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
- Comparison of the myometrial transcriptome from singleton and twin pregnancies by RNA-Seq (Sarah Arrowsmith, Yongxiang Fang, Andrew Sharp, )
- Molecular karyotyping of Siberian wild rye (Elymus sibiricus L.) with oligonucleotide fluorescence in situ hybridization (FISH) probes (Jihong Xie, Yan Zhao, Linqing Yu, Ruijuan Liu, Quanwen Dou, )
- Modeling the effect of prolonged ethanol exposure on global gene expression and chromatin accessibility in normal 3D colon organoids (Matthew Devall, Lucas T. Jennelle, Jennifer Bryant, Stephanie Bien, Ulrike Peters, Steven Powell, Graham Casey, )
- Computational simulation of the reactive oxygen species and redox network in the regulation of chloroplast metabolism (Melanie Gerken, Sergej Kakorin, Kamel Chibani, Karl-Josef Dietz, )
- Dating genomic variants and shared ancestry in population-scale sequencing data (Patrick K. Albers, Gil McVean, )
- Identification of putative Type-I sex pheromone biosynthesis-related genes expressed in the female pheromone gland of Streltzoviella insularis (Yuchao Yang, Jing Tao, Shixiang Zong, )
- Models of protein production along the cell cycle: An investigation of possible sources of noise (Renaud Dessalles, Vincent Fromion, Philippe Robert, )
BMC Genomics
- SMRT sequencing of a full-length transcriptome reveals transcript variants involved in C18 unsaturated fatty acid biosynthesis and metabolism pathways at chilling temperature in Pennisetum giganteum (Qingyuan Li, Conglin Xiang, Lin Xu, Jinghua Cui, Shao Fu, Baolin Chen, Shoukun Yang, Pan Wang, Yanfeng Xie, Ming Wei and Zhanchang Wang, )
- Correction to: Transcriptomic analysis of hepatic responses to testosterone deficiency in miniature pigs fed a high-cholesterol diet (Zhaowei Cai, Xiaoling Jiang, Yongming Pan, Liang Chen, Lifan Zhang, Keyan Zhu, Yueqin Cai, Yun Ling, Fangming Chen, Xiaoping Xu and Minli Chen, )
- Transcriptome-based screening of intracellular pathways and angiogenesis related genes at different stages of thiram induced tibial lesions in broiler chickens (Ali Raza Jahejo, Ding Zhang, Sheng Niu, Raza Ali Mangi, Afrasyab Khan, Muhammad Farhan Qadir, Ajab Khan, Huan-chun Chen and Wen-xia Tian, )
- Transcriptome analysis of Clinopodium gracile (Benth.) Matsum and identification of genes related to Triterpenoid Saponin biosynthesis (Chunmiao Shan, Chenkai Wang, Shengxiang Zhang, Yuanyuan Shi, Kelong Ma, Qingshan Yang and Jiawen Wu, )
- Intraspecific diversification of the crop wild relative Brassica cretica Lam. using demographic model selection (Antonios Kioukis, Vassiliki A. Michalopoulou, Laura Briers, Stergios Pirintsos, David J. Studholme, Pavlos Pavlidis and Panagiotis F. Sarris, )
- Changes in the expression of genes encoding type IV pili-associated proteins are seen when Clostridium perfringens is grown in liquid or on surfaces (Samantha R. Soncini, Andrea H. Hartman, Tara M. Gallagher, Gary J. Camper, Roderick V. Jensen and Stephen B. Melville, )
- Changes in life history traits and transcriptional regulation of Coccinellini ladybirds in using alternative prey (Mei-Lan Chen, Yu-Hao Huang, Bo-Yuan Qiu, Pei-Tao Chen, Xue-Yong Du, Hao-Sen Li and Hong Pang, )
RNA-Seq Blog
- Featured RNA-Seq Job – Quantitative Biologist/Bioinformatics ()
- A benchmark of batch-effect correction methods for single-cell RNA sequencing data ()
- ideal – an R/Bioconductor package for Interactive Differential Expression Analysis ()
- RNA and machine learning: rational design for multidimensional biomarkers ()
- SCDC – bulk gene expression deconvolution by multiple single-cell RNA sequencing references ()
- Illumina announces new sequencers ()
- BISR-RNAseq – an efficient and scalable RNAseq analysis workflow with interactive report generation ()
- Scientists improve crop yield predictions based on seedling RNA-Seq data ()
