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
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Visualizing climate catastrophes may spur people to act
XKCD Comic Strip
PLoS ONE
- Emergence of crucial evidence catalyzing the origin tracing of SARS-CoV-2 (Shunmei Chen, Cihan Ruan, Yutong Guo, Jia Chang, Haohao Yan, Liang Chen, Yongzhong Duan, Guangyou Duan, Jinlong Bei, Xin Li, Shan Gao, )
- Causal association of menstrual reproductive factors on the risk of osteoarthritis: A univariate and multivariate Mendelian randomization study (Xinzhe Tan, Yifang Mei, Yihao Zhou, Zhichao Liao, Pengqi Zhang, Yichang Liu, Yixiao Han, Dongyan Wang, )
- Identification of echinoderm metabolites as potential inhibitors targeting wild-type and mutant forms of Escherichia coli RNA polymerase (RpoB) for tuberculosis treatment (Fatimah M. Alsulais, Bayan A. Alhaidhal, Ramzi A. Mothana, Abdullah R. Alanzi, )
- ECD-CDGI: An efficient energy-constrained diffusion model for cancer driver gene identification (Tao Wang, Linlin Zhuo, Yifan Chen, Xiangzheng Fu, Xiangxiang Zeng, Quan Zou, )
- Validation of new tablet-based problem-solving tasks in primary school students (Jonas Schäfer, Timo Reuter, Miriam Leuchter, Julia Karbach, )
- Network analysis retrieving bioactive compounds from Spirulina (Arthrospira platensis) and their targets related to systemic lupus erythematosus (Amnart Chaiprasert, Ping Han, Teeraphan Laomettachit, Marasri Ruengjitchatchawalya, )
- Taenia solium TAF6 and TAF9 bind to a downstream promoter element present in the Tstbp1 gene core promoter (Oscar Rodríguez-Lima, Ponciano García-Gutiérrez, Lucía Jiménez, Laura A. Velázquez-Villegas, Angel Zarain-Herzberg, Roberto Lazzarini, Karel Estrada, Abraham Landa, )
BMC Genomics
- Transcriptome analysis and genome-wide identification of the dehydration-responsive element binding gene family in jackfruit under cold stress (Xiangwei Ma, Pengjin Zhu, Yingjun Du, Qiqi Song, Weiyan Ye, Xiuguan Tang, Jiang He, Yunjie Zhong, Jingli Ou and Xinhua Pang, )
- Transcriptome analysis reveals miRNA expression profiles in hypothalamus tissues during the sexual development of Jining grey goats (Qing Li, Tianle Chao, Yanyan Wang, Rong Xuan, Yanfei Guo, Peipei He, Lu Zhang and Jianmin Wang, )
- Benchmarking UMI-aware and standard variant callers for low frequency ctDNA variant detection (Rugare Maruzani, Liam Brierley, Andrea Jorgensen and Anna Fowler, )
- Predicting splicing patterns from the transcription factor binding sites in the promoter with deep learning (Tzu-Chieh Lin, Cheng-Hung Tsai, Cheng-Kai Shiau, Jia-Hsin Huang and Huai-Kuang Tsai, )
- Correction: Comparing methylation levels assayed in GCrich regions with current and emerging methods (Dominic Guanzon, Jason P. Ross, Chenkai Ma, Oliver Berry and Yi Jin Liew, )
- Signals of positive selection in genomes of palearctic Myotis-bats coexisting with a fungal pathogen (V. G. Twort, V. N. Laine, K. A. Field, F. Whiting-Fawcett, F. Ito, M. Reiman, T. Bartonicka, M. Fritze, V. A. Ilyukha, V. V. Belkin, E. A. Khizhkin, D. M. Reeder, D. Fukui, T. L. Jiang and T. M. Lilley, )
- Comparative transcriptome analysis reveals defense responses against soft rot induced by Pectobacterium aroidearum and Pectobacterium carotovorum in Pinellia ternata (Ming Luo, Mingxing Wang, Jiawei Xu, Kaili Qu, Yuhuan Miao and Dahui Liu, )
RNA-Seq Blog
- scAMF – single-cell analysis via manifold fitting – a framework for RNA clustering and beyond ()
- Unlocking the secrets of aging brains with snmCT-seq technology ()
- Eclipsebio Launches eSENSE dsRNA™ NGS Assay for Improved Detection and Optimization in RNA-based Therapeutics” ()
- PIP-seq – particle-templated instant partition sequencing ()
- scDist – robust identification of perturbed cell types in single-cell RNA-seq data ()
- Modified RNA sequencing method reveals how small RNAs boost immune response to tuberculosis ()
- NASC-seq2 – principles of transcription at the resolution of individual bursts ()
- RNA Sequencing reveals molecular mechanism behind MS and other autoimmune diseases ()
