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
- Cognitive workload evaluation of landmarks and routes using virtual reality (Usman Alhaji Abdurrahman, Lirong Zheng, Shih-Ching Yeh, )
- Evolution of tunnels in α/β-hydrolase fold proteins—What can we learn from studying epoxide hydrolases? (Maria Bzówka, Karolina Mitusińska, Agata Raczyńska, Tomasz Skalski, Aleksandra Samol, Weronika Bagrowska, Tomasz Magdziarz, Artur Góra, )
- A molecular view of amyotrophic lateral sclerosis through the lens of interaction network modules (Klaus Højgaard Jensen, Anna Katharina Stalder, Rasmus Wernersson, Tim-Christoph Roloff-Handschin, Daniel Hvidberg Hansen, Peter M. A. Groenen, )
- A custom ddPCR method for the detection of copy number variations in the nebulin triplicate region (Lydia Sagath, Vilma-Lotta Lehtokari, Carina Wallgren-Pettersson, Katarina Pelin, Kirsi Kiiski, )
- A model for isoform-level differential expression analysis using RNA-seq data without pre-specifying isoform structure (Yang Liu, Junying Wang, Song Wu, Jie Yang, )
- Robust inference of bi-directional causal relationships in presence of correlated pleiotropy with GWAS summary data (Haoran Xue, Wei Pan, )
- Annotating functional effects of non-coding variants in neuropsychiatric cell types by deep transfer learning (Boqiao Lai, Sheng Qian, Hanwei Zhang, Siwei Zhang, Alena Kozlova, Junbao Duan, Jinbo Xu, Xin He, )
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
- A LAMP sequencing approach for high-throughput co-detection of SARS-CoV-2 and influenza virus in human saliva ()
- The modulatory role of ions in stem cell transcriptome dynamics by regulating lineage-specific gene expression patterns ()
- Single cell RNA sequencing uncovers new mechanisms of heart disease ()
- ICARUS – an interactive web server for single cell RNA-seq analysis ()
- IMGG – integrating multiple single-cell datasets through connected graphs and generative adversarial networks ()
- Methylation of tRNA-derived fragments regulates gene-silencing activity in bladder cancer ()
- Upcoming Webinar – Cancer Cell Metastases: Understanding the Process Using Insights from Single Cell Sequencing ()
- Halo-seq – An RNA proximity labeling method for the isolation and analysis of subcellular RNA populations ()
Bioinformatics
- Building alternative consensus trees and supertrees using k-means and Robinson and Foulds distance ()
- PersonaDrive: A Method for the Identification and Prioritization of Personalized Cancer Drivers ()
- Kinetochore tracking in 3D from lattice light sheet imaging data with KiT ()
- CURC: A CUDA-based reference-free read compressor ()
- An R package VIGoR for joint estimation of multiple linear learners with variational Bayesian inference ()
- InterPepScore: A Deep Learning Score for Improving the FlexPepDock Refinement Protocol ()
- Assessing and assuring interoperability of a genomics file format ()
PLoS Computational Biology
- Evolution of tunnels in α/β-hydrolase fold proteins—What can we learn from studying epoxide hydrolases? (Maria Bzówka, Karolina Mitusińska, Agata Raczyńska, Tomasz Skalski, Aleksandra Samol, Weronika Bagrowska, Tomasz Magdziarz, Artur Góra, )
- Correlations from structure and phylogeny combine constructively in the inference of protein partners from sequences (Andonis Gerardos, Nicola Dietler, Anne-Florence Bitbol, )
- Appropriate relaxation of non-pharmaceutical interventions minimizes the risk of a resurgence in SARS-CoV-2 infections in spite of the Delta variant (Wadim Koslow, Martin J. Kühn, Sebastian Binder, Margrit Klitz, Daniel Abele, Achim Basermann, Michael Meyer-Hermann, )
- Annotating functional effects of non-coding variants in neuropsychiatric cell types by deep transfer learning (Boqiao Lai, Sheng Qian, Hanwei Zhang, Siwei Zhang, Alena Kozlova, Junbao Duan, Jinbo Xu, Xin He, )
- Predicting knee adduction moment response to gait retraining with minimal clinical data (Nataliya Rokhmanova, Katherine J. Kuchenbecker, Peter B. Shull, Reed Ferber, Eni Halilaj, )
- Accurate, high-coverage assignment of in vivo protein kinases to phosphosites from in vitro phosphoproteomic specificity data (Brandon M. Invergo, )
- CrowdGO: Machine learning and semantic similarity guided consensus Gene Ontology annotation (Maarten J. M. F. Reijnders, Robert M. Waterhouse, )
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
- Limited cross-variant immunity from SARS-CoV-2 Omicron without vaccination (Rahul K. Suryawanshi, Irene P. Chen, Tongcui Ma, Abdullah M. Syed, Noah Brazer, Prachi Saldhi, Camille R. Simoneau, Alison Ciling, Mir M. Khalid, Bharath Sreekumar, Pei-Yi Chen, G. Renuka Kumar, Mauricio Montano, Ronne Gascon, Chia-Lin Tsou, Miguel A. Gar, )
- Spillover threats, Moon quest — the week in infographics ()
- Parasite names, mouse rejuvenation and toxic sunscreen ()
- Science in Africa: lessons from the COVID-19 pandemic (Dom Byrne, )
- The pandemic’s true health cost: how much of our lives has COVID stolen? (Holly Else, )
- One statistical analysis must not rule them all (Eric-Jan Wagenmakers, Alexandra Sarafoglou, Balazs Aczel, )
- Structural insights into the HBV receptor and bile acid transporter NTCP (Jae-Hyun Park, Masashi Iwamoto, Ji-Hye Yun, Tomomi Uchikubo-Kamo, Donghwan Son, Zeyu Jin, Hisashi Yoshida, Mio Ohki, Naito Ishimoto, Kenji Mizutani, Mizuki Oshima, Masamichi Muramatsu, Takaji Wakita, Mikako Shirouzu, Kehong Liu, Tomoko Uemura, Norimichi N, )
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, )