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
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Scientists edited dogs' genes to correct a common form of muscle dystrophy
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Artificial Wood
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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
- The TPR domain of PgaA is a multifunctional scaffold that binds PNAG and modulates PgaB-dependent polymer processing (Roland Pfoh, Adithya S. Subramanian, Jingjing Huang, Dustin J. Little, Adam Forman, Benjamin R. DiFrancesco, Negar Balouchestani-Asli, Elena N. Kitova, John S. Klassen, Régis Pomès, Mark Nitz, P. Lynne Howell, )
- Comparative analysis of chloroplast genomes of three medicinal Carpesium species: Genome structures and phylogenetic relationships (Xingyu Shi, Wenfen Xu, Mingxiang Wan, Qingwen Sun, Qiyu Chen, Chao Zhao, Kaifen Sun, Yanxia Shu, )
- Identification of differentially expressed genes for Pseudomonas sp. Cr13 stimulated by hexavalent chromium (Bingbing Pang, Hongling Yu, Jin Zhang, Fengcai Ye, Haifeng Wu, Changhua Shang, )
- Genome insights from the identification of a novel Pandoraea sputorum isolate and its characteristics (Rui-Fang Gao, Ying Wang, Zhi-Wen Wang, Gui-Ming Zhang, )
- Complete chloroplast genomes and comparative analyses of Hippeastrum ‘milady’, Hippeastrum albertii and Hippeastrum reticulatum (Amaryllidaceae) (Xiao-fei Liu, Ying-bo Sun, Gen-fa Zhu, Li-li Huang, Bo Yu, )
- Recruitment strategies and lessons learned from a large genetic study of African Americans (Rebecca J. Salowe, Roy Lee, Selam Zenebe-Gete, Marquis Vaughn, Harini V. Gudiseva, Maxwell Pistilli, Ava Kikut, Emily Becker, David W. Collins, Jie He, Sayaka Merriam, Kristen Mulvihill, Nora Laberee, Sara Lomax-Reese, Windell Murphy, Jeffrey Henderer, Ve, )
- Causal relationships between sex hormone traits, lifestyle factors, and osteoporosis in men: A Mendelian randomization study (Hui Wang, Jianwen Cheng, Donglei Wei, Hong Wu, Jinmin Zhao, )
BMC Genomics
- Identification of novel key regulatory lncRNAs in gastric adenocarcinoma (Houri Razavi and Ali Katanforosh, )
- Association between high immune activity and worse prognosis in uveal melanoma and low-grade glioma in TCGA transcriptomic data (Hitoshi Matsuo, Takashi Kamatani, Yu Hamba, Keith A. Boroevich and Tatsuhiko Tsunoda, )
- Small RNA sequencing and bioinformatics analysis of RAW264.7-derived exosomes after Mycobacterium Bovis Bacillus Calmette-Guérin infection (Xuehua Zhan, Wenqi Yuan, Yueyong Zhou, Rong Ma and Zhaohui Ge, )
- Evolution and dispersal of mitochondrial DNA haplogroup U5 in Northern Europe: insights from an unsupervised learning approach to phylogeography (Dana Kristjansson, Jon Bohlin, Truc Trung Nguyen, Astanand Jugessur and Theodore G. Schurr, )
- Genomic features of the polyphagous cotton leafworm Spodoptera littoralis (Chao Wu, Lei Zhang, Bo Liu, Bojia Gao, Cong Huang, Ji Zhang, Minghui Jin, Hanyue Wang, Yan Peng, Annabel Rice, Esmat Hegazi, Kenneth Wilson, Pengjun Xu and Yutao Xiao, )
- Identification of condition-specific regulatory mechanisms in normal and cancerous human lung tissue (Yuqing Hang, Josh Burns, Benjamin T. Shealy, Rini Pauly, Stephen P. Ficklin and Frank A. Feltus, )
- Optimized Cas9:sgRNA delivery efficiently generates biallelic MSTN knockout sheep without affecting meat quality (Shiwei Zhou, Peter Kalds, Qi Luo, Kexin Sun, Xiaoe Zhao, Yawei Gao, Bei Cai, Shuhong Huang, Qifang Kou, Bjoern Petersen, Yulin Chen, Baohua Ma and Xiaolong Wang, )