Bioinformatics
- Guide assignment in single-cell CRISPR screens using crispat ()
- RCPedia: A global resource for studying and exploring retrocopies in diverse species ()
- SAAMBE-MEM: A Sequence-Based Method for Predicting Binding Free Energy Change upon Mutation in Membrane Protein-Protein Complexes ()
- CSV-Filter: a deep learning-based comprehensive structural variant filtering method for both short and long reads ()
- bio2Byte Tools deployment as a Python package and Galaxy tool to predict protein biophysical properties ()
- SCMeTA: A pipeline for single-cell metabolic analysis data processing ()
- A distribution-free and analytic method for power and sample size calculation in single-cell differential expression ()
PLoS Computational Biology
- Fitness models provide accurate short-term forecasts of SARS-CoV-2 variant frequency (Eslam Abousamra, Marlin Figgins, Trevor Bedford, )
- Cracking the neural code for word recognition in convolutional neural networks (Aakash Agrawal, Stanislas Dehaene, )
- Mutant fate in spatially structured populations on graphs: Connecting models to experiments (Alia Abbara, Lisa Pagani, Celia García-Pareja, Anne-Florence Bitbol, )
- Binomial models uncover biological variation during feature selection of droplet-based single-cell RNA sequencing (Breanne Sparta, Timothy Hamilton, Gunalan Natesan, Samuel D. Aragones, Eric J. Deeds, )
- Backtracking: Improved methods for identifying the source of a deliberate release of Bacillus anthracis from the temporal and spatial distribution of cases (Joseph Shingleton, David Mustard, Steven Dyke, Hannah Williams, Emma Bennett, Thomas Finnie, )
- Surveillance strategies for the detection of new pathogen variants across epidemiological contexts (Kirstin I. Oliveira Roster, Stephen M. Kissler, Enoma Omoregie, Jade C. Wang, Helly Amin, Steve Di Lonardo, Scott Hughes, Yonatan H. Grad, )
- MVST: Identifying spatial domains of spatial transcriptomes from multiple views using multi-view graph convolutional networks (Hao Duan, Qingchen Zhang, Feifei Cui, Quan Zou, Zilong Zhang, )
BMC Bioinformatics
- Cortexa: a comprehensive resource for studying gene expression and alternative splicing in the murine brain (Stephan Weißbach, Jonas Milkovits, Stefan Pastore, Martin Heine, Susanne Gerber and Hristo Todorov, )
- Inference of single-cell network using mutual information for scRNA-seq data analysis (Lan-Yun Chang, Ting-Yi Hao, Wei-Jie Wang and Chun-Yu Lin, )
- Answering open questions in biology using spatial genomics and structured methods (Siddhartha G. Jena, Archit Verma and Barbara E. Engelhardt, )
- Variant graph craft (VGC): a comprehensive tool for analyzing genetic variation and identifying disease-causing variants (Jennifer Li, Andy Yang, Benedito A. Carneiro, Ece D. Gamsiz Uzun, Lauren Massingham and Alper Uzun, )
- VCF observer: a user-friendly software tool for preliminary VCF file analysis and comparison (Abdullah Asım Emül, Mehmet Arif Ergün, Rumeysa Aslıhan Ertürk, Ömer Çinal and Mehmet Baysan, )
- Correction: Advancing drug–target interaction prediction: a comprehensive graph-based approach integrating knowledge graph embedding and ProtBert pretraining (Warith Eddine Djeddi, Khalil Hermi, Sadok Ben Yahia and Gayo Diallo, )
- PCP-GC-LM: single-sequence-based protein contact prediction using dual graph convolutional neural network and convolutional neural network (J. Ouyang, Y. Gao and Y. Yang, )
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 Amazon’s gargantuan gardeners: manatees ()
- Publisher Correction: Single-crystalline metal-oxide dielectrics for top-gate 2D transistors (Daobing Zeng, Ziyang Zhang, Zhongying Xue, Miao Zhang, Paul K. Chu, Yongfeng Mei, Ziao Tian, Zengfeng Di, )
- The baseless stat that could be harming Indigenous conservation efforts (Lucy Odling-Smee, Nick Petrić Howe, )
- Cough or sneeze? How the brain knows what to unleash ()
- Fur farming a ‘viral highway’ that could spark next pandemic, say scientists (Smriti Mallapaty, )
- How to change people’s minds about climate change: what the science says (Alix Soliman, )
