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Automated Author Profile

Souaiaia, Tade

Current S-Index

34.3

Sum of Dataset Indices for all datasets

Average Dataset Index per Dataset

1.0

Average Dataset Index per dataset

Total Datasets

34

Total datasets for this author

Average FAIR Score

44.8%

Average FAIR Score per dataset

Total Citations

18

Total citations to the author's datasets

Total Mentions

0

Total mentions of the author's datasets

S-Index Interpretation

S-Index Over Time

Cumulative Citations Over Time

Cumulative Mentions Over Time

Datasets

Additional file 12: of Assessing characteristics of RNA amplification methods for single cell RNA sequencing

Normalized read counts and expectation for ERCC transcripts. A–B. ERCC transcripts are found along the x-axis, ordered by expected number of input molecules. Axis labels are in the format of “ERCC spike-in ID, expected number of input molecules”. Points indicate the normalized read count for one transcript in one sample. Horizontal gray lines and background gray boxes indicate the expected normalized read count and a 95% CI under a Poisson model of dilution. Wide red horizontal lines indicate mean normalized read counts across all ERCC transcripts with a common expected number of input molecule, and red boxes indicate mean ± 2 × s.e.m. (A) aRNA. (B) SmartSeq Plus. (XLS 964 kb)

Authors

  • Dueck, Hannah ;
  • Rizi Ai ;
  • Camarena, Adrian ;
  • Ding, Bo ;
  • Reymundo Dominguez ;
  • Evgrafov, Oleg ;
  • Fan, Jian-Bing ;
  • Fisher, Stephen ;
  • Herstein, Jennifer ;
  • Kim, Tae ;
  • Kim, Jae ;
  • Lin, Ming-Yi ;
  • Liu, Rui ;
  • Mack, William ;
  • McGroty, Sean ;
  • Nguyen, Joseph ;
  • Salathia, Neeraj ;
  • Shallcross, Jamie ;
  • Souaiaia, Tade ;
  • Spaethling, Jennifer ;
  • Walker, Christopher ;
  • Jinhui Wang ;
  • Wang, Kai ;
  • Wang, Wei ;
  • Wildberg, Andre ;
  • Zheng, Lina ;
  • Chow, Robert ;
  • Eberwine, James ;
  • Knowles, James ;
  • Zhang, Kun ;
  • Junhyong Kim
1 Citation0 Mentions13% FAIR0.5 Dataset Index
10.6084/m9.figshare.c.3611564_d3.v1January 2016

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

Control dataset sample identification, protocol information, and RNA sequencing stats. Experimental group, protocol information and RNA sequencing statistics for each sample used in primary analyses. Alignment statistics were based on STAR alignment to hg19 and were with respect to reads retained after trimming for primer or poly-A sequences [21]. (XLS 62 kb)

Authors

  • Dueck, Hannah ;
  • Rizi Ai ;
  • Camarena, Adrian ;
  • Ding, Bo ;
  • Reymundo Dominguez ;
  • Evgrafov, Oleg ;
  • Fan, Jian-Bing ;
  • Fisher, Stephen ;
  • Herstein, Jennifer ;
  • Kim, Tae ;
  • Kim, Jae ;
  • Lin, Ming-Yi ;
  • Liu, Rui ;
  • Mack, William ;
  • McGroty, Sean ;
  • Nguyen, Joseph ;
  • Salathia, Neeraj ;
  • Shallcross, Jamie ;
  • Souaiaia, Tade ;
  • Spaethling, Jennifer ;
  • Walker, Christopher ;
  • Jinhui Wang ;
  • Wang, Kai ;
  • Wang, Wei ;
  • Wildberg, Andre ;
  • Zheng, Lina ;
  • Chow, Robert ;
  • Eberwine, James ;
  • Knowles, James ;
  • Zhang, Kun ;
  • Junhyong Kim
1 Citation0 Mentions13% FAIR0.5 Dataset Index
10.6084/m9.figshare.c.3611564_d4January 2016

Additional file 4: of Assessing characteristics of RNA amplification methods for single cell RNA sequencing

Number of detected genes for low-depth in silico samples. As Fig. 2a, except that each dilution replicate has been subsampled to a depth of 500,000 unique genic reads. (XLS 74 kb)

