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 ()
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
- Arbuscular mycorrhizal fungi induce the expression of specific retrotransposons in roots of sunflower (Helianthus annuus L.) (Alberto Vangelisti, Flavia Mascagni, Tommaso Giordani, Cristiana Sbrana, Alessandra Turrini, Andrea Cavallini, Manuela Giovannetti, Lucia Natali, )
- Applications of artificial neural networks in health care organizational decision-making: A scoping review (Nida Shahid, Tim Rappon, Whitney Berta, )
- Training set optimization of genomic prediction by means of EthAcc (Brigitte Mangin, Renaud Rincent, Charles-Elie Rabier, Laurence Moreau, Ellen Goudemand-Dugue, )
- Functional lability of RNA-dependent RNA polymerases in animals (Natalia Pinzón, Stéphanie Bertrand, Lucie Subirana, Isabelle Busseau, Hector Escrivá, Hervé Seitz, )
- Allosteric mechanism of the circadian protein Vivid resolved through Markov state model and machine learning analysis (Hongyu Zhou, Zheng Dong, Gennady Verkhivker, Brian D. Zoltowski, Peng Tao, )
- Multi-modality in gene regulatory networks with slow promoter kinetics (Muhammad Ali Al-Radhawi, Domitilla Del Vecchio, Eduardo D. Sontag, )
- A component overlapping attribute clustering (COAC) algorithm for single-cell RNA sequencing data analysis and potential pathobiological implications (He Peng, Xiangxiang Zeng, Yadi Zhou, Defu Zhang, Ruth Nussinov, Feixiong Cheng, )
BMC Genomics
- Sex differences in gene regulation in the dorsal root ganglion after nerve injury (Kimberly E. Stephens, Weiqiang Zhou, Zhicheng Ji, Zhiyong Chen, Shaoqiu He, Hongkai Ji, Yun Guan and Sean D. Taverna, )
- Metagenomic and metatranscriptomic analysis of human prostate microbiota from patients with prostate cancer (Ye Feng, Varune Rohan Ramnarine, Robert Bell, Stanislav Volik, Elai Davicioni, Vanessa M. Hayes, Shancheng Ren and Colin C. Collins, )
- RNA-seq based transcriptional analysis of Saccharomyces cerevisiae and Lachancea thermotolerans in mixed-culture fermentations under anaerobic conditions (Kirti Shekhawat, Hugh Patterton, Florian F. Bauer and Mathabatha E. Setati, )
- Involvement of jasmonic acid, ethylene and salicylic acid signaling pathways behind the systemic resistance induced by Trichoderma longibrachiatum H9 in cucumber (Min Yuan, Yuanyuan Huang, Weina Ge, Zhenhua Jia, Shuishan Song, Lan Zhang and Yali Huang, )
- A unique insight into the MiRNA profile during genital chlamydial infection (Ifeyinwa Benyeogor, Tankya Simoneaux, Yuehao Wu, Stephanie Lundy, Zenas George, Khamia Ryans, Danielle McKeithen, Roshan Pais, Debra Ellerson, W. Walter Lorenz, Tolulope Omosun, Winston Thompson, Francis O. Eko, Carolyn M. Black, Uriel Blas-Machado, Josep, )
- Genome-wide analysis and identification of the low potassium stress responsive gene SiMYB3 in foxtail millet (Setariaitalica L.) (Xinyou Cao, Liqin Hu, Xueyan Chen, Rongzhi Zhang, Dungong Cheng, Haosheng Li, Zhaoshi Xu, Liancheng Li, Yongbin Zhou, Aifeng Liu, Jianming Song, Cheng Liu, Jianjun Liu, Zhendong Zhao, Ming Chen and Youzhi Ma, )
- Analyses of histological and transcriptome differences in the skin of short-hair and long-hair rabbits (Haisheng Ding, Huiling Zhao, Guanglong Cheng, Yongxin Yang, Xiaofei Wang, Xiaowei Zhao, Yunxia Qi and Dongwei Huang, )
RNA-Seq Blog
- IRIS-EDA – An integrated RNA-Seq interpretation system for gene expression data analysis ()
- RNA-Seq reveals specialized lung cells appear very early in development ()
- EMBL Course: Shift your DNA and RNA Sequencing Library Preparation into Hyper-Drive ()
- In general, agreement among scRNA-Seq data analysis tools in calling DE genes is not high ()
- Fast interpolation-based t-SNE for improved visualization of single-cell RNA-seq data ()
- New infographic available from Technology Networks ()
- Upcoming LiveTutorial: RNA Sequencing Analysis ()
- Single-Cell RNA-Seq reveals how immune cells target different tissues ()
Bioinformatics
- The service is no longer available. Please refer to our RSS help page for information about changes to feeds. ()
