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
- Iron-mediated post-transcriptional regulation in Toxoplasma gondii (Megan A. Sloan, Adam Scott, Dana Aghabi, Lucia Mrvova, Clare R. Harding, )
- A CACTA-like transposon in the Anthocyanidin synthase 1 (Ans-1) gene is responsible for apricot fruit colour in the raspberry (Rubus idaeus) cultivar ‘Varnes’ (Daniel James Sargent, Matteo Buti, Stefan Martens, Claudio Pugliesi, Kjersti Aaby, Dag Røen, Chandra Bhan Yadav, Felicidad Fernández Fernández, Muath Alsheikh, Jahn Davik, R. Jordan Price, )
- Uncovering the genetic basis of milk production traits in Mexican Holstein cattle based on individual markers and genomic windows (José G. Cortes-Hernández, Adriana García-Ruiz, Francisco Peñagaricano, Hugo H. Montaldo, Felipe J. Ruiz-López, )
- A machine learning driven computationally efficient horse shoe shaped antenna design for internet of medical things (Umhara Rasool Khan, Javaid A. Sheikh, Aqib Junaid, Shazia Ashraf, Altaf A. Balkhi, )
- Integrative analysis of the metabolome and transcriptome provides insights into the mechanisms of flavonoid biosynthesis in Polygonatum (Xiaolin Wan, Qiang Xiao, )
- Computational and In silico study of novel fungicides against combating root rot, gray mold, fusarium wilt, and cereal rust (Mollah Naimuzzaman, Md Mahabub Hasan, Ajoy Kumer, Abu Yousuf Hossin, Mohammad Harun-Ur-Rashid, Swapan Kumar Roy, Abu Noman Faruq Ahmmed, Jamal Uddin, )
- Potential Azo-8-hydroxyquinoline derivatives as multi-target lead candidates for Alzheimer’s disease: An in-depth in silico study of monoamine oxidase and cholinesterase inhibitors (Fatima Zahra Guerguer, Bouchra Rossafi, Oussama Abchir, Yasir S. Raouf, Dhabya Bakhit Albalushi, Abdelouahid Samadi, Samir Chtita, )
BMC Genomics
- A computational HLA allele-typing protocol to de-noise and leverage nanopore amplicon data (Jalal Siddiqui, Rohita Sinha, James Grantham, Ronnie LaCombe, Judith R. Alonzo, Scott Cowden and Steven Kleiboeker, )
- Transcriptomic analysis of Myxococcus xanthus csgA, fruA, and mrpC mutants reveals extensive and diverse roles of key regulators in the multicellular developmental process (Mark A. Farrugia, Ramya Rajagopalan and Lee Kroos, )
- Genetic diversity and population structure in Ethiopian mustard (Brassica carinata A. Braun) revealed by high-density DArTSeq SNP genotyping (Yirssaw Demeke Ambaw, Andargachew Gedebo Abitea and Temesgen Magule Olango, )
- scAMZI: attention-based deep autoencoder with zero-inflated layer for clustering scRNA-seq data (Lin Yuan, Zhijie Xu, Boyuan Meng and Lan Ye, )
- Identification and expression profile analysis of circRNAs associated with goat uterus with different fecundity during estrous cycle (Xiaolong Du, Yufang Liu, Xiaoyun He, Lin Tao, Meiying Fang and Mingxing Chu, )
- Integrated analysis of tyrosine-induced MiRNA and mRNA expression profiles in melanocytes reveals the regulatory role of miR-1560-3p in melanin deposition in Xichuan black-bone chickens (Zhiyuan Zhang, Pengwei Zhang, Fumin He, Yingdong Hou, Xiaowen Geng, Ruilong Xu, Ruiting Li, Yadong Tian, Wenting Li, Guirong Sun, Ruirui Jiang, Xiaojun Liu, Ruili Han, Guoxi Li, Xiangtao Kang and Donghua Li, )
- RNA-sequencing demonstrates transcriptional differences between human vocal fold fibroblasts and myofibroblasts (Michelle Bretl, Lingxin Cheng, Christina Kendziorski and Susan L. Thibeault, )
RNA-Seq Blog
- scCRAFT – separates cell-type-related signals from batch effects for reliable multi-batch integration ()
- RNA sequencing reveals how cells ensure accurate mRNA splicing ()
- CHOIR improves significance-based detection of cell types and states from single-cell data ()
- Identification of lncRNAs differentially expressed in Alzheimer’s disease brains using RNA sequencing ()
- A practical guide for single-cell transcriptome data analysis in neuroscience ()
- SpaGRN – Investigating spatially informed regulatory paths for spatially resolved transcriptomics data ()
- CoupleVAE – coupled variational autoencoders for predicting perturbational single-cell RNA sequencing data ()
