Chen, Chien-Ming Lu, Yu-Lun Sio, Chi-Pong Wu, Guan-Chung Tzou, Wen-Shyong Pai, Tun-Wen
Published in
Methods
RNA-seq analysis provides a powerful tool for revealing relationships between gene expression level and biological function of proteins. In order to identify differentially expressed genes among various RNA-seq datasets obtained from different experimental designs, an appropriate normalization method for calibrating multiple experimental datasets i...
Jo, Kyuri Kwon, Hawk-Bin Kim, Sun
Published in
Methods
Measuring expression levels of genes at the whole genome level can be useful for many purposes, especially for revealing biological pathways underlying specific phenotype conditions. When gene expression is measured over a time period, we have opportunities to understand how organisms react to stress conditions over time. Thus many biologists routi...
Jeong, Byeong-Soo Golam Bari, A.T.M. Rokeya Reaz, Mst. Jeon, Seokhee Lim, Chae-Gyun Choi, Ho-Jin
Published in
Methods
With the exponential growth of biological sequence data (DNA or Protein Sequence), DNA sequence analysis has become an essential task for biologist to understand the features, functions, structures, and evolution of species. Encoding DNA sequences is an effective method to extract the features from DNA sequences. It is commonly used for visualizing...
Zeng, Tao Zhang, Chuan-chao Zhang, Wanwei Liu, Rui Liu, Juan Chen, Luonan
Published in
Methods
There is no effective cure nowadays for many complex diseases, and thus it is crucial to detect and further treat diseases in earlier stages. Generally, the development and progression of complex diseases include three stages: normal stage, pre-disease stage, and disease stage. For diagnosis and treatment, it is necessary to reveal dynamical organi...
Zhou, Jun Rosu, Frédéric Amrane, Samir Korkut, Dursun Nizam Gabelica, Valérie Mergny, Jean Louis
Published in
Methods
In this review, we introduce the biophysical and biochemical methods currently used to investigate the structures and stabilities of tetramolecular DNA G-quadruplexes containing chemical modifications. We hope this paper will guide others as they perform similar experiments leading to more information about the effects of chemical modifications on ...
Baccouche, Alexandre Montagne, Kevin Padirac, Adrien Fujii, Teruo Rondelez, Yannick
Published in
Methods
In living organisms, the integration of signals from the environment and the molecular computing leading to a cellular response are orchestrated by Gene Regulatory Networks (GRN). However, the molecular complexity of in vivo genetic regulation makes it next to impossible to describe in a quantitative manner. Reproducing, in vitro, reaction networks...
Koussa, Mounir A. Sotomayor, Marcos Wong, Wesley P.
Published in
Methods
Recent methods in DNA nanotechnology are enabling the creation of intricate nanostructures through the use of programmable, bottom-up self-assembly. However, structures consisting only of DNA are limited in their ability to act on other biomolecules. Proteins, on the other hand, perform a variety of functions on biological materials, but directed c...
Mazumder, Nirmal Hu, Chih-Wei Qiu, Jianjun Foreman, Matthew R. Romero, Carlos Macías Török, Peter Kao, Fu-Jen
Published in
Methods
We report on measurements and characterization of polarization properties of Second Harmonic (SH) signals using a four-channel photon counting based Stokes polarimeter. In this way, the critical polarization parameters can be obtained concurrently without the need of repeated image acquisition. The critical polarization parameters, including the de...
Li, Wenyuan Dai, Chao Kang, Shuli Zhou, Xianghong Jasmine
Published in
Methods
Alternative splicing is an important gene regulatory mechanism that dramatically increases the complexity of the proteome. However, how alternative splicing is regulated and how transcription and splicing are coordinated are still poorly understood, and functions of transcript isoforms have been studied only in a few limited cases. Nowadays, RNA-se...
Klein, O.J. Jung, Y.K. Evans, C.L.
Published in
Methods
In vitro three-dimensional models of cancer have the ability to recapitulate many features of tumors found in vivo, including cell–cell and cell–matrix interactions, microenvironments that become hypoxic and acidic, and other barriers to effective therapy. These model tumors can be large, highly complex, heterogeneous, and undergo time-dependent gr...