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
- Transcriptome analysis indicates dominant effects on ribosome and mitochondrial function of a premature termination codon mutation in the zebrafish gene psen2 (Haowei Jiang, Stephen Martin Pederson, Morgan Newman, Yang Dong, Karissa Barthelson, Michael Lardelli, )
- Assessing the performance of methods for copy number aberration detection from single-cell DNA sequencing data (Xian F. Mallory, Mohammadamin Edrisi, Nicholas Navin, Luay Nakhleh, )
- Whole cell biophysical modeling of codon-tRNA competition reveals novel insights related to translation dynamics (Doron Levin, Tamir Tuller, )
- Investigation of singular ordinary differential equations by a neuroevolutionary approach (Waseem Waseem, Muhammad Sulaiman, Poom Kumam, Muhammad Shoaib, Muhammad Asif Zahoor Raja, Saeed Islam, )
- Evaluation of variant calling for cpn60 barcode sequence-based microbiome profiling (Sarah J. Vancuren, Scott J. Dos Santos, Janet E. Hill, the Maternal Microbiome Legacy Project Team, )
- UFO: A tool for unifying biomedical ontology-based semantic similarity calculation, enrichment analysis and visualization (Duc-Hau Le, )
- Impact of insertion sequences on convergent evolution of Shigella species (Jane Hawkey, Jonathan M. Monk, Helen Billman-Jacobe, Bernhard Palsson, Kathryn E. Holt, )
BMC Genomics
- Genome analyses provide insights into the evolution and adaptation of the eukaryotic Picophytoplankton Mychonastes homosphaera (Changqing Liu, Xiaoli Shi, Fan Wu, Mingdong Ren, Guang Gao and Qinglong Wu, )
- Detecting fitness epistasis in recently admixed populations with genome-wide data (Xumin Ni, Mengshi Zhou, Heming Wang, Karen Y. He, Uli Broeckel, Craig Hanis, Sharon Kardia, Susan Redline, Richard S. Cooper, Hua Tang and Xiaofeng Zhu, )
- RNA-Seq transcriptome reveals different molecular responses during human and mouse oocyte maturation and fertilization (Zheng-Hui Zhao, Tie-Gang Meng, Ang Li, Heide Schatten, Zhen-Bo Wang and Qing-Yuan Sun, )
- Genome-wide identification and transcript profiles of walnut heat stress transcription factor involved in abiotic stress (Xuejiao Liu, Panpan Meng, Guiyan Yang, Mengyan Zhang, Shaobing Peng and Mei Zhi Zhai, )
- Quantitative characterization of tumor cell-free DNA shortening (Juntang Guo, Kefeng Ma, Hua Bao, Xiangyuan Ma, Yang Xu, Xue Wu, Yang W. Shao, Mei Jiang and Jin Huang, )
- VviERF6Ls: an expanded clade in Vitis responds transcriptionally to abiotic and biotic stresses and berry development (Haley S. Toups, Noé Cochetel, Dennis Gray and Grant R. Cramer, )
- Comparative analysis of single-cell transcriptomics in human and Zebrafish oocytes (Handan Can, Sree K. Chanumolu, Elena Gonzalez-Muñoz, Sukumal Prukudom, Hasan H. Otu and Jose B. Cibelli, )
RNA-Seq Blog
- ICRNASGE 2020: 14 – International Conference on RNA Sequencing and Gene Expression ()
- Single-cell RNA sequencing outlines the immune landscape of severe COVID-19 ()
- Methodologies for transcript profiling using long-read technologies ()
- scRNA-seq of glioblastoma complexity reveals its pattern of development ()
- Cell-free DNA and cell-free RNA NGS liquid biopsy technology can guide treatment for most aggressive prostate cancer ()
- St. Jude researchers integrate WGS and RNA-Seq to create an analytic tool that opens a new frontier of cancer discovery ()
- Comparison of high-throughput single-cell RNA sequencing data processing pipelines ()
- ACME dissociation – a versatile cell fixation-dissociation method for single-cell transcriptomics ()
Bioinformatics
- RTExtract: Time-series NMR spectra quantification based on 3D surface ridge tracking ()
- Predicting mechanism of action of cellular perturbations with pathway activity signatures ()
- Automatic classification of single-molecule force spectroscopy traces from heterogeneous samples ()
