Tweets on Gen/Transcript/Prote-Omics
News by Scientific American
- When Will We Learn? ()
- Letters ()
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Dereliction of Duty
()
The U.S. Congress has not protected health or the environment. Time to make it step up
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Income Inequality and Homicide
()
Where financial disparities are greatest, the murder rate tends to be high
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Fixing Wasting Muscles
()
Scientists edited dogs' genes to correct a common form of muscle dystrophy
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Artificial Wood
()
The synthetic material is both robust and versatile
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Flooding the Senses
()
Visualizing climate catastrophes may spur people to act
XKCD Comic Strip
PLoS ONE
- Bayesian integrative analysis of epigenomic and transcriptomic data identifies Alzheimer's disease candidate genes and networks (Hans-Ulrich Klein, Martin Schäfer, David A. Bennett, Holger Schwender, Philip L. De Jager, )
- Mechanistic models of PLC/PKC signaling implicate phosphatidic acid as a key amplifier of chemotactic gradient sensing (Jamie L. Nosbisch, Anisur Rahman, Krithika Mohan, Timothy C. Elston, James E. Bear, Jason M. Haugh, )
- Integrating GWAS with bulk and single-cell RNA-sequencing reveals a role for LY86 in the anti-Candida host response (Dylan H. de Vries, Vasiliki Matzaraki, Olivier B. Bakker, Harm Brugge, Harm-Jan Westra, Mihai G. Netea, Lude Franke, Vinod Kumar, Monique G. P. van der Wijst, )
- Opening the black box of artificial intelligence for clinical decision support: A study predicting stroke outcome (Esra Zihni, Vince Istvan Madai, Michelle Livne, Ivana Galinovic, Ahmed A. Khalil, Jochen B. Fiebach, Dietmar Frey, )
- Probing lasting cryoinjuries to oocyte-embryo transcriptome (Binnur Eroglu, Edyta A. Szurek, Peter Schall, Keith E. Latham, Ali Eroglu, )
- Risk prediction of two types of potential snail habitats in Anhui Province of China: Model-based approaches (Jun Zhang, Ming Yue, Yi Hu, Robert Bergquist, Chuan Su, Fenghua Gao, Zhi-Guo Cao, Zhijie Zhang, )
- Comparative genomics and full-length Tprk profiling of Treponema pallidum subsp. pallidum reinfection (Amin Addetia, Lauren C. Tantalo, Michelle J. Lin, Hong Xie, Meei-Li Huang, Christina M. Marra, Alexander L. Greninger, )
BMC Genomics
- Complete genome sequence and annotation of the laboratory reference strain Shigella flexneri serotype 5a M90T and genome-wide transcriptional start site determination (Ramón Cervantes-Rivera, Sophie Tronnet and Andrea Puhar, )
- Genome-wide analysis of Myo-inositol oxygenase gene family in tomato reveals their involvement in ascorbic acid accumulation (Shoaib Munir, Muhammad Ali Mumtaz, John Kojo Ahiakpa, Genzhong Liu, Weifang Chen, Guolin Zhou, Wei Zheng, Zhibiao Ye and Yuyang Zhang, )
- A qualitative transcriptional signature to reclassify histological grade of ER-positive breast cancer patients (Jing Li, Wenbin Jiang, Qirui Liang, Guanghao Liu, Yupeng Dai, Hailong Zheng, Jing Yang, Hao Cai and Guo Zheng, )
- Assessing graph-based read mappers against a baseline approach highlights strengths and weaknesses of current methods (Ivar Grytten, Knut D. Rand, Alexander J. Nederbragt and Geir K. Sandve, )
