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
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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
- Phenotypic and transcriptomic responses of cultivated sunflower seedlings (Helianthus annuus L.) to four abiotic stresses (Max H. Barnhart, Rishi R. Masalia, Liana J. Mosley, John M. Burke, )
- HAYSTAC: A Bayesian framework for robust and rapid species identification in high-throughput sequencing data (Evangelos A. Dimopoulos, Alberto Carmagnini, Irina M. Velsko, Christina Warinner, Greger Larson, Laurent A. F. Frantz, Evan K. Irving-Pease, )
- A transcriptome-wide association study of uterine fibroids to identify potential genetic markers and toxic chemicals (Gayeon Kim, Gyuyeon Jang, Jaeseung Song, Daeun Kim, Sora Lee, Jong Wha J. Joo, Wonhee Jang, )
- MetaWorks: A flexible, scalable bioinformatic pipeline for high-throughput multi-marker biodiversity assessments (Teresita M. Porter, Mehrdad Hajibabaei, )
- Aging-regulated TUG1 is dispensable for endothelial cell function (Anna Theresa Gimbel, Susanne Koziarek, Kosta Theodorou, Jana Felicitas Schulz, Laura Stanicek, Veerle Kremer, Tamer Ali, Stefan Günther, Sandeep Kumar, Hanjoong Jo, Norbert Hübner, Lars Maegdefessel, Stefanie Dimmeler, Sebastiaan van Heesch, Reinier A. Bo, )
- GWAS in the southern African context (Yolandi Swart, Gerald van Eeden, Caitlin Uren, Gian van der Spuy, Gerard Tromp, Marlo Möller, )
- Prostaglandins and calprotectin are genetically and functionally linked to the Inflammatory Bowel Diseases (Mohamad Karaky, Gabrielle Boucher, Saraï Mola, Sylvain Foisy, Claudine Beauchamp, Marie-Eve Rivard, Melanie Burnette, Hugues Gosselin, iGenoMed Consortium, Alain Bitton, Guy Charron, Philippe Goyette, John D. Rioux, )
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
- WMSA: a novel method for multiple sequence alignment of DNA sequences ()
- GeneNetTools: Tests for Gaussian graphical models with shrinkage ()
- GBZ File Format for Pangenome Graphs ()
- Integrating Phylogenetic and Functional Data in Microbiome Studies ()
- CITEdb: a manually curated database of cell-cell interactions in human ()
- Top-Down Crawl: A method for the ultra-rapid and motif-free alignment of sequences with associated binding metrics ()
- mHapTk: A comprehensive toolkit for the analysis of DNA methylation haplotypes ()
PLoS Computational Biology
- Computational multiplex panel reduction to maximize information retention in breast cancer tissue microarrays (Luke Ternes, Jia-Ren Lin, Yu-An Chen, Joe W. Gray, Young Hwan Chang, )
- HAYSTAC: A Bayesian framework for robust and rapid species identification in high-throughput sequencing data (Evangelos A. Dimopoulos, Alberto Carmagnini, Irina M. Velsko, Christina Warinner, Greger Larson, Laurent A. F. Frantz, Evan K. Irving-Pease, )
- A hierarchical process model links behavioral aging and lifespan in C. elegans (Natasha Oswal, Olivier M. F. Martin, Sofia Stroustrup, Monika Anna Matusiak Bruckner, Nicholas Stroustrup, )
- Individualised computational modelling of immune mediated disease onset, flare and clearance in psoriasis (Fedor Shmarov, Graham R. Smith, Sophie C. Weatherhead, Nick J. Reynolds, Paolo Zuliani, )
- Modeling enculturated bias in entrainment to rhythmic patterns (Thomas Kaplan, Jonathan Cannon, Lorenzo Jamone, Marcus Pearce, )
- Generative and interpretable machine learning for aptamer design and analysis of in vitro sequence selection (Andrea Di Gioacchino, Jonah Procyk, Marco Molari, John S. Schreck, Yu Zhou, Yan Liu, Rémi Monasson, Simona Cocco, Petr Šulc, )
- Estimation of the firing behaviour of a complete motoneuron pool by combining electromyography signal decomposition and realistic motoneuron modelling (Arnault H. Caillet, Andrew T. M. Phillips, Dario Farina, Luca Modenese, )
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
- Why scientists fear monkeypox spreading in wild animals (Emiliano Rodríguez Mega, )
- Will Nord Stream methane leaks make climate change worse? (Katharine Sanderson, )
- Audio long read: What scientists have learnt from COVID lockdowns (Dyani Lewis, Benjamin Thompson, )
- Genes’ effect on lifespan depends on sex and age, mouse study finds (Liam Drew, )
- Stroke genetics informs drug discovery and risk prediction across ancestries (Aniket Mishra, Rainer Malik, Tsuyoshi Hachiya, Tuuli Jürgenson, Shinichi Namba, Daniel C. Posner, Frederick K. Kamanu, Masaru Koido, Quentin Le Grand, Mingyang Shi, Yunye He, Marios K. Georgakis, Ilana Caro, Kristi Krebs, Yi-Ching Liaw, Felix C. Vaura, Ku, )
- Floods, fires and fluorescent fish — September’s best science images (Emma Stoye, )
- What Italy’s far-right election victory means for science (Giorgia Guglielmi, )
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, )