- Adaptive Multi-Orientation Resolution Analysis of Complex Filamentous Network Images ()
- RecBic: a fast and accurate algorithm recognizing trend-preserving biclusters ()
- DNA Chisel, a versatile sequence optimizer ()
- Exploring generative deep learning for omics data by using log-linear models ()
PLoS Computational Biology
- Heart failure-induced atrial remodelling promotes electrical and conduction alternans (Na Zhao, Qince Li, Kevin Zhang, Kuanquan Wang, Runnan He, Yongfeng Yuan, Henggui Zhang, )
- Assessing the performance of methods for copy number aberration detection from single-cell DNA sequencing data (Xian F. Mallory, Mohammadamin Edrisi, Nicholas Navin, Luay Nakhleh, )
- Heterogeneous, delayed-onset killing by multiple-hitting T cells: Stochastic simulations to assess methods for analysis of imaging data (Richard J. Beck, Dario I. Bijker, Joost B. Beltman, )
- Unravelling the γ-butyrolactone network in Streptomyces coelicolor by computational ensemble modelling (Areti Tsigkinopoulou, Eriko Takano, Rainer Breitling, )
- Whole cell biophysical modeling of codon-tRNA competition reveals novel insights related to translation dynamics (Doron Levin, Tamir Tuller, )
- The interplay between somatic and dendritic inhibition promotes the emergence and stabilization of place fields (Victor Pedrosa, Claudia Clopath, )
- AncesTree: An interactive immunoglobulin lineage tree visualizer (Mathilde Foglierini, Leontios Pappas, Antonio Lanzavecchia, Davide Corti, Laurent Perez, )
BMC Bioinformatics
- Keras R-CNN: library for cell detection in biological images using deep neural networks (Jane Hung, Allen Goodman, Deepali Ravel, Stefanie C. P. Lopes, Gabriel W. Rangel, Odailton A. Nery, Benoit Malleret, Francois Nosten, Marcus V. G. Lacerda, Marcelo U. Ferreira, Laurent Rénia, Manoj T. Duraisingh, Fabio T. M. Costa, Matthias Marti and Anne, )
- Leveraging Bayesian networks and information theory to learn risk factors for breast cancer metastasis (Xia Jiang, Alan Wells, Adam Brufsky, Darshan Shetty, Kahmil Shajihan and Richard E. Neapolitan, )
- Escher-Trace: a web application for pathway-based visualization of stable isotope tracing data (Avi Kumar, Jack Mitchener, Zachary A. King and Christian M. Metallo, )
- Efficient implied alignment (Alex J. Washburn and Ward C. Wheeler, )
- SOAPTyping: an open-source and cross-platform tool for sequence-based typing for HLA class I and II alleles (Yong Zhang, Yongsheng Chen, Huixin Xu, Junbin Fang, Zijian Zhao, Weipeng Hu, Xiaoqin Yang, Jia Ye, Yun Cheng, Jiayin Wang, Weiqiang Sun, Jian Wang, Huanming Yang, Jing Yan and Lin Fang, )
- SLFinder, a pipeline for the novel identification of splice-leader sequences: a good enough solution for a complex problem (Javier Calvelo, Hernán Juan, Héctor Musto, Uriel Koziol and Andrés Iriarte, )
- Bioinformatics recipes: creating, executing and distributing reproducible data analysis workflows (Natay Aberra, Aswathy Sebastian, Aaron P. Maloy, Christopher B. Rees, Meredith L. Bartron and Istvan Albert, )
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
- The four pillars of a successful science spin-off company (Barbara Domayne-Hayman, )
- Pangolin protectors, an inflatable lab and young stars — June’s best science images (Emma Stoye, )
- A perspective on potential antibody-dependent enhancement of SARS-CoV-2 (Ann M. Arvin, Katja Fink, Michael A. Schmid, Andrea Cathcart, Roberto Spreafico, Colin Havenar-Daughton, Antonio Lanzavecchia, Davide Corti, Herbert W. Virgin, )
- How scientific societies are weathering the pandemic’s financial storm (Diana Kwon, )
- Remote controller (Virginia Gewin, )
- Scientists call for pandemic investigations to focus on wildlife trade (Smriti Mallapaty, )
- Pandemic speeds largest test yet of universal basic income (Carrie Arnold, )
Science
- Teeth and jaws (Vignieri, S., )
