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Avantika Lal
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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
1492018
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
1272016
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
782018
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
45*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
36*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
362021
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
292019
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
172018
Quorum sensing: How bacteria talk to each other
A Lal
Resonance 14, 866-871, 2009
112009
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
92022
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
82021
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
82014
Genetic mutation detection using deep learning
J Israeli, A Lal, M Vella, N Yakovenko, Z Hu
US Patent App. 16/296,135, 2020
52020
Investigating the Human Host—ssRNA Virus Interaction Landscape Using the SMEAGOL Toolbox
A Lal, M Galvao Ferrarini, AJ Gruber
Viruses 14 (7), 1436, 2022
32022
regLM: Designing realistic regulatory DNA with autoregressive language models
A Lal, D Garfield, T Biancalani, G Eraslan
bioRxiv, 2024.02. 14.580373, 2024
22024
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
22021
Polygraph: A Software Framework for the Systematic Assessment of Synthetic Regulatory DNA Elements
A Gupta, A Lal, LM Gunsalus, T Biancalani, G Eraslan
bioRxiv, 2023.11. 27.568764, 2023
12023
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
12022
Genome variant calling with a deep averaging network
N Yakovenko, A Lal, J Israeli, B Catanzaro
arXiv preprint arXiv:2003.07220, 2020
12020
Bench-ML: A Benchmarking Web Interface for Machine Learning Methods and Models in Genomics
R Lopez, M Makita, L Ortega, A Lal, H De la Garza
bioRxiv, 2023.06. 05.543750, 2023
2023
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Articles 1–20