| Accurate proteome-wide missense variant effect prediction with AlphaMissense J Cheng, G Novati, J Pan, C Bycroft, A Žemgulytė, T Applebaum, A Pritzel, ... Science 381 (6664), eadg7492, 2023 | 1737 | 2023 |
| Deep learning: new computational modelling techniques for genomics G Eraslan, Ž Avsec, J Gagneur, FJ Theis Nature reviews genetics 20 (7), 389-403, 2019 | 1347 | 2019 |
| Effective gene expression prediction from sequence by integrating long-range interactions Ž Avsec, V Agarwal, D Visentin, JR Ledsam, A Grabska-Barwinska, ... Nature methods 18 (10), 1196-1203, 2021 | 1311 | 2021 |
| Base-resolution models of transcription-factor binding reveal soft motif syntax Ž Avsec, M Weilert, A Shrikumar, S Krueger, A Alexandari, K Dalal, ... Nature genetics 53 (3), 354-366, 2021 | 667 | 2021 |
| Mapping single-cell data to reference atlases by transfer learning M Lotfollahi, M Naghipourfar, MD Luecken, M Khajavi, M Büttner, ... Nature biotechnology 40 (1), 121-130, 2022 | 571 | 2022 |
| Technical note on transcription factor motif discovery from importance scores (TF-MoDISco) version 0.5. 6.5 A Shrikumar, K Tian, Ž Avsec, A Shcherbina, A Banerjee, M Sharmin, ... arXiv preprint arXiv:1811.00416, 2018 | 250 | 2018 |
| MMSplice: modular modeling improves the predictions of genetic variant effects on splicing J Cheng, TYD Nguyen, KJ Cygan, MH Çelik, WG Fairbrother, Ž Avsec, ... Genome biology 20 (1), 48, 2019 | 241 | 2019 |
| OUTRIDER: a statistical method for detecting aberrantly expressed genes in RNA sequencing data F Brechtmann, C Mertes, A Matusevičiūtė, VA Yépez, Ž Avsec, M Herzog, ... The American Journal of Human Genetics 103 (6), 907-917, 2018 | 231 | 2018 |
| The Kipoi repository accelerates community exchange and reuse of predictive models for genomics Ž Avsec, R Kreuzhuber, J Israeli, N Xu, J Cheng, A Shrikumar, A Banerjee, ... Nature biotechnology 37 (6), 592-600, 2019 | 183 | 2019 |
| The Kipoi repository accelerates community exchange and reuse of predictive models for genomics Ž Avsec, R Kreuzhuber, J Israeli, N Xu, J Cheng, A Shrikumar, A Banerjee, ... Nature biotechnology 37 (6), 592-600, 2019 | 183 | 2019 |
| An encyclopedia of enhancer-gene regulatory interactions in the human genome AR Gschwind, KS Mualim, A Karbalayghareh, MU Sheth, KK Dey, ... BioRxiv, 2023 | 108 | 2023 |
| Mutations in MDH2, encoding a Krebs cycle enzyme, cause early-onset severe encephalopathy S Ait-El-Mkadem, M Dayem-Quere, M Gusic, A Chaussenot, S Bannwarth, ... The American Journal of Human Genetics 100 (1), 151-159, 2017 | 105 | 2017 |
| Cis-regulatory elements explain most of the mRNA stability variation across genes in yeast J Cheng, KC Maier, Ž Avsec, P Rus, J Gagneur Rna 23 (11), 1648-1659, 2017 | 103 | 2017 |
| Technical note on transcription factor motif discovery from importance scores (TF-MoDISco) version 0.5. 6.5. arXiv A Shrikumar, K Tian, Ž Avsec, A Shcherbina, A Banerjee, M Sharmin, ... arXiv preprint arXiv:1811.00416, 2018 | 66 | 2018 |
| AlphaGenome: advancing regulatory variant effect prediction with a unified DNA sequence model Ž Avsec, N Latysheva, J Cheng, G Novati, KR Taylor, T Ward, C Bycroft, ... bioRxiv, 2025.06. 25.661532, 2025 | 57 | 2025 |
| AlphaFold Protein Structure Database and 3D-Beacons: New Data and Capabilities J Fleming, P Magana, S Nair, M Tsenkov, D Bertoni, I Pidruchna, ... Journal of Molecular Biology, 168967, 2025 | 55 | 2025 |
| CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods Genome biology 25 (1), 53, 2024 | 55 | 2024 |
| Predicting mean ribosome load for 5’UTR of any length using deep learning A Karollus, Ž Avsec, J Gagneur PLoS computational biology 17 (5), e1008982, 2021 | 54 | 2021 |
| Query to reference single-cell integration with transfer learning M Lotfollahi, M Naghipourfar, MD Luecken, M Khajavi, M Büttner, Z Avsec, ... bioRxiv, 2020.07. 16.205997, 2020 | 43 | 2020 |
| Modeling positional effects of regulatory sequences with spline transformations increases prediction accuracy of deep neural networks Ž Avsec, M Barekatain, J Cheng, J Gagneur Bioinformatics 34 (8), 1261-1269, 2018 | 39 | 2018 |
Julien GagneurProfessor, TUM, MunichVerified email at in.tum.de