- Engineering a toxin (Vinson, V., )
- Conserved redox regulation of kinases (Ferrarelli, L. K., )
- Beneficial bioartificial livers (Czajka, C., )
- An inherited disorder makes WAVEs (Scanlon, S. T., )
- Strongly coupled at distance (Osborne, I. S., )
- Food for thought (Smith, H. J., )
PNAS
- A systems approach delivers a functional microRNA catalog and expanded targets for seizure suppression in temporal lobe epilepsy [Neuroscience] (Morten T. Veno, Cristina R. Reschke, Gareth Morris, Niamh M. C. Connolly, Junyi Su, Yan Yan, Tobias Engel, Eva M. Jimenez–Mateos, Lea M. Harder, Dennis Pultz, Stefan J. Haunsberger, Aȷay Pal, Janosch P. Heller, Aoife Campbell, Elena Langa, Ga, )
- Cyclic GMP-AMP synthase promotes the inflammatory and autophagy responses in Huntington disease [Neuroscience] (Manish Sharma, Sumitha Raȷendrarao, Neelam Shahani, Uri Nimrod Ramirez–Jarquin, Srinivasa Subramaniam, )
- The role of carbonic anhydrases in extinction of contextual fear memory [Pharmacology] (Scheila Daiane Schmidt, Alessia Costa, Barbara Rani, Eduarda Godfried Nachtigall, Maria Beatrice Passani, Fabrizio Carta, Alessio Nocentini, Jociane de Carvalho Myskiw, Cristiane Regina Guerino Furini, Claudiu T. Supuran, Ivan Izquierdo, Patrizio Blandina, )
- Bacterial metabolism rescues the inhibition of intestinal drug absorption by food and drug additives [Pharmacology] (Ling Zou, Peter Spanogiannopoulos, Lindsey M. Pieper, Huan-Chieh Chien, Wenlong Cai, Natalia Khuri, Joshua Pottel, Bianca Vora, Zhanglin Ni, Eleftheria Tsakalozou, Wenjun Zhang, Brian K. Shoichet, Kathleen M. Giacomini, Peter J. Turnbaugh, )
- Real-time monitoring of the in vivo redox state transition using the ratiometric redox state sensor protein FROG/B [Plant Biology] (Kazunori Sugiura, Shoko Mihara, Nae Fu, Toru Hisabori, )
- Fluctuating auxin response gradients determine pavement cell-shape acquisition [Plant Biology] (Peter Grones, Mateusz Maȷda, Siamsa M. Doyle, Daniel Van Damme, Stephanie Robert, )
- Snapping mechanics of the Venus flytrap (Dionaea muscipula) [Plant Biology] (Renate Sachse, Anna Westermeier, Max Mylo, Joey Nadasdi, Manfred Bischoff, Thomas Speck, Simon Poppinga, )
Genome Biology
- DISC: a highly scalable and accurate inference of gene expression and structure for single-cell transcriptomes using semi-supervised deep learning (Yao He, Hao Yuan, Cheng Wu and Zhi Xie, )
- Genome-wide studies reveal the essential and opposite roles of ARID1A in controlling human cardiogenesis and neurogenesis from pluripotent stem cells (Juli Liu, Sheng Liu, Hongyu Gao, Lei Han, Xiaona Chu, Yi Sheng, Weinian Shou, Yue Wang, Yunlong Liu, Jun Wan and Lei Yang, )
- Genes adapt to outsmart gene-targeting strategies in mutant mouse strains by skipping exons to reinitiate transcription and translation (Vishnu Hosur, Benjamin E. Low, Daniel Li, Grace A. Stafford, Vivek Kohar, Leonard D. Shultz and Michael V. Wiles, )
- Sierra: discovery of differential transcript usage from polyA-captured single-cell RNA-seq data (Ralph Patrick, David T. Humphreys, Vaibhao Janbandhu, Alicia Oshlack, Joshua W.K. Ho, Richard P. Harvey and Kitty K. Lo, )
- Dysregulation of cancer genes by recurrent intergenic fusions (Jae Won Yun, Lixing Yang, Hye-Young Park, Chang-Woo Lee, Hongui Cha, Hyun-Tae Shin, Ka-Won Noh, Yoon-La Choi, Woong-Yang Park and Peter J. Park, )
- The regulatory landscape of early maize inflorescence development (Rajiv K. Parvathaneni, Edoardo Bertolini, Md Shamimuzzaman, Daniel L. Vera, Pei-Yau Lung, Brian R. Rice, Jinfeng Zhang, Patrick J. Brown, Alexander E. Lipka, Hank W. Bass and Andrea L. Eveland, )
- Exploring neighborhoods in large metagenome assembly graphs using spacegraphcats reveals hidden sequence diversity (C. Titus Brown, Dominik Moritz, Michael P. O’Brien, Felix Reidl, Taylor Reiter and Blair D. Sullivan, )