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
- Infrared and visible image fusion method of dual NSCT and PCNN (Chunming Wu, Long Chen, )
- A sequencing study of CTLA4 in Pakistani rheumatoid arthritis cases (Muhammad Muaaz Aslam, Fazal Jalil, Peter John, Kang-Hsien Fan, Attya Bhatti, Eleanor Feingold, F. Yesim Demirci, M. Ilyas Kamboh, )
- Short k-mer abundance profiles yield robust machine learning features and accurate classifiers for RNA viruses (Md. Nafis Ul Alam, Umar Faruq Chowdhury, )
- Genetic testing offer for inherited neuromuscular diseases within the EURO-NMD reference network: A European survey study (Borut Peterlin, Francesca Gualandi, Ales Maver, Serenella Servidei, Silvère M. van der Maarel, Francoise Lamy, Alexander Mejat, Teresinha Evangelista, Alessandra Ferlini, )
- coPLINK: A complementary tool to PLINK (Han-Ming Liu, Zhao-Fa Liu, Jin-Ping Zheng, Dan Yang, Sheng-Zhou Hu, Shen-Hai Yan, Xian-Wen He, )
- Functional gene categories differentiate maize leaf drought-related microbial epiphytic communities (Barbara A. Methe, David Hiltbrand, Jeffrey Roach, Wenwei Xu, Stuart G. Gordon, Brad W. Goodner, Ann E. Stapleton, )
- GCN sensitive protein translation in yeast (William A. Barr, Ruchi B. Sheth, Jack Kwon, Jungwoo Cho, Jacob W. Glickman, Felix Hart, Om K. Chatterji, Kristen Scopino, Karen Voelkel-Meiman, Daniel Krizanc, Kelly M. Thayer, Michael P. Weir, )
BMC Genomics
- Skeletal muscle and cardiac transcriptomics of a regionally endothermic fish, the Pacific bluefin tuna, Thunnus orientalis (Adam Ciezarek, Luke Gardner, Vincent Savolainen and Barbara Block, )
- Gene expression within the periaqueductal gray is linked to vocal behavior and early-onset parkinsonism in Pink1 knockout rats (Cynthia A. Kelm-Nelson and Stephen Gammie, )
- Full-length genome sequence of segmented RNA virus from ticks was obtained using small RNA sequencing data (Xiaofeng Xu, Jinlong Bei, Yibo Xuan, Jiayuan Chen, Defu Chen, Stephen C. Barker, Samuel Kelava, Xiaoai Zhang, Shan Gao and Ze Chen, )
- Long-read sequencing and de novo genome assembly of marine medaka (Oryzias melastigma) (Pingping Liang, Hafiz Sohaib Ahmed Saqib, Xiaomin Ni and Yingjia Shen, )
- Comparative transcriptome analysis of root, stem, and leaf tissues of Entada phaseoloides reveals potential genes involved in triterpenoid saponin biosynthesis (Weifang Liao, Zhinan Mei, Lihong Miao, Pulin Liu and Ruijie Gao, )
- Transcriptome response comparison between vector and non-vector aphids after feeding on virus-infected wheat plants (Dandan Li, Chi Zhang, Zeqian Tong, Dan Su, Gaisheng Zhang, Shize Zhang, Huiyan Zhao and Zuqing Hu, )
- CrustyBase: an interactive online database for crustacean transcriptomes (Cameron J. Hyde, Quinn P. Fitzgibbon, Abigail Elizur, Gregory G. Smith and Tomer Ventura, )
RNA-Seq Blog
- A sparse Bayesian factor model for the construction of gene co-expression networks from single-cell RNA sequencing count data ()
- New research identifies circulating RNA preeclampsia biomarkers ()
- Single cell transcriptome analysis reveals biomarker that predicts who will have severe COVID-19 ()
- Improved haplotype inference by exploiting long-range linking and allelic imbalance in RNA-seq datasets ()
- Shotgunning the messenger – Single-cell RNA sequencing ()
- Technology enabling research ()
- Comparison of RNA isolation and library preparation methods for small RNA sequencing of canine biofluids ()
- Shark – fishing relevant reads in an RNA-Seq sample ()
Bioinformatics
- The qBED track: a novel genome browser visualization for point processes ()
- Gene Circuit Explorer (GeneEx): an interactive web-app for visualizing, simulating and analyzing gene regulatory circuits ()
