| Droplet-based combinatorial indexing for massive-scale single-cell chromatin accessibility CA Lareau, FM Duarte, JG Chew, VK Kartha, ZD Burkett, AS Kohlway, ... Nature Biotechnology 37 (8), 916-924, 2019 | 386 | 2019 |
| Mammalian heat shock response and mechanisms underlying its genome-wide transcriptional regulation DB Mahat, HH Salamanca, FM Duarte, CG Danko, JT Lis Molecular cell 62 (1), 63-78, 2016 | 385 | 2016 |
| Genome structure of a Saccharomyces cerevisiae strain widely used in bioethanol production JL Argueso, MF Carazzolle, PA Mieczkowski, FM Duarte, OVC Netto, ... Genome research 19 (12), 2258-2270, 2009 | 301 | 2009 |
| Molecular mechanisms driving transcriptional stress responses A Vihervaara, FM Duarte, JT Lis Nature Reviews Genetics 19 (6), 385-397, 2018 | 224 | 2018 |
| Epigenomic state transitions characterize tumor progression in mouse lung adenocarcinoma LM LaFave, VK Kartha, S Ma, K Meli, I Del Priore, C Lareau, S Naranjo, ... Cancer cell 38 (2), 212-228. e13, 2020 | 176 | 2020 |
| Transcription factors GAF and HSF act at distinct regulatory steps to modulate stress-induced gene activation FM Duarte, NJ Fuda, DB Mahat, LJ Core, MJ Guertin, JT Lis Genes & Development 30 (15), 1731-1746, 2016 | 140 | 2016 |
| Functional inference of gene regulation using single-cell multi-omics VK Kartha, FM Duarte, Y Hu, S Ma, JG Chew, CA Lareau, A Earl, ... Cell genomics 2 (9), 2022 | 104 | 2022 |
| An improved auxin-inducible degron system preserves native protein levels and enables rapid and specific protein depletion KM Sathyan, BD McKenna, WD Anderson, FM Duarte, L Core, MJ Guertin Genes & development 33 (19-20), 1441-1455, 2019 | 102 | 2019 |
| Inference and effects of barcode multiplets in droplet-based single-cell assays CA Lareau, S Ma, FM Duarte, JD Buenrostro Nature Communications 11 (1), 866, 2020 | 54 | 2020 |
| Pioneer-like factor GAF cooperates with PBAP (SWI/SNF) and NURF (ISWI) to regulate transcription J Judd, FM Duarte, JT Lis Genes & Development 35 (1-2), 147-156, 2021 | 51 | 2021 |
| Multiplexed microcolumn-based process for efficient selection of RNA aptamers DR Latulippe, K Szeto, A Ozer, FM Duarte, CV Kelly, JM Pagano, ... Analytical chemistry 85 (6), 3417-3424, 2013 | 48 | 2013 |
| 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 | 39 | 2021 |
| High-throughput binding characterization of RNA aptamer selections using a microplate-based multiplex microcolumn device K Szeto, SJ Reinholt, FM Duarte, JM Pagano, A Ozer, L Yao, JT Lis, ... Analytical and bioanalytical chemistry 406, 2727-2732, 2014 | 30 | 2014 |
| Defining data-driven primary transcript annotations with primaryTranscriptAnnotation in R WD Anderson, FM Duarte, M Civelek, MJ Guertin Bioinformatics 36 (9), 2926-2928, 2020 | 11 | 2020 |
| Systematic benchmarking of single-cell ATAC-sequencing protocols FV De Rop, G Hulselmans, C Flerin, P Soler-Vila, A Rafels, V Christiaens, ... Nature biotechnology 42 (6), 916-926, 2024 | 10 | 2024 |
| AtacWorks: A deep convolutional neural network toolkit for epigenomics A Lal, ZD Chiang, N Yakovenko, FM Duarte, J Israeli, JD Buenrostro Biorxiv, 829481, 2019 | 9 | 2019 |
| Single-cell multi-scale footprinting reveals the modular organization of DNA regulatory elements Y Hu, S Ma, VK Kartha, FM Duarte, M Horlbeck, R Zhang, R Shrestha, ... bioRxiv, 2023 | 7 | 2023 |
| Kinetic networks identify TWIST2 as a key regulatory node in adipogenesis AB Dutta, DS Lank, RK Przanowska, P Przanowski, L Wang, B Nguyen, ... Genome Research 33 (3), 314-331, 2023 | 4 | 2023 |
| The Drosophila BEAF insulator protein interacts with the polybromo subunit of the PBAP chromatin remodeling complex JK McKowen, SVSP Avva, M Maharjan, FM Duarte, JM Tome, J Judd, ... G3 12 (11), jkac223, 2022 | 3 | 2022 |
| Pioneer factor GAF cooperates with PBAP and NURF to regulate transcription J Judd, FM Duarte, JT Lis bioRxiv, 2020.05. 10.087262, 2020 | 3 | 2020 |
