Deep Learning Applications in Single-Cell Multi-Omics Analysis: A Review

Authors: Taha, Manar H, El-Hadidi, Mohamed, Fawzi, Sahar Ali

Source: 2024 6th Novel Intelligent and Leading Emerging Sciences Conference (NILES) Novel Intelligent and Leading Emerging Sciences Conference (NILES), 2024 6th. :85-88 Oct, 2024

Relation: 2024 6th Novel Intelligent and Leading Emerging Sciences Conference (NILES)

Single-cell multi-omics in the study of digestive system cancers

Authors: Shuang Zhou, Nanfei Lin, Liying Yu, Xiaoshan Su, Zhenlong Liu, Xiaowan Yu, Hongzhi Gao, Shu Lin, Yiming Zeng

Source: Computational and Structural Biotechnology Journal, Vol 23, Iss , Pp 431-445 (2024)

Subject Terms: Digestive system cancer, Single-cell sequencing (SCS), Heterogeneity, Tumor microenvironment (TME), Single-cell omics, Single-cell transcriptomics (ST), Biotechnology, TP248.13-248.65

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2001037023004816; https://doaj.org/toc/2001-0370

Access URL: https://doaj.org/article/d011d875492847e59ece547666389729

Immune profiling of the macroenvironment in colorectal cancer unveils systemic dysfunction and plasticity of immune cells

Authors: Haoxian Ke, Peisi Li, Zhihao Li, Xian Zeng, Chi Zhang, Shuzhen Luo, Xiaofang Chen, Xinlan Zhou, Shichen Dong, Shaopeng Chen, Junfeng Huang, Ming Yuan, Runfeng Yu, Shubiao Ye, Tuo Hu, Zhonghui Tang, Dongbin Liu, Kui Wu, Xianrui Wu, Ping Lan

Source: Clinical and Translational Medicine, Vol 15, Iss 2, Pp n/a-n/a (2025)

Subject Terms: colorectal cancer, single‐cell omics, spatial transcription, tumour macroenvironment, Medicine (General), R5-920

File Description: electronic resource

Relation: https://doaj.org/toc/2001-1326

Access URL: https://doaj.org/article/056761c6f6ac429badf22d99ee93d442

Spatially-resolved analyses of muscle invasive bladder cancer microenvironment unveil a distinct fibroblast cluster associated with prognosis

Authors: Chao Feng, Yaobang Wang, Wuyue Song, Tao Liu, Han Mo, Hui Liu, Shulin Wu, Zezu Qin, Zhenxing Wang, Yuting Tao, Liangyu He, Shaomei Tang, Yuanliang Xie, Qiuyan Wang, Tianyu Li

Source: Frontiers in Immunology, Vol 15 (2024)

Subject Terms: MIBC, tumor microenvironment, spatial heterogeneity, single-cell omics, fibroblast, Immunologic diseases. Allergy, RC581-607

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fimmu.2024.1522582/full; https://doaj.org/toc/1664-3224

Access URL: https://doaj.org/article/c9323d095b3a48f3a415172b61f117c9

Computing cell state discriminates the aberrant hematopoiesis and activated microenvironment in Myelodysplastic syndrome (MDS) through a single cell genomic study

Authors: Xinyu Guo, Wenyan Jin, Yuchen Wen, Zhiqin Wang, Xiaotong Ren, Zhaoyun Liu, Rong Fu, Zhigang Cai, Lijuan Li

Source: Journal of Translational Medicine, Vol 22, Iss 1, Pp 1-16 (2024)

Subject Terms: Myelodysplastic syndrome, Single cell omics, Computational hematopoiesis, Bone marrow cell reference, HMGA1, Medicine

File Description: electronic resource

Relation: https://doaj.org/toc/1479-5876

Access URL: https://doaj.org/article/c5c0e8f4b0e844d2a0ad9963d12ce26e

A single cell RNA sequence atlas of the early Drosophila larval eye

Authors: Komal Kumar Bollepogu Raja, Kelvin Yeung, Yumei Li, Rui Chen, Graeme Mardon

Source: BMC Genomics, Vol 25, Iss 1, Pp 1-12 (2024)

Subject Terms: Drosophila eye, Single cell genomics, Eye disc single cell RNA, Drosophila single cell omics, Biotechnology, TP248.13-248.65, Genetics, QH426-470

