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
- Hypertensive APOL1 risk allele carriers demonstrate greater blood pressure reduction with angiotensin receptor blockade compared to low risk carriers (Patrick N. Cunningham, Zhiying Wang, Megan L. Grove, Rhonda M. Cooper-DeHoff, Amber L. Beitelshees, Yan Gong, John G. Gums, Julie A. Johnson, Stephen T. Turner, Eric Boerwinkle, Arlene B. Chapman, )
- Evolutionary analysis of six chloroplast genomes from three Persea americana ecological races: Insights into sequence divergences and phylogenetic relationships (Yu Ge, Xiangshu Dong, Bin Wu, Nan Wang, Di Chen, Haihong Chen, Minghong Zou, Zining Xu, Lin Tan, Rulin Zhan, )
- Gene dysregulation in peripheral blood of moyamoya disease and comparison with other vascular disorders (Xing Peng, Zhengshan Zhang, Dongqing Ye, Peiqi Xing, Zhengxing Zou, Hongxing Lei, Lian Duan, )
- Data in question: A survey of European biobank professionals on ethical, legal and societal challenges of biobank research (Melanie Goisauf, Gillian Martin, Heidi Beate Bentzen, Isabelle Budin-Ljøsne, Lars Ursin, Anna Durnová, Liis Leitsalu, Katharine Smith, Sara Casati, Marialuisa Lavitrano, Deborah Mascalzoni, Martin Boeckhout, Michaela Th. Mayrhofer, )
- Scope and efficacy of the broad-spectrum topical antiseptic choline geranate (Joshua R. Greene, Kahla L. Merrett, Alexanndra J. Heyert, Lucas F. Simmons, Camille M. Migliori, Kristen C. Vogt, Rebeca S. Castro, Paul D. Phillips, Joseph L. Baker, Gerrick E. Lindberg, David T. Fox, Rico E. Del Sesto, Andrew T. Koppisch, )
- Phylogenetic microbiota profiling in fecal samples depends on combination of sequencing depth and choice of NGS analysis method (Sukithar K. Rajan, Mårten Lindqvist, Robert Jan Brummer, Ida Schoultz, Dirk Repsilber, )
- In eubacteria, unlike eukaryotes, there is no evidence for selection favouring fail-safe 3’ additional stop codons (Alexander T. Ho, Laurence D. Hurst, )
BMC Genomics
- Ploidy level and nucleotide variations in inflorescence dichotomous cultivars of plantain (Musa spp. AAB genome) (Ebiamadon Andi Brisibe and Norah Godwin Ekanem, )
- Comparison between transcriptomic responses to short-term stress exposures of a common Holarctic and endemic Lake Baikal amphipods (Polina Drozdova, Lorena Rivarola-Duarte, Daria Bedulina, Denis Axenov-Gribanov, Stephan Schreiber, Anton Gurkov, Zhanna Shatilina, Kseniya Vereshchagina, Yulia Lubyaga, Ekaterina Madyarova, Christian Otto, Frank Jühling, Wibke Busch, Lena Jakob, Magnus Lu, )
- Mitochondrial and nuclear genetic analyses of the tropical black-lip rock oyster (Saccostrea echinata) reveals population subdivision and informs sustainable aquaculture development (Samantha J. Nowland, Catarina N. S. Silva, Paul C. Southgate and Jan M. Strugnell, )
- Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction (Olga M. Sigalova, Andrei V. Chaplin, Olga O. Bochkareva, Pavel V. Shelyakin, Vsevolod A. Filaretov, Evgeny E. Akkuratov, Valentina Burskaia and Mikhail S. Gelfand, )
- Deciphering epigenomic code for cell differentiation using deep learning (Pengyu Ni and Zhengchang Su, )
- Comparative proteomic analysis provides new insights into the specialization of shoots and stolons in bermudagrass (Cynodon dactylon L.) (Bing Zhang, Jibiao Fan and Jianxiu Liu, )
- The differences of gonadal hormones and uterine transcriptome during shell calcification of hens laying hard or weak-shelled eggs (Jiacai Zhang, Yanan Wang, Cong Zhang, Mingxin Xiong, Shahid Ali Rajput, Yun Liu and Desheng Qi, )
RNA-Seq Blog
- Self-assembling manifolds in single-cell RNA sequencing data ()
- DARPA taps Duke University’s RNA sequencing expertise to develop device for detecting exposure to WMDs ()
