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
- Ambiguity in logic-based models of gene regulatory networks: An integrative multi-perturbation analysis (Amir Reza Alizad-Rahvar, Mehdi Sadeghi, )
- De novo protein structure prediction using ultra-fast molecular dynamics simulation (Ngaam J. Cheung, Wookyung Yu, )
- Population sequencing reveals clonal diversity and ancestral inbreeding in the grapevine cultivar Chardonnay (Michael J. Roach, Daniel L. Johnson, Joerg Bohlmann, Hennie J. J. van Vuuren, Steven J. M. Jones, Isak S. Pretorius, Simon A. Schmidt, Anthony R. Borneman, )
- Evidence for gene-environment correlation in child feeding: Links between common genetic variation for BMI in children and parental feeding practices (Saskia Selzam, Tom A. McAdams, Jonathan R. I. Coleman, Susan Carnell, Paul F. O’Reilly, Robert Plomin, Clare H. Llewellyn, )
- Loss of the Mia40a oxidoreductase leads to hepato-pancreatic insufficiency in zebrafish (Anna M. Sokol, Barbara Uszczynska-Ratajczak, Michelle M. Collins, Michal Bazala, Ulrike Topf, Pia R. Lundegaard, Sreedevi Sugunan, Stefan Guenther, Carsten Kuenne, Johannes Graumann, Sherine S. L. Chan, Didier Y. R. Stainier, Agnieszka Chacinska, )
- Deepbinner: Demultiplexing barcoded Oxford Nanopore reads with deep convolutional neural networks (Ryan R. Wick, Louise M. Judd, Kathryn E. Holt, )
- RNA virus evasion of nonsense-mediated decay (Jared P. May, Xuefeng Yuan, Erika Sawicki, Anne E. Simon, )
BMC Genomics
- Parallel identification of novel antimicrobial peptide sequences from multiple anuran species by targeted DNA sequencing (Tomislav Rončević, Marco Gerdol, Francesca Spazzali, Fiorella Florian, Stjepan Mekinić, Alessandro Tossi and Alberto Pallavicini, )
- Combined genetic influence of the nicotinic receptor gene cluster CHRNA5/A3/B4 on nicotine dependence (Sung-Ha Lee, Woo-Young Ahn, Michał Seweryn and Wolfgang Sadee, )
- Dissecting clinical outcome of porcine circovirus type 2 with in vivo derived transcriptomic signatures of host tissue responses (Nicolaas Van Renne, Ruifang Wei, Nathalie Pochet and Hans J. Nauwynck, )
- Copper-induced increased expression of genes involved in photosynthesis, carotenoid synthesis and C assimilation in the marine alga Ulva compressa (Felipe E. Rodríguez, Daniel Laporte, Alberto González, Katterinne N. Mendez, Eduardo Castro-Nallar, Claudio Meneses, Juan Pablo Huidobro-Toro and Alejandra Moenne, )
- Exploration of exosomal microRNA expression profiles in pigeon ‘Milk’ during the lactation period (Yao Ma, Siyuan Feng, Xun Wang, Izhar Hyder Qazi, Keren Long, Yi Luo, Guojun Li, Chunyou Ning, Yixin Wang, Silu Hu, Juan Xiao, Xiaokai Li, Dan Lan, Yaodong Hu, Qianzi Tang, Jideng Ma…, )
- Transcriptomic time-series analysis of early development in olive from germinated embryos to juvenile tree (Jaime Jiménez-Ruiz, María de la O Leyva-Pérez, Isabel Vidoy-Mercado, Araceli Barceló and Francisco Luque, )
- RATEmiRs: the rat atlas of tissue-specific and enriched miRNAs database (Pierre R. Bushel, Florian Caiment, Han Wu, Raegan O’Lone, Frank Day, John Calley, Aaron Smith and Jianying Li, )
RNA-Seq Blog
- A practical implementation of large transcriptomic data analysis to resolve cryptic species diversity problems in microbial eukaryotes ()
- Single-cell RNA-Seq finds brain, muscle cells found lurking in kidney organoids grown in lab ()
- CisPi – a transcriptomic score for disclosing cis-acting disease-associated lincRNAs ()
