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
- Genetic characterisation of variants of the virulence plasmid, pSLT, in Salmonella enterica serovar Typhimurium provides evidence of a variety of evolutionary directions consistent with vertical rather than horizontal transmission (Lester Hiley, Rikki M. A. Graham, Amy V. Jennison, )
- Mine landslide susceptibility assessment using IVM, ANN and SVM models considering the contribution of affecting factors (Xiangang Luo, Feikai Lin, Shuang Zhu, Mengliang Yu, Zhuo Zhang, Lingsheng Meng, Jing Peng, )
- Genomic variants identified from whole-genome resequencing of indicine cattle breeds from Pakistan (Naveed Iqbal, Xin Liu, Ting Yang, Ziheng Huang, Quratulain Hanif, Muhammad Asif, Qaiser Mahmood Khan, Shahid Mansoor, )
- Reproducible big data science: A case study in continuous FAIRness (Ravi Madduri, Kyle Chard, Mike D’Arcy, Segun C. Jung, Alexis Rodriguez, Dinanath Sulakhe, Eric Deutsch, Cory Funk, Ben Heavner, Matthew Richards, Paul Shannon, Gustavo Glusman, Nathan Price, Carl Kesselman, Ian Foster, )
- Use of FFPE-derived DNA in next generation sequencing: DNA extraction methods (Samantha J. McDonough, Aditya Bhagwate, Zhifu Sun, Chen Wang, Michael Zschunke, Joshua A. Gorman, Karla J. Kopp, Julie M. Cunningham, )
- Reconciling high-throughput gene essentiality data with metabolic network reconstructions (Anna S. Blazier, Jason A. Papin, )
- Dhh1 promotes autophagy-related protein translation during nitrogen starvation (Xu Liu, Zhiyuan Yao, Meiyan Jin, Sim Namkoong, Zhangyuan Yin, Jun Hee Lee, Daniel J. Klionsky, )
BMC Genomics
- HumCFS: a database of fragile sites in human chromosomes (Rajesh Kumar, Gandharva Nagpal, Vinod Kumar, Salman Sadullah Usmani, Piyush Agrawal and Gajendra P. S. Raghava, )
- Analysis of microRNAs, phased small interfering RNAs and their potential targets in Rosarugosa Thunb. (Junqiang Guo, Qingyi Wang, Li Liu, Shuchao Ren, Shipeng Li, Peiran Liao, Zhigang Zhao, Chenyu Lu, Bingbing Jiang, Ramanjulu Sunkar and Yun Zheng, )
- HseSUMO: Sumoylation site prediction using half-sphere exposures of amino acids residues (Alok Sharma, Artem Lysenko, Yosvany López, Abdollah Dehzangi, Ronesh Sharma, Hamendra Reddy, Abdul Sattar and Tatsuhiko Tsunoda, )
- Correction to: low coverage sequencing for repetitive DNA analysis in Passiflora edulis Sims: citogenomic characterization of transposable elements and satellite DNA (Vanessa Carvalho Cayres Pamponét, Margarete Magalhães Souza, Gonçalo Santos Silva, Fabienne Micheli, Cláusio Antônio Ferreira de Melo, Sarah Gomes de Oliveira, Eduardo Almeida Costa and Ronan Xavier Corrêa, )
- APBioNet's annual International Conference on Bioinformatics (InCoB) returns to India in 2018 (Shandar Ahmad, Michael M. Gromiha, Gajendra P. S. Raghava, Christian Schönbach and Shoba Ranganathan, )
- The first draft genomes of the ant Formica exsecta, and its Wolbachia endosymbiont reveal extensive gene transfer from endosymbiont to host (Kishor Dhaygude, Abhilash Nair, Helena Johansson, Yannick Wurm and Liselotte Sundström, )
- Novel Stenotrophomonas maltophilia temperate phage DLP4 is capable of lysogenic conversion (Danielle L. Peters, Jaclyn G. McCutcheon, Paul Stothard and Jonathan J. Dennis, )
RNA-Seq Blog
- RNA sequencing reveals microRNA-like RNAs in fungi ()
- Comparison of RNA-Seq data alignment and qene expression quantification tools for clinical breast cancer research ()
- GSEPD – a Bioconductor package for RNA-seq gene set enrichment and projection display ()
