Article
Biochemical Research Methods
Sandra Hui, Rasmus Nielsen
Summary: In this study, we introduce SCONCE2, a method for jointly calling copy number alterations and estimating pairwise distances for single cell sequencing data. We demonstrate that SCONCE2 outperforms existing methods in copy number calling and phylogeny estimation. The method enables the inference of tumor phylogenies, providing deeper insights into tumor evolution.
BMC BIOINFORMATICS
(2022)
Article
Biochemical Research Methods
Zerun Lin, Le Ou-Yang
Summary: In this paper, a multi-view contrastive learning model (DeepMCL) is proposed to infer gene regulatory networks (GRNs) from single-cell RNA-seq (scRNA-seq) data collected from multiple data sources or time points. The experimental results validate the effectiveness of our contrastive learning and attention mechanisms, demonstrating the effectiveness of our model in integrating multiple data sources for GRN inference.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Biochemical Research Methods
Zerun Lin, Le Ou-Yang
Summary: The paper proposes a multi-view contrastive learning model, DeepMCL, for inferring gene regulatory networks from scRNA-seq data. By utilizing a deep Siamese convolutional neural network and attention mechanism, the model integrates information from multiple data sources, improving the accuracy of network inference.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Biochemistry & Molecular Biology
Matteo Schiavinato, Valentina del Olmo, Victor Njenga Muya, Toni Gabaldon
Summary: This study presents JLOH, a computational toolkit for inferring and exploring LOH blocks in heterozygous genomes. JLOH utilizes SNP density and read coverage to infer LOH blocks and assigns them to their subgenome of origin.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Biochemistry & Molecular Biology
Yuanxiao Chen, Xiao-Fei Zhang, Le Ou-Yang
Summary: Cancer is a complex disease primarily caused by genetic variants. Understanding the gene networks within tumors is crucial for comprehending the regulatory mechanisms of carcinogenesis. However, it is challenging to investigate the commonalities and specificities of gene networks in different cancer types due to the heterogeneity and similarities among them. This study proposes a new computational approach to jointly estimate the gene networks of multiple cancer types, which can identify both shared and unique regulatory components.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Biology
Mengni Liu, Jianyu Chen, Xin Wang, Chengwei Wang, Xiaolong Zhang, Yubin Xie, Zhixiang Zuo, Jian Ren, Qi Zhao
Summary: MesKit is a tool for interpreting ITH and tracing evolutionary trajectory based on MRS data, including functions such as ITH evaluation, metastatic route inference, and mutational signature identification.
Article
Biotechnology & Applied Microbiology
Mohammad Shahrokh Esfahani, Emily G. Hamilton, Mahya Mehrmohamadi, Barzin Y. Nabet, Stefan K. Alig, Daniel A. King, Chloe B. Steen, Charles W. Macaulay, Andre Schultz, Monica C. Nesselbush, Joanne Soo, Joseph G. Schroers-Martin, Binbin Chen, Michael S. Binkley, Henning Stehr, Jacob J. Chabon, Brian J. Sworder, Angela B-Y Hui, Matthew J. Frank, Everett J. Moding, Chih Long Liu, Aaron M. Newman, James M. Isbell, Charles M. Rudin, Bob T. Li, David M. Kurtz, Maximilian Diehn, Ash A. Alizadeh
Summary: EPIC-seq is a method that predicts gene expression levels at individual genes from cfDNA. We demonstrate the potential of EPIC-seq in cancer subtype classification and prediction of clinical response.
NATURE BIOTECHNOLOGY
(2022)
Article
Statistics & Probability
Shai He, Aaron Schein, Vishal Sarsani, Patrick Flaherty
Summary: There are distinguishing features of cancer that can be driven by specific genetic mutations, but individual tumors often exhibit genetic heterogeneity. This study aims to infer tumor subpopulation genotypes and distributions within individual tumors by integrating single-cell and bulk sequencing data, which is crucial for personalized targeted therapy and post-treatment monitoring. The proposed model shows improved inference quality and performance compared to standard methods, as demonstrated in simulation and real cancer sequencing datasets.
