Visual representation of CancerInSilico.

Visualizing the Dynamic Modelling of Gene Expressing Data

Leishi Zhang
Xiaohui Liu

February 2015

Modelling gene expressing data could help obtain a “global ” view of biological process and ultimate...

Simulation models for cancer immunotherapy and chemotherapy trials

Johannes Textor

March 2023

This repository contains code and data related to the following manuscript: In silico cancer immuno...

Visual depiction of correlations between gene co-expression modules and tissue/treatment with the inclusion of control samples.

Max H. Barnhart (13889579)
Rishi R. Masalia (3320439)
Liana J. Mosley (13889582)
John M. Burke (8031503)

September 2022

Correlation values (upper text) and P-values (lower, parenthetical text) are presented in each cell....

CancerInSilico: An R/Bioconductor package for combining mathematical and statistical modeling to simulate time course bulk and single cell gene expression data in cancer - Fig 3

Thomas D. Sherman (6615992)
Luciane T. Kagohara (6615995)
Raymon Cao (6615998)
Raymond Cheng (1466227)
Matthew Satriano (6616001)
Michael Considine (5269832)
Gabriel Krigsfeld (445907)
Ruchira Ranaweera (5269829)
Yong Tang (161879)
Sandra A. Jablonski (6616004)
Genevieve Stein-O'Brien (6616007)
Daria A. Gaykalova (121387)
Louis M. Weiner (506119)
Christine H. Chung (242076)
Elana J. Fertig (194738)

April 2019

T-SNE of simulated time course single cell RNA-sequencing data for a population with cells of types ...

The comparison of experimental results of gene expression levels and our theoretical predictions.

Chong Yu (847290)
Jin Wang (29560)

July 2016

The y-axis of left column of the each of the two figures represents fold changes of the gene expr...

Visualizing cancer data in the United States

Attali, Dean A

November 2014

The software provided here is an interactive application that allows users to explore data about can...

CancerInSilico: An R/Bioconductor package for combining mathematical and statistical modeling to simulate time course bulk and single cell gene expression data in cancer.

Thomas D Sherman
Luciane T Kagohara
Raymon Cao
Raymond Cheng
Matthew Satriano
Michael Considine
Gabriel Krigsfeld
Ruchira Ranaweera
Yong Tang
Sandra A Jablonski
Genevieve Stein-O'Brien
Daria A Gaykalova
Louis M Weiner
Christine H Chung
Elana J Fertig

June 2018

Bioinformatics techniques to analyze time course bulk and single cell omics data are advancing. The ...

CancerInSilico: An R/Bioconductor package for combining mathematical and statistical modeling to simulate time course bulk and single cell gene expression data in cancer

Thomas D. Sherman (6615992)
Luciane T. Kagohara (6615995)
Raymon Cao (6615998)
Raymond Cheng (1466227)
Matthew Satriano (6616001)
Michael Considine (5269832)
Gabriel Krigsfeld (445907)
Ruchira Ranaweera (5269829)
Yong Tang (161879)
Sandra A. Jablonski (6616004)
Genevieve Stein-O'Brien (6616007)
Daria A. Gaykalova (121387)
Louis M. Weiner (506119)
Christine H. Chung (242076)
Elana J. Fertig (194738)

April 2019

Bioinformatics techniques to analyze time course bulk and single cell omics data are advancing. The ...

Software implementations allowing new approaches toward data analysis, modeling and curation of biological knowledge for Systems Medicine

Zobolas, John

January 2021

Cancer is one of the leading causes of death globally. To combat cancer, scientists want to understa...

Schematic representation of well-known and hypothetical models of virus-associated carcinogenesis.

Daniele Viarisio (348197)
Karin Müller-Decker (4516681)
Rosita Accardi (269874)
Alexis Robitaille (4760709)
Matthias Dürst (155683)
Katrin Beer (4760712)
Lars Jansen (155662)
Christa Flechtenmacher (188350)
Matthias Bozza (4760715)
Richard Harbottle (1978729)
Catherine Voegele (107245)
Maude Ardin (737092)
Jiri Zavadil (10270)
Sandra Caldeira (4760718)
Lutz Gissmann (265124)
Massimo Tommasino (8382)

January 2018

Schematic representation of well-known and hypothetical models of virus-associated carcinogenesis...

Gene co-expression networks, modules and associations with clinicopathological attributes of BC patients.

Vanessa Dumeaux (72813)
Bjørn Fjukstad (4476352)
Hans E. Fjosne (4476343)
Jan-Ole Frantzen (4476349)
Marit Muri Holmen (4476355)
Enno Rodegerdts (4476358)
Ellen Schlichting (59878)
Anne-Lise Børresen-Dale (3413)
Lars Ailo Bongo (4476346)
Eiliv Lund (23601)
Michael Hallett (222516)

September 2017

(A) Network visualization using the edge-weighted spring embedded layout from Cytoscape (v3.2.1) ...