Authors

  • Dueck, Hannah ;
  • Rizi Ai ;
  • Camarena, Adrian ;
  • Ding, Bo ;
  • Reymundo Dominguez ;
  • Evgrafov, Oleg ;
  • Fan, Jian-Bing ;
  • Fisher, Stephen ;
  • Herstein, Jennifer ;
  • Kim, Tae ;
  • Kim, Jae ;
  • Lin, Ming-Yi ;
  • Liu, Rui ;
  • Mack, William ;
  • McGroty, Sean ;
  • Nguyen, Joseph ;
  • Salathia, Neeraj ;
  • Shallcross, Jamie ;
  • Souaiaia, Tade ;
  • Spaethling, Jennifer ;
  • Walker, Christopher ;
  • Jinhui Wang ;
  • Wang, Kai ;
  • Wang, Wei ;
  • Wildberg, Andre ;
  • Zheng, Lina ;
  • Chow, Robert ;
  • Eberwine, James ;
  • Knowles, James ;
  • Zhang, Kun ;
  • Junhyong Kim
1 Citation0 Mentions13% FAIR0.5 Dataset Index
10.6084/m9.figshare.c.3611564_d5January 2016

Additional file 5: of Assessing characteristics of RNA amplification methods for single cell RNA sequencing

Gene detection logistic regression model. See model details in Methods . Abbreviations: M expected number of input molecules; L gene length (kilobases); G gene GC content; S strength of gene local secondary structure (kilocalories per mole); hasA presence of A-hexamer internal to gene body; D Depth (per 10,000,000 reads); S.E. standard error; Wald Z Wald test statistic; Pr(>|Z|) Wald test p-value. (XLS 40 kb)

Authors

  • Dueck, Hannah ;
  • Rizi Ai ;
  • Camarena, Adrian ;
  • Ding, Bo ;
  • Reymundo Dominguez ;
  • Evgrafov, Oleg ;
  • Fan, Jian-Bing ;
  • Fisher, Stephen ;
  • Herstein, Jennifer ;
  • Kim, Tae ;
  • Kim, Jae ;
  • Lin, Ming-Yi ;
  • Liu, Rui ;
  • Mack, William ;
  • McGroty, Sean ;
  • Nguyen, Joseph ;
  • Salathia, Neeraj ;
  • Shallcross, Jamie ;
  • Souaiaia, Tade ;
  • Spaethling, Jennifer ;
  • Walker, Christopher ;
  • Jinhui Wang ;
  • Wang, Kai ;
  • Wang, Wei ;
  • Wildberg, Andre ;
  • Zheng, Lina ;
  • Chow, Robert ;
  • Eberwine, James ;
  • Knowles, James ;
  • Zhang, Kun ;
  • Junhyong Kim
1 Citation0 Mentions13% FAIR0.5 Dataset Index
10.6084/m9.figshare.c.3611564_d7January 2016

Additional file 10: of Assessing characteristics of RNA amplification methods for single cell RNA sequencing

Accuracy outliers. Genes were identified as accuracy outliers if its median fold deviation, taken across dilution replicates, was contained in the upper or lower 1%ile of all considered genes (see Methods ). Columns labeled by single-cell protocol contain an “H” if a gene was identified as an overestimated outlier, and an “L” if a gene was identified as an underestimated outlier. “Gene set” indicates whether gene is classified as computationally unambiguous (1) or not (2). (XLS 218 kb)

Authors

  • Dueck, Hannah ;
  • Rizi Ai ;
  • Camarena, Adrian ;
  • Ding, Bo ;
  • Reymundo Dominguez ;
  • Evgrafov, Oleg ;
  • Fan, Jian-Bing ;
  • Fisher, Stephen ;
  • Herstein, Jennifer ;
  • Kim, Tae ;
  • Kim, Jae ;
  • Lin, Ming-Yi ;
  • Liu, Rui ;
  • Mack, William ;
  • McGroty, Sean ;
  • Nguyen, Joseph ;
  • Salathia, Neeraj ;
  • Shallcross, Jamie ;
  • Souaiaia, Tade ;
  • Spaethling, Jennifer ;
  • Walker, Christopher ;
  • Jinhui Wang ;
  • Wang, Kai ;
  • Wang, Wei ;
  • Wildberg, Andre ;
  • Zheng, Lina ;
  • Chow, Robert ;
  • Eberwine, James ;
  • Knowles, James ;
  • Zhang, Kun ;
  • Junhyong Kim
1 Citation0 Mentions13% FAIR0.5 Dataset Index
10.6084/m9.figshare.c.3611564_d8January 2016