- 1CellBio Announces Custom Targeted Bead Program to Accelerate Next Phase in Single-Cell Analysis ()
- LIONESS – estimating sample-specific regulatory networks ()
- RNA-Seq enables discovery of ‘kingpin’ stem cells, greater understanding of cancerous tumours ()
- TSEE – an elastic embedding method to visualize the dynamic gene expression patterns of time series single-cell RNA sequencing data ()
- Seeking Postdoc – Knowledge of de novo genome assembly, transcriptomics analysis (RNA-seq and others), coding in Python, Perl, and/or R ()
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
- SPINDLE: End-to-end learning from EEG/EMG to extrapolate animal sleep scoring across experimental settings, labs and species (Đorđe Miladinović, Christine Muheim, Stefan Bauer, Andrea Spinnler, Daniela Noain, Mojtaba Bandarabadi, Benjamin Gallusser, Gabriel Krummenacher, Christian Baumann, Antoine Adamantidis, Steven A. Brown, Joachim M. Buhmann, )
- Toward a 3D model of phyllotaxis based on a biochemically plausible auxin-transport mechanism (Félix P. Hartmann, Pierre Barbier de Reuille, Cris Kuhlemeier, )
- Bet-hedging strategies in expanding populations (Paula Villa Martín, Miguel A. Muñoz, Simone Pigolotti, )
- Imperfect Bayesian inference in visual perception (Elina Stengård, Ronald van den Berg, )
- Predicting synthetic lethal interactions using conserved patterns in protein interaction networks (Graeme Benstead-Hume, Xiangrong Chen, Suzanna R. Hopkins, Karen A. Lane, Jessica A. Downs, Frances M. G. Pearl, )
- Learning and forgetting using reinforced Bayesian change detection (Vincent Moens, Alexandre Zénon, )
- Neural control of body-plan axis in regenerating planaria (Alexis Pietak, Johanna Bischof, Joshua LaPalme, Junji Morokuma, Michael Levin, )
BMC Bioinformatics
- Integration of transcriptomic data in a genome-scale metabolic model to investigate the link between obesity and breast cancer (Ilaria Granata, Enrico Troiano, Mara Sangiovanni and Mario Rosario Guarracino, )
- VIGLA-M: visual gene expression data analytics (Ismael Navas-Delgado, José García-Nieto, Esteban López-Camacho, Maciej Rybinski, Rocio Lavado, Miguel Ángel Berciano Guerrero and José F. Aldana-Montes, )
- Analyzing big datasets of genomic sequences: fast and scalable collection of k-mer statistics (Umberto Ferraro Petrillo, Mara Sorella, Giuseppe Cattaneo, Raffaele Giancarlo and Simona E. Rombo, )
- FEDRO: a software tool for the automatic discovery of candidate ORFs in plants with c →u RNA editing (Fabio Fassetti, Claudia Giallombardo, Ofelia Leone, Luigi Palopoli, Simona E. Rombo and Adolfo Saiardi, )
- Walking pathways with positive feedback loops reveal DNA methylation biomarkers of colorectal cancer (Alexander Kel, Ulyana Boyarskikh, Philip Stegmaier, Leonid S. Leskov, Andrey V. Sokolov, Ivan Yevshin, Nikita Mandrik, Daria Stelmashenko, Jeannette Koschmann, Olga Kel-Margoulis, Mathias Krull, Anna Martínez-Cardús, Sebastian Moran, Manel Esteller, Fedor, )
- Effect of stochasticity on coinfection dynamics of respiratory viruses (Lubna Pinky, Gilberto Gonzalez-Parra and Hana M. Dobrovolny, )
- Ryūtō: network-flow based transcriptome reconstruction (Thomas Gatter and Peter F Stadler, )
Nature
- Fearsome ancient carnivore discovered after fossil lingered for decades in museum drawer (Riley Black, )
- Algorithms spot millions of California’s tiniest quakes in historical data (Robin Andrews, )
- Daily briefing: Is brain death the end? (Anna Nagle, )
- How US–China political tensions are affecting science (Andrew Silver, Jeff Tollefson, Elizabeth Gibney, )