- Scale Bio Joins Chan Zuckerberg Initiative’s Billion Cells Project, Accelerating Single Cell Research at Unprecedented Scale ()
Bioinformatics
- Finding Antibodies in Cryo-EM maps with CrAI ()
- Approximating edit distances between complex tandem repeats efficiently ()
- Sawfish: Improving long-read structural variant discovery and genotyping with local haplotype modeling ()
- Rethinking GWAS: how lessons from genetic screens and artificial intelligence could reveal biological mechanisms ()
- Gradient matching accelerates mixed-effects inference for biochemical networks ()
- Predicting Explainable Dementia Types with LLM-aided Feature Engineering ()
- ROICellTrack: A deep learning framework for integrating cellular imaging modalities in subcellular spatial transcriptomic profiling of tumor tissues ()
PLoS Computational Biology
- Editorial Note: In silico knockout studies of xenophagic capturing of Salmonella (The PLOS Computational Biology Editors, )
- Transcriptomic landscape around wound bed defines regenerative versus non-regenerative outcomes in mouse digit amputation (Archana Prabahar, Connie S. Chamberlain, Ray Vanderby, William L. Murphy, William Dangelo, Kulkarni Mangesh, Bryan Brown, Barsanjit Mazumder, Stephen Badylak, Peng Jiang, )
- Comprehensive characterization of respiratory genes based on a computational framework in pan-cancer to develop stratified treatment strategies (Caiyu Zhang, Chenyu Liu, Zhuoru Wang, Di Wang, Wenli Chen, Jian Li, Qianyi Lu, Jiajun Zhou, Yetong Chang, Peng Wang, Yue Gao, Junwei Wang, Hui Zhi, Shangwei Ning, )
- Multiple patterns of persistent inward currents with multiple types of repetitive firings in medullary serotonergic neurons of mice: An experimental and modeling study (Yi Cheng, Xingyu Wang, Qiang Zhang, Renkai Ge, Mei Zhou, Yue Dai, )
- Chromatin structures from integrated AI and polymer physics model (Eric R. Schultz, Soren Kyhl, Rebecca Willett, Juan J. de Pablo, )
- Mathematical modeling unveils the timeline of CAR-T cell therapy and macrophage-mediated cytokine release syndrome (Daniela S Santurio, Luciana R C Barros, Ingmar Glauche, Artur c Fassoni, )
- DelaySSA: stochastic simulation of biochemical systems and gene regulatory networks with or without time delays (Ziyan Jin, Xinyi Zhou, Zhaoyuan Fang, )
BMC Bioinformatics
- Bayesian compositional generalized linear mixed models for disease prediction using microbiome data (Li Zhang, Xinyan Zhang, Justin M. Leach, A. K. M. F. Rahman, Carrie R. Howell and Nengjun Yi, )
- Goistrat: gene-of-interest-based sample stratification for the evaluation of functional differences (Carlos Uziel Pérez Malla, Jessica Kalla, Andreas Tiefenbacher, Gabriel Wasinger, Kilian Kluge, Gerda Egger and Raheleh Sheibani-Tezerji, )
- DconnLoop: a deep learning model for predicting chromatin loops based on multi-source data integration (Junfeng Wang, Kuikui Cheng, Chaokun Yan, Huimin Luo and Junwei Luo, )
- optRF: Optimising random forest stability by determining the optimal number of trees (Thomas M. Lange, Mehmet Gültas, Armin O. Schmitt and Felix Heinrich, )
- Amogel: a multi-omics classification framework using associative graph neural networks with prior knowledge for biomarker identification (Chia Yan Tan, Huey Fang Ong, Chern Hong Lim, Mei Sze Tan, Ean Hin Ooi and KokSheik Wong, )
- SCITUNA: single-cell data integration tool using network alignment (Aissa Houdjedj, Yacine Marouf, Mekan Myradov, Süleyman Onur Doğan, Burak Onur Erten, Oznur Tastan, Cesim Erten and Hilal Kazan, )
- DMoVGPE: predicting gut microbial associated metabolites profiles with deep mixture of variational Gaussian Process experts (Qinghui Weng, Mingyi Hu, Guohao Peng and Jinlin Zhu, )
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
- Unlocking the secrets of sleep (Herb Brody, )
- The infuriating, expensive road to a good night’s sleep (Rachel Nuwer, )
- Microbial warfare brought us CRISPR. What big breakthroughs could be next? (Amber Dance, )
- New treatments to put insomnia to bed (Rachel Nuwer, )
- How do I explain the publication gap I ended up with after a hostile manager? (Bianca Nogrady, )
- Research round-up: sleep (Bianca Nogrady, )
