Publications
- See google scholar and ORCID.
- Co-first and co-last authors are indicated by * and †, respectively.
- For publications grouped by context, see research.
Papers
P34 The scverse project provides a computational ecosystem for single-cell omics data analysis
I Virshup*, D Bredikhin*, L Heumos*, G Palla, G Sturm, A Gayoso, I Kats, M Koutrouli, S Community, B Berger, D Pe’er, A Regev, SA Teichmann, F Finotello†, FA Wolf†, N Yosef†, O Stegle†, FJ Theis†
Nature Biotechnology (2023)
P33 anndata: Annotated data
I Virshup, S Rybakov, FJ Theis, P Angerer†, FA Wolf†
bioRxiv (2021) pdf code
P32 Predicting cellular responses to complex perturbations in high‐throughput screens
M Lotfollahi*, A Klimovskaia*, CD Donno**, Y Ji**, IL Ibarra, FA Wolf, N Yakubova, FJ Theis†, D Lopez-Paz†
Molecular Systems Biology (2023) Facebook AI blog bioRxiv pdf code
P31 Machine learning for perturbational single-cell omics
Y Ji, M Lotfollahi, FA Wolf, FJ Theis
Cell Systems (2021) resource
P30 Learning interpretable latent autoencoder representations with annotations of feature sets
S Rybakov, M Lotfollahi, FJ Theis†, FA Wolf†
Machine Learning in Computational Biology (2020) conference proceeding bioRxiv pdf code
P29 Conditional out-of-distribution generation for unpaired data using transfer VAE
M Lotfollahi, M Naghipourfar, FJ Theis†, FA Wolf†
Bioinformatics (2020) talk at ECCB arXiv pdf code
P28 Generalizing RNA velocity to transient cell states through dynamical modeling
V Bergen, M Lange, S Peidli, FA Wolf†, FJ Theis†
Nature Biotechnology (2020) cover story bioRxiv pdf code
P27 scGen predicts single-cell perturbation responses
M Lotfollahi, FA Wolf†, FJ Theis†
Nature Methods (2019) bioRxiv pdf code
P26 PAGA: graph abstraction reconciles clustering with trajectory inference through a topology preserving map of single cells
FA Wolf, F Hamey, M Plass, J Solana, JS Dahlin, B Göttgens, N Rajewsky, L Simon, FJ Theis
Genome Biology (2019) talk at SCG bioRxiv pdf code
P25 A test metric for assessing single-cell RNA-seq batch correction
M Büttner*, Z Miao*, FA Wolf, SA Teichmann†, FJ Theis†
Nature Methods (2018) bioRxiv pdf code
P24 Cell type atlas and lineage tree of a whole complex animal by single-cell transcriptomics
M Plass*, J Solana*, FA Wolf, S Ayoub, A Misios, P Glažar, B Obermayer, FJ Theis, C Kocks, N Rajewsky
Science (2018) pdf code
P23 Scanpy: large-scale single-cell gene expression data analysis
FA Wolf, P Angerer, FJ Theis
Genome Biology (2018) bioRxiv pdf code
P22 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 (2017)
P21 Model-based branching point detection in single-cell data by K-Branches clustering
NK Chlis, FA Wolf, FJ Theis
Bioinformatics (2017) bioRxiv code
P20 Reconstructing cell cycle and disease progression using deep learning
P Eulenberg*, N Köhler*, T Blasi, A Filby, AE Carpenter, P Rees, FJ Theis†, FA Wolf†
Nature Communications (2017) bioRxiv pdf code
P19 Diffusion pseudotime robustly reconstructs branching cellular lineages
L Haghverdi, M Büttner, FA Wolf, F Buettner, FJ Theis
Nature Methods (2016) bioRxiv pdf
P18 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 (2015) arXiv pdf
P17 How to discretize a quantum bath for real-time evolution
Id Vega, U Schollwöck, FA Wolf
Physical Review B (2015) arXiv pdf
P16 Non-thermal melting of Neel order in the Hubbard model
K Balzer, FA Wolf, IP McCulloch, P Werner, M Eckstein
Physical Review X (2015) arXiv pdf
