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Alex Wolf
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SCANPY: large-scale single-cell gene expression data analysis
FA Wolf, P Angerer, FJ Theis
Genome Biology 19, 15, 2018
47842018
Generalizing RNA velocity to transient cell states through dynamical modeling
V Bergen, M Lange, S Peidli, FA Wolf†, FJ Theis†
Nature Biotechnology, 2020
17122020
Diffusion pseudotime robustly reconstructs lineage branching
L Haghverdi, M Buettner, FA Wolf, F Buettner, FJ Theis
Nature Methods 13, 845-848, 2016
11832016
PAGA: graph abstraction reconciles clustering with trajectory inference through a topology preserving map of single cells
FA Wolf, FK Hamey, M Plass, [...], N Rajewsky, L Simon, FJ Theis
Genome Biology 20, 59, 2019
11232019
Cell type atlas and lineage tree of a whole complex animal by single-cell transcriptomics
M Plass*, J Solana*, FA Wolf, [...], FJ Theis, C Kocks, N Rajewsky
Science 360 (6391), eaaq1723, 2018
4622018
A test metric for assessing single-cell RNA-seq batch correction
M Büttner*, Z Miao*, FA Wolf, SA Teichmann†, FJ Theis†
Nature Methods 16, 43, 2019
3532019
scGen predicts single-cell perturbation responses
M Lotfollahi, FA Wolf†, FJ Theis†
Nature methods 16 (8), 715-721, 2019
3452019
Generalized Gibbs ensemble prediction of prethermalization plateaus and their relation to nonthermal steady states in integrable systems
M Kollar, FA Wolf, M Eckstein
Physical Review B 84 (5), 054304, 2011
3452011
Reconstructing cell cycle and disease progression using deep learning
P Eulenberg*, N Koehler*, T Blasi, [...], P Rees, FJ Theis†, FA Wolf†
Nature Communications 8, 463, 2017
2712017
Single cells make big data: new challenges and opportunities in transcriptomics
P Angerer, L Simon, S Tritschler, FA Wolf, D Fischer, FJ Theis
Current Opinion in Systems Biology 4, 85-91, 2017
2132017
Strictly Single-Site DMRG Algorithm with Subspace Expansion
C Hubig, IP McCulloch, U Schollwöck, FA Wolf
Physical Review B 91 (15), 155115, 2015
1832015
Solving nonequilibrium dynamical mean-field theory using matrix product states
FA Wolf, IP McCulloch, U Schollwöck
Physical Review B 90 (23), 235131, 2014
1282014
Chebyshev matrix product state impurity solver for dynamical mean-field theory
FA Wolf, IP McCulloch, O Parcollet, U Schollwöck
Physical Review B 90 (11), 115124, 2014
1152014
anndata: Annotated data
I Virshup, S Rybakov, FJ Theis, P Angerer†, FA Wolf†
bioRxiv, 2021
1062021
Imaginary-time matrix product state impurity solver for dynamical mean-field theory
FA Wolf, A Go, IP McCulloch, AJ Millis, U Schollwöck
Physical Review X 5 (4), 041032, 2015
1052015
Predicting cellular responses to complex perturbations in high‐throughput screens
M Lotfollahi, A Klimovskaia Susmelj, C De Donno, L Hetzel, Y Ji, IL Ibarra, ...
Molecular systems biology 19 (6), e11517, 2023
100*2023
Conditional out-of-distribution generation for unpaired data using transfer VAE
M Lotfollahi, M Naghipourfar, FJ Theis†, FA Wolf†
Bioinformatics 36 (Supplement_2), i610-i617, 2020
90*2020
Exact real-time dynamics of the quantum Rabi model
FA Wolf, M Kollar, D Braak
Physical Review A 85 (5), 053817, 2012
792012
New theoretical approaches for correlated systems in nonequilibrium
M Eckstein, A Hackl, S Kehrein, M Kollar, M Moeckel, P Werner, FA Wolf
The European Physical Journal Special Topics 180, 217-235, 2009
782009
Machine learning for perturbational single-cell omics
Y Ji, M Lotfollahi, FA Wolf, FJ Theis
Cell Systems 12 (6), 522-537, 2021
742021
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Articles 1–20