| Multi-omic tumor data reveal diversity of molecular mechanisms that correlate with survival D Ramazzotti, A Lal, B Wang, S Batzoglou, A Sidow Nature communications 9 (1), 1-14, 2018 | 160 | 2018 |
| Genome scale patterns of supercoiling in a bacterial chromosome A Lal, A Dhar, A Trostel, F Kouzine, ASN Seshasayee, S Adhya Nature communications 7 (1), 11055, 2016 | 133 | 2016 |
| Integrative proteomics and bioinformatic prediction enable a high-confidence apicoplast proteome in malaria parasites MJ Boucher, S Ghosh, L Zhang, A Lal, SW Jang, A Ju, S Zhang, X Wang, ... PLoS biology 16 (9), e2005895, 2018 | 92 | 2018 |
| Deep learning-based enhancement of epigenomics data with AtacWorks A Lal, ZD Chiang, N Yakovenko, FM Duarte, J Israeli, JD Buenrostro Nature communications 12 (1), 1507, 2021 | 48* | 2021 |
| Genome-wide bioinformatic analyses predict key host and viral factors in SARS-CoV-2 pathogenesis MG Ferrarini, A Lal, R Rebollo, AJ Gruber, A Guarracino, IM Gonzalez, ... Communications biology 4 (1), 590, 2021 | 41 | 2021 |
| De novo mutational signature discovery in tumor genomes using SparseSignatures A Lal, K Liu, R Tibshirani, A Sidow, D Ramazzotti PLoS computational biology 17 (6), e1009119, 2021 | 38* | 2021 |
| Comprehensive genomic characterization of breast tumors with BRCA1 and BRCA2 mutations A Lal, D Ramazzotti, Z Weng, K Liu, JM Ford, A Sidow BMC Medical Genomics 12, 1-13, 2019 | 31 | 2019 |
| Regulation of Global Transcription in Escherichia coli by Rsd and 6S RNA A Lal, S Krishna, ASN Seshasayee G3: Genes, Genomes, Genetics 8 (6), 2079-2089, 2018 | 21 | 2018 |
| Accelerating single-cell genomic analysis with GPUs C Nolet, A Lal, R Ilango, T Dyer, R Movva, J Zedlewski, J Israeli bioRxiv, 2022.05. 26.493607, 2022 | 12 | 2022 |
| Quorum sensing: How bacteria talk to each other A Lal Resonance 14, 866-871, 2009 | 12 | 2009 |
| Improving long-read consensus sequencing accuracy with deep learning A Lal, M Brown, R Mohan, J Daw, J Drake, J Israeli BioRxiv, 2021.06. 28.450238, 2021 | 8 | 2021 |
| The impact of next-generation sequencing technology on bacterial genomics A Lal, ASN Seshasayee A systems theoretic approach to systems and synthetic biology II: Analysis …, 2014 | 8 | 2014 |
| Investigating the Human Host—ssRNA Virus Interaction Landscape Using the SMEAGOL Toolbox A Lal, M Galvao Ferrarini, AJ Gruber Viruses 14 (7), 1436, 2022 | 5 | 2022 |
| regLM: Designing realistic regulatory DNA with autoregressive language models. A Lal, T Biancalani, G Eraslan NeurIPS 2023 Generative AI and Biology (GenBio) Workshop, 2023 | 4 | 2023 |
| Gepsi: A python library to simulate gwas phenotype data DA Reidenbach, A Lal, L Slim, O Mosafi, J Israeli BioRxiv, 2021.08. 04.455085, 2021 | 2 | 2021 |
| Bridging Model-Based Optimization and Generative Modeling via Conservative Fine-Tuning of Diffusion Models M Uehara, Y Zhao, E Hajiramezanali, G Scalia, G Eraslan, A Lal, S Levine, ... arXiv preprint arXiv:2405.19673, 2024 | 1 | 2024 |
| Polygraph: A Software Framework for the Systematic Assessment of Synthetic Regulatory DNA Elements A Lal, LM Gunsalus, A Gupta, T Biancalani, G Eraslan bioRxiv, 2023.11. 27.568764, 2024 | 1* | 2024 |
| SparseSignatures: An R package using LASSO-regularized non-negative matrix factorization to identify mutational signatures from human tumor samples L Mella, A Lal, F Angaroni, D Maspero, R Piazza, A Sidow, M Antoniotti, ... STAR protocols 3 (3), 101513, 2022 | 1 | 2022 |
| Genome variant calling with a deep averaging network N Yakovenko, A Lal, J Israeli, B Catanzaro arXiv preprint arXiv:2003.07220, 2020 | 1 | 2020 |
| Bench-ML: A Benchmarking Web Interface for Machine Learning Methods and Models in Genomics L Rene, M Mario, O Laura, L Avantika, DLG Hernan bioRxiv, 2023.06. 05.543750, 2023 | | 2023 |
Daniele RamazzottiDepartment of Medicine and Surgery, University of Milano-Bicocca, Milano, ItalyVerified email at unimib.it