File Description: electronic resource

Relation: https://doaj.org/toc/1471-2164

Access URL: https://doaj.org/article/5e03546cc0204130927c7bb86ef5bb06

Charting the cellular landscape of pulmonary arterial hypertension through single-cell omics

Authors: Brian Tang, Arjun Vadgama, Bryce Redmann, Jason Hong

Source: Respiratory Research, Vol 25, Iss 1, Pp 1-9 (2024)

Subject Terms: Pulmonary arterial hypertension, Single-cell RNA sequencing, Single-cell omics, Diseases of the respiratory system, RC705-779

File Description: electronic resource

Relation: https://doaj.org/toc/1465-993X

Access URL: https://doaj.org/article/d35f57d68afa4dd9aa1b3db58e7eb01e

K-Volume Clustering Algorithms for scRNA-Seq Data Analysis

Authors: Yong Chen, Fei Li

Source: Biology, Vol 14, Iss 3, p 283 (2025)

Subject Terms: single-cell omics, clustering algorithms, gene regulatory networks, Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://www.mdpi.com/2079-7737/14/3/283; https://doaj.org/toc/2079-7737

Access URL: https://doaj.org/article/14a138edb2544c029031dc3e713934be

Visual cohort comparison for spatial single-cell omics-data

Authors: Somarakis, A., Ijsselsteijn, M.E., Luk, S.J., Kenkhuis, B., de Miranda, N.F., Lelieveldt, B.P., Hollt, T.

Source: IEEE Transactions on Visualization and Computer Graphics IEEE Trans. Visual. Comput. Graphics Visualization and Computer Graphics, IEEE Transactions on. 27(2):733-743 Feb, 2021

Editorial: Novelties in acute myeloid leukemia: from biology to clinical applications

Authors: Luca Vincenzo Cappelli, Nico Gagelmann, Hassan Awada, Carmelo Gurnari

Source: Frontiers in Oncology, Vol 14 (2024)

Subject Terms: acute myeloid leukemia, prognostic biomarker, oncogenes, single cell omics, chemotherapy, CAR T cell, Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fonc.2024.1499272/full; https://doaj.org/toc/2234-943X

Access URL: https://doaj.org/article/f8548cfd4bce48b89f21de407e10b78a

Single Cell Atlas: a single-cell multi-omics human cell encyclopedia

Authors: Lu Pan, Paolo Parini, Roman Tremmel, Joseph Loscalzo, Volker M. Lauschke, Bradley A. Maron, Paola Paci, Ingemar Ernberg, Nguan Soon Tan, Zehuan Liao, Weiyao Yin, Sundararaman Rengarajan, Xuexin Li, The SCA Consortium

Source: Genome Biology, Vol 25, Iss 1, Pp 1-21 (2024)

Subject Terms: Single-cell omics, Multi-omics, Single Cell Atlas, Human database, Single-cell RNA-sequencing, Spatial transcriptomics, Biology (General), QH301-705.5, Genetics, QH426-470

File Description: electronic resource

Relation: https://doaj.org/toc/1474-760X

Access URL: https://doaj.org/article/bfac2c6a06f6422a8ceb3444a8f601fb

Metabolic regulation of tumor-associated macrophage heterogeneity: insights into the tumor microenvironment and immunotherapeutic opportunities

Authors: Yujing Qian, Yujia Yin, Xiaocui Zheng, Zhaoyuan Liu, Xipeng Wang

Source: Biomarker Research, Vol 12, Iss 1, Pp 1-28 (2024)

Subject Terms: Tumor-associated macrophages, Tumor microenvironment, Metabolic reprogramming, Single-cell omics, Immunotherapy, Therapeutics. Pharmacology, RM1-950

File Description: electronic resource

Relation: https://doaj.org/toc/2050-7771

Access URL: https://doaj.org/article/185594542fa441fdb008711f7a0a1b6f

Range of chromatin accessibility configurations are permissive of GABAergic fate acquisition in developing mouse brain

Authors: Sami Kilpinen, Heidi Heliölä, Kaia Achim

Source: BMC Genomics, Vol 24, Iss 1, Pp 1-17 (2023)

Subject Terms: Cell type, Cell state, Single-cell -omics, Genetic regulation of cell fate, GABAergic neurons, Selector gene, Biotechnology, TP248.13-248.65, Genetics, QH426-470