- Mount Sinai researchers develop tool that analyzes RNA-Seq data within minutes ()
- A step-by-step guide to submitting RNA-Seq data to NCBI ()
- Neural nets supplant marker genes in analyzing single cell RNA sequencing ()
- BioLegend partners on TotalSeqTM antibodies to boost single cell surface protein profiling within VIB ()
- Amaryllis Nucleics Adds Dual-Indexing Capabilities to its Dual-Mode RNAseq Kit ()
Bioinformatics
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- 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
- Deepbinner: Demultiplexing barcoded Oxford Nanopore reads with deep convolutional neural networks (Ryan R. Wick, Louise M. Judd, Kathryn E. Holt, )
- Adaptive feature detection from differential processing in parallel retinal pathways (Yusuf Ozuysal, David B. Kastner, Stephen A. Baccus, )
- Rosetta FunFolDes – A general framework for the computational design of functional proteins (Jaume Bonet, Sarah Wehrle, Karen Schriever, Che Yang, Anne Billet, Fabian Sesterhenn, Andreas Scheck, Freyr Sverrisson, Barbora Veselkova, Sabrina Vollers, Roxanne Lourman, Mélanie Villard, Stéphane Rosset, Thomas Krey, Bruno E. Correia, )
- Simulations of blood as a suspension predicts a depth dependent hematocrit in the circulation throughout the cerebral cortex (Grant Hartung, Claudia Vesel, Ryan Morley, Ali Alaraj, John Sled, David Kleinfeld, Andreas Linninger, )
- Towards a molecular basis of ubiquitin signaling: A dual-scale simulation study of ubiquitin dimers (Andrej Berg, Oleksandra Kukharenko, Martin Scheffner, Christine Peter, )
- Metabolic models and gene essentiality data reveal essential and conserved metabolism in prokaryotes (Joana C. Xavier, Kiran Raosaheb Patil, Isabel Rocha, )
- Cytoplasmic flows in starfish oocytes are fully determined by cortical contractions (Nils Klughammer, Johanna Bischof, Nikolas D. Schnellbächer, Andrea Callegari, Péter Lénárt, Ulrich S. Schwarz, )
BMC Bioinformatics
- The poly-omics of ageing through individual-based metabolic modelling (Elisabeth Yaneske and Claudio Angione, )
- DNA sequences alignment in multi-GPUs: acceleration and energy payoff (Jesús Pérez-Serrano, Edans Sandes, Alba Cristina Magalhaes Alves de Melo and Manuel Ujaldón, )
- Evaluating the impact of topological protein features on the negative examples selection (Paolo Boldi, Marco Frasca and Dario Malchiodi, )
- Deep learning architectures for prediction of nucleosome positioning from sequences data (Mattia Di Gangi, Giosuè Lo Bosco and Riccardo Rizzo, )
- Computational discovery of direct associations between GO terms and protein domains (Seyed Ziaeddin Alborzi, David W. Ritchie and Marie-Dominique Devignes, )
- Learning protein binding affinity using privileged information (Wajid Arshad Abbasi, Amina Asif, Asa Ben-Hur and Fayyaz ul Amir Afsar Minhas, )
- Empirical assessment of the impact of sample number and read depth on RNA-Seq analysis workflow performance (Alyssa Baccarella, Claire R. Williams, Jay Z. Parrish and Charles C. Kim, )
Nature
- When skin’s defence against pollution fails (Elizabeth Svoboda, )
- A voyage to map Earth’s polar ice from the skies — in pictures (Angela Posada-Swafford, )
- Stop exploitation of foreign postdocs in the United States ()
- Moving skin beyond the biological (Katherine Bourzac, )
- Lab life — when privileged are a minority, equity stands a chance (Amin Aalipour, )
- How it feels to be swallowed by a black hole (Gretchen Tessmer, )
