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
- Essential gene prediction using limited gene essentiality information–An integrative semi-supervised machine learning strategy (Sutanu Nandi, Piyali Ganguli, Ram Rup Sarkar, )
- Novel methods for epistasis detection in genome-wide association studies (Lotfi Slim, Clément Chatelain, Chloé-Agathe Azencott, Jean-Philippe Vert, )
- The complete mitochondrial genome of a cold seep gastropod Phymorhynchus buccinoides (Neogastropoda: Conoidea: Raphitomidae) (Lvpei Du, Shanya Cai, Jun Liu, Ruoyu Liu, Haibin Zhang, )
- The Number Symbol Coding Task: A brief measure of executive function to detect dementia and cognitive impairment (James E. Galvin, Magdalena I. Tolea, Claudia Moore, Stephanie Chrisphonte, )
- Analysis of mutations of defensin protein using accelerated molecular dynamics simulations (Bharati Pandey, Chetna Tyagi, Gopal Kumar Prajapati, Awdhesh Kumar Mishra, Abeer Hashem, Abdulaziz A. Alqarawi, Elsayed Fathi Abd_Allah, Tapan Kumar Mohanta, )
- Mining GWAS and eQTL data for CF lung disease modifiers by gene expression imputation (Hong Dang, Deepika Polineni, Rhonda G. Pace, Jaclyn R. Stonebraker, Harriet Corvol, Garry R. Cutting, Mitchell L. Drumm, Lisa J. Strug, Wanda K. O’Neal, Michael R. Knowles, )
- Identifying longevity associated genes by integrating gene expression and curated annotations (F. William Townes, Kareem Carr, Jeffrey W. Miller, )
BMC Genomics
- Virulence characterization and comparative genomics of Listeria monocytogenes sequence type 155 strains (Eva Wagner, Andreas Zaiser, Rebekka Leitner, Narciso M. Quijada, Nadja Pracser, Ariane Pietzka, Werner Ruppitsch, Stephan Schmitz-Esser, Martin Wagner and Kathrin Rychli, )
- Deep sampling and pooled amplicon sequencing reveals hidden genic variation in heterogeneous rye accessions (Anna Hawliczek, Leszek Bolibok, Katarzyna Tofil, Ewa Borzęcka, Joanna Jankowicz-Cieślak, Piotr Gawroński, Adam Kral, Bradley J. Till and Hanna Bolibok-Brągoszewska, )
- Competitive mapping allows for the identification and exclusion of human DNA contamination in ancient faunal genomic datasets (Tatiana R. Feuerborn, Eleftheria Palkopoulou, Tom van der Valk, Johanna von Seth, Arielle R. Munters, Patrícia Pečnerová, Marianne Dehasque, Irene Ureña, Erik Ersmark, Vendela Kempe Lagerholm, Maja Krzewińska, Ricardo Rodríguez-Varela, Anders Götherström,, )
- Differential gene expression analysis reveals pathways important in early post-traumatic osteoarthritis in an equine model (Annette M. McCoy, Ann M. Kemper, Mary K. Boyce, Murray P. Brown and Troy N. Trumble, )
- Highly diversified core promoters in the human genome and their effects on gene expression and disease predisposition (Hemant Gupta, Khyati Chandratre, Siddharth Sinha, Teng Huang, Xiaobing Wu, Jian Cui, Michael Q. Zhang and San Ming Wang, )
- Identification and population genetic analyses of copy number variations in six domestic goat breeds and Bezoar ibexes using next-generation sequencing (Jiazhong Guo, Jie Zhong, George E. Liu, Liu Yang, Li Li, Guangling Chen, Tianzeng Song and Hongping Zhang, )
- Molecular convergent and parallel evolution among four high-elevation anuran species from the Tibetan region (Bin Lu, Hong Jin and Jinzhong Fu, )
RNA-Seq Blog
- RNA-Seq signatures normalized by mRNA abundance allow absolute deconvolution of human immune cell types ()
- Potential new therapies for Alzheimer’s disease are revealed through network modeling of its complex molecular interactions ()
- RNA sequencing reveals the link between obesity and puberty ()
- Featured RNA-Seq Job – Molecular, Cell & Developmental Biology ()
- HMS Initiative for RNA Medicine ()
- Deep feature extraction of single-cell transcriptomes by generative adversarial network ()
- Targeting drug-resistant cancers with fluctuation analysis and RNA MemorySeq ()
