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
- Position preference of essential genes in prokaryotic operons (Tao Liu, Hao Luo, Feng Gao, )
- TriatoDex, an electronic identification key to the Triatominae (Hemiptera: Reduviidae), vectors of Chagas disease: Development, description, and performance (Rodrigo Gurgel-Gonçalves, Fernando Abad-Franch, Maxwell Ramos de Almeida, Marcos Takashi Obara, Rita de Cássia Moreira de Souza, Jainaine Abrantes de Sena Batista, Douglas de Almeida Rocha, )
- Forecasting ocean acidification impacts on kelp forest ecosystems (Adam J. Schlenger, Rodrigo Beas-Luna, Richard F. Ambrose, )
- Single nucleotide polymorphisms affect miRNA target prediction in bovine (Marco Antônio Perpétuo de Sousa, Flavia Regina Florêncio de Athayde, Mariângela Bueno Cordeiro Maldonado, Andressa Oliveira de Lima, Marina Rufino S. Fortes, Flavia Lombardi Lopes, )
- The copy number variation and stroke (CaNVAS) risk and outcome study (John W. Cole, Taiwo Adigun, Rufus Akinyemi, Onoja Matthew Akpa, Steven Bell, Bowang Chen, Jordi Jimenez Conde, Uxue Lazcano Dobao, Israel Fernandez, Myriam Fornage, Cristina Gallego-Fabrega, Christina Jern, Michael Krawczak, Arne Lindgren, Hugh S. Markus,, )
- MRLocus: Identifying causal genes mediating a trait through Bayesian estimation of allelic heterogeneity (Anqi Zhu, Nana Matoba, Emma P. Wilson, Amanda L. Tapia, Yun Li, Joseph G. Ibrahim, Jason L. Stein, Michael I. Love, )
- Sequence deeper without sequencing more: Bayesian resolution of ambiguously mapped reads (Rohan N. Shah, Alexander J. Ruthenburg, )
BMC Genomics
- Comprehensive analysis and identification of drought-responsive candidate NAC genes in three semi-arid tropics (SAT) legume crops (Sadhana Singh, Himabindu Kudapa, Vanika Garg and Rajeev K. Varshney, )
- Dynamics of rumen gene expression, microbiome colonization, and their interplay in goats (Xiangyu Pan, Zongjun Li, Bibo Li, Chen Zhao, Yu Wang, Yulin Chen and Yu Jiang, )
- Variation of microRNA expression in the human placenta driven by population identity and sex of the newborn (Song Guo, Shuyun Huang, Xi Jiang, Haiyang Hu, Dingding Han, Carlos S. Moreno, Genevieve L. Fairbrother, David A. Hughes, Mark Stoneking and Philipp Khaitovich, )
- Zea mays RNA-seq estimated transcript abundances are strongly affected by read mapping bias (Shuhua Zhan, Cortland Griswold and Lewis Lukens, )
- Effects of AGXT2 variants on blood pressure and blood sugar among 750 older Japanese subjects recruited by the complete enumeration survey method (Yuta Yoshino, Hiroshi Kumon, Takaaki Mori, Taku Yoshida, Ayumi Tachibana, Hideaki Shimizu, Jun-ichi Iga and Shu-ichi Ueno, )
- Identification of the specific long-noncoding RNAs involved in night-break mediated flowering retardation in Chenopodium quinoa (Qi Wu, Yiming Luo, Xiaoyong Wu, Xue Bai, Xueling Ye, Changying Liu, Yan Wan, Dabing Xiang, Qiang Li, Liang Zou and Gang Zhao, )
- Genome-wide analysis of SET-domain group histone methyltransferases in apple reveals their role in development and stress responses (Wenjie Li, Jinjiao Yan, Shicong Wang, Qianying Wang, Caixia Wang, Zhongxing Li, Dehui Zhang, Fengwang Ma, Qingmei Guan and Jidi Xu, )
RNA-Seq Blog
- XYZeq – a better map of cell diversity ()
- Sequence deeper without sequencing more ()
- miRMaster 2.0 – multi-species non-coding RNA sequencing analyses at scale ()
- New urine-based test holds promise for detecting aggressive prostate cancer ()
- Gene expression variation in disseminated prostate cancer tumors can inform treatment ()
- ROSALIND, HELiXrUS and Geninus partner to bring powerful new single cell analysis services to cancer researchers ()
- SIS-seq – a new single cell method to understand the programming behind stem cell fate ()
- scGNN – a novel graph neural network framework for single-cell RNA-Seq analyses ()
Bioinformatics
- Integrative Survival Analysis of Breast Cancer with Gene Expression and DNA Methylation Data ()
