Results 1 to 10 of about 398,969 (379)

Deep generative modeling for single-cell transcriptomics. [PDF]

Nature Methods, 2018
Single-cell transcriptome measurements can reveal unexplored biological diversity, but they suffer from technical noise and bias that must be modeled to account for the resulting uncertainty in downstream analyses.
A Regev, A Tanay, A Wagner, A Zeisel, AP Patel, B Wang, BK Tusi, CA Vallejos, CA Vallejos, D DeTomaso, D Grün, D Risso, DM Blei, E Pierson, FA Wolf, G Finak, G Görgün, GXY Zheng, HI Nakaya, J Ding, J Fan, Jeffrey Regier, JT Gaublomme, K Shekhar, L Haghverdi, L Held, M Stoeckius, MD Robinson, MI Love, Michael B. Cole, Michael I. Jordan, Nir Yosef, PV Kharchenko, Q Li, RE Kass, Romain Lopez, S Prabhakaran, S Semrau, U Shaham, WE Johnson   +39 more
core   +2 more sources

Advances in spatial transcriptomics and its applications in cancer research

Molecular Cancer
Malignant tumors have increasing morbidity and high mortality, and their occurrence and development is a complicate process. The development of sequencing technologies enabled us to gain a better understanding of the underlying genetic and molecular ...
Yang Jin, Yuanli Zuo, Gang Li, Wenrong Liu, Yitong Pan, Ting Fan, Xin Fu, Xiaojun Yao, Yong Peng   +8 more
doaj   +2 more sources

Spatially informed clustering, integration, and deconvolution of spatial transcriptomics with GraphST

bioRxiv, 2023
Spatial transcriptomics technologies generate gene expression profiles with spatial context, requiring spatially informed analysis tools for three key tasks, spatial clustering, multisample integration, and cell-type deconvolution.
Yahui Long, Kok Siong Ang, Mengwei Li, Kian Long Kelvin Chong, R. Sethi, Chengwei Zhong, Hang Xu, Zhiwei Ong, K. Sachaphibulkij, Ao Chen, Zeng Li, H. Fu, Min Wu, Hsiu Kim Lina Lim, Longqi Liu, Jinmiao Chen   +15 more
semanticscholar   +1 more source

Large Scale Foundation Model on Single-cell Transcriptomics

bioRxiv, 2023
Large-scale pretrained models have become foundation models leading to breakthroughs in natural language processing and related fields. Developing foundation models in life science for deciphering the “languages” of cells and facilitating biomedical ...
Minsheng Hao, Jing Gong, Xin Zeng, Chiming Liu, Yucheng Guo, Xingyi Cheng, Taifeng Wang, Jianzhu Ma, Leo T. Song, Xuegong Zhang   +9 more
semanticscholar   +1 more source

Screening cell–cell communication in spatial transcriptomics via collective optimal transport

Nature Methods, 2023
This work presents a computational framework, COMMOT, to spatially infer cell–cell communication from transcriptomics data based on a variant of optimal transport (OT).
Zixuan Cang, Yanxiang Zhao, Axel A. Almet, Adam R. Stabell, Raul Ramos, M. Plikus, Scott X. Atwood, Qing Nie   +7 more
semanticscholar   +1 more source

Improving ancient DNA genome assembly [PDF]

PeerJ, 2017
Most reconstruction methods for genomes of ancient origin that are used today require a closely related reference. In order to identify genomic rearrangements or the deletion of whole genes, de novo assembly has to be used.
Alexander Seitz, Kay Nieselt
doaj   +2 more sources

Identification and characterization of a novel enhancer in the HTLV-1 proviral genome

Nature Communications, 2022
Human T-cell leukemia virus type 1 (HTLV-1) is an oncogenic virus with constantly active antisense transcription from the proviral genome. Here, Matsuo et al.
Misaki Matsuo, Takaharu Ueno, Kazuaki Monde, Kenji Sugata, Benjy Jek Yang Tan, Akhinur Rahman, Paola Miyazato, Kyosuke Uchiyama, Saiful Islam, Hiroo Katsuya, Shinsuke Nakajima, Masahito Tokunaga, Kisato Nosaka, Hiroyuki Hata, Atae Utsunomiya, Jun-ichi Fujisawa, Yorifumi Satou   +16 more
doaj   +1 more source

HTLV-1 persistence and leukemogenesis: A game of hide-and-seek with the host immune system

Frontiers in Immunology, 2022
Human T-cell leukemia virus type 1 (HTLV-1), a retrovirus which mainly infects CD4+ T cells and causes adult T-cell leukemia/lymphoma (ATL), is primarily transmitted via direct cell-to-cell transmission.
Benjy J. Y. Tan, Kenji Sugata, Masahiro Ono, Yorifumi Satou   +3 more
doaj   +1 more source

Review of precision cancer medicine: Evolution of the treatment paradigm. [PDF]

, 2020
In recent years, biotechnological breakthroughs have led to identification of complex and unique biologic features associated with carcinogenesis. Tumor and cell-free DNA profiling, immune markers, and proteomic and RNA analyses are used to identify ...
Fountzilas, Elena, Kurzrock, Razelle, Nikanjam, Mina, Tsimberidou, Apostolia M   +3 more
core   +1 more source

A single–cell type transcriptomics map of human tissues

Science Advances, 2021
Single-cell RNA analysis has been integrated with spatial protein profiling to create a single–cell type map of human tissues. Advances in molecular profiling have opened up the possibility to map the expression of genes in cells, tissues, and organs in ...
Max J. Karlsson, Cheng Zhang, Loren Méar, Wen Zhong, A. Digre, Borbala Katona, E. Sjöstedt, L. Butler, J. Odeberg, P. Dusart, F. Edfors, P. Oksvold, K. von Feilitzen, M. Zwahlen, M. Arif, O. Altay, Xiangyu Li, M. Ozcan, Adil Mardonoglu, Linn Fagerberg, J. Mulder, Yonglun Luo, F. Pontén, M. Uhlén, C. Lindskog   +24 more
semanticscholar   +1 more source