- Chan Zuckerburg proposes an initative to advance support and development of the open source Salmon and Alevin software for gene expression quantification of single-cell and bulk RNA-seq ()
Bioinformatics
- Colour Deconvolution – stain unmixing in histological imaging ()
- BEST: a Shiny/R web–based application to easily retrieve cross–related enzyme functional parameters and information from BRENDA ()
- Fijiyama: a registration tool for 3D multimodal time-lapse imaging ()
- NoPeak: k-mer based motif discovery in ChIP-Seq data without peak calling ()
- A systems-biology model of the tumor necrosis factor (TNF) interactions with TNF receptor 1 and 2 ()
- Swan: a library for the analysis and visualization of long-read transcriptomes ()
- PBSIM2: a simulator for long read sequencers with a novel generative model of quality scores ()
PLoS Computational Biology
- An exact method for quantifying the reliability of end-of-epidemic declarations in real time (Kris V. Parag, Christl A. Donnelly, Rahul Jha, Robin N. Thompson, )
- Inference of mutability landscapes of tumors from single cell sequencing data (Viachaslau Tsyvina, Alex Zelikovsky, Sagi Snir, Pavel Skums, )
- Deconvolution of heterogeneous tumor samples using partial reference signals (Yufang Qin, Weiwei Zhang, Xiaoqiang Sun, Siwei Nan, Nana Wei, Hua-Jun Wu, Xiaoqi Zheng, )
- Modelling pathogen spread in a healthcare network: Indirect patient movements (Monika J. Piotrowska, Konrad Sakowski, Andre Karch, Hannan Tahir, Johannes Horn, Mirjam E. Kretzschmar, Rafael T. Mikolajczyk, )
- Inferring a network from dynamical signals at its nodes (Corey Weistuch, Luca Agozzino, Lilianne R. Mujica-Parodi, Ken A. Dill, )
- Pre-existing resistance in the latent reservoir can compromise VRC01 therapy during chronic HIV-1 infection (Ananya Saha, Narendra M. Dixit, )
- Acetate and glycerol are not uniquely suited for the evolution of cross-feeding in E. coli (Magdalena San Roman, Andreas Wagner, )
BMC Bioinformatics
- Multiple imputation and direct estimation for qPCR data with non-detects (Valeriia Sherina, Helene R. McMurray, Winslow Powers, Harmut Land, Tanzy M. T. Love and Matthew N. McCall, )
- CGINet: graph convolutional network-based model for identifying chemical-gene interaction in an integrated multi-relational graph (Wei Wang, Xi Yang, Chengkun Wu and Canqun Yang, )
- Improving biomedical named entity recognition with syntactic information (Yuanhe Tian, Wang Shen, Yan Song, Fei Xia, Min He and Kenli Li, )
- Mixed logistic regression in genome-wide association studies (Jacqueline Milet, David Courtin, André Garcia and Hervé Perdry, )
- MADloy: robust detection of mosaic loss of chromosome Y from genotype-array-intensity data (Juan R. González, Marcos López-Sánchez, Alejandro Cáceres, Pere Puig, Tonu Esko and Luis A. Pérez-Jurado, )
- TruNeo: an integrated pipeline improves personalized true tumor neoantigen identification (Yunxia Tang, Yu Wang, Jiaqian Wang, Miao Li, Linmin Peng, Guochao Wei, Yixing Zhang, Jin Li and Zhibo Gao, )
- An alignment-free heuristic for fast sequence comparisons with applications to phylogeny reconstruction (Sriram P. Chockalingam, Jodh Pannu, Sahar Hooshmand, Sharma V. Thankachan and Srinivas Aluru, )
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
- Alarm as execution looms for scientist on death row in Iran (Michele Catanzaro, )
- Watching the sentinels (Amber Dance, )
- How COVID vaccines are being divvied up around the world (Asher Mullard, )
- If you can’t be kind in peer review, be neutral ()
- Arthur Ashkin (1922–2020) (Steven Chu, )
- Daily briefing: ‘Sistine Chapel of the ancients’ discovered in Colombia (Flora Graham, )
- ‘It will change everything’: DeepMind’s AI makes gigantic leap in solving protein structures (Ewen Callaway, )
Science
- A dangerous trend (Smith, H. J., )
- Quality control in mitochondria (Vinson, V., )
- When all routes are exceptional (Osborne, I. S., )
- Driving the pores away (Grocholski, B., )