Additional file 6: of Assessing characteristics of RNA amplification methods for single cell RNA sequencing

Gene detection logistic regression fit and validation. Model was fit using randomly selected 90% of 10 pg. data, excluding 17 large influence genes. Fit was evaluated on the remaining 10% of the data. Fit was also evaluated on sequence data that was in silico truncated to 50 base pair single end (“Truncated”), ERCC read counts (“ERCC”), and 100 pg. dilution replicates (“100 pg.”). AUC (area under receiver operating characteristic curve) reported as mean values ± 2 Sd. calculated over 10,000 bootstrap samples. AUC (molecules) predicts detection based on number of input molecules alone. See Methods for further details. (XLS 29 kb)

Authors

  • Dueck, Hannah ;
  • Rizi Ai ;
  • Camarena, Adrian ;
  • Ding, Bo ;
  • Reymundo Dominguez ;
  • Evgrafov, Oleg ;
  • Fan, Jian-Bing ;
  • Fisher, Stephen ;
  • Herstein, Jennifer ;
  • Kim, Tae ;
  • Kim, Jae ;
  • Lin, Ming-Yi ;
  • Liu, Rui ;
  • Mack, William ;
  • McGroty, Sean ;
  • Nguyen, Joseph ;
  • Salathia, Neeraj ;
  • Shallcross, Jamie ;
  • Souaiaia, Tade ;
  • Spaethling, Jennifer ;
  • Walker, Christopher ;
  • Jinhui Wang ;
  • Wang, Kai ;
  • Wang, Wei ;
  • Wildberg, Andre ;
  • Zheng, Lina ;
  • Chow, Robert ;
  • Eberwine, James ;
  • Knowles, James ;
  • Zhang, Kun ;
  • Junhyong Kim
1 Citation0 Mentions13% FAIR0.5 Dataset Index
10.6084/m9.figshare.c.3611564_d9January 2016

Additional file 9: of Assessing characteristics of RNA amplification methods for single cell RNA sequencing

Precision outliers. Genes with residuals within the upper or lower 1%ile with respect to regression of standard deviation on the mean (see Methods ). â Gene setâ indicates whether gene is classified as computationally unambiguous (1) or not (2). Only genes whose mean is within the range of fitted model were included. Column values indicate whether indicate whether the gene standard deviation is unexpectedly low (L) or high (H), given mean. (XLS 114 kb)

Authors

  • Dueck, Hannah ;
  • Rizi Ai ;
  • Camarena, Adrian ;
  • Ding, Bo ;
  • Reymundo Dominguez ;
  • Evgrafov, Oleg ;
  • Fan, Jian-Bing ;
  • Fisher, Stephen ;
  • Herstein, Jennifer ;
  • Kim, Tae ;
  • Kim, Jae ;
  • Lin, Ming-Yi ;
  • Liu, Rui ;
  • Mack, William ;
  • McGroty, Sean ;
  • Nguyen, Joseph ;
  • Salathia, Neeraj ;
  • Shallcross, Jamie ;
  • Souaiaia, Tade ;
  • Spaethling, Jennifer ;
  • Walker, Christopher ;
  • Jinhui Wang ;
  • Wang, Kai ;
  • Wang, Wei ;
  • Wildberg, Andre ;
  • Zheng, Lina ;
  • Chow, Robert ;
  • Eberwine, James ;
  • Knowles, James ;
  • Zhang, Kun ;
  • Junhyong Kim
1 Citation0 Mentions85% FAIR1.3 Dataset Index
10.6084/m9.figshare.c.3611564_d10January 2016

Additional file 11: of Assessing characteristics of RNA amplification methods for single cell RNA sequencing

