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
- Iron-mediated post-transcriptional regulation in Toxoplasma gondii (Megan A. Sloan, Adam Scott, Dana Aghabi, Lucia Mrvova, Clare R. Harding, )
- A CACTA-like transposon in the Anthocyanidin synthase 1 (Ans-1) gene is responsible for apricot fruit colour in the raspberry (Rubus idaeus) cultivar ‘Varnes’ (Daniel James Sargent, Matteo Buti, Stefan Martens, Claudio Pugliesi, Kjersti Aaby, Dag Røen, Chandra Bhan Yadav, Felicidad Fernández Fernández, Muath Alsheikh, Jahn Davik, R. Jordan Price, )
- Uncovering the genetic basis of milk production traits in Mexican Holstein cattle based on individual markers and genomic windows (José G. Cortes-Hernández, Adriana García-Ruiz, Francisco Peñagaricano, Hugo H. Montaldo, Felipe J. Ruiz-López, )
- A machine learning driven computationally efficient horse shoe shaped antenna design for internet of medical things (Umhara Rasool Khan, Javaid A. Sheikh, Aqib Junaid, Shazia Ashraf, Altaf A. Balkhi, )
- Integrative analysis of the metabolome and transcriptome provides insights into the mechanisms of flavonoid biosynthesis in Polygonatum (Xiaolin Wan, Qiang Xiao, )
- Computational and In silico study of novel fungicides against combating root rot, gray mold, fusarium wilt, and cereal rust (Mollah Naimuzzaman, Md Mahabub Hasan, Ajoy Kumer, Abu Yousuf Hossin, Mohammad Harun-Ur-Rashid, Swapan Kumar Roy, Abu Noman Faruq Ahmmed, Jamal Uddin, )
- Potential Azo-8-hydroxyquinoline derivatives as multi-target lead candidates for Alzheimer’s disease: An in-depth in silico study of monoamine oxidase and cholinesterase inhibitors (Fatima Zahra Guerguer, Bouchra Rossafi, Oussama Abchir, Yasir S. Raouf, Dhabya Bakhit Albalushi, Abdelouahid Samadi, Samir Chtita, )
BMC Genomics
- Detecting and characterizing copy number variation in a large commercial U.S. Holstein cattle population (Giovanni C. Ladeira, Pablo J. Pinedo, José E. P. Santos, William W. Thatcher and Fernanda M. Rezende, )
- A detailed transcriptome study uncovers the epigenetic characteristics associated with Aromatase inhibitor-induced masculinization in Takifugu rubripes larvae gonads (Xufang Shen, Hongwei Yan, Mingtao Hu, Huiting Zhou, Qi Zhang, Rui Gao, Qi Liu and Qunwen Sun, )
- Optimizing Cost-Effective gene expression phenotyping approaches in cattle using 3′ mRNA sequencing (Ruwaa I. Mohamed, Taylor B. Ault-Seay, Sonia J. Moisá, Jonathan E. Beever, Agustín G. Ríus and Troy N. Rowan, )
- Design and verification of a 25 K multiple-SNP liquid-capture chip by target sequencing for dairy goat (Jianqing Zhao, Yaling Wang, Jiayidaer Kamalibieke, Ping Gong, Fuhong Zhang, Huaiping Shi, Wei Wang and Jun Luo, )
- Fine mapping and candidate gene analysis of major QTLs for number of seeds per pod in Arachis hypogaea L. (Long Li, Shunli Cui, Xiukun Li, Mingyu Hou, Yingru Liu and Lifeng Liu, )
- Dynamic transcriptome and metabolome analyses of two sweet corn lines under artificial aging treatment (Zili Zhang, Ruichun Yang, Lei Gao, Shilin Huang, Feng Jiang, Qingchun Chen, Pengfei Liu and Faqiang Feng, )
- Direct RNA sequencing reveals chicken post-transcriptional modifications in response to Campylobacter jejuni inoculation (Yanan Zhao, Yuanmei Wang, Yanru Ren, Long Liu, Tianyi Wang, Liying Liu and Xianyao Li, )
RNA-Seq Blog
- A simplified preparation method for single-nucleus RNA-sequencing using long-term frozen brain tumor tissues ()
- Cyber-biosecurity risks threaten RNA sequencing and genomic data integrity ()
- RNA sequencing reveals ADAR1 as a key driver of lenalidomide resistance in multiple myeloma ()
- adverSCarial – assessing the vulnerability of single-cell RNA-sequencing classifiers to adversarial attacks ()
- Deep dive into plant signalling data reveals a noisy “elephant in the room” ()
- Genome Research publishes a special issue on long-read DNA and RNA sequencing applications in biology and medicine ()
- RIBOSS detects novel translational events by combining long- and short-read transcriptome and translatome profiling ()
- Identification of high-resolution gene expression atlas of woody tissue ()
Bioinformatics
- CAFE: An Integrated Web App for High-Dimensional Analysis and Visualization in Spectral Flow Cytometry ()
- Colora: A Snakemake Workflow for Complete Chromosome-scale De Novo Genome Assembly ()
- argNorm: normalization of antibiotic resistance gene annotations to the Antibiotic Resistance Ontology (ARO) ()
- A Multi-View Graph Convolutional Network Framework Based on Adaptive Adjacency Matrix and Multi-Strategy Fusion Mechanism for Identifying Spatial Domains ()
- ProtNote: a multimodal method for protein-function annotation ()
- adverSCarial: assessing the vulnerability of single-cell RNA-sequencing classifiers to adversarial attacks ()
- MS1FA: Shiny App for the Annotation of Redundant Features in Untargeted Metabolomics Datasets ()
