Additional file 1 of Analyzing Th17 cell differentiation dynamics using a novel integrative modeling framework for time-course RNA sequencing data

Additional file 1: of A transcriptome-based model of central memory CD4 T cell death in HIV infection

Gustavo Olvera-García (3471683)
Tania Aguilar-García (3471674)
Fany Gutiérrez-Jasso (3471677)
Iván Imaz-Rosshandler (2586292)
Claudia Rangel-Escareño (321873)
Lorena Orozco (180145)
Irma Aguilar-Delfín (3471668)
Joel Vázquez-Pérez (3471671)
Joaquín Zúñiga (461855)
Santiago Pérez-Patrigeon (3471680)
Enrique Espinosa (175501)

November 2016

CD4 T cell subpopulations were separated with at least 90% purity. Dot plots showing the sequential ...

Additional file 1: of Mapping human pluripotent stem cell differentiation pathways using high throughput single-cell RNA-sequencing

Xiaoping Han (5069165)
Haide Chen (762797)
Daosheng Huang (5069171)
Huidong Chen (3520568)
Lijiang Fei (5069168)
Chen Cheng (76970)
He Huang (50693)
Guo-Cheng Yuan (39064)
Guoji Guo (3441431)

April 2018

Figure S1. Quality control of the dataset. Figure S2. Surface marker analysis and GO enrichment anal...

Additional file 4: of Identification and characterization of genes with absolute mRNA abundances changes in tumor cells with varied transcriptome sizes

Hao Cai (1324782)
Xiangyu Li (1475548)
Jun He (46556)
Wenbin Zhou (295899)
Kai Song (107003)
You Guo (4622707)
Huaping Liu (769096)
Qingzhou Guan (3728839)
Haidan Yan (3728836)
Xianlong Wang (432284)
Zheng Guo (14989)

February 2019

The simulation experiments in data with global transcriptome size changes due to the genome size cha...

Additional file 3 of Analyzing Th17 cell differentiation dynamics using a novel integrative modeling framework for time-course RNA sequencing data

Jukka Intosalmi (3464243)
Helena Ahlfors (433264)
Sini Rautio (3464246)
Henrik MannerstĂśm (3464261)
Zhi Chen (222749)
Riitta Lahesmaa (61009)
Brigitta Stockinger (277480)
Harri LĂ¤hdesmĂ¤ki (3464258)

November 2015

Implementation of population-based Markov chain Monte Carlo in Matlab. (ZIP 46 kb

Additional file 1: of MAST: a flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data

Greg Finak (236903)
Andrew McDavid (393555)
Masanao Yajima (3424436)
Jingyuan Deng (250051)
Vivian Gersuk (3424442)
Alex Shalek (3424427)
Chloe Slichter (3424430)
Hannah Miller (3424439)
M. McElrath (3424433)
Martin Prlic (330776)
Peter Linsley (3424445)
Raphael Gottardo (1558)

December 2015

Supplemental methods, extended derivations, and supplementary figures and tables. (PDF 3940 kb

Additional file 1: of UMI-count modeling and differential expression analysis for single-cell RNA sequencing

Wenan Chen (5127059)
Yan Li (23143)
John Easton (4615627)
David Finkelstein (222792)
Gang Wu (23885)
Xiang Chen (10398)

May 2018

This file includes: (1) supplementary methods describing details in single cell quality control and ...

Additional file 3: of A mathematical model as a tool to identify microRNAs with highest impact on transcriptome changes

Marzena Mura (6309653)
Roman Jaksik (6309656)
Anna Lalik (6309659)
Krzysztof Biernacki (1695766)
Marek Kimmel (39636)
Joanna Rzeszowska-Wolny (286036)
Krzysztof Fujarewicz (286030)

February 2019

Table S2. Summary of each dataset (number of expressed mRNAs and miRNAs), experimental conditions (r...

Additional file 2 of DTWscore: differential expression and cell clustering analysis for time-series single-cell RNA-seq data

Zhuo Wang (18668)
Shuilin Jin (522328)
Guiyou Liu (224712)
Xiurui Zhang (4043528)
Nan Wang (21935)
Deliang Wu (4043534)
Yang Hu (315392)
Chiping Zhang (4043531)
Qinghua Jiang (522330)
Li Xu (108702)
Yadong Wang (82064)

May 2017

Figure S2. DTWscore identifies heterogeneous genes and non-heterogeneous genes from the synthetic da...