RNA-Seq Blog
- Researchers use single-cell approaches and deep learning to map all stages of fruit fly embryo development ()
- DeLTa-Seq – direct-lysate targeted RNA-Seq from crude tissue lysate ()
- Tumor bulk-RNA seq identifies patients at high risk of progression in non-complete pathological responders from NADIM trial ()
- STRIDE – a topic-model-based method to deconvolve spatial transcriptomics using scRNA-seq ()
- Researchers find heart failure arises from mutations in numerous distinct genes ()
- Transcriptome diversity in human tissues mapped with emerging long-read RNA sequencing technology ()
- Significance analysis for clustering with single-cell RNA-sequencing data ()
- BacDrop – droplet-based single-cell RNA-seq reveals heterogeneity in bacterial populations and in response to antibiotic perturbation ()
Bioinformatics
- MICER: A Pre-trained Encoder-Decoder Architecture for Molecular Image Captioning ()
- Neural Collective Matrix Factorization for Integrated Analysis of Heterogeneous Biomedical Data ()
- Hierarchical deep learning for predicting GO annotations by integrating protein knowledge ()
- Prediction of Gene Co-expression from Chromatin Contacts with Graph Attention Network ()
- DBFE: Distribution-based feature extraction from structural variants in whole-genome data ()
- ASURAT: Functional annotation-driven unsupervised clustering of single-cell transcriptomes ()
- DiNAMIC.Duo: detecting somatic DNA copy number differences without a normal reference ()
PLoS Computational Biology
- Spatiotemporal dynamics of human high gamma discriminate naturalistic behavioral states (Abdulwahab Alasfour, Paolo Gabriel, Xi Jiang, Isaac Shamie, Lucia Melloni, Thomas Thesen, Patricia Dugan, Daniel Friedman, Werner Doyle, Orin Devinsky, David Gonda, Shifteh Sattar, Sonya Wang, Eric Halgren, Vikash Gilja, )
- From kill the winner to eliminate the winner in open phage-bacteria systems (Anastasios Marantos, Namiko Mitarai, Kim Sneppen, )
- Insertions and deletions as phylogenetic signal in an alignment-free context (Niklas Birth, Thomas Dencker, Burkhard Morgenstern, )
- Correction: Understanding narwhal diving behaviour using Hidden Markov Models with dependent state distributions and long range dependence (Manh Cuong Ngô, Mads Peter Heide-Jørgensen, Susanne Ditlevsen, )
- Quantification of hypoxic regions distant from occlusions in cerebral penetrating arteriole trees (Yidan Xue, Theodosia Georgakopoulou, Anne-Eva van der Wijk, Tamás I. Józsa, Ed van Bavel, Stephen J. Payne, )
- Signal neutrality, scalar property, and collapsing boundaries as consequences of a learned multi-timescale strategy (Luca Manneschi, Guido Gigante, Eleni Vasilaki, Paolo Del Giudice, )
- Computational approach to modeling microbiome landscapes associated with chronic human disease progression (Lu Li, Jiho Sohn, Robert J. Genco, Jean Wactawski-Wende, Steve Goodison, Patricia I. Diaz, Yijun Sun, )
BMC Bioinformatics
- An optimal variant to gene distance window derived from an empirical definition of cis and trans protein QTLs (Eric B. Fauman and Craig Hyde, )
- Sparse sliced inverse regression for high dimensional data analysis (Haileab Hilafu and Sandra E. Safo, )
- HGGA: hierarchical guided genome assembler (Riku Walve and Leena Salmela, )
- SPINNAKER: an R-based tool to highlight key RNA interactions in complex biological networks (Paola Paci and Giulia Fiscon, )
- RSNET: inferring gene regulatory networks by a redundancy silencing and network enhancement technique (Xiaohan Jiang and Xiujun Zhang, )