- Lessons from recordings lost in Brazil fire: deposit and back up (Simone Dena, Raoni Rebouças, Guilherme Augusto-Alves, Luís Felipe Toledo, )
Science
- Warm water and big winds (Smith, H. J., )
- The science of art advancement (Jasny, B. R., )
- Innovating to be nondisruptive (Vinson, V., )
- A programmable type of CRISPR system (Mao, S., )
- Patterned fiber formation (Lavine, M. S., )
- DNA binding as an anti-inflammatory (Scanlon, S. T., )
- Chemically reversible hydrogels (Szuromi, P., )
PNAS
- Is “choline and geranate” an ionic liquid or deep eutectic solvent system? [Biological Sciences] (Robin D. Rogers, Gabriela Gurau, )
- Reply to Rogers and Gurau: Definitions of ionic liquids and deep eutectic solvents [Biological Sciences] (Amrita Banerjee, Kelly Ibsen, Tyler Brown, Renwei Chen, Christian Agatemor, Samir Mitragotri, )
- Tagging the musical beat: Neural entrainment or event-related potentials? [Biological Sciences] (Giacomo Novembre, Gian Domenico Iannetti, )
- Reply to Novembre and Iannetti: Conceptual and methodological issues [Biological Sciences] (Tomas Lenc, Peter E. Keller, Manuel Varlet, Sylvie Nozaradan, )
- Ocean circulation, ice shelf, and sea ice interactions explain Dansgaard-Oeschger cycles [Earth, Atmospheric, and Planetary Sciences] (Niklas Boers, Michael Ghil, Denis-Didier Rousseau, )
- A flexible organic reflectance oximeter array [Engineering] (Yasser Khan, Donggeon Han, Adrien Pierre, Jonathan Ting, Xingchun Wang, Claire M. Lochner, Gianluca Bovo, Nir Yaacobi-Gross, Chris Newsome, Richard Wilson, Ana C. Arias, )
- Engineering the protein secretory pathway of Saccharomyces cerevisiae enables improved protein production [Applied Biological Sciences] (Mingtao Huang, Guokun Wang, Jiufu Qin, Dina Petranovic, Jens Nielsen, )
Genome Biology
- N6-methyldeoxyadenosine directs nucleosome positioning in Tetrahymena DNA (Guan-Zheng Luo, Ziyang Hao, Liangzhi Luo, Mingren Shen, Daniela Sparvoli, Yuqing Zheng, Zijie Zhang, Xiaocheng Weng, Kai Chen, Qiang Cui, Aaron P. Turkewitz and Chuan He, )
- N6-methyldeoxyadenosine directs nucleosome positioning in Tetrahymena DNA (Guan-Zheng Luo, Ziyang Hao, Liangzhi Luo, Mingren Shen, Daniela Sparvoli, Yuqing Zheng, Zijie Zhang, Xiaocheng Weng, Kai Chen, Qiang Cui, Aaron P. Turkewitz and Chuan He, )
- Ten things you should know about transposable elements (Guillaume Bourque, Kathleen H. Burns, Mary Gehring, Vera Gorbunova, Andrei Seluanov, Molly Hammell, Michaël Imbeault, Zsuzsanna Izsvák, Henry L. Levin, Todd S. Macfarlan, Dixie L. Mager and Cédric Feschotte, )
- Ten things you should know about transposable elements (Guillaume Bourque, Kathleen H. Burns, Mary Gehring, Vera Gorbunova, Andrei Seluanov, Molly Hammell, Michaël Imbeault, Zsuzsanna Izsvák, Henry L. Levin, Todd S. Macfarlan, Dixie L. Mager and Cédric Feschotte, )
- KrakenUniq: confident and fast metagenomics classification using unique k-mer counts (F. P. Breitwieser, D. N. Baker and S. L. Salzberg, )
- Genomes reveal marked differences in the adaptive evolution between orangutan species (Maja P. Mattle-Greminger, Tugce Bilgin Sonay, Alexander Nater, Marc Pybus, Tariq Desai, Guillem de Valles, Ferran Casals, Aylwyn Scally, Jaume Bertranpetit, Tomas Marques-Bonet, Carel P. van Schaik, Maria Anisimova and Michael Krützen, )
- Conferring DNA virus resistance with high specificity in plants using virus-inducible genome-editing system (Xiang Ji, Xiaomin Si, Yi Zhang, Huawei Zhang, Feng Zhang and Caixia Gao, )