Additional file 14: of Mapping human pluripotent stem cell differentiation pathways using high throughput single-cell RNA-sequencing

Xiaoping Han (5069165)
Haide Chen (762797)
Daosheng Huang (5069171)
Huidong Chen (3520568)
Lijiang Fei (5069168)
Chen Cheng (76970)
He Huang (50693)
Guo-Cheng Yuan (39064)
Guoji Guo (3441431)

April 2018

Table S13. List of signaling pathways used in Additional fileÂ 1: Figure S7a. (XLSX 20Â kb

Additional file 1: of A cell size- and cell cycle-aware stochastic model for predicting time-dynamic gene network activity in individual cells

Ruijie Song (3543251)
Weilin Peng (3543254)
Ping Liu (156158)
Murat Acar (3543257)

December 2015

Contains Notes S1 (derivation of the functional form of the GAL network) and S2 (description of phen...

Additional file 6 of DTWscore: differential expression and cell clustering analysis for time-series single-cell RNA-seq data

Zhuo Wang (18668)
Shuilin Jin (522328)
Guiyou Liu (224712)
Xiurui Zhang (4043528)
Nan Wang (21935)
Deliang Wu (4043534)
Yang Hu (315392)
Chiping Zhang (4043531)
Qinghua Jiang (522330)
Li Xu (108702)
Yadong Wang (82064)

May 2017

Figure S6. Model-based clustering of HSMM dataset by any three highly variable genes. (PDF 68 kb

Additional file 1: of Assessing characteristics of RNA amplification methods for single cell RNA sequencing

Hannah Dueck (3461837)
Rizi Ai (2343607)
Adrian Camarena (3461816)
Bo Ding (210928)
Reymundo Dominguez (3461819)
Oleg Evgrafov (392965)
Jian-Bing Fan (28237)
Stephen Fisher (3461825)
Jennifer Herstein (3461804)
Tae Kim (3405566)
Jae Kim (2100565)
Ming-Yi Lin (237662)
Rui Liu (54031)
William Mack (3461807)
Sean McGroty (3461831)
Joseph Nguyen (3461810)
Neeraj Salathia (18709)
Jamie Shallcross (3461834)
Tade Souaiaia (3291015)
Jennifer Spaethling (3461813)
Christopher Walker (200465)
Jinhui Wang (37220)
Kai Wang (21246)
Wei Wang (17594)
Andre Wildberg (3461828)
Lina Zheng (331151)
Robert Chow (3443600)
James Eberwine (253973)
James Knowles (3461822)
Kun Zhang (108291)
Junhyong Kim (6423)

November 2016

Control dataset sample identification, protocol information, and RNA sequencing stats. Experimental ...

Additional file 7: of Mapping human pluripotent stem cell differentiation pathways using high throughput single-cell RNA-sequencing

Xiaoping Han (5069165)
Haide Chen (762797)
Daosheng Huang (5069171)
Huidong Chen (3520568)
Lijiang Fei (5069168)
Chen Cheng (76970)
He Huang (50693)
Guo-Cheng Yuan (39064)
Guoji Guo (3441431)

April 2018

Table S6. List of ligand-receptor pairs and cell–cell pairs used in Fig. 4c for heatmap. (XLSX 12 kb

Additional file 2 of Analysis of a mechanistic Markov model for gene duplicates evolving under subfunctionalization

Tristan Stark (3706726)
David Liberles (3492842)
Barbara Holland (1776)
MaĹgorzata OâReilly (3706729)

January 2017

Contains the data set analyzed in this work. The data was originally published and analyzed by Hughe...

Additional file 1 of Integrating mutation and gene expression cross-sectional data to infer cancer progression

Julia Fleck (3491156)
Ana Pavel (3491159)
Christos Cassandras (3491153)

January 2016

The partition of 72 mutation and 319 expression genes in 3 phases of cancer progression. The values ...

Additional file 1: of A transcriptome-based model of central memory CD4 T cell death in HIV infection

Gustavo Olvera-García (3471683)
Tania Aguilar-García (3471674)
Fany Gutiérrez-Jasso (3471677)
Iván Imaz-Rosshandler (2586292)
Claudia Rangel-Escareño (321873)
Lorena Orozco (180145)
Irma Aguilar-Delfín (3471668)
Joel Vázquez-Pérez (3471671)
Joaquín Zúñiga (461855)
Santiago Pérez-Patrigeon (3471680)
Enrique Espinosa (175501)

November 2016

CD4 T cell subpopulations were separated with at least 90% purity. Dot plots showing the sequential ...

Additional file 1: of Mapping human pluripotent stem cell differentiation pathways using high throughput single-cell RNA-sequencing

Xiaoping Han (5069165)
Haide Chen (762797)
Daosheng Huang (5069171)
Huidong Chen (3520568)
Lijiang Fei (5069168)
Chen Cheng (76970)
He Huang (50693)
Guo-Cheng Yuan (39064)
Guoji Guo (3441431)

April 2018

Figure S1. Quality control of the dataset. Figure S2. Surface marker analysis and GO enrichment anal...

