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1

Computational and analytical challenges in single-cell transcriptomics

Stegle, Oliver, Teichmann, Sarah A., Marioni, John C.

Journal:

Nature Reviews Genetics

Year:

2015

Language:

english

File:

PDF, 925 KB

english, 2015

2

Single-cell epigenomics: Recording the past and predicting the future

Kelsey, Gavin, Stegle, Oliver, Reik, Wolf

Journal:

Year:

2017

Language:

english

File:

PDF, 3.72 MB

english, 2017

3

A Pan-cancer Transcriptome Analysis Reveals Pervasive Regulation through Alternative Promoters

Demircioğlu, Deniz, Cukuroglu, Engin, Kindermans, Martin, Nandi, Tannistha, Calabrese, Claudia, Fonseca, Nuno A., Kahles, André, Lehmann, Kjong-Van, Stegle, Oliver, Brazma, Alvis, Brooks, Angela N., R

Journal:

Year:

2019

Language:

english

File:

PDF, 5.43 MB

english, 2019

4

Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells

Buettner, Florian, Natarajan, Kedar N, Casale, F Paolo, Proserpio, Valentina, Scialdone, Antonio, Theis, Fabian J, Teichmann, Sarah A, Marioni, John C, Stegle, Oliver

Journal:

Nature Biotechnology

Year:

2015

Language:

english

File:

PDF, 1.08 MB

english, 2015

5

pyseer: a comprehensive tool for microbial pangenome-wide association studies

Lees, John A, Galardini, Marco, Bentley, Stephen D, Weiser, Jeffrey N, Corander, Jukka, Stegle, Oliver

Journal:

Year:

2018

Language:

english

File:

PDF, 105 KB

english, 2018

6

Efficient Computation of the Kinship Coefficients

Kirkpatrick, Brent, Ge, Shufei, Wang, Liangliang, Stegle, Oliver

Journal:

Year:

2018

Language:

english

File:

PDF, 152 KB

english, 2018

7

Reply

Howell, Kate, Kraiczy, Judith, Stegle, Oliver, Zilbauer, Matthias

Journal:

Gastroenterology

Year:

2018

Language:

english

File:

PDF, 225 KB

english, 2018

8

Comprehensive Analysis of Alternative Splicing Across Tumors from 8,705 Patients

Kahles, André, Lehmann, Kjong-Van, Toussaint, Nora C., Hüser, Matthias, Stark, Stefan G., Sachsenberg, Timo, Stegle, Oliver, Kohlbacher, Oliver, Sander, Chris, Rätsch, Gunnar, Caesar-Johnson, Samantha

Journal:

Year:

2018

Language:

english

File:

PDF, 42.00 MB

english, 2018

9

METACLUSTER - an R package for context-specific expression analysis of metabolic gene clusters

Banf, Michael, Zhao, Kangmei, Rhee, Seung Y, Stegle, Oliver

Journal:

Year:

2019

Language:

english

File:

PDF, 296 KB

english, 2019

10

ELMER v.2: An R/Bioconductor package to reconstruct gene regulatory networks from DNA methylation and transcriptome profiles

Silva, Tiago C, Coetzee, Simon G, Gull, Nicole, Yao, Lijing, Hazelett, Dennis J, Noushmehr, Houtan, Lin, De-Chen, Berman, Benjamin P, Stegle, Oliver

Journal:

Year:

2018

Language:

english

File:

PDF, 946 KB

english, 2018

11

Simulation assisted machine learning

Deist, Timo M, Patti, Andrew, Wang, Zhaoqi, Krane, David, Sorenson, Taylor, Craft, David, Stegle, Oliver

Journal:

Year:

2019

Language:

english

File:

PDF, 2.43 MB

english, 2019

12

Extensive cis -Regulatory Variation Robust to Environmental Perturbation in Arabidopsis

Cubillos, Francisco A., Stegle, Oliver, Grondin, Cécile, Canut, Matthieu, Tisné, Sébastien, Gy, Isabelle, Loudet, Olivier

Journal:

Year:

2014

Language:

english

File:

PDF, 849 KB

english, 2014

13

DeepCpG: accurate prediction of single-cell DNA methylation states using deep learning

Angermueller, Christof, Lee, Heather J., Reik, Wolf, Stegle, Oliver

Journal:

Year:

2017

Language:

english

File:

PDF, 1.22 MB

english, 2017

14

A linear mixed-model approach to study multivariate gene–environment interactions