- A novel method for predicting activity of cis-regulatory modules, based on a diverse training set (Yang, W., Sinha, S., )
- signeR: an empirical Bayesian approach to mutational signature discovery (Rosales, R. A., Drummond, R. D., Valieris, R., Dias-Neto, E., da Silva, I. T., )
- Multivariate two-part statistics for analysis of correlated mass spectrometry data from multiple biological specimens (Taylor, S. L., Ruhaak, L. R., Weiss, R. H., Kelly, K., Kim, K., )
- SiNVICT: ultra-sensitive detection of single nucleotide variants and indels in circulating tumour DNA (Kockan, C., Hach, F., Sarrafi, I., Bell, R. H., McConeghy, B., Beja, K., Haegert, A., Wyatt, A. W., Volik, S. V., Chi, K. N., Collins, C. C., Sahinalp, S. C., )
- iRSpot-EL: identify recombination spots with an ensemble learning approach (Liu, B., Wang, S., Long, R., Chou, K.-C., )
- Prediction of nucleosome positioning by the incorporation of frequencies and distributions of three different nucleotide segment lengths into a general pseudo k-tuple nucleotide composition (Awazu, A., )
PLoS Computational Biology
- Multiscale modeling of influenza A virus replication in cell cultures predicts infection dynamics for highly different infection conditions (Daniel Rüdiger, Sascha Young Kupke, Tanja Laske, Pawel Zmora, Udo Reichl, )
- Allosteric mechanism of the circadian protein Vivid resolved through Markov state model and machine learning analysis (Hongyu Zhou, Zheng Dong, Gennady Verkhivker, Brian D. Zoltowski, Peng Tao, )
- A saturated reaction in repressor synthesis creates a daytime dead zone in circadian clocks (Koichiro Uriu, Hajime Tei, )
- Multi-modality in gene regulatory networks with slow promoter kinetics (Muhammad Ali Al-Radhawi, Domitilla Del Vecchio, Eduardo D. Sontag, )
- A component overlapping attribute clustering (COAC) algorithm for single-cell RNA sequencing data analysis and potential pathobiological implications (He Peng, Xiangxiang Zeng, Yadi Zhou, Defu Zhang, Ruth Nussinov, Feixiong Cheng, )
- A numerical approach for a discrete Markov model for progressing drug resistance of cancer (Masayuki Maeda, Hideaki Yamashita, )
- Graph Peak Caller: Calling ChIP-seq peaks on graph-based reference genomes (Ivar Grytten, Knut D. Rand, Alexander J. Nederbragt, Geir O. Storvik, Ingrid K. Glad, Geir K. Sandve, )
BMC Bioinformatics
- ElemCor: accurate data analysis and enrichment calculation for high-resolution LC-MS stable isotope labeling experiments (Di Du, Lin Tan, Yumeng Wang, Bo Peng, John N. Weinstein, Fredric E. Wondisford, Xiaoyang Su and Philip L. Lorenzi, )
- SLIM: a flexible web application for the reproducible processing of environmental DNA metabarcoding data (Yoann Dufresne, Franck Lejzerowicz, Laure Apotheloz Perret-Gentil, Jan Pawlowski and Tristan Cordier, )
- Prediction of lncRNA-disease associations by integrating diverse heterogeneous information sources with RWR algorithm and positive pointwise mutual information (Xiao-Nan Fan, Shao-Wu Zhang, Song-Yao Zhang, Kunju Zhu and Songjian Lu, )
- DeepUbi: a deep learning framework for prediction of ubiquitination sites in proteins (Hongli Fu, Yingxi Yang, Xiaobo Wang, Hui Wang and Yan Xu, )
- Identifying cancer prognostic modules by module network analysis (Xiong-Hui Zhou, Xin-Yi Chu, Gang Xue, Jiang-Hui Xiong and Hong-Yu Zhang, )
- CirGO: an alternative circular way of visualising gene ontology terms (Irina Kuznetsova, Artur Lugmayr, Stefan J. Siira, Oliver Rackham and Aleksandra Filipovska, )
- Statistical assessment and visualization of synergies for large-scale sparse drug combination datasets (Arnaud Amzallag, Sridhar Ramaswamy and Cyril H. Benes, )
Nature
- Author Correction: El Niño–Southern Oscillation complexity (Axel Timmermann, Soon-Il An, Jong-Seong Kug, Fei-Fei Jin, Wenju Cai, Antonietta Capotondi, Kim M. Cobb, Matthieu Lengaigne, Michael J. McPhaden, Malte F. Stuecker, Karl Stein, Andrew T. Wittenberg, Kyung-Sook Yun, Tobias Bayr, Han-Ching Chen, Yoshimitsu C, )
- Space-junk spear, depression drug and the EU’s digital copyright ()
- A new model for disease research in Africa ()
- Frozen arias for the Anthropocene epoch (Patrick Goymer, )