Additional file 4: of Identification and characterization of genes with absolute mRNA abundances changes in tumor cells with varied transcriptome sizes

Hao Cai (1324782)
Xiangyu Li (1475548)
Jun He (46556)
Wenbin Zhou (295899)
Kai Song (107003)
You Guo (4622707)
Huaping Liu (769096)
Qingzhou Guan (3728839)
Haidan Yan (3728836)
Xianlong Wang (432284)
Zheng Guo (14989)

February 2019

The simulation experiments in data with global transcriptome size changes due to the genome size cha...

Additional file 3 of Analyzing Th17 cell differentiation dynamics using a novel integrative modeling framework for time-course RNA sequencing data

Jukka Intosalmi (3464243)
Helena Ahlfors (433264)
Sini Rautio (3464246)
Henrik MannerstĂśm (3464261)
Zhi Chen (222749)
Riitta Lahesmaa (61009)
Brigitta Stockinger (277480)
Harri LĂ¤hdesmĂ¤ki (3464258)

November 2015

Implementation of population-based Markov chain Monte Carlo in Matlab. (ZIP 46 kb

Additional file 1: of MAST: a flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data

Greg Finak (236903)
Andrew McDavid (393555)
Masanao Yajima (3424436)
Jingyuan Deng (250051)
Vivian Gersuk (3424442)
Alex Shalek (3424427)
Chloe Slichter (3424430)
Hannah Miller (3424439)
M. McElrath (3424433)
Martin Prlic (330776)
Peter Linsley (3424445)
Raphael Gottardo (1558)

December 2015

Supplemental methods, extended derivations, and supplementary figures and tables. (PDF 3940 kb

Additional file 1: of UMI-count modeling and differential expression analysis for single-cell RNA sequencing

Wenan Chen (5127059)
Yan Li (23143)
John Easton (4615627)
David Finkelstein (222792)
Gang Wu (23885)
Xiang Chen (10398)

May 2018

This file includes: (1) supplementary methods describing details in single cell quality control and ...

Additional file 3: of A mathematical model as a tool to identify microRNAs with highest impact on transcriptome changes

Marzena Mura (6309653)
Roman Jaksik (6309656)
Anna Lalik (6309659)
Krzysztof Biernacki (1695766)
Marek Kimmel (39636)
Joanna Rzeszowska-Wolny (286036)
Krzysztof Fujarewicz (286030)

February 2019

Table S2. Summary of each dataset (number of expressed mRNAs and miRNAs), experimental conditions (r...

Additional file 2 of DTWscore: differential expression and cell clustering analysis for time-series single-cell RNA-seq data

Zhuo Wang (18668)
Shuilin Jin (522328)
Guiyou Liu (224712)
Xiurui Zhang (4043528)
Nan Wang (21935)
Deliang Wu (4043534)
Yang Hu (315392)
Chiping Zhang (4043531)
Qinghua Jiang (522330)
Li Xu (108702)
Yadong Wang (82064)

May 2017

Figure S2. DTWscore identifies heterogeneous genes and non-heterogeneous genes from the synthetic da...

Additional file 14: of Mapping human pluripotent stem cell differentiation pathways using high throughput single-cell RNA-sequencing

Xiaoping Han (5069165)
Haide Chen (762797)
Daosheng Huang (5069171)
Huidong Chen (3520568)
Lijiang Fei (5069168)
Chen Cheng (76970)
He Huang (50693)
Guo-Cheng Yuan (39064)
Guoji Guo (3441431)

April 2018

Table S13. List of signaling pathways used in Additional fileÂ 1: Figure S7a. (XLSX 20Â kb

Additional file 1: of A cell size- and cell cycle-aware stochastic model for predicting time-dynamic gene network activity in individual cells

Ruijie Song (3543251)
Weilin Peng (3543254)
Ping Liu (156158)
Murat Acar (3543257)

December 2015

Contains Notes S1 (derivation of the functional form of the GAL network) and S2 (description of phen...