- Neoantimon: A multifunctional R package for identification of tumor-specific neoantigens ()
- HiSCF: leveraging higher-order structures for clustering analysis in biological networks ()
- SEEDS: Data driven inference of structural model errors and unknown inputs for dynamic systems biology ()
- AFid: A tool for automated identification and exclusion of autofluorescent objects from microscopy images ()
- COGENT: evaluating the consistency of gene co-expression networks ()
PLoS Computational Biology
- Nonlinear stimulus representations in neural circuits with approximate excitatory-inhibitory balance (Cody Baker, Vicky Zhu, Robert Rosenbaum, )
- Capturing cell type-specific chromatin compartment patterns by applying topic modeling to single-cell Hi-C data (Hyeon-Jin Kim, Galip Gurkan Yardımcı, Giancarlo Bonora, Vijay Ramani, Jie Liu, Ruolan Qiu, Choli Lee, Jennifer Hesson, Carol B. Ware, Jay Shendure, Zhijun Duan, William Stafford Noble, )
- All-atom simulation of the HET-s prion replication (Luca Terruzzi, Giovanni Spagnolli, Alberto Boldrini, Jesús R. Requena, Emiliano Biasini, Pietro Faccioli, )
- Genetic grouping of SARS-CoV-2 coronavirus sequences using informative subtype markers for pandemic spread visualization (Zhengqiao Zhao, Bahrad A. Sokhansanj, Charvi Malhotra, Kitty Zheng, Gail L. Rosen, )
- Ten simple rules for writing scientific op-ed articles (Hoe-Han Goh, Philip Bourne, )
- A new Graph Gaussian embedding method for analyzing the effects of cognitive training (Mengjia Xu, Zhijiang Wang, Haifeng Zhang, Dimitrios Pantazis, Huali Wang, Quanzheng Li, )
- Response nonlinearities in networks of spiking neurons (Alessandro Sanzeni, Mark H. Histed, Nicolas Brunel, )
BMC Bioinformatics
- PAWER: protein array web exploreR (Dmytro Fishman, Ivan Kuzmin, Priit Adler, Jaak Vilo and Hedi Peterson, )
- A learning-based method for drug-target interaction prediction based on feature representation learning and deep neural network (Jiajie Peng, Jingyi Li and Xuequn Shang, )
- Multi-omics profiling reveals microRNA-mediated insulin signaling networks (Yang-Chi-Dung Lin, Hsi-Yuan Huang, Sirjana Shrestha, Chih-Hung Chou, Yen-Hua Chen, Chi-Ru Chen, Hsiao-Chin Hong, Jing Li, Yi-An Chang, Men-Yee Chiew, Ya-Rong Huang, Siang-Jyun Tu, Ting-Hsuan Sun, Shun-Long Weng, Ching-Ping Tseng and Hsien-Da Huang, )
- NEDD: a network embedding based method for predicting drug-disease associations (Renyi Zhou, Zhangli Lu, Huimin Luo, Ju Xiang, Min Zeng and Min Li, )
- Prediction of hot spots in protein–DNA binding interfaces based on supervised isometric feature mapping and extreme gradient boosting (Ke Li, Sijia Zhang, Di Yan, Yannan Bin and Junfeng Xia, )
- Seagull: lasso, group lasso and sparse-group lasso regularization for linear regression models via proximal gradient descent (Jan Klosa, Noah Simon, Pål Olof Westermark, Volkmar Liebscher and Dörte Wittenburg, )
- ADEPT: a domain independent sequence alignment strategy for gpu architectures (Muaaz G. Awan, Jack Deslippe, Aydin Buluc, Oguz Selvitopi, Steven Hofmeyr, Leonid Oliker and Katherine Yelick, )
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
- New York and Boston maintain their lead (Neil Savage, )
- A guide to the Nature Index ()
- Nature Index’s top five science cities, by the numbers ()
- Science cities seek new connections (György Csomós, Zsófia Viktória Vida, Balázs Lengyel, )
- Beijing, the seat of science capital (Hepeng Jia, )
- The top cities for research in the Nature Index (Catherine Armitage, )