- Brazil’s ban on X: how scientists are coping with the cutoff (Meghie Rodrigues, )
Science
- A broad defense against SARS-like viruses (Vinson, V., )
- RNA editing restricts ciliary kinases (Jiang, D., )
- Not your usual superconductor (Stajic, J., )
- Blocking heat in two ways (Grocholski, B., )
- SagA promotes immunotherapy response (Kelly, P. N., )
- Machine learning solves RNA puzzles (Jiang, D., )
- Taking a BiTE out of tumors (Malo, C. S., )
PNAS
- A multiomic study uncovers a bZIP23-PER1A-mediated detoxification pathway to enhance seed vigor in rice [Agricultural Sciences] (Wei-Qing Wang, Ding-Yi Xu, Ya-Ping Sui, Xiao-Hui Ding, Xian-Jun Song, )
- Indirect influence in social networks as an induced percolation phenomenon [Applied Mathematics] (Jiarong Xie, Xiangrong Wang, Ling Feng, Jin-Hua Zhao, Wenyuan Liu, Yamir Moreno, Yanqing Hu, )
- Precision targeting tumor cells using cancer-specific InDel mutations with CRISPR-Cas9 [Medical Sciences] (Taejoon Kwon, Jae Sun Ra, Soyoung Lee, In-Joon Baek, Keon Woo Khim, Eun A Lee, Eun Kyung Song, Daniyar Otarbayev, Woojae Jung, Yong Hwan Park, Minwoo Wie, Juyoung Bae, Himchan Cheng, Jun Hong Park, Namwoo Kim, Yuri Seo, Seongmin Yun, Ha Eun Kim, Hyo Eun M, )
- An in-frame deletion mutation in the degron tail of auxin coreceptor IAA2 confers resistance to the herbicide 2,4-D in Sisymbrium orientale [Agricultural Sciences] (Marcelo R. A. de Figueiredo, Anita Kupper, Jenna M. Malone, Tiȷana Petrovic, Ana Beatriz T. B. de Figueiredo, Grace Campagnola, Olve B. Peersen, Kasavaȷhala V. S. K. Prasad, Eric L. Patterson, Anireddy S. N. Reddy, Martin F. Kubeš, Ri, )
- Scaling laws in enzyme function reveal a new kind of biochemical universality [Biophysics and Computational Biology] (Dylan C. Gagler, Bradley Karas, Christopher P. Kempes, John Malloy, Veronica Mierzejewski, Aaron D. Goldman, Hyunju Kim, Sara I. Walker, )
- Modeling suggests gene editing combined with vaccination could eliminate a persistent disease in livestock [Genetics] (Gertje Eta Leony Petersen, Jaap B. Buntjer, Fiona S. Hely, Timothy John Byrne, Andrea Doeschl-Wilson, )
- BEND3 safeguards pluripotency by repressing differentiation-associated genes [Genetics] (Fredy Kurniawan, Neha Chetlangia, Mohammad Kamran, Christophe E. Redon, Lorinc Pongor, Qinyu Sun, Yo-Chuen Lin, Vijay Mohan, Oways Shaqildi, Darya Asoudegi, Qinyu Hao, Abid Khan, Mirit I. Aladjem, Kannanganattu V. Prasanth, Supriya G. Prasanth, )
Genome Biology
- A comprehensive map of the aging blood methylome in humans (Kirsten Seale, Andrew Teschendorff, Alexander P. Reiner, Sarah Voisin and Nir Eynon, )
- DeepKINET: a deep generative model for estimating single-cell RNA splicing and degradation rates (Chikara Mizukoshi, Yasuhiro Kojima, Satoshi Nomura, Shuto Hayashi, Ko Abe and Teppei Shimamura, )
- Author Correction: A benchmark of computational methods for correcting biases of established and unknown origin in CRISPR-Cas9 screening data (Alessandro Vinceti, Rafaele M. Iannuzzi, Isabella Boyle, Lucia Trastulla, Catarina D. Campbell, Francisca Vazquez, Joshua M. Dempster and Francesco Iorio, )
- Publisher Correction: scParser: sparse representation learning for scalable single-cell RNA sequencing data analysis (Kai Zhao, Hon-Cheong So and Zhixiang Lin, )
- Improved simultaneous mapping of epigenetic features and 3D chromatin structure via ViCAR (Sean M. Flynn, Somdutta Dhir, Krzysztof Herka, Colm Doyle, Larry Melidis, Angela Simeone, Winnie W. I. Hui, Rafael de Cesaris Araujo Tavares, Stefan Schoenfelder, David Tannahill and Shankar Balasubramanian, )
- RNAseqCovarImpute: a multiple imputation procedure that outperforms complete case and single imputation differential expression analysis (Brennan H. Baker, Sheela Sathyanarayana, Adam A. Szpiro, James W. MacDonald and Alison G. Paquette, )
- Enhlink infers distal and context-specific enhancer–promoter linkages (Olivier B. Poirion, Wulin Zuo, Catrina Spruce, Candice N. Baker, Sandra L. Daigle, Ashley Olson, Daniel A. Skelly, Elissa J. Chesler, Christopher L. Baker and Brian S. White, )