ANNALS OF APPLIED STATISTICS
(2021)
Article
Plant Sciences
Hiroki Takahashi, Arihiro Iwasaki, Naoaki Kurisawa, Ryota Suzuki, Ghulam Jeelani, Teruhiko Matsubara, Toshinori Sato, Tomoyoshi Nozaki, Kiyotake Suenaga
Summary: Motobamide, a novel cyclic peptide containing a C-prenylated cyclotryptophan residue, was isolated from a marine cyanobacterium. It showed moderate inhibition of Trypanosoma brucei rhodesiense growth, but exhibited weaker cytotoxicity against normal human cells.
JOURNAL OF NATURAL PRODUCTS
(2021)
Article
Genetics & Heredity
Wei Vivian Li, Yanzeng Li
Summary: The study presents a method called scLink, which utilizes single-cell RNA sequencing technologies for gene co-expression network analysis. Through simulation and real data studies, the advantages of scLink in improving single-cell gene network analysis are demonstrated.
GENOMICS PROTEOMICS & BIOINFORMATICS
(2021)
Article
Biochemical Research Methods
Simone Ciccolella, Camir Ricketts, Mauricio Soto Gomez, Murray Patterson, Dana Silverbush, Paola Bonizzoni, Iman Hajirasouliha, Gianluca Della Vedova
Summary: Recent studies have identified limitations in current computational methods for inferring tumor phylogenies. The new SASC approach, based on simulated annealing and using the Dollo-k model, demonstrates high accuracy in inferring cancer progressions.
Review
Chemistry, Physical
Yingwen Chen, Jia Song, Qingyu Ruan, Xi Zeng, Lingling Wu, Linfeng Cai, Xuanqun Wang, Chaoyong Yang
Summary: Cells are fundamental building blocks of biological systems, and studying single cells can provide insights into cell diversity and disease processes. Single-cell RNA sequencing technologies allow cellular heterogeneity to be dissected at unprecedented resolution.
Article
Genetics & Heredity
Shaofeng Lin, Yanping Chen, Jianchao Wang, Yibin Cai, Xiaohui Chen, Yuanmei Chen, Yi Shi, Gang Chen, Kunshou Zhu
Summary: In this study, whole-exome sequencing was performed on tissue samples from six esophageal cancer patients with lymph node metastasis. Significant differences in somatic mutations between metastatic lymph nodes and primary lesions were identified, and pathway enrichment analysis and subclonality analysis revealed commonalities and heterogeneity among the patients, highlighting the potential of identifying tumor-specific mutations for effective intervention and improving prognosis.
FRONTIERS IN GENETICS
(2022)
Article
Immunology
Yixuan Wang, Xin Lai, Jiayin Wang, Ying Xu, Xuanping Zhang, Xiaoyan Zhu, Yuqian Liu, Yang Shao, Li Zhang, Wenfeng Fang
Summary: TMB is a key indicator for predicting the efficacy of immunotherapy. Our study introduces a new TMB categorization method (TMBcat) and confirms the non-linear relationship between TMB and immunotherapy, which varies across different types of cancer. The reliability of our categorization method is validated through research.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Computer Science, Interdisciplinary Applications
Yue Zhang, Chengtao Peng, Ruofeng Tong, Lanfen Lin, Yen-Wei Chen, Qingqing Chen, Hongjie Hu, S. Kevin Zhou
Summary: In this paper, we propose a novel multi-modal tumor segmentation method with deformable feature fusion and uncertain region refinement to address the deficiencies of known methods. Experimental results demonstrate that our method achieves promising tumor segmentation results and outperforms state-of-the-art methods.