- Editorial Expression of Concern: Living annulative π-extension polymerization for graphene nanoribbon synthesis (Yuuta Yano, Nobuhiko Mitoma, Kaho Matsushima, Feijiu Wang, Keisuke Matsui, Akira Takakura, Yuhei Miyauchi, Hideto Ito, Kenichiro Itami, )
Science
- Horses were not domesticated in Anatolia (Aldenderfer, M., )
- Inosine modulates antitumor immunity (Kelly, P. N., )
- How ribosomes are made (Vinson, V., )
- A mess of plastic (Smith, H. J., )
- Nature of the molecule-surface encounter (Suleymanov, Y., )
- Supercooled water structures (Szuromi, P., )
- Complex stellar winds from evolved stars (Smith, K. T., )
PNAS
- Mechanism for analogous illusory motion perception in flies and humans [Neuroscience] (Margarida Agrochao, Ryosuke Tanaka, Emilio Salazar-Gatzimas, Damon A. Clark, )
- Fusogen-mediated neuron-neuron fusion disrupts neural circuit connectivity and alters animal behavior [Neuroscience] (Rosina Giordano-Santini, Eva Kaulich, Kate M. Galbraith, Fiona K. Ritchie, Wei Wang, Zhaoyu Li, Massimo A. Hilliard, )
- Finding the neural correlates of collaboration using a three-person fMRI hyperscanning paradigm [Neuroscience] (Hua Xie, Iliana I. Karipidis, Amber Howell, Meredith Schreier, Kristen E. Sheau, Mai K. Manchanda, Rafi Ayub, Gary H. Glover, Malte Jung, Allan L. Reiss, Manish Saggar, )
- CRL5-dependent regulation of the small GTPases ARL4C and ARF6 controls hippocampal morphogenesis [Neuroscience] (Jisoo S. Han, Keiko Hino, Wenzhe Li, Raenier V. Reyes, Cesar P. Canales, Adam M. Miltner, Yasmin Haddadi, Junqing Sun, Chao–Yin Chen, Anna La Torre, Sergi Simo, )
- Active vision shapes and coordinates flight motor responses in flies [Neuroscience] (Benjamin Cellini, Jean-Michel Mongeau, )
- Analysis of {beta}2AR-Gs and {beta}2AR-Gi complex formation by NMR spectroscopy [Pharmacology] (Xiuyan Ma, Yunfei Hu, Hossein Batebi, Jie Heng, Jun Xu, Xiangyu Liu, Xiaogang Niu, Hongwei Li, Peter W. Hildebrand, Changwen Jin, Brian K. Kobilka, )
- Hypnotic effect of thalidomide is independent of teratogenic ubiquitin/proteasome pathway [Pharmacology] (Yuki Hirose, Tomohiro Kitazono, Maiko Sezaki, Manabu Abe, Kenji Sakimura, Hiromasa Funato, Hiroshi Handa, Kaspar E. Vogt, Masashi Yanagisawa, )
Genome Biology
- Chromatin regulates expression of small RNAs to help maintain transposon methylome homeostasis in Arabidopsis (Ranjith K. Papareddy, Katalin Páldi, Subramanian Paulraj, Ping Kao, Stefan Lutzmayer and Michael D. Nodine, )
- Removing reference bias and improving indel calling in ancient DNA data analysis by mapping to a sequence variation graph (Rui Martiniano, Erik Garrison, Eppie R. Jones, Andrea Manica and Richard Durbin, )
- Bifrost: highly parallel construction and indexing of colored and compacted de Bruijn graphs (Guillaume Holley and Páll Melsted, )
- Ultrasensitive deletion detection links mitochondrial DNA replication, disease, and aging (Scott A. Lujan, Matthew J. Longley, Margaret H. Humble, Christopher A. Lavender, Adam Burkholder, Emma L. Blakely, Charlotte L. Alston, Grainne S. Gorman, Doug M. Turnbull, Robert McFarland, Robert W. Taylor, Thomas A. Kunkel and William C. Copeland, )
- Cancer-specific CTCF binding facilitates oncogenic transcriptional dysregulation (Celestia Fang, Zhenjia Wang, Cuijuan Han, Stephanie L. Safgren, Kathryn A. Helmin, Emmalee R. Adelman, Valentina Serafin, Giuseppe Basso, Kyle P. Eagen, Alexandre Gaspar-Maia, Maria E. Figueroa, Benjamin D. Singer, Aakrosh Ratan, Panagiotis Ntziachristos , )
- AuthentiCT: a model of ancient DNA damage to estimate the proportion of present-day DNA contamination (Stéphane Peyrégne and Benjamin M. Peter, )
- Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies (Arang Rhie, Brian P. Walenz, Sergey Koren and Adam M. Phillippy, )