Nature Search

Interfacial water confers transcription factors with dinucleotide specificity

The study highlights the importance of water-mediated interactions in recognition of dinucleotides by transcription factors. Water’s influence on enthalpy and entropy modulates binding affinity and temperature sensitivity of TF binding.

Ekaterina Morgunova
Gabor Nagy
Jussi Taipale
ResearchOpen Access03 Jan 2025
Nature Structural & Molecular Biology

Volume: 32, P: 650-661
Respiratory tract infections in children with allergic asthma on allergen immunotherapy during influenza season

Yuyun Li
Dongming Wang
Guangxing Yan
ResearchOpen Access22 Jan 2021
Scientific Reports

Volume: 11, P: 1-6
A protein activity assay to measure global transcription factor activity reveals determinants of chromatin accessibility

A method to analyze global transcription factor activity in cells reveals that a small number of factors determines the landscape of accessible chromatin.

Bei Wei
Arttu Jolma
Jussi Taipale
Research21 May 2018
Nature Biotechnology

Volume: 36, P: 521-529
Sequence determinants of human gene regulatory elements

Analysis of massively parallel reporter assays measuring the transcriptional activity of DNA sequences indicates that most transcription factor (TF) activity is additive and does not rely on specific TF–TF interactions. Individual TFs can have different gene regulatory activities.

Biswajyoti Sahu
Tuomo Hartonen
Jussi Taipale
ResearchOpen Access21 Feb 2022
Nature Genetics

Volume: 54, P: 283-294
In-situ transfer vat photopolymerization for transparent microfluidic device fabrication

Despite many advantages of vat photopolymerization in microfluidic device fabrication, well-controlled μm-sized (< 100 μm) channels in the layer building direction remains a challenge. Here, authors present a general high resolution and low-cost 3D printing process that can produce devices within the 10 μm scale.

Yang Xu
Fangjie Qi
Yong Chen
ResearchOpen Access17 Feb 2022
Nature Communications

Volume: 13, P: 1-11
A retrospective study to compare the clinical effects of individualized anatomic single- and double-bundle anterior cruciate ligament reconstruction surgery

Kang Chen
Weimin Zhu
Wei Lu
ResearchOpen Access07 Sept 2020
Scientific Reports

Volume: 10, P: 1-8
The interaction landscape between transcription factors and the nucleosome

A method for systematically exploring interactions between the nucleosome and transcription factors identifies five major interaction patterns.

Fangjie Zhu
Lucas Farnung
Jussi Taipale
Research24 Sept 2018
Nature

Volume: 562, P: 76-81
Nucleosome-bound SOX2 and SOX11 structures elucidate pioneer factor function

Cryo-electron microscopy structures of the DNA-binding domains of the pioneer transcription factor SOX2 and its close homologue SOX11 elucidate the role of these factors in initiating chromatin opening and nucleosome remodelling.

Svetlana O. Dodonova
Fangjie Zhu
Patrick Cramer
Research22 Apr 2020
Nature

Volume: 580, P: 669-672
A molecular switch in sulfur metabolism to reduce arsenic and enrich selenium in rice grain

Contamination of paddy soils can lead to toxic arsenic accumulation in rice grains and low levels of the micronutrient selenium. Here the authors show that a gain of function mutant affecting an O-acetylserine (thiol) lyase enhances sulfur and selenium assimilation while reducing arsenic accumulation in grains.

Sheng-Kai Sun
Xuejie Xu
Fang-Jie Zhao
ResearchOpen Access02 Mar 2021
Nature Communications

Volume: 12, P: 1-14
Associations between condylar height relative to occlusal plane and condylar osseous condition and TMJ loading based on 3D measurements and finite element analysis

Yanji Gong
Jinyi Zhu
Deqiang Yin
ResearchOpen Access22 Nov 2024
Scientific Reports

Volume: 14, P: 1-14
MBLSTM is a contextual interaction refined method for time series prediction

Weihan Qiu
Fangjie Zhu
Runyue Huang
ResearchOpen Access27 May 2025
Scientific Reports

Volume: 15, P: 1-15
Parthanatos initiated by ROS-induced DNA damage is involved in intestinal epithelial injury during necrotizing enterocolitis

Lingqi Xu
Shurong Ma
Huiting Zhou
ResearchOpen Access31 Jul 2024
Cell Death Discovery

Volume: 10, P: 1-14
Organic/inorganic fusion materials: cyclodextrin-based polymer/CaCO₃ hybrids incorporating dye molecules through host–guest interactions

Thin-film inorganic/organic hybrids of CaCO₃ and poly(cyclodextrin) were prepared. The cavities of CDs inside the hybrids facilitated functionalization of these fusion materials by dye molecules.

Fangjie Zhu
Tatsuya Nishimura
Takashi Kato
Research17 Dec 2014
Polymer Journal

Volume: 47, P: 122-127
Methylotrophic methanogens and bacteria synergistically demethylate dimethylarsenate in paddy soil and alleviate rice straighthead disease

Chuan Chen
Lingyan Li
Fang-Jie Zhao
ResearchOpen Access21 Aug 2023
The ISME Journal

Volume: 17, P: 1851-1861
Sulfate-reducing bacteria and methanogens are involved in arsenic methylation and demethylation in paddy soils

Chuan Chen
Lingyan Li
Fang-Jie Zhao
ResearchOpen Access21 Jun 2019
The ISME Journal

Volume: 13, P: 2523-2535

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