- Fine mapping of a Phytophthora-resistance locus RpsGZ in soybean using genotyping-by-sequencing (Bingzhi Jiang, Yanbo Cheng, Zhandong Cai, Mu Li, Ze Jiang, Ruirui Ma, Yeshan Yuan, Qiuju Xia and Hai Nian, )
- Re-annotation of the Theileria parva genome refines 53% of the proteome and uncovers essential components of N-glycosylation, a conserved pathway in many organisms (Kyle Tretina, Roger Pelle, Joshua Orvis, Hanzel T. Gotia, Olukemi O. Ifeonu, Priti Kumari, Nicholas C. Palmateer, Shaikh B. A. Iqbal, Lindsay M. Fry, Vishvanath M. Nene, Claudia A. Daubenberger, Richard P. Bishop and Joana C. Silva, )
- ddRADseq-assisted construction of a high-density SNP genetic map and QTL fine mapping for growth-related traits in the spotted scat (Scatophagus argus) (Wei Yang, Yaorong Wang, Dongneng Jiang, Changxu Tian, Chunhua Zhu, Guangli Li and Huapu Chen, )
RNA-Seq Blog
- A cheaper way to study the immune system, one cell at a time ()
- Viral RNA structure analysis using DMS-MaPseq ()
- Researchers benchmark single-cell transcriptome profiling methods ()
- SILVER-SEQ enables discovery of new exRNA biomarker in blood for Alzheimer’s disease ()
- Direct RNA sequencing and early evolution of SARS-CoV-2 ()
- Scientists find a practical approach to improve differential gene expression analysis ()
- Direct-capture Perturb-seq – sequencing expressed sgRNAs alongside single-cell transcriptomes ()
- Obstacles to detecting isoforms using full-length scRNA-seq data ()
Bioinformatics
- CircMiner: Accurate and Rapid Detection of Circular RNA through Splice-Aware Pseudo-Alignment Scheme ()
- FASPR: an open-source tool for fast and accurate protein side-chain packing ()
- MaveQuest: a web resource for planning experimental tests of human variant effects ()
- Learning transferable deep convolutional neural networks for the classification of bacterial virulence factors ()
- T-Gene: Improved target gene prediction ()
- ADFinder: accurate detection of programmed DNA elimination using NGS high-throughput sequencing data ()
- Prioritizing genetic variants in GWAS with lasso using permutation-assisted tuning ()
PLoS Computational Biology
- Bayesian integrative analysis of epigenomic and transcriptomic data identifies Alzheimer's disease candidate genes and networks (Hans-Ulrich Klein, Martin Schäfer, David A. Bennett, Holger Schwender, Philip L. De Jager, )
- Mechanistic models of PLC/PKC signaling implicate phosphatidic acid as a key amplifier of chemotactic gradient sensing (Jamie L. Nosbisch, Anisur Rahman, Krithika Mohan, Timothy C. Elston, James E. Bear, Jason M. Haugh, )
- MAGIC: A tool for predicting transcription factors and cofactors driving gene sets using ENCODE data (Avtar Roopra, )
- Ion channel noise shapes the electrical activity of endocrine cells (David M. Richards, Jamie J. Walker, Joel Tabak, )
- 3D mesh processing using GAMer 2 to enable reaction-diffusion simulations in realistic cellular geometries (Christopher T. Lee, Justin G. Laughlin, Nils Angliviel de La Beaumelle, Rommie E. Amaro, J. Andrew McCammon, Ravi Ramamoorthi, Michael Holst, Padmini Rangamani, )
- Robustness of the Dorsal morphogen gradient with respect to morphogen dosage (Hadel Al Asafen, Prasad U. Bandodkar, Sophia Carrell-Noel, Allison E. Schloop, Jeramey Friedman, Gregory T. Reeves, )
- Complementary computational and experimental evaluation of missense variants in the ROMK potassium channel (Luca Ponzoni, Nga H. Nguyen, Ivet Bahar, Jeffrey L. Brodsky, )