- Bipartite graph-based approach for clustering of cell lines by gene expression-drug response associations ()
- S3V2-IDEAS: a package for normalizing, denoising and integrating epigenomic datasets across different cell types ()
- Characterizing protein conformers by cross-linking mass spectrometry and pattern recognition ()
- Normalization of single-cell RNA-seq counts by log(x + 1)* or log(1 + x)* ()
- DeepS: A web server for image optical sectioning and super resolution microscopy based on a deep learning framework ()
- Biphasic regulation of transcriptional surge generated by the gene feedback loop in a two-component system ()
PLoS Computational Biology
- Correction: An antigenic diversification threshold for falciparum malaria transmission at high endemicity (The PLOS Computational Biology Staff, )
- Vessel network extraction and analysis of mouse pulmonary vasculature via X-ray micro-computed tomographic imaging (Eric A. Chadwick, Takaya Suzuki, Michael G. George, David A. Romero, Cristina Amon, Thomas K. Waddell, Golnaz Karoubi, Aimy Bazylak, )
- Systematic comparison and prediction of the effects of missense mutations on protein-DNA and protein-RNA interactions (Yao Jiang, Hui-Fang Liu, Rong Liu, )
- The landscape of metabolic pathway dependencies in cancer cell lines (James H. Joly, Brandon T. L. Chew, Nicholas A. Graham, )
- Sequence deeper without sequencing more: Bayesian resolution of ambiguously mapped reads (Rohan N. Shah, Alexander J. Ruthenburg, )
- MAUI (MBI Analysis User Interface)—An image processing pipeline for Multiplexed Mass Based Imaging (Alex Baranski, Idan Milo, Shirley Greenbaum, John-Paul Oliveria, Dunja Mrdjen, Michael Angelo, Leeat Keren, )
- Convolutional neural networks improve species distribution modelling by capturing the spatial structure of the environment (Benjamin Deneu, Maximilien Servajean, Pierre Bonnet, Christophe Botella, François Munoz, Alexis Joly, )
BMC Bioinformatics
- FINDER: an automated software package to annotate eukaryotic genes from RNA-Seq data and associated protein sequences (Sagnik Banerjee, Priyanka Bhandary, Margaret Woodhouse, Taner Z. Sen, Roger P. Wise and Carson M. Andorf, )
- AutoDTI++: deep unsupervised learning for DTI prediction by autoencoders (Seyedeh Zahra Sajadi, Mohammad Ali Zare Chahooki, Sajjad Gharaghani and Karim Abbasi, )
- Constructing and analysing dynamic models with modelbase v1.2.3: a software update (Marvin van Aalst, Oliver Ebenhöh and Anna Matuszyńska, )
- MAPS: machine-assisted phenotype scoring enables rapid functional assessment of genetic variants by high-content microscopy (Jesse T. Chao, Calvin D. Roskelley and Christopher J. R. Loewen, )
- A flexible ChIP-sequencing simulation toolkit (An Zheng, Michael Lamkin, Yutong Qiu, Kevin Ren, Alon Goren and Melissa Gymrek, )
- Modeling transcriptional regulation using gene regulatory networks based on multi-omics data sources (Neel Patel and William S. Bush, )
- Correction to: Automatic reconstruction of metabolic pathways from identified biosynthetic gene clusters (Snorre Sulheim, Fredrik A. Fossheim, Alexander Wentzel and Eivind Almaas, )
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
- High-dimensional characterization of post-acute sequalae of COVID-19 (Ziyad Al-Aly, Yan Xie, Benjamin Bowe, )
- The world’s lightest uranium atom reveals nuclear secrets ()
- ‘Less pipetting and more thinking’: scientists carry on through the pandemic (Chris Woolston, )
- Three million COVID deaths is a grim milestone ()
- Rivers give off stealth carbon at night ()
- Pseudoscience, zero waste, and female scientists save the world: Books in brief (Andrew Robinson, )
- Restore autonomy for Pakistan’s Higher Education Commission (Farasat Zaman , Amir Rashid , )
Science
- Change in the air (Smith, H. J., )
- Replication timing organizes epigenome (Jiang, D., )
- A junction for single-photon detection (Osborne, I. S., )
- Backtracking a pandemic (Ash, C., )
- Astrotherapy for stroke (Maroso, M., )
