackenbush, John
Haibe-Kains, Benjamin

January 2013

BreastOutput_SubScaled.RData is an R-workspace contains the objects: allPs, allPs.adj, sumTable. The...

Univariate and multivariate analyses of OS/RFS in patients with primary ovarian cancer in TCGA-OV.

Lianzhi Qin (4560334)
Ting Li (117885)
Yuhua Liu (37269)

November 2017

Univariate and multivariate analyses of OS/RFS in patients with primary ovarian cancer in TCGA-OV...

Forest plot of estimated DOR for quantitative analysis of circulating cell free DNA in the diagnosis of ovarian cancer.

Quan Zhou (492529)
Wei Li (7081)
Bingjie Leng (2814445)
Wenfei Zheng (2814439)
Ze He (549047)
Manzhen Zuo (2814442)
Aihua Chen (663136)

June 2016

Forest plot of estimated DOR for quantitative analysis of circulating cell free DNA in the diagno...

A novel algorithm for better distinction of primary mucinous ovarian carcinomas and mucinous carcinomas metastatic to the ovary

Simons, M.
Bolhuis, Thomas
Haan, A.F. de
Bruggink, Annette H.
Bulten, J.
Massuger, L.F.
Nagtegaal, I.D.

January 2019

Contains fulltext : 201898.pdf (publisher's version ) (Open Access

Analytical Code for "Cross-population analysis of high-grade serous ovarian cancer reveals only two robust subtypes"

Gregory Way
James Rudd
Casey Greene

October 2015

Analytical code to accompany the manuscript: "High-grade serous ovarian cancer subtypes are similar ...

Replication Data for: Performance of the MasSpec Pen for Rapid Diagnosis of Ovarian Cancer

Sans, Marta
Zhang, Jialing
Lin, John Q.
Feider, Clara L.
Giese, Noah
Breen, Michael
Sebastian, Katherine
Liu, Jinsong
Sood, Anil K.
S. Eberlin, Livia

Replication Data for: Performance of the MasSpec Pen for Rapid Diagnosis of Ovarian Cance

Validation of angiogenic ovarian cancer classification in our dataset and ten independent validation datasets.

Stefan Bentink (183842)
Benjamin Haibe-Kains (183845)
Thomas Risch (183849)
Jian-Bing Fan (28237)
Michelle S. Hirsch (183854)
Kristina Holton (183857)
Renee Rubio (15771)
Craig April (176343)
Jing Chen (4762)
Eliza Wickham-Garcia (183860)
Joyce Liu (183861)
Aedin Culhane (183862)
Ronny Drapkin (130800)
John Quackenbush (1213)
Ursula A. Matulonis (183863)

February 2012

Panels A, D and G display the gene expression of the 100 genes used to classify ovarian tumors in...

Four binary classifications of high grade ovarian serous cancer.

Stefan Bentink (183842)
Benjamin Haibe-Kains (183845)
Thomas Risch (183849)
Jian-Bing Fan (28237)
Michelle S. Hirsch (183854)
Kristina Holton (183857)
Renee Rubio (15771)
Craig April (176343)
Jing Chen (4762)
Eliza Wickham-Garcia (183860)
Joyce Liu (183861)
Aedin Culhane (183862)
Ronny Drapkin (130800)
John Quackenbush (1213)
Ursula A. Matulonis (183863)

February 2012

The ISIS algorithm identified four independent binary partition classifications (splits) of 129 o...

Comparison between 45 ovarian cancer (39 epithelial carcinoma and 6 borderline tissues) and 14 normal ovarian tissues.

Lin Wang (11986)
Miao-Jun Zhu (562073)
Ai-Min Ren (562074)
Hong-Fei Wu (562075)
Wu-Mei Han (562076)
Ruo-Ying Tan (562077)
Rui-Qin Tu (562078)

May 2014

A) The plot of miRNA assays used to profile compared samples: fold change (y-axis) against normal...

FinalOutput_Ovary

Abstract

Extracted data

FinalOutput_Ovary

Abstract

Extracted data

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