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
- Maternal immune activation induces methylation changes in schizophrenia genes (Thomas Johnson, Defne Saatci, Lahiru Handunnetthi, )
- Audit lead selection and yield prediction from historical tax data using artificial neural networks (Trevor Chan, Cheng-En Tan, Ilias Tagkopoulos, )
- Optimized conditions for Listeria, Salmonella and Escherichia whole genome sequencing using the Illumina iSeq100 platform with point-and-click bioinformatic analysis (Sonsiray Alvarez Narvaez, Zhenyu Shen, Lifang Yan, Brianna L. S. Stenger, Laura B. Goodman, Ailam Lim, Ruth H. Nissly, Meera Surendran Nair, Shuping Zhang, Susan Sanchez, )
- Sampling effects and measurement overlap can bias the inference of neuronal avalanches (Joao Pinheiro Neto, F. Paul Spitzner, Viola Priesemann, )
- Increasing plant group productivity through latent genetic variation for cooperation (Samuel E. Wuest, Nuno D. Pires, Shan Luo, Francois Vasseur, Julie Messier, Ueli Grossniklaus, Pascal A. Niklaus, )
- Multicenter evaluation of the GenomEra SARS-CoV-2 assay kit (Mika Lång, Annika Allard, Soile Blomqvist, Irmeli Iranto, Tytti Vuorinen, Antti-Heikki Tapio, Jiri Vainio, )
- A stochastic numerical approach for a class of singular singularly perturbed system (Zulqurnain Sabir, Thongchai Botmart, Muhammad Asif Zahoor Raja, Wajaree Weera, Fevzi Erdoğan, )
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
- scRNA-Seq analysis reveals that the cells regulating blood stem cell maintenance are more diverse than expected ()
- Kodoja – a workflow for virus detection in plants using k-mer analysis of RNA-sequencing data ()
- Live-seq – sequencing a cell without killing it ()
- CellRegMap – a statistical framework for mapping context-specific regulatory variants using scRNA-seq ()
- TGIRT sequencing reveals abundant non-microRNA-small RNAs in BLCA tumor samples ()
- totRNAseq – high-throughput muscle fiber typing from RNA sequencing data ()
- THRONE – a new approach for accurate prediction of human RNA N7-methylguanosine sites ()
- Pan-cancer single-cell RNA-sequencing analysis reveals cancer cell states recur across tumor types ()
Bioinformatics
- SCExecute: custom cell barcode-stratified analyses of scRNA-seq data ()
- Systematic identification of biochemical networks in cancer cells by Functional Pathway Inference Analysis ()
- PoDCall: positive droplet calling and normalisation of droplet digital PCR DNA methylation data ()
- Unbiased pangenome graphs ()
- Active Learning for Efficient Analysis of High-throughput Nanopore Data ()
- dnadna: a deep learning framework for population genetics inference ()
- Distinguishing imported cases from locally acquired cases within a geographically limited genomic sample of an infectious disease ()
PLoS Computational Biology
- Modelling the synergistic effect of bacteriophage and antibiotics on bacteria: Killers and drivers of resistance evolution (Quentin J. Leclerc, Jodi A. Lindsay, Gwenan M. Knight, )
- Optimized phylogenetic clustering of HIV-1 sequence data for public health applications (Connor Chato, Yi Feng, Yuhua Ruan, Hui Xing, Joshua Herbeck, Marcia Kalish, Art F. Y. Poon, )
- Cluster detection with random neighbourhood covering: Application to invasive Group A Streptococcal disease (Massimo Cavallaro, Juliana Coelho, Derren Ready, Valerie Decraene, Theresa Lamagni, Noel D. McCarthy, Dan Todkill, Matt J. Keeling, )
- Tracking human skill learning with a hierarchical Bayesian sequence model (Noémi Éltető, Dezső Nemeth, Karolina Janacsek, Peter Dayan, )
- Sampling effects and measurement overlap can bias the inference of neuronal avalanches (Joao Pinheiro Neto, F. Paul Spitzner, Viola Priesemann, )
- Efficient inference and identifiability analysis for differential equation models with random parameters (Alexander P. Browning, Christopher Drovandi, Ian W. Turner, Adrianne L. Jenner, Matthew J. Simpson, )
- Role of path information in visual perception of joint stiffness (A. Michael West Jr., Meghan E. Huber, Neville Hogan, )
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
- Publisher Correction: Distinguishing externally from saccade-induced motion in visual cortex (Satoru K. Miura, Massimo Scanziani, )
- Publisher Correction: A brainstem map for visceral sensations (Chen Ran, Jack C. Boettcher, Judith A. Kaye, Catherine E. Gallori, Stephen D. Liberles, )
- Soaring energy costs mean we are using less — but for how long? (Heidi Ledford, )
- Violent conservation, and your brain on magic: Books in brief (Andrew Robinson, )
- Conflict resolution (Holly Schofield, )
- Charge dropped against New Zealand science agency after deadly volcano eruption (Dyani Lewis, )
- Surprise! The UK is spending way more on research than it thought (Holly Else, )
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, )