- Transcriptome profiling methods reveal mRNA processing events ()
- RNA whole-transcriptome sequencing test informs thyroid cancer treatment decisions at time of diagnosis ()
- Valid Post-clustering Differential Analysis for Single-Cell RNA-Seq ()
- UCSF researchers recommend that all patients without Ras mutations undergo RNA sequencing to identify any fusions that might be treated with targeted therapies ()
- Upcoming Live Chat Sessions: rRNA removal – The most underestimated step for RNA-seq optimization ()
- Interactive Workshop – RNA-seq for Mendelian Diseases Diagnostics ()
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
- Complex genetic and epigenetic regulation deviates gene expression from a unifying global transcriptional program (Mónica Chagoyen, Juan F. Poyatos, )
- Predicting gene regulatory interactions based on spatial gene expression data and deep learning (Yang Yang, Qingwei Fang, Hong-Bin Shen, )
- Unified feature association networks through integration of transcriptomic and proteomic data (Ryan S. McClure, Jason P. Wendler, Joshua N. Adkins, Jesica Swanstrom, Ralph Baric, Brooke L. Deatherage Kaiser, Kristie L. Oxford, Katrina M. Waters, Jason E. McDermott, )
- 3D spatial organization and network-guided comparison of mutation profiles in Glioblastoma reveals similarities across patients (Cansu Dincer, Tugba Kaya, Ozlem Keskin, Attila Gursoy, Nurcan Tuncbag, )
- Frequency spectrum of chemical fluctuation: A probe of reaction mechanism and dynamics (Sanggeun Song, Gil-Suk Yang, Seong Jun Park, Sungguan Hong, Ji-Hyun Kim, Jaeyoung Sung, )
- A flexible and generalizable model of online latent-state learning (Amy L. Cochran, Josh M. Cisler, )
- Fast and near-optimal monitoring for healthcare acquired infection outbreaks (Bijaya Adhikari, Bryan Lewis, Anil Vullikanti, José Mauricio Jiménez, B. Aditya Prakash, )
BMC Bioinformatics
- A purely bioinformatic pipeline for the prediction of mammalian odorant receptor gene enhancers (Andrea Degl’Innocenti, Gabriella Meloni, Barbara Mazzolai and Gianni Ciofani, )
- HH-suite3 for fast remote homology detection and deep protein annotation (Martin Steinegger, Markus Meier, Milot Mirdita, Harald Vöhringer, Stephan J. Haunsberger and Johannes Söding, )
- Towards pixel-to-pixel deep nucleus detection in microscopy images (Fuyong Xing, Yuanpu Xie, Xiaoshuang Shi, Pingjun Chen, Zizhao Zhang and Lin Yang, )
- Identifying protein complexes based on an edge weight algorithm and core-attachment structure (Rongquan Wang, Guixia Liu and Caixia Wang, )
- A multiscale mathematical model of cell dynamics during neurogenesis in the mouse cerebral cortex (Marie Postel, Alice Karam, Guillaume Pézeron, Sylvie Schneider-Maunoury and Frédérique Clément, )
- A network embedding-based multiple information integration method for the MiRNA-disease association prediction (Yuchong Gong, Yanqing Niu, Wen Zhang and Xiaohong Li, )
- CytoConverter: a web-based tool to convert karyotypes to genomic coordinates (Janet Wang and Thomas LaFramboise, )
Nature
- Deep learning for multi-year ENSO forecasts (Yoo-Geun Ham, Jeong-Hwan Kim, Jing-Jia Luo, )
- A new scenario logic for the Paris Agreement long-term temperature goal (Joeri Rogelj, Daniel Huppmann, Volker Krey, Keywan Riahi, Leon Clarke, Matthew Gidden, Zebedee Nicholls, Malte Meinshausen, )
- Stunted microbiota and opportunistic pathogen colonization in caesarean-section birth (Yan Shao, Samuel C. Forster, Evdokia Tsaliki, Kevin Vervier, Angela Strang, Nandi Simpson, Nitin Kumar, Mark D. Stares, Alison Rodger, Peter Brocklehurst, Nigel Field, Trevor D. Lawley, )
- A sticking point for rapid flu tests? (Elizabeth Svoboda, )
- Podcast: XKCD, and Extinction Rebellion ()