BioCPR : a tool for correlation plots

Fey, Vidal
Jambulingam, Dhanaprakash
Sara, Henri
Heron, Samuel
Sipeky, Csilla
Schleutker, Johanna

September 2021

A gene is a sequence of DNA bases through which genetic information is passed on to the next generat...

Bubble chart of Cancer-Gene associations from literature.

Uma S. Mudunuri (463683)
Mohamad Khouja (491887)
Stephen Repetski (491888)
Girish Venkataraman (491889)
Anney Che (491890)
Brian T. Luke (171128)
F. Pascal Girard (491891)
Robert M. Stephens (17045)

December 2013

A bubble chart representation with cancer terms on the x-axis and genes on the y-axis. The size o...

Representation of the most important data format, plots and visualization results, used in data mining and prioritization of candidate biomarkers, using the CACNA1D gene as an example.

Saeid Alinezhad (2795053)
Riina-Minna Väänänen (2795047)
Jesse Mattsson (2795044)
Yifeng Li (1265229)
Terhi Tallgrén (2795050)
Natalia Tong Ochoa (2795041)
Anders Bjartell (199682)
Malin Åkerfelt (561696)
Pekka Taimen (773545)
Peter J. Boström (470005)
Kim Pettersson (501978)
Matthias Nees (229635)

May 2016

A) Dot plot chart illustrating the association of mRNA gene expression of CACNA1D in normal and c...

CANCERTOOL: A Visualization and Representation Interface to Exploit Cancer Datasets

Cortazar, Ana
Torrano, Veronica
Martin-Martin, Natalia
Caro-Maldonado, Alfredo
Camacho, Laura
Hermanova, Ivana
Guruceaga, Elizabeth
Lorenzo-Martín, L.
Caloto, Ruben
Gomis, Roger
Apaolaza, Iñigo
Quesada, Víctor
Trka, Jan
Gomez-Muñoz, Antonio
Vicent, Silvestre
Bustelo, Xosé
Planes, Francisco
Aransay, Ana
Carracedo, Arkaitz

November 2018

With the advent of OMICs technologies, both individual research groups and consortia have spear-head...

Visualizing the Dynamic Modelling of Gene Expressing Data

Leishi Zhang
Xiaohui Liu

February 2015

Modelling gene expressing data could help obtain a “global ” view of biological process and ultimate...

Simulation models for cancer immunotherapy and chemotherapy trials

Johannes Textor

March 2023

This repository contains code and data related to the following manuscript: In silico cancer immuno...

Visual depiction of correlations between gene co-expression modules and tissue/treatment with the inclusion of control samples.

Max H. Barnhart (13889579)
Rishi R. Masalia (3320439)
Liana J. Mosley (13889582)
John M. Burke (8031503)

September 2022

Correlation values (upper text) and P-values (lower, parenthetical text) are presented in each cell....

CancerInSilico: An R/Bioconductor package for combining mathematical and statistical modeling to simulate time course bulk and single cell gene expression data in cancer - Fig 3

Thomas D. Sherman (6615992)
Luciane T. Kagohara (6615995)
Raymon Cao (6615998)
Raymond Cheng (1466227)
Matthew Satriano (6616001)
Michael Considine (5269832)
Gabriel Krigsfeld (445907)
Ruchira Ranaweera (5269829)
Yong Tang (161879)
Sandra A. Jablonski (6616004)
Genevieve Stein-O'Brien (6616007)
Daria A. Gaykalova (121387)
Louis M. Weiner (506119)
Christine H. Chung (242076)
Elana J. Fertig (194738)

April 2019

T-SNE of simulated time course single cell RNA-sequencing data for a population with cells of types ...

The comparison of experimental results of gene expression levels and our theoretical predictions.

Chong Yu (847290)
Jin Wang (29560)

July 2016

The y-axis of left column of the each of the two figures represents fold changes of the gene expr...

Visualizing cancer data in the United States

Attali, Dean A

November 2014

The software provided here is an interactive application that allows users to explore data about can...

CancerInSilico: An R/Bioconductor package for combining mathematical and statistical modeling to simulate time course bulk and single cell gene expression data in cancer.

Thomas D Sherman
Luciane T Kagohara
Raymon Cao
Raymond Cheng
Matthew Satriano
Michael Considine
Gabriel Krigsfeld
Ruchira Ranaweera
Yong Tang
Sandra A Jablonski
Genevieve Stein-O'Brien
Daria A Gaykalova
Louis M Weiner
Christine H Chung
Elana J Fertig

June 2018

Bioinformatics techniques to analyze time course bulk and single cell omics data are advancing. The ...