BMC Bioinformatics
- Enhanced identification of significant regulators of gene expression (Rezvan Ehsani and Finn Drabløs, )
- RDb2C2: an improved method to identify the residue-residue pairing in β strands (Di Shao, Wenzhi Mao, Yaoguang Xing and Haipeng Gong, )
- Modeling of shotgun sequencing of DNA plasmids using experimental and theoretical approaches (Sergey Shityakov, Elena Bencurova, Carola Förster and Thomas Dandekar, )
- MI-MAAP: marker informativeness for multi-ancestry admixed populations (Siqi Chen, Sudhir Ghandikota, Yadu Gautam and Tesfaye B. Mersha, )
- pyCancerSig: subclassifying human cancer with comprehensive single nucleotide, structural and microsatellite mutational signature deconstruction from whole genome sequencing (Jessada Thutkawkorapin, Jesper Eisfeldt, Emma Tham and Daniel Nilsson, )
- A novel virtual barcode strategy for accurate panel-wide variant calling in circulating tumor DNA (Leilei Wu, Qinfang Deng, Ze Xu, Songwen Zhou, Chao Li and Yi-Xue Li, )
- A random forest based computational model for predicting novel lncRNA-disease associations (Dengju Yao, Xiaojuan Zhan, Xiaorong Zhan, Chee Keong Kwoh, Peng Li and Jinke Wang, )
NEWS
- Roca-Ayats et al, N. Eng. J. Med., 2017 ()
- Hjelmsø et al, PLoS ONE, 2017 ()
- Gabre et al, Marine Genomics, 2015 ()
- RPGeNet: Boloc et al, PLoS ONE, 2015 ()
- Rodríguez-Esteban et al, BMC Genomics, 2015 ()
- Joint 23rd ISMB / 14th ECCB ()
- Applying Next Generation Sequencing in Metagenomics Studies ()
- Perea-Atienza et al, J Exp Biol, 2015 ()
- 3rd CNAG Symposium on Genome Resarch: Rare Diseases ()
- Metagenomics for Food and Water Safety ()
Nature
- The gluconeogenic enzyme PCK1 phosphorylates INSIG1/2 for lipogenesis (Daqian Xu, Zheng Wang, Yan Xia, Fei Shao, Weiya Xia, Yongkun Wei, Xinjian Li, Xu Qian, Jong-Ho Lee, Linyong Du, Yanhua Zheng, Guishuai Lv, Jia-shiun Leu, Hongyang Wang, Dongming Xing, Tingbo Liang, Mien-Chie Hung, Zhimin Lu, )
- The projected timing of abrupt ecological disruption from climate change (Christopher H. Trisos, Cory Merow, Alex L. Pigot, )
- A reference map of the human binary protein interactome (Katja Luck, Dae-Kyum Kim, Luke Lambourne, Kerstin Spirohn, Bridget E. Begg, Wenting Bian, Ruth Brignall, Tiziana Cafarelli, Francisco J. Campos-Laborie, Benoit Charloteaux, Dongsic Choi, Atina G. Coté, Meaghan Daley, Steven Deimling, Alice Desbuleux, Amél, )
- Coronavirus in cats, climate cancellation and missing African trials ()
- A neural circuit mechanism for mechanosensory feedback control of ingestion (Dong-Yoon Kim, Gyuryang Heo, Minyoo Kim, Hyunseo Kim, Ju Ae Jin, Hyun-Kyung Kim, Sieun Jung, Myungmo An, Benjamin H. Ahn, Jong Hwi Park, Han-Eol Park, Myungsun Lee, Jung Weon Lee, Gary J. Schwartz, Sung-Yon Kim, )
- AIM2 inflammasome surveillance of DNA damage shapes neurodevelopment (Catherine R. Lammert, Elizabeth L. Frost, Calli E. Bellinger, Ashley C. Bolte, Celia A. McKee, Mariah E. Hurt, Matt J. Paysour, Hannah E. Ennerfelt, John R. Lukens, )
- Podcast: A plastic-recycling enzyme, and supercooled molecules ()
Science
- How to read the face of a mouse (Stern, P., )
- Seeing subtle nanoparticle differences (Lavine, M. S., )
- New ideas about neoantigens (Nusinovich, Y., )
- Slipping on till (Smith, H. J., )
- Airway-hugging macrophages (Williams, I., )