- US health agency pours $350 million into fight against opioid crisis (Sara Reardon, )
- Predicting disruptive instabilities in controlled fusion plasmas through deep learning (Julian Kates-Harbeck, Alexey Svyatkovskiy, William Tang, )
- Publisher Correction: No detection of methane on Mars from early ExoMars Trace Gas Orbiter observations (Oleg Korablev, Ann Carine Vandaele, Franck Montmessin, Anna A. Fedorova, Alexander Trokhimovskiy, François Forget, Franck Lefèvre, Frank Daerden, Ian R. Thomas, Loïc Trompet, Justin T. Erwin, Shohei Aoki, Séverine Robert, Lori Neary, Sébastien Viscardy, A, )
Science
- Spectrin in mammalian hearing mechanisms (Yeagle, P., Post, K., )
- Spotting off-targets from gene editing (Mao, S., )
- Tissue specificity of tumor suppression (Ray, L. B., )
- Samarium supersensors (Grocholski, B., )
- Wet surface sightings in clusters (Yeston, J., )
- Motion measurement (Kline, R., )
- Hayabusa2 at the asteroid Ryugu (Smith, K. T., )
PNAS
- In This Issue [This Week in PNAS] ()
- Plague, camels, and lice [Biological Sciences] (Remi Barbieri, M. Drancourt, D. Raoult, )
- Reply to Barbieri et al.: Out of the Land of Darkness: Plague on the fur trade routes [Biological Sciences] (Barbara Bramanti, Amine Namouchi, Boris V. Schmid, Katharine R. Dean, Nils Chr. Stenseth, )
- Profile of Dame Carol Robinson [Profiles] (Jennifer Viegas, )
- Theory and experiments join forces to characterize the electrocatalytic interface [Chemistry] (Stephan N. Steinmann, Zi-Yang Wei, Philippe Sautet, )
- Synthetic ubiquitinated proteins meet the proteasome: Distinct roles of ubiquitin in a chain [Biochemistry] (Gerbrand J. van der Heden van Noort, Jin Gan, Huib Ovaa, )
- Shining light on microbial signaling to distant organs [Microbiology] (Fredrik Backhed, )
Genome Biology
- Bazam: a rapid method for read extraction and realignment of high-throughput sequencing data (Simon P. Sadedin and Alicia Oshlack, )
- DegNorm: normalization of generalized transcript degradation improves accuracy in RNA-seq analysis (Bin Xiong, Yiben Yang, Frank R. Fineis and Ji-Ping Wang, )
- Machine learning and complex biological data (Chunming Xu and Scott A. Jackson, )
- Analysis of the recombination landscape of hexaploid bread wheat reveals genes controlling recombination and gene conversion frequency (Laura-Jayne Gardiner, Luzie U. Wingen, Paul Bailey, Ryan Joynson, Thomas Brabbs, Jonathan Wright, James D. Higgins, Neil Hall, Simon Griffiths, Bernardo J. Clavijo and Anthony Hall, )
- Comparative analysis of sequencing technologies for single-cell transcriptomics (Kedar Nath Natarajan, Zhichao Miao, Miaomiao Jiang, Xiaoyun Huang, Hongpo Zhou, Jiarui Xie, Chunqing Wang, Shishang Qin, Zhikun Zhao, Liang Wu, Naibo Yang, Bo Li, Yong Hou, Shiping Liu and Sarah A. Teichmann, )
- Correction to: Comprehensive benchmarking and ensemble approaches for metagenomic classifiers (Alexa B. R. McIntyre, Rachid Ounit, Ebrahim Afshinnekoo, Robert J. Prill, Elizabeth Hénaff, Noah Alexander, Samuel S. Minot, David Danko, Jonathan Foox, Sofia Ahsanuddin, Scott Tighe, Nur A. Hasan, Poorani Subramanian, Kelly Moffat, Shawn Levy, Stefano Lo, )
- Molecular evolutionary trends and feeding ecology diversification in the Hemiptera, anchored by the milkweed bug genome (Kristen A. Panfilio, Iris M. Vargas Jentzsch, Joshua B. Benoit, Deniz Erezyilmaz, Yuichiro Suzuki, Stefano Colella, Hugh M. Robertson, Monica F. Poelchau, Robert M. Waterhouse, Panagiotis Ioannidis, Matthew T. Weirauch, Daniel S. T. Hughes, Shwetha C. Mur, )