Computational challenges and opportunities in spatially resolved transcriptomic data analysis

por Atta, Lyla, Fan, Jean
Publicado 2021

Single-cell transcriptomics in cancer: computational challenges and opportunities

por Fan, Jean, Slowikowski, Kamil, Zhang, Fan
Publicado 2020

Gene count normalization in single-cell imaging-based spatially resolved transcriptomics

por Atta, Lyla, Clifton, Kalen, Anant, Manjari, Fan, Jean
Publicado 2023

Spatial transcriptome profiling by MERFISH reveals subcellular RNA compartmentalization and cell cycle-dependent gene expression

por Xia, Chenglong, Fan, Jean, Emanuel, George, Hao, Junjie, Zhuang, Xiaowei
Publicado 2019

Reference-free cell type deconvolution of multi-cellular pixel-resolution spatially resolved transcriptomics data

por Miller, Brendan F., Huang, Feiyang, Atta, Lyla, Sahoo, Arpan, Fan, Jean
Publicado 2022

Characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomic data with nonuniform cellular densities

por Miller, Brendan F., Bambah-Mukku, Dhananjay, Dulac, Catherine, Zhuang, Xiaowei, Fan, Jean
Publicado 2021

Effects of Ketoconazole on the Pharmacokinetics of Lenvatinib (E7080) in Healthy Participants

por Shumaker, Robert, Aluri, Jagadeesh, Fan, Jean, Martinez, Gresel, Thompson, Gary A, Ren, Min
Publicado 2015

Effect of Rifampicin on the Pharmacokinetics of Lenvatinib in Healthy Adults

por Shumaker, Robert C., Aluri, Jagadeesh, Fan, Jean, Martinez, Gresel, Thompson, Gary A., Ren, Min
Publicado 2014

Alignment of spatial transcriptomics data using diffeomorphic metric mapping

por Clifton, Kalen, Anant, Manjari, Aihara, Gohta, Atta, Lyla, Aimiuwu, Osagie K., Kebschull, Justus M., Miller, Michael I., Tward, Daniel, Fan, Jean
Publicado 2023

Fast, sensitive, and accurate integration of single cell data with Harmony

por Korsunsky, Ilya, Millard, Nghia, Fan, Jean, Slowikowski, Kamil, Zhang, Fan, Wei, Kevin, Baglaenko, Yuriy, Brenner, Michael, Loh, Po-ru, Raychaudhuri, Soumya
Publicado 2019

Characterizing transcriptional heterogeneity through pathway and gene set overdispersion analysis

por Fan, Jean, Salathia, Neeraj, Liu, Rui, Kaeser, Gwendolyn E., Yung, Yun C., Herman, Joseph L., Kaper, Fiona, Fan, Jian-Bing, Zhang, Kun, Chun, Jerold, Kharchenko, Peter V.
Publicado 2016

Integrative single-cell analysis of transcriptional and epigenetic states in the human adult brain

por Lake, Blue B., Chen, Song, Sos, Brandon C., Fan, Jean, Kaeser, Gwendolyn E., Yung, Yun C., Duong, Thu E., Gao, Derek, Chun, Jerold, Kharchenko, Peter V., Zhang, Kun
Publicado 2017

Linking transcriptional and genetic tumor heterogeneity through allele analysis of single-cell RNA-seq data

por Fan, Jean, Lee, Hae-Ock, Lee, Soohyun, Ryu, Da-eun, Lee, Semin, Xue, Catherine, Kim, Seok Jin, Kim, Kihyun, Barkas, Nikolaos, Park, Peter J., Park, Woong-Yang, Kharchenko, Peter V.
Publicado 2018

Afatinib versus gemcitabine/cisplatin for first-line treatment of Chinese patients with advanced non-small-cell lung cancer harboring EGFR mutations: subgroup analysis of the LUX-L...

por Wu, Yi-Long, Xu, Chong-Rui, Hu, Cheng-Ping, Feng, Jifeng, Lu, Shun, Huang, Yunchao, Li, Wei, Hou, Mei, Shi, Jian Hua, Märten, Angela, Fan, Jean, Peil, Barbara, Zhou, Caicun
Publicado 2018

Single cell and spatial transcriptomics analysis of kidney double negative T lymphocytes in normal and ischemic mouse kidneys

por Gharaie, Sepideh, Lee, Kyungho, Noller, Kathleen, Lo, Emily K., Miller, Brendan, Jung, Hyun Jun, Newman-Rivera, Andrea M., Kurzhagen, Johanna T., Singla, Nirmish, Welling, Paul A., Fan, Jean, Cahan, Patrick, Noel, Sanjeev, Rabb, Hamid
Publicado 2023

Integrated single-cell genetic and transcriptional analysis suggests novel drivers of chronic lymphocytic leukemia

por Wang, Lili, Fan, Jean, Francis, Joshua M., Georghiou, George, Hergert, Sarah, Li, Shuqiang, Gambe, Rutendo, Zhou, Chensheng W., Yang, Chunxiao, Xiao, Sheng, Cin, Paola Dal, Bowden, Michaela, Kotliar, Dylan, Shukla, Sachet A., Brown, Jennifer R., Neuberg, Donna, Alessi, Dario R., Zhang, Cheng-Zhong, Kharchenko, Peter V., Livak, Kenneth J., Wu, Catherine J.
Publicado 2017

RNA velocity of single cells

por La Manno, Gioele, Soldatov, Ruslan, Zeisel, Amit, Braun, Emelie, Hochgerner, Hannah, Petukhov, Viktor, Lidschreiber, Katja, Kastriti, Maria E., Lönnerberg, Peter, Furlan, Alessandro, Fan, Jean, Borm, Lars E., Liu, Zehua, van Bruggen, David, Guo, Jimin, He, Xiaoling, Barker, Roger, Sundström, Erik, Castelo-Branco, Gonçalo, Cramer, Patrick, Adameyko, Igor, Linnarsson, Sten, Kharchenko, Peter V.
Publicado 2018

Clonal evolution in patients with chronic lymphocytic leukaemia developing resistance to BTK inhibition

por Burger, Jan A., Landau, Dan A., Taylor-Weiner, Amaro, Bozic, Ivana, Zhang, Huidan, Sarosiek, Kristopher, Wang, Lili, Stewart, Chip, Fan, Jean, Hoellenriegel, Julia, Sivina, Mariela, Dubuc, Adrian M., Fraser, Cameron, Han, Yulong, Li, Shuqiang, Livak, Kenneth J., Zou, Lihua, Wan, Youzhong, Konoplev, Sergej, Sougnez, Carrie, Brown, Jennifer R., Abruzzo, Lynne V., Carter, Scott L., Keating, Michael J., Davids, Matthew S., Wierda, William G., Cibulskis, Kristian, Zenz, Thorsten, Werner, Lillian, Cin, Paola Dal, Kharchencko, Peter, Neuberg, Donna, Kantarjian, Hagop, Lander, Eric, Gabriel, Stacey, O'Brien, Susan, Letai, Anthony, Weitz, David A., Nowak, Martin A., Getz, Gad, Wu, Catherine J.
Publicado 2016