P15 Strictly single-site DMRG algorithm with subspace expansion
C Hubig, IP McCulloch, U Schollwöck, FA Wolf
Physical Review B (2015) arXiv pdf
P14 Spectral functions and time evolution from the Chebyshev recursion
FA Wolf, JA Justiniano, IP McCulloch, U Schollwöck
Physical Review B (2015) arXiv pdf
P13 Solving nonequilibrium dynamical mean-field theory using matrix product states
FA Wolf, IP McCulloch, U Schollwöck
Physical Review B (2014) arXiv pdf
P12 Chebyshev matrix product state impurity solver for dynamical mean-field theory
FA Wolf, IP McCulloch, O Parcollet, U Schollwöck
Physical Review B (2014) arXiv pdf
P11 Electrical and structural analysis of crystal defects after high-temperature rapid thermal annealing of highly boron ion-implanted emitters
J Krügener, R Peibst, FA Wolf, E Bugiel, T Ohrdes, F Kiefer, C Schollhorn, A Grohe, R Brendel, HJ Osten
IEEE Journal of Photovoltaics (2014) ResearchGate pdf
P10 Diffusion and segregation model for the annealing of silicon solar cells implanted with phosphorus
FA Wolf, A Martinez-Limia, D Grote, D Stichtenoth, P Pichler
IEEE Journal of Photovoltaics (2014) ResearchGate pdf
P9 Modeling the annealing of dislocation loops in implanted c-Si solar cells
FA Wolf, A Martinez-Limia, D Stichtenoth, P Pichler
IEEE Journal of Photovoltaics (2014) ResearchGate pdf
P8 A comprehensive model for the diffusion of boron in silicon in presence of fluorine
FA Wolf, A Martinez-Limia, P Pichler
Solid-State Electronics (2013) ResearchGate pdf
P7 Dynamical correlation functions and the quantum Rabi model
FA Wolf, F Vallone, G Romero, M Kollar, E Solano, D Braak
Physical Review A (2013) arXiv pdf
P6 Exact real-time dynamics of the quantum Rabi model
FA Wolf, M Kollar, D Braak
Physical Review A (2012) arXiv pdf
P5 Supercurrent through grain boundaries in the presence of strong correlations
FA Wolf, S Graser, F Loder, T Kopp
Physical Review Letters (2012) arXiv pdf
P4 Expansion of Bose-Hubbard Mott insulators in optical lattices
M Jreissaty, J Carrasquilla, FA Wolf, M Rigol
Physical Review A (2011) arXiv pdf
P3 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 (2011) arXiv pdf
P2 Collapse and revival oscillations as a probe for the tunneling amplitude in an ultra-cold Bose gas
FA Wolf, I Hen, M Rigol
Physical Review A (2010) arXiv pdf
P1 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 (2009) arXiv pdf
Patents
Pa2 Molecule design
U Eser, FA Wolf, NM Plugis
Patent (2020)
Pa1 Methods of analyzing cells
A Kahvejian, NM Plugis, MR Retchin, FA Wolf, P Hosseini
Patent (2019)
Other publications
O7 Predicting cancer from three dimensional computer tomography scans of the lung
N Köhler, J Jungwirth, M Berthold, FA Wolf
Report (2017) pdf code
O6 Solving dynamical mean-field theory using matrix product states
FA Wolf
PhD Thesis (2015) pdf
O5 Modeling of annealing processes for ion-implanted single-crystalline silicon solar cells
FA Wolf
PhD Thesis (2014) pdf
O4 Supercurrent through grain boundaries in the presence of strong correlations
FA Wolf
Master’s Thesis (2011) pdf
O3 Collapse and revival oscillations as a probe for the tunneling amplitude in an ultra-cold Bose gas
FA Wolf
Report (2010) pdf
O2 Orbital order in a spin-polarized two-band Hubbard model
FA Wolf
Bachelor’s Thesis (2009) pdf
O1 Sartre à Stammheim: son éxistentialisme et l'idéologie de la fraction armée rouge
FA Wolf
High School Thesis (2005) pdf