Measurement reliability at low sequencing depth. As Fig. 4kâ m, but using low-depth in silico samples in place of individual 10 pg. replicates. (A) aRNA. (B) SmartSeq Plus. (C) NuGen. (XLS 329 kb)

Authors

  • Dueck, Hannah ;
  • Rizi Ai ;
  • Camarena, Adrian ;
  • Ding, Bo ;
  • Reymundo Dominguez ;
  • Evgrafov, Oleg ;
  • Fan, Jian-Bing ;
  • Fisher, Stephen ;
  • Herstein, Jennifer ;
  • Kim, Tae ;
  • Kim, Jae ;
  • Lin, Ming-Yi ;
  • Liu, Rui ;
  • Mack, William ;
  • McGroty, Sean ;
  • Nguyen, Joseph ;
  • Salathia, Neeraj ;
  • Shallcross, Jamie ;
  • Souaiaia, Tade ;
  • Spaethling, Jennifer ;
  • Walker, Christopher ;
  • Jinhui Wang ;
  • Wang, Kai ;
  • Wang, Wei ;
  • Wildberg, Andre ;
  • Zheng, Lina ;
  • Chow, Robert ;
  • Eberwine, James ;
  • Knowles, James ;
  • Zhang, Kun ;
  • Junhyong Kim
1 Citation0 Mentions13% FAIR0.5 Dataset Index
10.6084/m9.figshare.c.3611564_d11January 2016

Additional file 13: of Assessing characteristics of RNA amplification methods for single cell RNA sequencing

Optimization dataset sample identification, protocol information, and RNA sequencing stats. As Additional file 1 for samples used in protocol optimization analyses. (XLS 37 kb)

Authors

  • Dueck, Hannah ;
  • Rizi Ai ;
  • Camarena, Adrian ;
  • Ding, Bo ;
  • Reymundo Dominguez ;
  • Evgrafov, Oleg ;
  • Fan, Jian-Bing ;
  • Fisher, Stephen ;
  • Herstein, Jennifer ;
  • Kim, Tae ;
  • Kim, Jae ;
  • Lin, Ming-Yi ;
  • Liu, Rui ;
  • Mack, William ;
  • McGroty, Sean ;
  • Nguyen, Joseph ;
  • Salathia, Neeraj ;
  • Shallcross, Jamie ;
  • Souaiaia, Tade ;
  • Spaethling, Jennifer ;
  • Walker, Christopher ;
  • Jinhui Wang ;
  • Wang, Kai ;
  • Wang, Wei ;
  • Wildberg, Andre ;
  • Zheng, Lina ;
  • Chow, Robert ;
  • Eberwine, James ;
  • Knowles, James ;
  • Zhang, Kun ;
  • Junhyong Kim
1 Citation0 Mentions13% FAIR0.5 Dataset Index
10.6084/m9.figshare.c.3611564_d12January 2016

Additional file 13: of Assessing characteristics of RNA amplification methods for single cell RNA sequencing

Optimization dataset sample identification, protocol information, and RNA sequencing stats. As Additional file 1 for samples used in protocol optimization analyses. (XLS 37 kb)

Authors

  • Dueck, Hannah ;
  • Rizi Ai ;
  • Camarena, Adrian ;
  • Ding, Bo ;
  • Reymundo Dominguez ;
  • Evgrafov, Oleg ;
  • Fan, Jian-Bing ;
  • Fisher, Stephen ;
  • Herstein, Jennifer ;
  • Kim, Tae ;
  • Kim, Jae ;
  • Lin, Ming-Yi ;
  • Liu, Rui ;
  • Mack, William ;
  • McGroty, Sean ;
  • Nguyen, Joseph ;
  • Salathia, Neeraj ;
  • Shallcross, Jamie ;
  • Souaiaia, Tade ;
  • Spaethling, Jennifer ;
  • Walker, Christopher ;
  • Jinhui Wang ;
  • Wang, Kai ;
  • Wang, Wei ;
  • Wildberg, Andre ;
  • Zheng, Lina ;
  • Chow, Robert ;
  • Eberwine, James ;
  • Knowles, James ;
  • Zhang, Kun ;
  • Junhyong Kim
1 Citation0 Mentions13% FAIR0.5 Dataset Index
10.6084/m9.figshare.c.3611564_d12.v1January 2016