Moore, Rachel, Casale, Francesco Paolo, Jan Bonder, Marc, Horta, Danilo, Franke, Lude, Barroso, Inês, Stegle, Oliver

Journal:

Nature Genetics

Year:

2018

Language:

english

File:

PDF, 5.38 MB

english, 2018

15

Precision Lasso: Accounting for Correlations and Linear Dependencies in High-Dimensional Genomic Data

Wang, Haohan, Lengerich, Benjamin J, Aragam, Bryon, Xing, Eric P, Stegle, Oliver

Journal:

Year:

2018

Language:

english

File:

PDF, 377 KB

english, 2018

16

The Kipoi repository accelerates community exchange and reuse of predictive models for genomics

Avsec, Žiga, Kreuzhuber, Roman, Israeli, Johnny, Xu, Nancy, Cheng, Jun, Shrikumar, Avanti, Banerjee, Abhimanyu, Kim, Daniel S., Beier, Thorsten, Urban, Lara, Kundaje, Anshul, Stegle, Oliver, Gagneur,

Journal:

Nature Biotechnology

Year:

2019

Language:

english

File:

PDF, 1.59 MB

english, 2019

17

Heavy-tailed prior distributions for sequence count data: removing the noise and preserving large differences

Zhu, Anqi, Ibrahim, Joseph G, Love, Michael I, Stegle, Oliver

Journal:

Year:

2018

Language:

english

File:

PDF, 1.83 MB

english, 2018

18

Promoter shape varies across populations and affects promoter evolution and expression noise

Schor, Ignacio E, Degner, Jacob F, Harnett, Dermot, Cannavò, Enrico, Casale, Francesco P, Shim, Heejung, Garfield, David A, Birney, Ewan, Stephens, Matthew, Stegle, Oliver, Furlong, Eileen E M

Journal:

Nature Genetics

Year:

2017

Language:

english

File:

PDF, 1.64 MB

english, 2017

19

A Single-Cell Transcriptomics CRISPR-Activation Screen Identifies Epigenetic Regulators of the Zygotic Genome Activation Program

Alda-Catalinas, Celia, Bredikhin, Danila, Hernando-Herraez, Irene, Santos, FÃ¡tima, Kubinyecz, Oana, Eckersley-Maslin, MÃ©lanie A., Stegle, Oliver, Reik, Wolf

Journal:

Year:

2020

File:

PDF, 12.80 MB

2020

20

A Robust Bayesian Two-Sample Test for Detecting Intervals of Differential Gene Expression in Microarray Time Series

Stegle, Oliver, Denby, Katherine J., Cooke, Emma J., Wild, David L., Ghahramani, Zoubin, Borgwardt, Karsten M.

Journal:

Journal of Computational Biology

Year:

2010

Language:

english

File:

PDF, 2.28 MB

english, 2010

21

Efficient set tests for the genetic analysis of correlated traits

Casale, Francesco Paolo, Rakitsch, Barbara, Lippert, Christoph, Stegle, Oliver

Journal:

Year:

2015

Language:

english

File:

PDF, 717 KB

english, 2015

22

Properties of structural variants and short tandem repeats associated with gene expression and complex traits

Jakubosky, David, DâAntonio, Matteo, Bonder, Marc Jan, Smail, Craig, Donovan, Margaret K. R., Young Greenwald, William W., Matsui, Hiroko, DâAntonio-Chronowska, Agnieszka, Stegle, Oliver, Smith, E

Journal:

Nature Communications

Year:

2020

File:

PDF, 2.22 MB

2020

23

A Toolbox for Predicting G-Quadruplex Formation and Stability

Wong, Han Min, Stegle, Oliver, Rodgers, Simon, Huppert, Julian Leon

Journal:

Journal of Nucleic Acids

Year:

2010

Language:

english

File:

PDF, 2.30 MB

english, 2010

24

Flux tope analysis: studying the coordination of reaction directions in metabolic networks

Gerstl, Matthias P, Müller, Stefan, Regensburger, Georg, Zanghellini, Jürgen, Stegle, Oliver

Journal:

Year:

2018

Language:

english

File:

PDF, 453 KB

english, 2018

25

Estimating error models for whole genome sequencing using mixtures of Dirichlet-multinomial distributions

Wu, Steven H, Schwartz, Rachel S, Winter, David J, Conrad, Donald F, Cartwright, Reed A, Stegle, Oliver

Journal:

Year:

2017

Language:

english

File:

PDF, 508 KB

english, 2017

26

Breaking the paradigm: Dr Insight empowers signature-free, enhanced drug repurposing

Chan, Jinyan, Wang, Xuan, Turner, Jacob A, Baldwin, Nicole E, Gu, Jinghua, Stegle, Oliver

Journal:

Year:

2019

File:

PDF, 591 KB

2019

27

Benchmarking optimization methods for parameter estimation in large kinetic models

Villaverde, Alejandro F, Fröhlich, Fabian, Weindl, Daniel, Hasenauer, Jan, Banga, Julio R, Stegle, Oliver

Journal:

Year:

2018

Language:

english

File:

PDF, 1.40 MB

english, 2018

28

The Distance Precision Matrix: computing networks from non-linear relationships

Ghanbari, Mahsa, Lasserre, Julia, Vingron, Martin, Stegle, Oliver

Journal:

Year:

2018

Language:

english

File:

PDF, 495 KB

english, 2018

29

ngsLD : evaluating linkage disequilibrium using genotype likelihoods

Fox, Emma A, Wright, Alison E, Fumagalli, Matteo, Vieira, Filipe G, Stegle, Oliver

Journal:

Year:

2019

Language:

english

File:

PDF, 234 KB

english, 2019

30

Robustness and applicability of transcription factor and pathway analysis tools on single-cell RNA-seq data

Holland, Christian H., Tanevski, Jovan, Perales-PatÃ³n, Javier, Gleixner, Jan, Kumar, Manu P., Mereu, Elisabetta, Joughin, Brian A., Stegle, Oliver, Lauffenburger, Douglas A., Heyn, Holger, Szalai, Be

Journal:

Year:

2020

File:

PDF, 1.66 MB

2020

31

Computational assignment of cell-cycle stage from single-cell transcriptome data

Scialdone, Antonio, Natarajan, Kedar N., Saraiva, Luis R., Proserpio, Valentina, Teichmann, Sarah A., Stegle, Oliver, Marioni, John C., Buettner, Florian

Journal:

Year:

2015

Language:

english

File:

PDF, 2.65 MB

english, 2015

32

A high-content platform to characterise human induced pluripotent stem cell lines

Leha, Andreas, Moens, Nathalie, Meleckyte, Ruta, Culley, Oliver J., Gervasio, Mia K., Kerz, Maximilian, Reimer, Andreas, Cain, Stuart A., Streeter, Ian, Folarin, Amos, Stegle, Oliver, Kielty, Cay M.,

Journal:

Year:

2015

Language:

english

File:

PDF, 4.46 MB

english, 2015

33

Erratum to: DeepCpG: accurate prediction of single-cell DNA methylation states using deep learning

Angermueller, Christof, Lee, Heather J., Reik, Wolf, Stegle, Oliver

Journal:

Year:

2017

Language:

english

File:

PDF, 211 KB

english, 2017

34

L1000FWD: Fireworks visualization of drug-induced transcriptomic signatures

Wang, Zichen, Lachmann, Alexander, Keenan, Alexandra B, Ma’ayan, Avi, Stegle, Oliver

Journal:

Year:

2018

Language:

english

File:

PDF, 322 KB

english, 2018

35

pedigreejs: a web-based graphical pedigree editor

Carver, Tim, Cunningham, Alex P, Babb de Villiers, Chantal, Lee, Andrew, Hartley, Simon, Tischkowitz, Marc, Walter, Fiona M, Easton, Douglas F, Antoniou, Antonis C, Stegle, Oliver

Journal:

Year:

2018

Language:

english

File:

PDF, 103 KB

english, 2018

36

f-scLVM: scalable and versatile factor analysis for single-cell RNA-seq

Buettner, Florian, Pratanwanich, Naruemon, McCarthy, Davis J., Marioni, John C., Stegle, Oliver

Journal:

Year:

2017

Language:

english

File:

PDF, 1.22 MB

english, 2017

37

pyABC: distributed, likelihood-free inference

Klinger, Emmanuel, Rickert, Dennis, Hasenauer, Jan, Stegle, Oliver

Journal:

Year:

2018

Language:

english

File:

PDF, 100 KB

english, 2018

38

Genetic Variation in the Social Environment Contributes to Health and Disease

Baud, Amelie, Mulligan, Megan K., Casale, Francesco Paolo, Ingels, Jesse F., Bohl, Casey J., Callebert, Jacques, Launay, Jean-Marie, Krohn, Jon, Legarra, Andres, Williams, Robert W., Stegle, Oliver, F