Bioinformatics
- Visualization of circular RNAs and their internal splicing events from transcriptomic data ()
- RxnBLAST: Molecular Scaffold and Reactive Chemical Environment Feature Extractor for Biochemical Reactions ()
- Simulating trees with millions of species ()
- 3D-Cell-Annotator: an open-source active surface tool for single cell segmentation in 3D microscopy images ()
- BMDx: a graphical Shiny application to perform Benchmark Dose analysis for transcriptomics data ()
- Inference of Gene Regulatory Networks Based on Nonlinear Ordinary Differential Equations ()
- Targeted Realignment of LC-MS Profiles by Neighbor-wise Compound-specific Graphical Time Warping with Misalignment Detection ()
PLoS Computational Biology
- Transient amplifiers of selection and reducers of fixation for death-Birth updating on graphs (Benjamin Allen, Christine Sample, Robert Jencks, James Withers, Patricia Steinhagen, Lori Brizuela, Joshua Kolodny, Darren Parke, Gabor Lippner, Yulia A. Dementieva, )
- Limits on amplifiers of natural selection under death-Birth updating (Josef Tkadlec, Andreas Pavlogiannis, Krishnendu Chatterjee, Martin A. Nowak, )
- Computational simulation of the reactive oxygen species and redox network in the regulation of chloroplast metabolism (Melanie Gerken, Sergej Kakorin, Kamel Chibani, Karl-Josef Dietz, )
- A new method for inferring timetrees from temporally sampled molecular sequences (Sayaka Miura, Koichiro Tamura, Qiqing Tao, Louise A. Huuki, Sergei L. Kosakovsky Pond, Jessica Priest, Jiamin Deng, Sudhir Kumar, )
- Eco-evolutionary agriculture: Host-pathogen dynamics in crop rotations (Maria Bargués-Ribera, Chaitanya S. Gokhale, )
- A single reaction-diffusion equation for the multifarious eruptions of urticaria (Sungrim Seirin-Lee, Yuhki Yanase, Shunsuke Takahagi, Michihiro Hide, )
- BrainIAK tutorials: User-friendly learning materials for advanced fMRI analysis (Manoj Kumar, Cameron T. Ellis, Qihong Lu, Hejia Zhang, Mihai Capotă, Theodore L. Willke, Peter J. Ramadge, Nicholas B. Turk-Browne, Kenneth A. Norman, )
BMC Bioinformatics
- ShinyOmics: collaborative exploration of omics-data (Defne Surujon and Tim van Opijnen, )
- Lag penalized weighted correlation for time series clustering (Thevaa Chandereng and Anthony Gitter, )
- PRAP: Pan Resistome analysis pipeline (Yichen He, Xiujuan Zhou, Ziyan Chen, Xiangyu Deng, Andrew Gehring, Hongyu Ou, Lida Zhang and Xianming Shi, )
- Automatic construction of metabolic models with enzyme constraints (Pavlos Stephanos Bekiaris and Steffen Klamt, )
- A pipeline to create predictive functional networks: application to the tumor progression of hepatocellular carcinoma (Maxime Folschette, Vincent Legagneux, Arnaud Poret, Lokmane Chebouba, Carito Guziolowski and Nathalie Théret, )
- Deep neural networks for human microRNA precursor detection (Xueming Zheng, Xingli Fu, Kaicheng Wang and Meng Wang, )
- Guidelines for cell-type heterogeneity quantification based on a comparative analysis of reference-free DNA methylation deconvolution software (Clémentine Decamps, Florian Privé, Raphael Bacher, Daniel Jost, Arthur Waguet, Eugene Andres Houseman, Eugene Lurie, Pavlo Lutsik, Aleksandar Milosavljevic, Michael Scherer, Michael G. B. Blum and Magali Richard, )
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
- Catastrophic Australian bushfires derail research (Dyani Lewis, )
- Daily briefing: A supercomputer is mining fossil records to uncover unknown extinctions (Flora Graham, )
- Research on embryo-like structures struggles to win US government funding (Nidhi Subbaraman, )
- The manicured wetland that sucks up more carbon than a natural marsh ()
- Atomic-bomb carbon unmasks fraudulent luxury whisky ()
- Large African herbivores have helped to repair their environment (Andrew Mitchinson, )
- Supercomputer scours fossil record for Earth’s hidden extinctions (Ewen Callaway, )