Additional file 6 of DTWscore: differential expression and cell clustering analysis for time-series single-cell RNA-seq data

Zhuo Wang (18668)
Shuilin Jin (522328)
Guiyou Liu (224712)
Xiurui Zhang (4043528)
Nan Wang (21935)
Deliang Wu (4043534)
Yang Hu (315392)
Chiping Zhang (4043531)
Qinghua Jiang (522330)
Li Xu (108702)
Yadong Wang (82064)

May 2017

Figure S6. Model-based clustering of HSMM dataset by any three highly variable genes. (PDF 68 kb

Additional file 1: of Assessing characteristics of RNA amplification methods for single cell RNA sequencing

Hannah Dueck (3461837)
Rizi Ai (2343607)
Adrian Camarena (3461816)
Bo Ding (210928)
Reymundo Dominguez (3461819)
Oleg Evgrafov (392965)
Jian-Bing Fan (28237)
Stephen Fisher (3461825)
Jennifer Herstein (3461804)
Tae Kim (3405566)
Jae Kim (2100565)
Ming-Yi Lin (237662)
Rui Liu (54031)
William Mack (3461807)
Sean McGroty (3461831)
Joseph Nguyen (3461810)
Neeraj Salathia (18709)
Jamie Shallcross (3461834)
Tade Souaiaia (3291015)
Jennifer Spaethling (3461813)
Christopher Walker (200465)
Jinhui Wang (37220)
Kai Wang (21246)
Wei Wang (17594)
Andre Wildberg (3461828)
Lina Zheng (331151)
Robert Chow (3443600)
James Eberwine (253973)
James Knowles (3461822)
Kun Zhang (108291)
Junhyong Kim (6423)

November 2016

Control dataset sample identification, protocol information, and RNA sequencing stats. Experimental ...

Additional file 7: of Mapping human pluripotent stem cell differentiation pathways using high throughput single-cell RNA-sequencing

Xiaoping Han (5069165)
Haide Chen (762797)
Daosheng Huang (5069171)
Huidong Chen (3520568)
Lijiang Fei (5069168)
Chen Cheng (76970)
He Huang (50693)
Guo-Cheng Yuan (39064)
Guoji Guo (3441431)

April 2018

Table S6. List of ligand-receptor pairs and cell–cell pairs used in Fig. 4c for heatmap. (XLSX 12 kb

Additional file 2 of Analysis of a mechanistic Markov model for gene duplicates evolving under subfunctionalization

Tristan Stark (3706726)
David Liberles (3492842)
Barbara Holland (1776)
MaĹgorzata OâReilly (3706729)

January 2017

Contains the data set analyzed in this work. The data was originally published and analyzed by Hughe...

Additional file 1 of Integrating mutation and gene expression cross-sectional data to infer cancer progression

Julia Fleck (3491156)
Ana Pavel (3491159)
Christos Cassandras (3491153)

January 2016

The partition of 72 mutation and 319 expression genes in 3 phases of cancer progression. The values ...

Additional file 1: of A transcriptome-based model of central memory CD4 T cell death in HIV infection

Gustavo Olvera-García (3471683)
Tania Aguilar-García (3471674)
Fany Gutiérrez-Jasso (3471677)
Iván Imaz-Rosshandler (2586292)
Claudia Rangel-Escareño (321873)
Lorena Orozco (180145)
Irma Aguilar-Delfín (3471668)
Joel Vázquez-Pérez (3471671)
Joaquín Zúñiga (461855)
Santiago Pérez-Patrigeon (3471680)
Enrique Espinosa (175501)

November 2016

CD4 T cell subpopulations were separated with at least 90% purity. Dot plots showing the sequential ...

Additional file 1: of Mapping human pluripotent stem cell differentiation pathways using high throughput single-cell RNA-sequencing

Xiaoping Han (5069165)
Haide Chen (762797)
Daosheng Huang (5069171)
Huidong Chen (3520568)
Lijiang Fei (5069168)
Chen Cheng (76970)
He Huang (50693)
Guo-Cheng Yuan (39064)
Guoji Guo (3441431)

April 2018

Figure S1. Quality control of the dataset. Figure S2. Surface marker analysis and GO enrichment anal...

Additional file 4: of Identification and characterization of genes with absolute mRNA abundances changes in tumor cells with varied transcriptome sizes

Hao Cai (1324782)
Xiangyu Li (1475548)
Jun He (46556)
Wenbin Zhou (295899)
Kai Song (107003)
You Guo (4622707)
Huaping Liu (769096)
Qingzhou Guan (3728839)
Haidan Yan (3728836)
Xianlong Wang (432284)
Zheng Guo (14989)

February 2019

The simulation experiments in data with global transcriptome size changes due to the genome size cha...

Additional file 1 of Analyzing Th17 cell differentiation dynamics using a novel integrative modeling framework for time-course RNA sequencing data

Abstract

Extracted data

Additional file 1 of Analyzing Th17 cell differentiation dynamics using a novel integrative modeling framework for time-course RNA sequencing data

Abstract

Extracted data

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