- A logic to cell-cell recognition (Vinson, V., )
- Paternal factor specifies female wasps (Purnell, B. A., )
- Deep dive (Lee, M. M., )
PNAS
- Reversing the direction of drug transport mediated by the human multidrug transporter P-glycoprotein [Biochemistry] (Andaleeb Sajid, Sabrina Lusvarghi, Megumi Murakami, Eduardo E. Chufan, Biebele Abel, Michael M. Gottesman, Stewart R. Durell, Suresh V. Ambudkar, )
- Evolution of insulin at the edge of foldability and its medical implications [Biochemistry] (Nischay K. Rege, Ming Liu, Yanwu Yang, Balamurugan Dhayalan, Nalinda P. Wickramasinghe, Yen-Shan Chen, Leili Rahimi, Huan Guo, Leena Haataja, Jinhong Sun, Faramarz Ismail-Beigi, Nelson B. Phillips, Peter Arvan, Michael A. Weiss, )
- Water oxidation by photosystem II is the primary source of electrons for sustained H2 photoproduction in nutrient-replete green algae [Biochemistry] (Sergey Kosourov, Valeria Nagy, Dmitry Shevela, Martina Jokel, Johannes Messinger, Yagut Allahverdiyeva, )
- Structural and functional characterization of the pore-forming domain of pinholin S2168 [Biochemistry] (Lena M. E. Steger, Annika Kohlmeyer, Parvesh Wadhwani, Jochen Burck, Erik Strandberg, Johannes Reichert, Stephan L. Grage, Sergii Afonin, Marin Kempfer, Anne C. Gorner, Julia Koch, Torsten H. Walther, Anne S. Ulrich, )
- The 3 x 120{degrees} rotary mechanism of Paracoccus denitrificans F1-ATPase is different from that of the bacterial and mitochondrial F1-ATPases [Biochemistry] (Mariel Zarco–Zavala, Ryo Watanabe, Duncan G. G. McMillan, Toshiharu Suzuki, Hiroshi Ueno, Francisco Mendoza–Hoffmann, Jose J. Garcia–Treȷo, Hiroyuki Noȷi, )
- A majority of Rhodobacter sphaeroides promoters lack a crucial RNA polymerase recognition feature, enabling coordinated transcription activation [Biochemistry] (Kemardo K. Henry, Wilma Ross, Kevin S. Myers, Kimberly C. Lemmer, Jessica M. Vera, Robert Landick, Timothy J. Donohue, Richard L. Gourse, )
- Lipoteichoic acid polymer length is determined by competition between free starter units [Biochemistry] (Anthony R. Hesser, Kaitlin Schaefer, Wonsik Lee, Suzanne Walker, )
Genome Biology
- DNA polymerase epsilon is required for heterochromatin maintenance in Arabidopsis (Pierre Bourguet, Leticia López-González, Ángeles Gómez-Zambrano, Thierry Pélissier, Amy Hesketh, Magdalena E. Potok, Marie-Noëlle Pouch-Pélissier, Magali Perez, Olivier Da Ines, David Latrasse, Charles I. White, Steven E. Jacobsen, Moussa Benhamed and Oli, )
- From FAANG to fork: application of highly annotated genomes to improve farmed animal production (Emily L. Clark, Alan L. Archibald, Hans D. Daetwyler, Martien A. M. Groenen, Peter W. Harrison, Ross D. Houston, Christa Kühn, Sigbjørn Lien, Daniel J. Macqueen, James M. Reecy, Diego Robledo, Mick Watson, Christopher K. Tuggle and Elisabetta Giuffra, )
- The evolution of relapse of adult T cell acute lymphoblastic leukemia (Inés Sentís, Santiago Gonzalez, Eulalia Genescà, Violeta García-Hernández, Ferran Muiños, Celia Gonzalez, Erika López-Arribillaga, Jessica Gonzalez, Lierni Fernandez-Ibarrondo, Loris Mularoni, Lluís Espinosa, Beatriz Bellosillo, Josep-Maria Ribera, Anna B, )
- A pitfall for machine learning methods aiming to predict across cell types (Jacob Schreiber, Ritambhara Singh, Jeffrey Bilmes and William Stafford Noble, )
- Deep sequencing reveals a DAP1 regulatory haplotype that potentiates autoimmunity in systemic lupus erythematosus (Prithvi Raj, Ran Song, Honglin Zhu, Linley Riediger, Dong-Jae Jun, Chaoying Liang, Carlos Arana, Bo Zhang, Yajing Gao, Benjamin E. Wakeland, Igor Dozmorov, Jinchun Zhou, Jennifer A. Kelly, Bernard R. Lauwerys, Joel M. Guthridge, Nancy J. Olsen…, )
- Stairway Plot 2: demographic history inference with folded SNP frequency spectra (Xiaoming Liu and Yun-Xin Fu, )
- A versatile toolkit for CRISPR-Cas13-based RNA manipulation in Drosophila (Nhan Huynh, Noah Depner, Raegan Larson and Kirst King-Jones, )