Reconstruction of cell-type specific interactomes at single-cell resolution

le Mohammadi, Shahin, Davila-Velderrain, Jose, Kellis, Manolis
Foilsithe in Cell Syst (2019)

A multiresolution framework to characterize single-cell state landscapes

le Mohammadi, Shahin, Davila-Velderrain, Jose, Kellis, Manolis
Foilsithe in Nat Commun (2020)

Reshaping the epigenetic landscape during early flower development: induction of attractor transitions by relative differences in gene decay rates

le Davila-Velderrain, Jose, Villarreal, Carlos, Alvarez-Buylla, Elena R
Foilsithe in BMC Syst Biol (2015)

Integrative construction of regulatory region networks in 127 human reference epigenomes by matrix factorization

le Liu, Dianbo, Davila-Velderrain, Jose, Zhang, Zhizhuo, Kellis, Manolis
Foilsithe in Nucleic Acids Res (2019)

Modeling the epigenetic attractors landscape: toward a post-genomic mechanistic understanding of development

le Davila-Velderrain, Jose, Martinez-Garcia, Juan C., Alvarez-Buylla, Elena R.
Foilsithe in Front Genet (2015)

NEBULA is a fast negative binomial mixed model for differential or co-expression analysis of large-scale multi-subject single-cell data

le He, Liang, Davila-Velderrain, Jose, Sumida, Tomokazu S., Hafler, David A., Kellis, Manolis, Kulminski, Alexander M.
Foilsithe in Commun Biol (2021)

In vivo and in vitro human gene essentiality estimations capture contrasting functional constraints

le Caldu-Primo, Jose Luis, Verduzco-Martínez, Jorge Armando, Alvarez-Buylla, Elena R, Davila-Velderrain, Jose
Foilsithe in NAR Genom Bioinform (2021)

Gene regulatory network underlying the immortalization of epithelial cells

le Méndez-López, Luis Fernando, Davila-Velderrain, Jose, Domínguez-Hüttinger, Elisa, Enríquez-Olguín, Christian, Martínez-García, Juan Carlos, Alvarez-Buylla, Elena R.
Foilsithe in BMC Syst Biol (2017)

Mapping the epigenomic and transcriptomic interplay during memory formation and recall in the hippocampal engram ensemble

le Marco, Asaf, Meharena, Hiruy S., Dileep, Vishnu, Raju, Ravikiran M., Davila-Velderrain, Jose, Zhang, Amy, Adaikkan, Chinnakkaruppan, Young, Jennie Z., Gao, Fan, Kellis, Manolis, Tsai, Li-Huei
Foilsithe in Nat Neurosci (2020)

Single-cell transcriptomic atlas of the human retina identifies cell types associated with age-related macular degeneration

le Menon, Madhvi, Mohammadi, Shahin, Davila-Velderrain, Jose, Goods, Brittany A., Cadwell, Tanina D., Xing, Yu, Stemmer-Rachamimov, Anat, Shalek, Alex K., Love, John Christopher, Kellis, Manolis, Hafler, Brian P.
Foilsithe in Nat Commun (2019)

Cell Type-Specific Transcriptomics Reveals that Mutant Huntingtin Leads to Mitochondrial RNA Release and Neuronal Innate Immune Activation

le Lee, Hyeseung, Fenster, Robert J., Pineda, S. Sebastian, Gibbs, Whitney S., Mohammadi, Shahin, Davila-Velderrain, Jose, Garcia, Francisco J., Therrien, Martine, Novis, Hailey S., Gao, Fan, Wilkinson, Hilary, Vogt, Thomas, Kellis, Manolis, LaVoie, Matthew J., Heiman, Myriam
Foilsithe in Neuron (2020)

Single-cell transcriptomic analysis of Alzheimer’s disease

le Mathys, Hansruedi, Davila-Velderrain, Jose, Peng, Zhuyu, Gao, Fan, Mohammadi, Shahin, Young, Jennie Z., Menon, Madhvi, He, Liang, Abdurrob, Fatema, Jiang, Xueqiao, Martorell, Anthony J., Ransohoff, Richard M., Hafler, Brian P., Bennett, David A., Kellis, Manolis, Tsai, Li-Huei
Foilsithe in Nature (2019)

