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

par Mohammadi, Shahin, Davila-Velderrain, Jose, Kellis, Manolis
Publié dans Cell Syst (2019)

A multiresolution framework to characterize single-cell state landscapes

par Mohammadi, Shahin, Davila-Velderrain, Jose, Kellis, Manolis
Publié dans Nat Commun (2020)

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

par Davila-Velderrain, Jose, Villarreal, Carlos, Alvarez-Buylla, Elena R
Publié dans BMC Syst Biol (2015)

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

par Liu, Dianbo, Davila-Velderrain, Jose, Zhang, Zhizhuo, Kellis, Manolis
Publié dans Nucleic Acids Res (2019)

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

par Davila-Velderrain, Jose, Martinez-Garcia, Juan C., Alvarez-Buylla, Elena R.
Publié dans 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

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

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

par Caldu-Primo, Jose Luis, Verduzco-Martínez, Jorge Armando, Alvarez-Buylla, Elena R, Davila-Velderrain, Jose
Publié dans NAR Genom Bioinform (2021)

Gene regulatory network underlying the immortalization of epithelial cells

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

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

par 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
Publié dans Nat Neurosci (2020)

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

par 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.
Publié dans Nat Commun (2019)

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

par 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
Publié dans Neuron (2020)

Single-cell transcriptomic analysis of Alzheimer’s disease

par 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
Publié dans Nature (2019)

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

par 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
Publié dans Nat Med (2020)

Inferring multimodal latent topics from electronic health records

par 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
Publié dans Nat Commun (2020)

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

par 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
Publié dans Nat Genet (2019)