IEEE TRANSACTIONS ON MEDICAL IMAGING
(2023)
Article
Biochemistry & Molecular Biology
Yuezheng Zhang, Yawei Li, Tao Li, Xu Shen, Tianqi Zhu, Yong Tao, Xueying Li, Di Wang, Qin Ma, Zheng Hu, Jialin Liu, Jue Ruan, Jun Cai, Hurng-Yi Wang, Xuemei Lu
MOLECULAR BIOLOGY AND EVOLUTION
(2019)
Article
Multidisciplinary Sciences
Jennifer L. Caswell-Jin, Katherine McNamara, Johannes G. Reiter, Ruping Sun, Zheng Hu, Zhicheng Ma, Jie Ding, Carlos J. Suarez, Susanne Tilk, Akshara Raghavendra, Victoria Forte, Suet-Feung Chin, Helen Bardwell, Elena Provenzano, Carlos Caldas, Julie Lang, Robert West, Debu Tripathy, Michael F. Press, Christina Curtis
NATURE COMMUNICATIONS
(2019)
Article
Biochemistry & Molecular Biology
Jose A. Seoane, Jacob G. Kirkland, Jennifer L. Caswell-Jin, Gerald R. Crabtree, Christina Curtis
Article
Genetics & Heredity
Zheng Hu, Zan Li, Zhicheng Ma, Christina Curtis
Article
Genetics & Heredity
Nastaran Zahir, Ruping Sun, Daniel Gallahan, Robert A. Gatenby, Christina Curtis
Article
Multidisciplinary Sciences
Zheng Hu, Christina Curtis
NATURE COMMUNICATIONS
(2020)
Review
Oncology
Iris Nederlof, Hugo M. Horlings, Christina Curtis, Marleen Kok
Summary: TNBC exhibits significant genomic, cellular, and phenotypic heterogeneity, with disease progression dependent on the interaction between cancer cells and the TME. New high-dimensional technologies have been instrumental in further elucidating the TME through comprehensive analysis at the single cell level or studying spatial relationships. Understanding cellular phenotypes and spatial patterns in the TNBC microenvironment is crucial for effective personalized immunotherapy.
Editorial Material
Biochemistry & Molecular Biology
Jennifer L. Caswell-Jin, Christina Curtis
Article
Oncology
Brittany M. Flowers, Hang Xu, Abigail S. Mulligan, Kathryn J. Hanson, Jose A. Seoane, Hannes Vogel, Christina Curtis, Laura D. Wood, Laura D. Attardi
Summary: Cell of origin and Trp53 alleles play crucial roles in the development of PDAC, influencing the molecular subtypes of the tumor. Tumor signatures derived from ductal cells and acinar cells are enriched in different subtypes of human PDAC.
Review
Biochemistry & Molecular Biology
Zhaolian Lu, Beina Nie, Weiwei Zhai, Zheng Hu
Summary: This study discusses the genetic and epigenetic alterations in cancer evolution, the advantages and challenges of using organoids to study cancer evolution, and proposes the establishment of an experimental evolutionary model to study tumor evolution dynamics and patterns over time.
JOURNAL OF GENETICS AND GENOMICS
(2021)
Article
Biochemistry & Molecular Biology
Zhongjie Tang, Zhaolian Lu, Baizhen Chen, Weixing Zhang, Howard Y. Chang, Zheng Hu, Jin Xu
Summary: In this study, the researchers analyzed mitochondrial DNA mutations in over 30,000 human cells and found an overrepresentation of mutations in lymphocytes compared to hematopoietic progenitors and myeloid cells. They also found that mtDNA replication lags behind cell proliferation in lymphoid cells, potentially causing a genetic bottleneck. This study reveals a lymphoid-specific mtDNA genetic bottleneck, shedding light on how highly metabolically active immune cells limit their mtDNA mutation load.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Biology
Susanne Tilk, Svyatoslav Tkachenko, Christina Curtis, Dmitri A. Petrov, Christopher D. McFarland
Summary: The lack of observed negative selection in most tumors is not due to relaxed selective pressures, but rather the inability of selection to remove deleterious mutations in the presence of genome-wide linkage.
Article
Biotechnology & Applied Microbiology
Kun Wang, Liangzhen Hou, Xin Wang, Xiangwei Zhai, Zhaolian Lu, Zhike Zi, Weiwei Zhai, Xionglei He, Christina Curtis, Da Zhou, Zheng Hu
Summary: PhyloVelo is a computational framework that accurately estimates the velocity of transcriptomic dynamics by using monotonically expressed genes or genes with specific expression patterns. It integrates scRNA-seq data with lineage information to identify key genes and reconstruct the transcriptomic velocity field. PhyloVelo has been validated using simulated and real datasets, and has shown high accuracy and robustness in inferring complex lineage trajectories.
NATURE BIOTECHNOLOGY
(2023)
