Search Results - "Tan, Ge"

TFBSTools: an R/bioconductor package for transcription factor binding site analysis by Tan, Ge, Lenhard, Boris

“…: The ability to efficiently investigate transcription factor binding sites (TFBSs) genome-wide is central to computational studies of gene regulation…”
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Current Methods for Automated Filtering of Multiple Sequence Alignments Frequently Worsen Single-Gene Phylogenetic Inference by Tan, Ge, Muffato, Matthieu, Ledergerber, Christian, Herrero, Javier, Goldman, Nick, Gil, Manuel, Dessimoz, Christophe

“…Phylogenetic inference is generally performed on the basis of multiple sequence alignments (MSA). Because errors in an alignment can lead to errors in tree…”
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Topologically associating domains are ancient features that coincide with Metazoan clusters of extreme noncoding conservation by Harmston, Nathan, Ing-Simmons, Elizabeth, Tan, Ge, Perry, Malcolm, Merkenschlager, Matthias, Lenhard, Boris

“…Developmental genes in metazoan genomes are surrounded by dense clusters of conserved noncoding elements (CNEs). CNEs exhibit unexplained extreme levels of…”
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Distribution of ACE2, CD147, CD26, and other SARS‐CoV‐2 associated molecules in tissues and immune cells in health and in asthma, COPD, obesity, hypertension, and COVID‐19 risk factors by Radzikowska, Urszula, Ding, Mei, Tan, Ge, Zhakparov, Damir, Peng, Yaqi, Wawrzyniak, Paulina, Wang, Ming, Li, Shuo, Morita, Hideaki, Altunbulakli, Can, Reiger, Matthias, Neumann, Avidan U., Lunjani, Nonhlanhla, Traidl‐Hoffmann, Claudia, Nadeau, Kari C., O’Mahony, Liam, Akdis, Cezmi, Sokolowska, Milena

“…Background Morbidity and mortality from COVID‐19 caused by novel coronavirus SARS‐CoV‐2 is accelerating worldwide, and novel clinical presentations of COVID‐19…”
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JASPAR 2020: update of the open-access database of transcription factor binding profiles by Fornes, Oriol, Castro-Mondragon, Jaime A, Khan, Aziz, van der Lee, Robin, Zhang, Xi, Richmond, Phillip A, Modi, Bhavi P, Correard, Solenne, Gheorghe, Marius, Baranašić, Damir, Santana-Garcia, Walter, Tan, Ge, Chèneby, Jeanne, Ballester, Benoit, Parcy, François, Sandelin, Albin, Lenhard, Boris, Wasserman, Wyeth W, Mathelier, Anthony

“…Abstract JASPAR (http://jaspar.genereg.net) is an open-access database of curated, non-redundant transcription factor (TF)-binding profiles stored as position…”
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JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework by Khan, Aziz, Fornes, Oriol, Stigliani, Arnaud, Gheorghe, Marius, Castro-Mondragon, Jaime A, van der Lee, Robin, Bessy, Adrien, Chèneby, Jeanne, Kulkarni, Shubhada R, Tan, Ge, Baranasic, Damir, Arenillas, David J, Sandelin, Albin, Vandepoele, Klaas, Lenhard, Boris, Ballester, Benoît, Wasserman, Wyeth W, Parcy, François, Mathelier, Anthony

“…Abstract JASPAR (http://jaspar.genereg.net) is an open-access database of curated, non-redundant transcription factor (TF)-binding profiles stored as position…”
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Clinical, radiological, and laboratory characteristics and risk factors for severity and mortality of 289 hospitalized COVID‐19 patients by Zhang, Jin‐jin, Cao, Yi‐yuan, Tan, Ge, Dong, Xiang, Wang, Bin‐chen, Lin, Jun, Yan, You‐qin, Liu, Guang‐hui, Akdis, Mübeccel, Akdis, Cezmi A., Gao, Ya‐dong

“…Background The coronavirus disease 2019 (COVID‐19) has become a global pandemic, with 10%‐20% of severe cases and over 508 000 deaths worldwide. Objective This…”
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JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles by Mathelier, Anthony, Fornes, Oriol, Arenillas, David J, Chen, Chih-Yu, Denay, Grégoire, Lee, Jessica, Shi, Wenqiang, Shyr, Casper, Tan, Ge, Worsley-Hunt, Rebecca, Zhang, Allen W, Parcy, François, Lenhard, Boris, Sandelin, Albin, Wasserman, Wyeth W

“…JASPAR (http://jaspar.genereg.net) is an open-access database storing curated, non-redundant transcription factor (TF) binding profiles representing…”
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Transcriptional profiling of mouse peripheral nerves to the single-cell level to build a sciatic nerve ATlas (SNAT) by Gerber, Daniel, Pereira, Jorge A, Gerber, Joanne, Tan, Ge, Dimitrieva, Slavica, Yángüez, Emilio, Suter, Ueli

“…Peripheral nerves are organ-like structures containing diverse cell types to optimize function. This interactive assembly includes mostly axon-associated…”
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JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework by Khan, Aziz, Fornes, Oriol, Stigliani, Arnaud, Gheorghe, Marius, Castro-Mondragon, Jaime A, van der Lee, Robin, Bessy, Adrien, Chèneby, Jeanne, Kulkarni, Shubhada R, Tan, Ge, Baranasic, Damir, Arenillas, David J, Sandelin, Albin, Vandepoele, Klaas, Lenhard, Boris, Ballester, Benoît, Wasserman, Wyeth W, Parcy, François, Mathelier, Anthony