Journal:

Year:

2017

Language:

english

File:

PDF, 2.71 MB

english, 2017

39

GrandPrix: scaling up the Bayesian GPLVM for single-cell data

Ahmed, Sumon, Rattray, Magnus, Boukouvalas, Alexis, Stegle, Oliver

Journal:

Year:

2018

Language:

english

File:

PDF, 1.19 MB

english, 2018

40

A Clustering Linear Combination Approach to Jointly Analyze Multiple Phenotypes for GWAS

Sha, Qiuying, Wang, Zhenchuan, Zhang, Xiao, Zhang, Shuanglin, Stegle, Oliver

Journal:

Year:

2018

Language:

english

File:

PDF, 1.21 MB

english, 2018

41

LASER server: ancestry tracing with genotypes or sequence reads

Taliun, Daniel, Chothani, Sonia P, Schönherr, Sebastian, Forer, Lukas, Boehnke, Michael, Abecasis, Gonçalo R, Wang, Chaolong, Stegle, Oliver

Journal:

Year:

2017

Language:

english

File:

PDF, 256 KB

english, 2017

42

Cardelino: computational integration of somatic clonal substructure and single-cell transcriptomes

McCarthy, Davis J., Rostom, Raghd, Huang, Yuanhua, Kunz, Daniel J., Danecek, Petr, Bonder, Marc Jan, Hagai, Tzachi, Lyu, Ruqian, Wang, Wenyi, Gaffney, Daniel J., Simons, Benjamin D., Stegle, Oliver, T

Journal:

Year:

2020

Language:

english

File:

PDF, 5.23 MB

english, 2020

43

[ACM Press the 25th international conference - Helsinki, Finland (2008.07.05-2008.07.09)] Proceedings of the 25th international conference on Machine learning - ICML '08 - Gaussian process product models for nonparametric nonstationarity

Adams, Ryan Prescott, Stegle, Oliver

Year:

2008

Language:

english

File:

PDF, 563 KB

english, 2008

44

PlateDesigner: a web-based application for the design of microplate experiments

Suprun, Maria, Suárez-Fariñas, Mayte, Stegle, Oliver

Journal:

Year:

2018

Language:

english

File:

PDF, 310 KB

english, 2018

45

Modeling Cell-Cell Interactions from Spatial Molecular Data with Spatial Variance Component Analysis

Arnol, Damien, Schapiro, Denis, Bodenmiller, Bernd, Saez-Rodriguez, Julio, Stegle, Oliver

Journal:

Year:

2019

Language:

english

File:

PDF, 1.91 MB

english, 2019

46

Joint Genetic Analysis of Gene Expression Data with Inferred Cellular Phenotypes

Parts, Leopold, Stegle, Oliver, Winn, John, Durbin, Richard, Storey, John D.

Journal:

Year:

2011

Language:

english

File:

PDF, 1.02 MB

english, 2011

47

easyGWAS: A Cloud-Based Platform for Comparing the Results of Genome-Wide Association Studies

Grimm, Dominik G., Roqueiro, Damian, Salomé, Patrice A., Kleeberger, Stefan, Greshake, Bastian, Zhu, Wangsheng, Liu, Chang, Lippert, Christoph, Stegle, Oliver, Schölkopf, Bernhard, Weigel, Detlef, Bor

Journal:

Year:

2017

Language:

english

File:

PDF, 4.77 MB

english, 2017

48

PANDA: A comprehensive and flexible tool for proteomics data quantitative analysis

Chang, Cheng, Li, Mansheng, Guo, Chaoping, Ding, Yuqing, Xu, Kaikun, Han, Mingfei, He, Fuchu, Zhu, Yunping, Stegle, Oliver

Journal:

Year:

2018

Language:

english

File:

PDF, 159 KB

english, 2018

49

Gimpute: An efficient genetic data imputation pipeline

Chen, Junfang, Lippold, Dietmar, Frank, Josef, Rayner, William, Meyer-Lindenberg, Andreas, Schwarz, Emanuel, Stegle, Oliver

Journal:

Year:

2018

Language:

english

File:

PDF, 208 KB

english, 2018

50

ABC random forests for Bayesian parameter inference

Raynal, Louis, Marin, Jean-Michel, Pudlo, Pierre, Ribatet, Mathieu, Robert, Christian P, Estoup, Arnaud, Stegle, Oliver

Journal:

Year:

2018

Language:

english

File:

PDF, 368 KB

english, 2018

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