- CircMiMi: a stand-alone software for constructing circular RNA-microRNA-mRNA interactions across species (Tai-Wei Chiang, Te-Lun Mai and Trees-Juen Chuang, )
- A novel approach to predicting the synergy of anti-cancer drug combinations using document-based feature extraction (Yongsun Shim, Munhwan Lee, Pil-Jong Kim and Hong-Gee Kim, )
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
- Autoantibody mimicry of hormone action at the thyrotropin receptor (Bryan Faust, Christian B. Billesbølle, Carl-Mikael Suomivuori, Isha Singh, Kaihua Zhang, Nicholas Hoppe, Antonio F. M. Pinto, Jolene K. Diedrich, Yagmur Muftuoglu, Mariusz W. Szkudlinski, Alan Saghatelian, Ron O. Dror, Yifan Cheng, Aashish Manglik, )
- Diverse Tsunamigenesis Triggered by the Hunga Tonga-Hunga Ha’apai Eruption (Patrick Lynett, Maile McCann, Zili Zhou, Willington Renteria, Jose Borrero, Dougal Greer, Ofa Fa’anunu, Cyprien Bosserelle, Bruce Jaffe, SeanPaul La Selle, Andrew Ritchie, Alexander Snyder, Brandon Nasr, Jacqueline Bott, Nicholas Graehl, Costas Synolakis,, )
- Hormone- and antibody-mediated activation of the thyrotropin receptor (Jia Duan, Peiyu Xu, Xiaodong Luan, Yujie Ji, Xinheng He, Ning Song, Qingning Yuan, Ye Jin, Xi Cheng, Hualiang Jiang, Jie Zheng, Shuyang Zhang, Yi Jiang, H. Eric Xu, )
- Author Correction: An open science study of ageing in companion dogs (Kate E. Creevy, Joshua M. Akey, Matt Kaeberlein, Daniel E. L. Promislow, Brian G. Barnett, Brooke Benton, Elhanan Borenstein, Marta G. Castelhano, Lucy Chou, Devin Collins, Amanda E. Coleman, Kyle Crowder, Matthew D. Dunbar, Jeremy Evans, Virginia R. Fajt, )
- Cancer cells hijack nerve cells to storm through the brain ()
- Potato-gene wrangler (Virginia Gewin, )
- DOCK2 is involved in the host genetics and biology of severe COVID-19 (Ho Namkoong, Ryuya Edahiro, Tomomi Takano, Hiroshi Nishihara, Yuya Shirai, Kyuto Sonehara, Hiromu Tanaka, Shuhei Azekawa, Yohei Mikami, Ho Lee, Takanori Hasegawa, Koji Okudela, Daisuke Okuzaki, Daisuke Motooka, Masahiro Kanai, Tatsuhiko Naito, Kenichi Yam, )
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
- TT-Mars: structural variants assessment based on haplotype-resolved assemblies (Jianzhi Yang and Mark J.P. Chaisson, )
- Enhancer transcription detected in the nascent transcriptomic landscape of bread wheat (Yilin Xie, Yan Chen, Zijuan Li, Jiafu Zhu, Min Liu, Yijing Zhang and Zhicheng Dong, )
- Systematic evaluation of colorectal cancer organoid system by single-cell RNA-Seq analysis (Rui Wang, Yunuo Mao, Wendong Wang, Xin Zhou, Wei Wang, Shuai Gao, Jingyun Li, Lu Wen, Wei Fu and Fuchou Tang, )
- DeepRepeat: direct quantification of short tandem repeats on signal data from nanopore sequencing (Li Fang, Qian Liu, Alex Mas Monteys, Pedro Gonzalez-Alegre, Beverly L. Davidson and Kai Wang, )
- Author Correction: Mutational signatures reveal the role of RAD52 in p53-independent p21-driven genomic instability (Panagiotis Galanos, George Pappas, Alexander Polyzos, Athanassios Kotsinas, Ioanna Svolaki, Nickolaos N. Giakoumakis, Christina Glytsou, Ioannis S. Pateras, Umakanta Swain, Vassilis L. Souliotis, Alexandros G. Georgakilas, Nicholas Geacintov, Luca Scorran, )
- Comprehensive enhancer-target gene assignments improve gene set level interpretation of genome-wide regulatory data (Tingting Qin, Christopher Lee, Shiting Li, Raymond G. Cavalcante, Peter Orchard, Heming Yao, Hanrui Zhang, Shuze Wang, Snehal Patil, Alan P. Boyle and Maureen A. Sartor, )
- Predicting RNA splicing from DNA sequence using Pangolin (Tony Zeng and Yang I Li, )