- Cancer cells have ‘unsettling’ ability to hijack the brain’s nerves (Heidi Ledford, )
- Cyclic GMP–AMP signalling protects bacteria against viral infection (Daniel Cohen, Sarah Melamed, Adi Millman, Gabriela Shulman, Yaara Oppenheimer-Shaanan, Assaf Kacen, Shany Doron, Gil Amitai, Rotem Sorek, )
Science
- Role play between rats and humans (Stern, P., )
- Flipping a lipid (Vinson, V., )
- Stabilizing rougher nanoparticles (Szuromi, P., )
- Catching a copper nitrene (Yeston, J., )
- How to define a light path topologically (Osborne, I. S., )
- Hazardous delays (Vignieri, S., )
- Taming tonic signaling for immunotherapy (Williams, E., )
PNAS
- Structural insight into multistage inhibition of CRISPR-Cas12a by AcrVA4 [Biochemistry] (Ruchao Peng, Zhiteng Li, Ying Xu, Shaoshuai He, Qi Peng, Lian-ao Wu, Ying Wu, Jianxun Qi, Peiyi Wang, Yi Shi, George F. Gao, )
- Hydrophobic gasket mutation produces gating pore currents in closed human voltage-gated proton channels [Biophysics and Computational Biology] (Richard Banh, Vladimir V. Cherny, Deri Morgan, Boris Musset, Sarah Thomas, Kethika Kulleperuma, Susan M. E. Smith, Regis Pomes, Thomas E. DeCoursey, )
- Leveraging protein dynamics to identify cancer mutational hotspots using 3D structures [Biophysics and Computational Biology] (Sushant Kumar, Declan Clarke, Mark B. Gerstein, )
- Historical records reveal the distinctive associations of human disturbance and extreme climate change with local extinction of mammals [Ecology] (Xinru Wan, Guangshun Jiang, Chuan Yan, Fangliang He, Rongsheng Wen, Jiayin Gu, Xinhai Li, Jianzhang Ma, Nils Chr. Stenseth, Zhibin Zhang, )
- Weak warning signals can persist in the absence of gene flow [Evolution] (J. P. Lawrence, Bibiana Rojas, Antoine Fouquet, Johanna Mappes, Annelise Blanchette, Ralph A. Saporito, Renan Janke Bosque, Elodie A. Courtois, Brice P. Noonan, )
- Cooption of the pteridine biosynthesis pathway underlies the diversification of embryonic colors in water striders [Evolution] (Aidamalia Vargas–Lowman, David Armisen, Carla Fernanda Burguez Floriano, Isabelle da Rocha Silva Cordeiro, Severine Viala, Mathilde Bouchet, Marie Bernard, Augustin Le Bouquin, M. Emilia Santos, Alexandra Berlioz–Barbier, Arnaud Salvador, Feli, )
- Medullary thymic epithelial NF-kB-inducing kinase (NIK)/IKK{alpha} pathway shapes autoimmunity and liver and lung homeostasis in mice [Immunology and Inflammation] (Hong Shen, Yewei Ji, Yi Xiong, Hana Kim, Xiao Zhong, Michelle G. Jin, Yatrik M. Shah, M. Bishr Omary, Yong Liu, Ling Qi, Liangyou Rui, )
Genome Biology
- How to meet your ‘silent partner’: tips for approaching editors at conferences (Yixin Yao, )
- When the levee breaks: a practical guide to sketching algorithms for processing the flood of genomic data (Will P. M. Rowe, )
- Quantitative MNase-seq accurately maps nucleosome occupancy levels (Răzvan V. Chereji, Terri D. Bryson and Steven Henikoff, )
- The first enhancer in an enhancer chain safeguards subsequent enhancer-promoter contacts from a distance (Wei Song, Roded Sharan and Ivan Ovcharenko, )
- Reproducible biomedical benchmarking in the cloud: lessons from crowd-sourced data challenges (Kyle Ellrott, Alex Buchanan, Allison Creason, Michael Mason, Thomas Schaffter, Bruce Hoff, James Eddy, John M. Chilton, Thomas Yu, Joshua M. Stuart, Julio Saez-Rodriguez, Gustavo Stolovitzky, Paul C. Boutros and Justin Guinney, )
- A comparison of automatic cell identification methods for single-cell RNA sequencing data (Tamim Abdelaal, Lieke Michielsen, Davy Cats, Dylan Hoogduin, Hailiang Mei, Marcel J. T. Reinders and Ahmed Mahfouz, )
- scBFA: modeling detection patterns to mitigate technical noise in large-scale single-cell genomics data (Ruoxin Li and Gerald Quon, )