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Tight junction, mucin, and inflammasome‐related molecules are differentially expressed in eosinophilic, mixed, and neutrophilic experimental asthma in mice by Tan, Hern‐Tze Tina, Hagner, Stefanie, Ruchti, Fiorella, Radzikowska, Urszula, Tan, Ge, Altunbulakli, Can, Eljaszewicz, Andrzej, Moniuszko, Marcin, Akdis, Mübeccel, Akdis, Cezmi A., Garn, Holger, Sokolowska, Milena

“…Background Asthma is a chronic respiratory disease with marked clinical and pathophysiological heterogeneity. Specific pathways are thought to be involved in…”
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CNEr: A toolkit for exploring extreme noncoding conservation by Tan, Ge, Polychronopoulos, Dimitris, Lenhard, Boris

“…Conserved Noncoding Elements (CNEs) are elements exhibiting extreme noncoding conservation in Metazoan genomes. They cluster around developmental genes and act…”
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JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles by Mathelier, Anthony, Zhao, Xiaobei, Zhang, Allen W, Parcy, François, Worsley-Hunt, Rebecca, Arenillas, David J, Buchman, Sorana, Chen, Chih-yu, Chou, Alice, Ienasescu, Hans, Lim, Jonathan, Shyr, Casper, Tan, Ge, Zhou, Michelle, Lenhard, Boris, Sandelin, Albin, Wasserman, Wyeth W

“…JASPAR (http://jaspar.genereg.net) is the largest open-access database of matrix-based nucleotide profiles describing the binding preference of transcription…”
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Role of Der p 1–specific B cells in immune tolerance during 2 years of house dust mite–specific immunotherapy by Boonpiyathad, Tadech, van de Veen, Willem, Wirz, Oliver, Sokolowska, Milena, Rückert, Beate, Tan, Ge, Sangasapaviliya, Atik, Pradubpongsa, Panitan, Fuengthong, Rattanaporn, Thantiworasit, Pattarawat, Sirivichayakul, Sunee, Ruxrungtham, Kiat, Akdis, Cezmi A., Akdis, Mübeccel

“…Long-term follow-up of allergen-specific B cells in terms of immunoglobulin isotype expression, plasmablast differentiation, and regulatory B (Breg) cell…”
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Effect of the phthalates exposure on sex steroid hormones in the US population by Zhu, Yuan-duo, Han, Xu, Wang, Xin-qi, Ge, Tan-xi, Liu, Hang, Fan, Lin, Li, Li, Su, Li-qin, Wang, Xian-liang

“…New alternative phthalates have been increasingly substituted for certain phthalates in some consumer products due to safety concerns. However, research on the…”
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Assessing the impacts of urban functional form on anthropogenic carbon emissions: A case study of 31 major cities in China by Tan, Ge, Zhang, Xiuyuan, Xiong, Shuping, Sun, Zihao, Lei, Yichen, Wang, Haoyu, Du, Shihong

“…•Functional heterogeneity within cities is taken into account when measuring urban form.•The grid size of 6 km is the optimal scale for analyzing the…”
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Induction of human regulatory innate lymphoid cells from group 2 innate lymphoid cells by retinoic acid by Morita, Hideaki, Kubo, Terufumi, Rückert, Beate, Ravindran, Avinash, Soyka, Michael B., Rinaldi, Arturo Ottavio, Sugita, Kazunari, Wawrzyniak, Marcin, Wawrzyniak, Paulina, Motomura, Kenichiro, Tamari, Masato, Orimo, Keisuke, Okada, Naoko, Arae, Ken, Saito, Kyoko, Altunbulakli, Can, Castro-Giner, Francesc, Tan, Ge, Neumann, Avidan, Sudo, Katsuko, O'Mahony, Liam, Honda, Kenya, Nakae, Susumu, Saito, Hirohisa, Mjösberg, Jenny, Nilsson, Gunnar, Matsumoto, Kenji, Akdis, Mübeccel, Akdis, Cezmi A.

“…Group 2 innate lymphoid cells (ILC2s) play critical roles in induction and exacerbation of allergic airway inflammation. Thus clarification of the mechanisms…”
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Excessively increased thalamocortical connectivity and poor initial antiseizure medication response in epilepsy patients by Zhong, Jiyuan, Tan, Ge, Wang, Haijiao, Chen, Yangmei

“…The network mechanism underlying the initial response to antiseizure medication in epilepsy has not been revealed yet. Given the central role of the thalamus…”
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Self-assembled morphologies of polyelectrolyte-grafted nanoparticles directed by oppositely charged polymer matrices by Hao, Qing-Hai, Cheng, Jie, Yang, Fan, Tan, Hong-Ge

“…Self-assembled structure of polymer grafted nanoparticles is an interesting and growing subject in the field of hybrid electronics and high energy density…”
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The Role and Regulation of the NKG2D/NKG2D Ligand System in Cancer by Tan, Ge, Spillane, Katelyn M, Maher, John

“…The family of human NKG2D ligands (NKG2DL) consists of eight stress-induced molecules. Over 80% of human cancers express these ligands on the surface of tumour…”
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