PLoS Computational Biology
- Expression of Concern: HiSV: A control-free method for structural variation detection from Hi-C data (The PLOS Computational Biology Editors, )
- Traveling waves in the human visual cortex: An MEG-EEG model-based approach (Laetitia Grabot, Garance Merholz, Jonathan Winawer, David J. Heeger, Laura Dugué, )
- Joint estimation of hand-foot-mouth disease model and prediction in korea using the ensemble kalman filter (Wasim Abbas, Sieun Lee, Sangil Kim, )
- A spectral framework to map QTLs affecting joint differential networks of gene co-expression (Jiaxin Hu, Jesse N. Weber, Lauren E. Fuess, Natalie C. Steinel, Daniel I. Bolnick, Miaoyan Wang, )
- Eleven quick tips to unlock the power of in vivo data science (Troy J. Kieran, Taronna R. Maines, Jessica A. Belser, )
- RMPJ: An ImageJ plugin for morphological information processing in biomedical images (Yoshitaka Kimori, )
- Perceptual learning improves discrimination but does not reduce distortions in appearance (Sarit F.A. Szpiro, Charlie S. Burlingham, Eero P. Simoncelli, Marisa Carrasco, )
BMC Bioinformatics
- PRED-LD: efficient imputation of GWAS summary statistics (Georgios A. Manios, Aikaterini Michailidi, Panagiota I. Kontou and Pantelis G. Bagos, )
- DeBasher: a flow-based programming bash extension for the implementation of complex and interactive workflows with stateful processes (Daniel Ortiz-Martínez, )
- Phoenics: a novel statistical approach for longitudinal metabolomic pathway analysis (Camille Guilmineau, Marie Tremblay-Franco, Nathalie Vialaneix and Rémi Servien, )
- Redefining the high variable genes by optimized LOESS regression with positive ratio (Yue Xie, Zehua Jing, Hailin Pan, Xun Xu and Qi Fang, )
- M01 tool: an automated, comprehensive computational tool for generating small molecule-peptide hybrids and docking them into curated protein structures (Mahsa Sheikholeslami, Mohammad Hasan Nazari and Afshin Fassihi, )
- Improving data interpretability with new differential sample variance gene set tests (Yasir Rahmatallah and Galina Glazko, )
- DTreePred: an online viewer based on machine learning for pathogenicity prediction of genomic variants (Daniel Henrique Ferreira Gomes, Inácio Gomes Medeiros, Tirzah Braz Petta, Beatriz Stransky and Jorge Estefano Santana de Souza, )
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
- Author Correction: Continued Atlantic overturning circulation even under climate extremes (J. A. Baker, M. J. Bell, L. C. Jackson, G. K. Vallis, A. J. Watson, R. A. Wood, )
- Microplastic pollution found in insect casing from 1971 (Shamini Bundell, )
- The lunatic is on the grass: Books in brief (Andrew Robinson, )
- Sowing solutions: my quest to save Kenya’s maize from a devastating invader (Linda Nordling, )
- Martian rock hints at ancient dense atmosphere ()
- Exclusive: Trump team freezes new NSF awards — and could soon axe hundreds of grants (Dan Garisto, )
- Whole-genome sequencing susses out rare diseases (Amanda B. Keener, )
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
- Post-cleavage target residence determines asymmetry in non-homologous end joining of Cas12a-induced DNA double strand breaks (Ruo-Dan Chen, Yi Yang, Kun-Ming Liu, Jing-Zhen Hu, Yi-Li Feng, Chun-Yi Yang, Rui-Rui Jiang, Si-Cheng Liu, Yue Wang, Ping-An Han, Ru-Gang Tian, Yu-Long Wang, Shi-Ming Xu and An-Yong Xie, )
- Extracellular vesicle-derived miRNA-mediated cell–cell communication inference for single-cell transcriptomic data with miRTalk (Xin Shao, Lingqi Yu, Chengyu Li, Jingyang Qian, Xinyu Yang, Haihong Yang, Jie Liao, Xueru Fan, Xiao Xu and Xiaohui Fan, )
- Genomic evidence for low genetic diversity but purging of strong deleterious variants in snow leopards (Lin Yang, Hong Jin, Qien Yang, Andrey Poyarkov, Miroslav Korablev, Viatcheslav Rozhnov, Junjie Shao, Qiaomei Fu, Jose Antonio Hernandez-Blanco, Xiangjiang Zhan, Li Yu, Dmitry Alexandrov, Qingyan Dai, Bariushaa Munkhtsog, Xin Du, Bayaraa Munkhtsog…, )
- Spatiotemporal transcriptomics reveals key gene regulation for grain yield and quality in wheat (Xiaohui Li, Yiman Wan, Dongzhi Wang, Xingguo Li, Jiajie Wu, Jun Xiao, Kunming Chen, Xue Han and Yuan Chen, )
- TF Profiler: a transcription factor inference method that broadly measures transcription factor activity and identifies mechanistically distinct networks (Taylor Jones, Rutendo F. Sigauke, Lynn Sanford, Dylan J. Taatjes, Mary A. Allen and Robin D. Dowell, )
- Filtering cells with high mitochondrial content depletes viable metabolically altered malignant cell populations in cancer single-cell studies (Josephine Yates, Agnieszka Kraft and Valentina Boeva, )
- MIDAA: deep archetypal analysis for interpretable multi-omic data integration based on biological principles (Salvatore Milite, Giulio Caravagna and Andrea Sottoriva, )