File Description: electronic resource

Relation: https://doaj.org/toc/1471-2164

Access URL: https://doaj.org/article/c97863e09d7c49dab090a6788d3c8122

Editorial: Single-cell OMICs analyses in cardiovascular diseases

Authors: Abhijeet Rajendra Sonawane, Michel Pucéat, Hanjoong Jo

Source: Frontiers in Cardiovascular Medicine, Vol 11 (2024)

Subject Terms: cardiovascular diseases, single-cell omics, data analysis, atherosclerosis, heart valve disease (HVD), Diseases of the circulatory (Cardiovascular) system, RC666-701

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fcvm.2024.1413184/full; https://doaj.org/toc/2297-055X

Access URL: https://doaj.org/article/33479fce00784d0aaa14e0a46239f0ff

Decoding Human Biology and Disease Using Single-cell Omics Technologies

Authors: Qiang Shi, Xueyan Chen, Zemin Zhang

Source: Genomics, Proteomics & Bioinformatics, Vol 21, Iss 5, Pp 926-949 (2023)

Subject Terms: Single-cell omics, Computational method, Cellular heterogeneity, Disease, Cancer research, Biology (General), QH301-705.5, Computer applications to medicine. Medical informatics, R858-859.7

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S1672022923001043; https://doaj.org/toc/1672-0229

Access URL: https://doaj.org/article/832cf527058e43fd871109b13a4cccc5

Omics Views of Mechanisms for Cell Fate Determination in Early Mammalian Development

Authors: Lin-Fang Ju, Heng-Ji Xu, Yun-Gui Yang, Ying Yang

Source: Genomics, Proteomics & Bioinformatics, Vol 21, Iss 5, Pp 950-961 (2023)

Subject Terms: Cell fate determination, Cellular heterogeneity, Cell polarity, Single-cell omics, Mammalian preimplantation embryo, Biology (General), QH301-705.5, Computer applications to medicine. Medical informatics, R858-859.7

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S1672022923000670; https://doaj.org/toc/1672-0229

Access URL: https://doaj.org/article/64db95cec60b401b929b34f8275d0f3f

Single-cell omics traces the heterogeneity of prostate cancer cells and the tumor microenvironment

Authors: Xudong Yu, Ruijia Liu, Wenfeng Gao, Xuyun Wang, Yaosheng Zhang

Source: Cellular & Molecular Biology Letters, Vol 28, Iss 1, Pp 1-16 (2023)

Subject Terms: Prostate cancer, Single-cell omics, Spatial transcriptomics, Heterogeneity, Cytology, QH573-671

File Description: electronic resource

Relation: https://doaj.org/toc/1689-1392

Access URL: https://doaj.org/article/15fe07b6b3464cb88308811845855fb1

Editorial: Single-cell and spatial-omics in delineating immune-related diseases

Authors: Shaodi Wen, Steven Mo, Jin Zhou, Yufeng Lv, Khashayarsha Khazaie, Guangchuang Yu

Source: Frontiers in Cell and Developmental Biology, Vol 12 (2024)

Subject Terms: immune-related diseases, single-cell omics, spatial transcriptome, inflamation, immune response, Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fcell.2024.1365242/full; https://doaj.org/toc/2296-634X

Access URL: https://doaj.org/article/7998f3e681ee4f01b94c945eb19c55f9

PSF toolkit: an R package for pathway curation and topology-aware analysis

Authors: Siras Hakobyan, Ani Stepanyan, Lilit Nersisyan, Hans Binder, Arsen Arakelyan

Source: Frontiers in Genetics, Vol 14 (2023)

Subject Terms: biological networks, systems biology, pathway analysis, gene expression, single cell omics, Genetics, QH426-470

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fgene.2023.1264656/full; https://doaj.org/toc/1664-8021

Access URL: https://doaj.org/article/2e0d5a7c6f454d4cad6d7bb242139720

Gene network inference from single-cell omics data and domain knowledge for constructing COVID-19-specific ICAM1-associated pathways

Authors: Mitsuhiro Odaka, Morgan Magnin, Katsumi Inoue

Source: Frontiers in Genetics, Vol 14 (2023)

Subject Terms: ICAM-1, cell-to-cell transmission, COVID-19, single-cell omics data analysis, model validation, pathway enrichment analysis, Genetics, QH426-470

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fgene.2023.1250545/full; https://doaj.org/toc/1664-8021

Access URL: https://doaj.org/article/1db6826c08e64267908081d09751a2b7