- Blowing a crater in asteroid Ryugu (Smith, K. T., )
- Designer gates (Vinson, V., )
PNAS
- Ddi1 is a ubiquitin-dependent protease [Biochemistry] (Matthew C. J. Yip, Nicholas O. Bodnar, Tom A. Rapoport, )
- Coordination of mRNA and tRNA methylations by TRMT10A [Biochemistry] (R. Jordan Ontiveros, Hui Shen, Julian Stoute, Amber Yanas, Yixiao Cui, Yuyu Zhang, Kathy Fange Liu, )
- The TMEM189 gene encodes plasmanylethanolamine desaturase which introduces the characteristic vinyl ether double bond into plasmalogens [Biochemistry] (Ernst R. Werner, Markus A. Keller, Sabrina Sailer, Katharina Lackner, Jakob Koch, Martin Hermann, Stefan Coassin, Georg Golderer, Gabriele Werner-Felmayer, Raphael A. Zoeller, Nicolas Hulo, Johannes Berger, Katrin Watschinger, )
- Self-organized networks: Darwinian evolution of dynein rings, stalks, and stalk heads [Biophysics and Computational Biology] (J. C. Phillips, )
- Defining how multiple lipid species interact with inward rectifier potassium (Kir2) channels [Biophysics and Computational Biology] (Anna L. Duncan, Robin A. Corey, Mark S. P. Sansom, )
- Kinetics of the conformational cycle of Hsp70 reveals the importance of the dynamic and heterogeneous nature of Hsp70 for its function [Biophysics and Computational Biology] (Si Wu, Liu Hong, Yuqing Wang, Jieqiong Yu, Jie Yang, , Hong Zhang, Sarah Perrett, )
- Bayesian inference of chromatin structure ensembles from population-averaged contact data [Biophysics and Computational Biology] (Simeon Carstens, Michael Nilges, Michael Habeck, )
Genome Biology
- Principles of RNA processing from analysis of enhanced CLIP maps for 150 RNA binding proteins (Eric L. Van Nostrand, Gabriel A. Pratt, Brian A. Yee, Emily C. Wheeler, Steven M. Blue, Jasmine Mueller, Samuel S. Park, Keri E. Garcia, Chelsea Gelboin-Burkhart, Thai B. Nguyen, Ines Rabano, Rebecca Stanton, Balaji Sundararaman, Ruth Wang, Xiang-Dong Fu,, )
- The preceding root system drives the composition and function of the rhizosphere microbiome (Yi Zhou, David R. Coventry, Vadakattu V. S. R. Gupta, David Fuentes, Andrew Merchant, Brent N. Kaiser, Jishun Li, Yanli Wei, Huan Liu, Yayu Wang, Shuheng Gan and Matthew D. Denton, )
- Leveraging biological and statistical covariates improves the detection power in epigenome-wide association testing (Jinyan Huang, Ling Bai, Bowen Cui, Liang Wu, Liwen Wang, Zhiyin An, Shulin Ruan, Yue Yu, Xianyang Zhang and Jun Chen, )
- Lamina-associated domains: peripheral matters and internal affairs (Nolwenn Briand and Philippe Collas, )
- TADsplimer reveals splits and mergers of topologically associating domains for epigenetic regulation of transcription (Guangyu Wang, Qingshu Meng, Bo Xia, Shuo Zhang, Jie Lv, Dongyu Zhao, Yanqiang Li, Xin Wang, Lili Zhang, John P. Cooke, Qi Cao and Kaifu Chen, )
- Successful generation of epigenetic disease model mice by targeted demethylation of the epigenome (Takuro Horii, Sumiyo Morita, Shinjiro Hino, Mika Kimura, Yuko Hino, Hiroshi Kogo, Mitsuyoshi Nakao and Izuho Hatada, )
- CRISPRi-based radiation modifier screen identifies long non-coding RNA therapeutic targets in glioma (S. John Liu, Martina Malatesta, Brian V. Lien, Parna Saha, Shivani S. Thombare, Sung Jun Hong, Leslie Pedraza, Mark Koontz, Kyounghee Seo, Max A. Horlbeck, Daniel He, Harjus S. Birk, Miten Jain, Hugh E. Olsen, Mark Akeson, Jonathan S. Weissman…, )