Science
- Wing shapes take flight (Lavine, M. S., )
- An impact with a dash of volcanism (Grocholski, B., )
- Spin-charge entanglement (Stajic, J., )
- Ion fluxes resolve organellar volume (Hurtley, S. M., )
- Making a mammalian ear (Vignieri, S., )
- Magnetic energy release in a solar flare (Smith, K. T., )
- Teaching bismuth to make and break bonds (Yeston, J., )
PNAS
- A general-purpose protein design framework based on mining sequence-structure relationships in known protein structures [Biophysics and Computational Biology] (Jianfu Zhou, Alexandra E. Panaitiu, Gevorg Grigoryan, )
- Corazonin signaling integrates energy homeostasis and lunar phase to regulate aspects of growth and sexual maturation in Platynereis [Developmental Biology] (Gabriele Andreatta, Caroline Broyart, Charline Borghgraef, Karim Vadiwala, Vitaly Kozin, Alessandra Polo, Andrea Bileck, Isabel Beets, Liliane Schoofs, Christopher Gerner, Florian Raible, )
- Intratumoral injection of the seasonal flu shot converts immunologically cold tumors to hot and serves as an immunotherapy for cancer [Immunology and Inflammation] (Jenna H. Newman, C. Brent Chesson, Nora L. Herzog, Praveen K. Bommareddy, Salvatore M. Aspromonte, Russell Pepe, Ricardo Estupinian, Mones M. Aboelatta, Stuti Buddhadev, Saeed Tarabichi, Michael Lee, Shengguo Li, Daniel J. Medina, Eileena F. Giurini, Ka&#, )
- Rescue of tomato spotted wilt virus entirely from complementary DNA clones [Microbiology] (Mingfeng Feng, Ruixiang Cheng, Minglong Chen, Rong Guo, Luyao Li, Zhike Feng, Jianyan Wu, Li Xie, Jian Hong, Zhongkai Zhang, Richard Kormelink, Xiaorong Tao, )
- High-yield monolayer graphene grids for near-atomic resolution cryoelectron microscopy [Biophysics and Computational Biology] (Yimo Han, Xiao Fan, Haozhe Wang, Fang Zhao, Christopher G. Tully, Jing Kong, Nan Yao, Nieng Yan, )
- Proteome-wide observation of the phenomenon of life on the edge of solubility [Biophysics and Computational Biology] (Giulia Vecchi, Pietro Sormanni, Benedetta Mannini, Andrea Vandelli, Gian Gaetano Tartaglia, Christopher M. Dobson, F. Ulrich Hartl, Michele Vendruscolo, )
- The functionally relevant site for paxilline inhibition of BK channels [Biophysics and Computational Biology] (Yu Zhou, Xiao-Ming Xia, Christopher J. Lingle, )
Genome Biology
- A benchmark of batch-effect correction methods for single-cell RNA sequencing data (Hoa Thi Nhu Tran, Kok Siong Ang, Marion Chevrier, Xiaomeng Zhang, Nicole Yee Shin Lee, Michelle Goh and Jinmiao Chen, )
- HIFI: estimating DNA-DNA interaction frequency from Hi-C data at restriction-fragment resolution (Christopher JF Cameron, Josée Dostie and Mathieu Blanchette, )
- DENDRO: genetic heterogeneity profiling and subclone detection by single-cell RNA sequencing (Zilu Zhou, Bihui Xu, Andy Minn and Nancy R. Zhang, )
- Chromatin interactome mapping at 139 independent breast cancer risk signals (Jonathan Beesley, Haran Sivakumaran, Mahdi Moradi Marjaneh, Luize G. Lima, Kristine M. Hillman, Susanne Kaufmann, Natasha Tuano, Nehal Hussein, Sunyoung Ham, Pamela Mukhopadhyay, Stephen Kazakoff, Jason S. Lee, Kyriaki Michailidou, Daniel R. Barnes, Anton, )
- Non-coding RNAs underlie genetic predisposition to breast cancer (Mahdi Moradi Marjaneh, Jonathan Beesley, Tracy A. O’Mara, Pamela Mukhopadhyay, Lambros T. Koufariotis, Stephen Kazakoff, Nehal Hussein, Laura Fachal, Nenad Bartonicek, Kristine M. Hillman, Susanne Kaufmann, Haran Sivakumaran, Chanel E. Smart, Amy E. McCar, )
- Clustered CTCF binding is an evolutionary mechanism to maintain topologically associating domains (Elissavet Kentepozidou, Sarah J. Aitken, Christine Feig, Klara Stefflova, Ximena Ibarra-Soria, Duncan T. Odom, Maša Roller and Paul Flicek, )
- Functional consequences of archaic introgression and their impact on fitness (Maxime Rotival and Lluis Quintana-Murci, )