Reconstruction of the Human Blood-Brain Barrier in vitro reveals a Pathogenic Mechanism of APOE4 in Pericytes

le Blanchard, Joel W., Bula, Michael, Davila-Velderrain, Jose, Akay, Leyla Anne, Zhu, Lena, Frank, Alexander, Victor, Matheus B., Bonner, Julia Maeve, Mathys, Hansruedi, Lin, Yuan-Ta, Ko, Tak, Bennett, David A., Cam, Hugh P., Kellis, Manolis, Tsai, Li-Huei
Foilsithe in Nat Med (2020)

Inferring multimodal latent topics from electronic health records

le Li, Yue, Nair, Pratheeksha, Lu, Xing Han, Wen, Zhi, Wang, Yuening, Dehaghi, Amir Ardalan Kalantari, Miao, Yan, Liu, Weiqi, Ordog, Tamas, Biernacka, Joanna M., Ryu, Euijung, Olson, Janet E., Frye, Mark A., Liu, Aihua, Guo, Liming, Marelli, Ariane, Ahuja, Yuri, Davila-Velderrain, Jose, Kellis, Manolis
Foilsithe in Nat Commun (2020)

Association studies of up to 1.2 million individuals yield new insights into the genetic etiology of tobacco and alcohol use

le Liu, Mengzhen, Jiang, Yu, Wedow, Robbee, Li, Yue, Brazel, David M., Chen, Fang, Datta, Gargi, Davila-Velderrain, Jose, McGuire, Daniel, Tian, Chao, Zhan, Xiaowei, Choquet, Hélène, Docherty, Anna R., Faul, Jessica D., Foerster, Johanna R., Fritsche, Lars G., Gabrielsen, Maiken Elvestad, Gordon, Scott D., Haessler, Jeffrey, Hottenga, Jouke-Jan, Huang, Hongyan, Jang, Seon-Kyeong, Jansen, Philip R., Ling, Yueh, Mägi, Reedik, Matoba, Nana, McMahon, George, Mulas, Antonella, Orrù, Valeria, Palviainen, Teemu, Pandit, Anita, Reginsson, Gunnar W., Skogholt, Anne Heidi, Smith, Jennifer A., Taylor, Amy E., Turman, Constance, Willemsen, Gonneke, Young, Hannah, Young, Kendra A., Zajac, Gregory J. M., Zhao, Wei, Zhou, Wei, Bjornsdottir, Gyda, Boardman, Jason D., Boehnke, Michael, Boomsma, Dorret I., Chen, Chu, Cucca, Francesco, Davies, Gareth E., Eaton, Charles B., Ehringer, Marissa A., Esko, Tõnu, Fiorillo, Edoardo, Gillespie, Nathan A., Gudbjartsson, Daniel F., Haller, Toomas, Harris, Kathleen Mullan, Heath, Andrew C., Hewitt, John K., Hickie, Ian B., Hokanson, John E., Hopfer, Christian J., Hunter, David J., Iacono, William G., Johnson, Eric O., Kamatani, Yoichiro, Kardia, Sharon L. R., Keller, Matthew C., Kellis, Manolis, Kooperberg, Charles, Kraft, Peter, Krauter, Kenneth S., Laakso, Markku, Lind, Penelope A., Loukola, Anu, Lutz, Sharon M., Madden, Pamela A. F., Martin, Nicholas G., McGue, Matt, McQueen, Matthew B., Medland, Sarah E., Metspalu, Andres, Mohlke, Karen L., Nielsen, Jonas B., Okada, Yukinori, Peters, Ulrike, Polderman, Tinca J. C., Posthuma, Danielle, Reiner, Alexander P., Rice, John P., Rimm, Eric, Rose, Richard J., Runarsdottir, Valgerdur, Stallings, Michael C., Stančáková, Alena, Stefansson, Hreinn, Thai, Khanh K., Tindle, Hilary A., Tyrfingsson, Thorarinn, Wall, Tamara L., Weir, David R., Weisner, Constance, Whitfield, John B., Winsvold, Bendik Slagsvold, Yin, Jie, Zuccolo, Luisa, Bierut, Laura J., Hveem, Kristian, Lee, James J., Munafo, Marcus R., Saccone, Nancy L., Willer, Cristen J., Cornelis, Marilyn C., David, Sean P., Hinds, David, Jorgenson, Eric, Kaprio, Jaakko, Stitzel, Jerry A., Stefansson, Kari, Thorgeirsson, Thorgeir E., Abecasis, Goncalo, Liu, Dajiang J., Vrieze, Scott
Foilsithe in Nat Genet (2019)