- The life aquatic: this board game lets you dip into marine ecology (Angela Chuang, Orlando Schwery, )
Science
- A broad defense against SARS-like viruses (Vinson, V., )
- RNA editing restricts ciliary kinases (Jiang, D., )
- Not your usual superconductor (Stajic, J., )
- Blocking heat in two ways (Grocholski, B., )
- SagA promotes immunotherapy response (Kelly, P. N., )
- Machine learning solves RNA puzzles (Jiang, D., )
- Taking a BiTE out of tumors (Malo, C. S., )
PNAS
- A multiomic study uncovers a bZIP23-PER1A-mediated detoxification pathway to enhance seed vigor in rice [Agricultural Sciences] (Wei-Qing Wang, Ding-Yi Xu, Ya-Ping Sui, Xiao-Hui Ding, Xian-Jun Song, )
- Indirect influence in social networks as an induced percolation phenomenon [Applied Mathematics] (Jiarong Xie, Xiangrong Wang, Ling Feng, Jin-Hua Zhao, Wenyuan Liu, Yamir Moreno, Yanqing Hu, )
- Precision targeting tumor cells using cancer-specific InDel mutations with CRISPR-Cas9 [Medical Sciences] (Taejoon Kwon, Jae Sun Ra, Soyoung Lee, In-Joon Baek, Keon Woo Khim, Eun A Lee, Eun Kyung Song, Daniyar Otarbayev, Woojae Jung, Yong Hwan Park, Minwoo Wie, Juyoung Bae, Himchan Cheng, Jun Hong Park, Namwoo Kim, Yuri Seo, Seongmin Yun, Ha Eun Kim, Hyo Eun M, )
- An in-frame deletion mutation in the degron tail of auxin coreceptor IAA2 confers resistance to the herbicide 2,4-D in Sisymbrium orientale [Agricultural Sciences] (Marcelo R. A. de Figueiredo, Anita Kupper, Jenna M. Malone, Tiȷana Petrovic, Ana Beatriz T. B. de Figueiredo, Grace Campagnola, Olve B. Peersen, Kasavaȷhala V. S. K. Prasad, Eric L. Patterson, Anireddy S. N. Reddy, Martin F. Kubeš, Ri, )
- Scaling laws in enzyme function reveal a new kind of biochemical universality [Biophysics and Computational Biology] (Dylan C. Gagler, Bradley Karas, Christopher P. Kempes, John Malloy, Veronica Mierzejewski, Aaron D. Goldman, Hyunju Kim, Sara I. Walker, )
- Modeling suggests gene editing combined with vaccination could eliminate a persistent disease in livestock [Genetics] (Gertje Eta Leony Petersen, Jaap B. Buntjer, Fiona S. Hely, Timothy John Byrne, Andrea Doeschl-Wilson, )
- BEND3 safeguards pluripotency by repressing differentiation-associated genes [Genetics] (Fredy Kurniawan, Neha Chetlangia, Mohammad Kamran, Christophe E. Redon, Lorinc Pongor, Qinyu Sun, Yo-Chuen Lin, Vijay Mohan, Oways Shaqildi, Darya Asoudegi, Qinyu Hao, Abid Khan, Mirit I. Aladjem, Kannanganattu V. Prasanth, Supriya G. Prasanth, )
Genome Biology
- MIDAA: deep archetypal analysis for interpretable multi-omic data integration based on biological principles (Salvatore Milite, Giulio Caravagna and Andrea Sottoriva, )
- The histone acetyltransferase CBP participates in regulating the DNA damage response through ATM after double-strand breaks (Wafaa S. Ramadan, Samrein B. M. Ahmed, Iman M. Talaat, Lama Lozon, Soraya Mouffak, Timo Gemoll, Wael Y. Mansour and Raafat El-Awady, )
- Benchmark of cellular deconvolution methods using a multi-assay dataset from postmortem human prefrontal cortex (Louise A. Huuki-Myers, Kelsey D. Montgomery, Sang Ho Kwon, Sophia Cinquemani, Nicholas J. Eagles, Daianna Gonzalez-Padilla, Sean K. Maden, Joel E. Kleinman, Thomas M. Hyde, Stephanie C. Hicks, Kristen R. Maynard and Leonardo Collado-Torres, )
- CNRein: an evolution-aware deep reinforcement learning algorithm for single-cell DNA copy number calling (Stefan Ivanovic and Mohammed El-Kebir, )
- Missing cell types in single-cell references impact deconvolution of bulk data but are detectable (Adriana Ivich, Natalie R. Davidson, Laurie Grieshober, Weishan Li, Stephanie C. Hicks, Jennifer A. Doherty and Casey S. Greene, )
- Systematic optimization and prediction of cre recombinase for precise genome editing in mice (Valerie Erhardt, Elli Hartig, Kristian Lorenzo, Hannah R. Megathlin, Basile Tarchini and Vishnu Hosur, )
- Genomic prediction with kinship-based multiple kernel learning produces hypothesis on the underlying inheritance mechanisms of phenotypic traits (Daniele Raimondi, Nora Verplaetse, Antoine Passemiers, Deborah Sarah Jans, Isabelle Cleynen and Yves Moreau, )