@article{kim2024moments,title={Method of moments framework for differential expression analysis of single-cell {RNA} sequencing data},author={Kim, Min Cheol and Gate, Rachel and Lee, David S. and Tolopko, Andrew and Lu, Andrew and Gordon, Erin and Shifrut, Eric and Garcia-Nieto, Pablo E. and Marson, Alexander and Ntranos, Vasilis and Ye, Chun Jimmie},journal={Cell},volume={187},number={22},pages={6393--6410},year={2024},doi={10.1016/j.cell.2024.09.044},}
2023
bioRxiv
CZ CELL×GENE Discover: A single-cell data platform for scalable exploration, analysis and modeling of aggregated data
CZI Single-Cell Biology Program, Shibla Abdulla, Brian Aevermann, and 51 more authors
@article{cellxgene2023,title={{CZ} {CELL}×{GENE} Discover: A single-cell data platform for scalable exploration, analysis and modeling of aggregated data},author={Program, CZI Single-Cell Biology and Abdulla, Shibla and Aevermann, Brian and Assis, Pedro and Badajoz, Seve and Bell, Sidney M. and Bezzi, Emanuele and Cakir, Batuhan and Chaffer, Jim and Chambers, Signe and Cherry, J. Michael and Chi, Tiffany and Chien, Jennifer and Dorman, Leah and Garcia-Nieto, Pablo and Gloria, Nayib and Hastie, Mim and Hegeman, Daniel and Hilton, Jason and Huang, Timmy and Infeld, Amanda and Istrate, Ana-Maria and Jelic, Ivana and Katsuya, Kuni and Kim, Yang Joon and Liang, Karen and Lin, Mike and Lombardo, Maximilian and Marshall, Bailey and Martin, Bruce and McDade, Fran and Megill, Colin and Patel, Nikhil and Predeus, Alexander and Raymor, Brian and Robatmili, Behnam and Rogers, Dave and Rutherford, Erica and Sadgat, Dana and Shin, Andrew and Small, Corinn and Smith, Trent and Sridharan, Prathap and Tarashansky, Alexander and Tavares, Norbert and Thomas, Harley and Tolopko, Andrew and Urisko, Meghan and Yan, Joyce and Yeretssian, Garabet and Zamanian, Jennifer and Mani, Arathi and Cool, Jonah and Carr, Ambrose},journal={bioRxiv},year={2023},doi={10.1101/2023.10.30.563174},}
2022
PLoS Comput Biol
Transcriptome diversity is a systematic source of variation in RNA-sequencing data
Pablo E. Garcia-Nieto, Ban Wang, and Hunter B. Fraser
@article{garciani2022transcriptome,title={Transcriptome diversity is a systematic source of variation in {RNA}-sequencing data},author={Garcia-Nieto, Pablo E. and Wang, Ban and Fraser, Hunter B.},journal={PLOS Computational Biology},year={2022},}
2021
Mutat Res
Genome-wide profiles of UV lesion susceptibility, repair, and mutagenic potential in melanoma
Brian S. Perez, Ka Man Wong, Erin K. Schwartz, and 4 more authors
@article{perez2021uv,title={Genome-wide profiles of {UV} lesion susceptibility, repair, and mutagenic potential in melanoma},author={Perez, Brian S. and Wong, Ka Man and Schwartz, Erin K. and Herrera, Rafael E. and King, Devin A. and Garcia-Nieto, Pablo E. and Morrison, Ashby J.},journal={Mutation Research},year={2021},}
2019
Genome Biol
The somatic mutation landscape of the human body
Pablo E. Garcia-Nieto, Ashby J. Morrison, and Hunter B. Fraser
@article{garciani2019somatic,title={The somatic mutation landscape of the human body},author={Garcia-Nieto, Pablo E. and Morrison, Ashby J. and Fraser, Hunter B.},journal={Genome Biology},year={2019},}
2018
PLoS Genet
The INO80 chromatin remodeler sustains metabolic stability by promoting TOR signaling and regulating histone acetylation
Sean L. Beckwith, Erin K. Schwartz, Pablo E. Garcia-Nieto, and 9 more authors
@article{beckwith2018ino80,title={The {INO80} chromatin remodeler sustains metabolic stability by promoting {TOR} signaling and regulating histone acetylation},author={Beckwith, Sean L. and Schwartz, Erin K. and Garcia-Nieto, Pablo E. and King, Devin A. and Gowans, Graeme J. and Wong, Ka Man and Eckley, Tessa L. and Paraschuk, Alexander P. and Peltan, Egan L. and Lee, Laura R. and Yao, Wei and Morrison, Ashby J.},journal={PLOS Genetics},year={2018},}
2017
EMBO J
Carcinogen susceptibility is regulated by genome architecture and predicts cancer mutagenesis
Pablo E. Garcia-Nieto, Erin K. Schwartz, Devin A. King, and 4 more authors
@article{garciani2017carcinogen,title={Carcinogen susceptibility is regulated by genome architecture and predicts cancer mutagenesis},author={Garcia-Nieto, Pablo E. and Schwartz, Erin K. and King, Devin A. and Paulsen, Jonas and Collas, Philippe and Herrera, Rafael E. and Morrison, Ashby J.},journal={The EMBO Journal},year={2017},}
2014
Epigenetics
Set5 and Set1 cooperate to repress gene expression at telomeres and retrotransposons
Glòria Mas Martín, Devin A. King, Erin M. Green, and 6 more authors
@article{martin2014set5,title={Set5 and Set1 cooperate to repress gene expression at telomeres and retrotransposons},author={Mart{\'i}n, Gl{\`o}ria Mas and King, Devin A. and Green, Erin M. and Garcia-Nieto, Pablo E. and Alexander, Richard and Collins, Sean R. and Krogan, Nevan J. and Gozani, Or P. and Morrison, Ashby J.},journal={Epigenetics},year={2014},}