- Adding methyl groups with good timing (Yeston, J., )
- Broadband thermal beaming (Grocholski, B., )
PNAS
- Electrical unfolding of cytochrome c during translocation through a nanopore constriction [Biophysics and Computational Biology] (Prabhat Tripathi, Abdelkrim Benabbas, Behzad Mehrafrooz, Hirohito Yamazaki, Aleksei Aksimentiev, Paul M. Champion, Meni Wanunu, )
- HIM-17 regulates the position of recombination events and GSP-1/2 localization to establish short arm identity on bivalents in meiosis [Genetics] (Saravanapriah Nadaraȷan, Elisabeth Altendorfer, Takamune T. Saito, Marina Martinez–Garcia, Monica P. Colaiacovo, )
- Systems level profiling of chemotherapy-induced stress resolution in cancer cells reveals druggable trade-offs [Medical Sciences] (Paula Saavedra–Garcia, Monica Roman–Trufero, Hibah A. Al–Sadah, Kevin Blighe, Elena Lopez–Jimenez, Marilena Christoforou, Lucy Penfold, Daria Capece, Xiaobei Xiong, Yirun Miao, Katarzyna Parzych, Valentina S. Caputo, Alexandros P. , )
- Parallel evolution of UbiA superfamily proteins into aromatic O-prenyltransferases in plants [Plant Biology] (Ryosuke Munakata, Alexandre Olry, Tomoya Takemura, Kanade Tatsumi, Takuȷi Ichino, Cloe Villard, Joȷi Kageyama, Tetsuya Kurata, Masaru Nakayasu, Florence Jacob, Takao Koeduka, Hirobumi Yamamoto, Eiko Moriyoshi, Tetsuya Matsukawa, Jeremy Gros&, )
- Incipient genome erosion and metabolic streamlining for antibiotic production in a defensive symbiont [Evolution] (Taras Y. Nechitaylo, Mario Sandoval–Calderon, Tobias Engl, Natalie Wielsch, Diane M. Dunn, Alexander Goesmann, Erhard Strohm, Aleš Svatoš, Colin Dale, Robert B. Weiss, Martin Kaltenpoth, )
- Direct validation of dune instability theory [Earth, Atmospheric, and Planetary Sciences] (Ping Lu, Clement Narteau, Zhibao Dong, Philippe Claudin, Sebastien Rodriguez, Zhishan An, Laura Fernandez–Cascales, Cyril Gadal, Sylvain Courrech du Pont, )
- Role of bacterial RNA polymerase gate opening dynamics in DNA loading and antibiotics inhibition elucidated by quasi-Markov State Model [Biophysics and Computational Biology] (Ilona Christy Unarta, Siqin Cao, Shintaroh Kubo, Wei Wang, Peter Pak-Hang Cheung, Xin Gao, Shoji Takada, Xuhui Huang, )
Genome Biology
- scMET: Bayesian modeling of DNA methylation heterogeneity at single-cell resolution (Chantriolnt-Andreas Kapourani, Ricard Argelaguet, Guido Sanguinetti and Catalina A. Vallejos, )
- Genomic insights into the origin, domestication and genetic basis of agronomic traits of castor bean (Wei Xu, Di Wu, Tianquan Yang, Chao Sun, Zaiqing Wang, Bing Han, Shibo Wu, Anmin Yu, Mark A. Chapman, Sammy Muraguri, Qing Tan, Wenbo Wang, Zhigui Bao, Aizhong Liu and De-Zhu Li, )
- Personalized genome structure via single gamete sequencing (Ruqian Lyu, Vanessa Tsui, Davis J. McCarthy and Wayne Crismani, )
- A verified genomic reference sample for assessing performance of cancer panels detecting small variants of low allele frequency (Wendell Jones, Binsheng Gong, Natalia Novoradovskaya, Dan Li, Rebecca Kusko, Todd A. Richmond, Donald J. Johann Jr, Halil Bisgin, Sayed Mohammad Ebrahim Sahraeian, Pierre R. Bushel, Mehdi Pirooznia, Katherine Wilkins, Marco Chierici, Wenjun Bao, Lee Scott, )
- Identification of X-chromosomal genes that drive sex differences in embryonic stem cells through a hierarchical CRISPR screening approach (Oriana Genolet, Anna A. Monaco, Ilona Dunkel, Michael Boettcher and Edda G. Schulz, )
- Cross-oncopanel study reveals high sensitivity and accuracy with overall analytical performance depending on genomic regions (Binsheng Gong, Dan Li, Rebecca Kusko, Natalia Novoradovskaya, Yifan Zhang, Shangzi Wang, Carlos Pabón-Peña, Zhihong Zhang, Kevin Lai, Wanshi Cai, Jennifer S. LoCoco, Eric Lader, Todd A. Richmond, Vinay K. Mittal, Liang-Chun Liu, Donald J. Johann Jr&hellip, )
- Publisher Correction: MTSplice predicts effects of genetic variants on tissue-specific splicing (Jun Cheng, Muhammed Hasan Çelik, Anshul Kundaje and Julien Gagneur, )