- Daily briefing: Israel is sending the first privately built lander to the Moon (Flora Graham, )
- How evolutionary theory guides policy (Monique Borgerhoff Mulder, )
- China sets sights on first solar power stations in space (David Cyranoski, )
Science
- There's no place like home (Kline, R., )
- B1 or B2? The BCR decides (Scanlon, S. T., )
- Elastic ceramics (Grocholski, B., )
- A path through a crowd (Szuromi, P., )
- Low-power organic transistors (Szuromi, P., )
- An integrated route to quantum detection (Osborne, I. S., )
- Mechanism of ribosome rescue (Mao, S., )
PNAS
- Experimental evolutionary studies on the genetic autonomy of the cytoplasmic genome “plasmon” in the Triticum (wheat)-Aegilops complex [Genetics] (Koichiro Tsunewaki, Naoki Mori, Shigeo Takumi, )
- Comparative transcriptomics method to infer gene coexpression networks and its applications to maize and rice leaf transcriptomes [Genetics] (Yao-Ming Chang, Hsin-Hung Lin, Wen-Yu Liu, Chun-Ping Yu, Hsiang-June Chen, Putu Puja Wartini, Yi-Ying Kao, Yeh-Hua Wu, Jinn-Jy Lin, Mei-Yeh Jade Lu, Shih-Long Tu, Shu-Hsing Wu, Shin-Han Shiu, Maurice S. B. Ku, Wen-Hsiung Li, )
- High ambient temperature dampens adaptive immune responses to influenza A virus infection [Immunology and Inflammation] (Miyu Moriyama, Takeshi Ichinohe, )
- DGAT1 inhibits retinol-dependent regulatory T cell formation and mediates autoimmune encephalomyelitis [Immunology and Inflammation] (Kareem L. Graham, Bonnie J. Werner, Kimberly M. Moyer, Alycia K. Patton, Charles R. Krois, Hong Sik Yoo, Maria Tverskoy, Melissa LaJevic, Joseph L. Napoli, Raymond A. Sobel, Brian A. Zabel, Eugene C. Butcher, )
- Breaking tolerance with engineered class I antigen-presenting molecules [Immunology and Inflammation] (Christopher A. Parks, Kalli R. Henning, Kevin D. Pavelko, Michael J. Hansen, Virginia P. Van Keulen, Brendan K. Reed, Jennifer D. Stone, Adam G. Schrum, Diana Gil, David M. Kranz, Andrew J. Bordner, Michael A. Barry, Larry R. Pease, )
- A collaborative multiyear, multimodel assessment of seasonal influenza forecasting in the United States [Medical Sciences] (Nicholas G. Reich, Logan C. Brooks, Spencer J. Fox, Sasikiran Kandula, Craig J. McGowan, Evan Moore, Dave Osthus, Evan L. Ray, Abhinav Tushar, Teresa K. Yamana, Matthew Biggerstaff, Michael A. Johansson, Roni Rosenfeld, Jeffrey Shaman, )
- Increased gene copy number of DEFA1/DEFA3 worsens sepsis by inducing endothelial pyroptosis [Medical Sciences] (QiXing Chen, Yang Yang, JinChao Hou, Qiang Shu, YiXuan Yin, WeiTao Fu, Feng Han, TingJun Hou, CongLi Zeng, Elizabeta Nemeth, Rose Linzmeier, Tomas Ganz, XiangMing Fang, )
Genome Biology
- Rapid turnover of life-cycle-related genes in the brown algae (A. P. Lipinska, M. L. Serrano-Serrano, A. Cormier, A. F. Peters, K. Kogame, J. M. Cock and S. M. Coelho, )
- Dynamic inosinome profiles reveal novel patient stratification and gender-specific differences in glioblastoma (Domenico Alessandro Silvestris, Ernesto Picardi, Valeriana Cesarini, Bruno Fosso, Nicolò Mangraviti, Luca Massimi, Maurizio Martini, Graziano Pesole, Franco Locatelli and Angela Gallo, )
- Skmer: assembly-free and alignment-free sample identification using genome skims (Shahab Sarmashghi, Kristine Bohmann, M. Thomas P. Gilbert, Vineet Bafna and Siavash Mirarab, )
- Combined single-cell profiling of expression and DNA methylation reveals splicing regulation and heterogeneity (Stephanie M. Linker, Lara Urban, Stephen J. Clark, Mariya Chhatriwala, Shradha Amatya, Davis J. McCarthy, Ingo Ebersberger, Ludovic Vallier, Wolf Reik, Oliver Stegle and Marc Jan Bonder, )
- CellFishing.jl: an ultrafast and scalable cell search method for single-cell RNA sequencing (Kenta Sato, Koki Tsuyuzaki, Kentaro Shimizu and Itoshi Nikaido, )
- NCBoost classifies pathogenic non-coding variants in Mendelian diseases through supervised learning on purifying selection signals in humans (Barthélémy Caron, Yufei Luo and Antonio Rausell, )
- Paleogenomics: reconstruction of plant evolutionary trajectories from modern and ancient DNA (Caroline Pont, Stefanie Wagner, Antoine Kremer, Ludovic Orlando, Christophe Plomion and Jerome Salse, )