CancerInSilico: An R/Bioconductor package for combining mathematical and statistical modeling to simulate time course bulk and single cell gene expression data in cancer

Thomas D. Sherman (6615992)
Luciane T. Kagohara (6615995)
Raymon Cao (6615998)
Raymond Cheng (1466227)
Matthew Satriano (6616001)
Michael Considine (5269832)
Gabriel Krigsfeld (445907)
Ruchira Ranaweera (5269829)
Yong Tang (161879)
Sandra A. Jablonski (6616004)
Genevieve Stein-O'Brien (6616007)
Daria A. Gaykalova (121387)
Louis M. Weiner (506119)
Christine H. Chung (242076)
Elana J. Fertig (194738)

April 2019

Bioinformatics techniques to analyze time course bulk and single cell omics data are advancing. The ...

Software implementations allowing new approaches toward data analysis, modeling and curation of biological knowledge for Systems Medicine

Zobolas, John

January 2021

Cancer is one of the leading causes of death globally. To combat cancer, scientists want to understa...

Schematic representation of well-known and hypothetical models of virus-associated carcinogenesis.

Daniele Viarisio (348197)
Karin Müller-Decker (4516681)
Rosita Accardi (269874)
Alexis Robitaille (4760709)
Matthias Dürst (155683)
Katrin Beer (4760712)
Lars Jansen (155662)
Christa Flechtenmacher (188350)
Matthias Bozza (4760715)
Richard Harbottle (1978729)
Catherine Voegele (107245)
Maude Ardin (737092)
Jiri Zavadil (10270)
Sandra Caldeira (4760718)
Lutz Gissmann (265124)
Massimo Tommasino (8382)

January 2018

Schematic representation of well-known and hypothetical models of virus-associated carcinogenesis...

Gene co-expression networks, modules and associations with clinicopathological attributes of BC patients.

Vanessa Dumeaux (72813)
Bjørn Fjukstad (4476352)
Hans E. Fjosne (4476343)
Jan-Ole Frantzen (4476349)
Marit Muri Holmen (4476355)
Enno Rodegerdts (4476358)
Ellen Schlichting (59878)
Anne-Lise Børresen-Dale (3413)
Lars Ailo Bongo (4476346)
Eiliv Lund (23601)
Michael Hallett (222516)

September 2017

(A) Network visualization using the edge-weighted spring embedded layout from Cytoscape (v3.2.1) ...

BioCPR : a tool for correlation plots

Fey, Vidal
Jambulingam, Dhanaprakash
Sara, Henri
Heron, Samuel
Sipeky, Csilla
Schleutker, Johanna

September 2021

A gene is a sequence of DNA bases through which genetic information is passed on to the next generat...

Bubble chart of Cancer-Gene associations from literature.

Uma S. Mudunuri (463683)
Mohamad Khouja (491887)
Stephen Repetski (491888)
Girish Venkataraman (491889)
Anney Che (491890)
Brian T. Luke (171128)
F. Pascal Girard (491891)
Robert M. Stephens (17045)

December 2013

A bubble chart representation with cancer terms on the x-axis and genes on the y-axis. The size o...

Representation of the most important data format, plots and visualization results, used in data mining and prioritization of candidate biomarkers, using the CACNA1D gene as an example.

Saeid Alinezhad (2795053)
Riina-Minna Väänänen (2795047)
Jesse Mattsson (2795044)
Yifeng Li (1265229)
Terhi Tallgrén (2795050)
Natalia Tong Ochoa (2795041)
Anders Bjartell (199682)
Malin Åkerfelt (561696)
Pekka Taimen (773545)
Peter J. Boström (470005)
Kim Pettersson (501978)
Matthias Nees (229635)

May 2016

A) Dot plot chart illustrating the association of mRNA gene expression of CACNA1D in normal and c...

CANCERTOOL: A Visualization and Representation Interface to Exploit Cancer Datasets

Cortazar, Ana
Torrano, Veronica
Martin-Martin, Natalia
Caro-Maldonado, Alfredo
Camacho, Laura
Hermanova, Ivana
Guruceaga, Elizabeth
Lorenzo-Martín, L.
Caloto, Ruben
Gomis, Roger
Apaolaza, Iñigo
Quesada, Víctor
Trka, Jan
Gomez-Muñoz, Antonio
Vicent, Silvestre
Bustelo, Xosé
Planes, Francisco
Aransay, Ana
Carracedo, Arkaitz

November 2018

With the advent of OMICs technologies, both individual research groups and consortia have spear-head...

Visualizing the Dynamic Modelling of Gene Expressing Data

Leishi Zhang
Xiaohui Liu

February 2015

Modelling gene expressing data could help obtain a “global ” view of biological process and ultimate...

Simulation models for cancer immunotherapy and chemotherapy trials

Johannes Textor

March 2023

This repository contains code and data related to the following manuscript: In silico cancer immuno...

Visual depiction of correlations between gene co-expression modules and tissue/treatment with the inclusion of control samples.

Max H. Barnhart (13889579)
Rishi R. Masalia (3320439)
Liana J. Mosley (13889582)
John M. Burke (8031503)

September 2022

Correlation values (upper text) and P-values (lower, parenthetical text) are presented in each cell....

Visual representation of CancerInSilico.

Abstract

Extracted data

Visual representation of CancerInSilico.

Abstract

Extracted data

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