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
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Where financial disparities are greatest, the murder rate tends to be high
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Fixing Wasting Muscles
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Scientists edited dogs' genes to correct a common form of muscle dystrophy
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Artificial Wood
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The synthetic material is both robust and versatile
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Flooding the Senses
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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
- Stage-specific transcriptomic analysis reveals insights into the development, reproduction and biological function of allergens in the European house dust mite Dermatophagoides pteronyssinus (José Cristian Vidal-Quist, Félix Ortego, Bart N. Lambrecht, Stephane Rombauts and Pedro Hernández-Crespo, )
- Correction: Genome-wide identification and expression analysis of the JMJ-C gene family in melon (Cucumis melo L.) reveals their potential role in fruit development (Wuyun Jin, Wei Yan, Ming Ma, Agula Hasi and Gen Che, )
- A Mg2+-dependent high-yield method for extracting high-molecular-weight genomic DNA from a single planarian specimen (Ao Li, Bingrui Sun, Ying Zhang, Ping Yu, Jicheng Qu, Hongkuan Deng, Qiuxiang Pang and Fengtang Yang, )
- Transcriptome analysis reveals age-specific growth characteristics in the rumen of Hanwoo (Korean native cattle) steers (Yejee Park, Sunsik Jang, Han-Ha Chai, Ju-Whan Son, Dajeong Lim and Woncheoul Park, )
- Transcriptomic analysis of wild Cannabis sativa: insights into tissue- and stage-specific expression and secondary metabolic regulation (Jinyuan Hu, Zishi Wang, He Xu, Zhenlong Wang, Ning Li, Rui Feng, Jianyu Yin, Fangru Liu and Baishi Wang, )
- Identification and expression analysis of N6-methyltransferase and demethylase in rapeseed (Brassica napus L.) (Xiaoyu Chen, Yu Kang, Shun Li, Bo Yang, Xiaoyan Xia, Zhonghua Wang, Lunwen Qian, Xinhua Xiong, Lei Kang and Xin He, )
- Preservation of milk in liquid nitrogen during sample collection does not affect the RNA quality for RNA-seq analysis (Lucía Jiménez-Montenegro, Leopoldo Alfonso, Beatriz Soret, José A. Mendizabal and Olaia Urrutia, )
RNA-Seq Blog
- Worm Perturb-Seq – massively parallel whole-animal RNAi and RNA-seq ()
- Summit Health expands precision medicine with RNA sequencing and liquid biopsy services ()
- The Curated Cancer Cell Atlas provides a comprehensive characterization of tumors at single-cell resolution ()
- New method helps identify hormone-disrupting chemicals – without animal testing ()
- RNA sequencing reveals early mitochondrial dysfunction shared across ALS mutations ()
- PHOTON – subcellular level spatial transcriptomics ()
- Lexogen Launches miRVEL Discovery – Cutting-edge Small RNA-Seq Library Prep Kit for sRNA Discovery and Biomarker studies ()
- Immunopipe – a comprehensive and flexible scRNA-seq and scTCR-seq data analysis pipeline ()
Bioinformatics
- A Deep Learning-based Method for Predicting the Frequency Classes of Drug Side Effects Based on Multi-Source Similarity Fusion ()
- scNucMap: mapping the nucleosome landscapes at single-cell resolution ()
- Simple controls exceed best deep learning algorithms and reveal foundation model effectiveness for predicting genetic perturbations ()
- MIMIC: A Python Package for Simulating, Inferring, and Predicting Microbial Community Interactions and Dynamics ()
- TRENDY: Gene Regulatory Network Inference Enhanced by Transformer ()
- esMPRA: an easy-to-use systematic pipeline for MPRA experiment quality control and data analysis ()
- OrthologAL: A Shiny application for quality- aware humanization of non-human pre-clinical high-dimensional gene expression data ()
PLoS Computational Biology
- The respiratory cycle modulates distinct dynamics of affective and perceptual decision-making (Malthe Brændholt, Niia Nikolova, Melina Vejlø, Leah Banellis, Francesca Fardo, Daniel S. Kluger, Micah Allen, )
- Geometric and mechanical guidance: Role of stigmatic epidermis in early pollen tube pathfinding in arabidopsis (Lucie Riglet, Catherine Quilliet, Christophe Godin, Karin John, Isabelle Fobis-Loisy, )
- Relating sparse and predictive coding to divisive normalization (Yanbo Lian, Anthony N. Burkitt, )
- Stimulus uncertainty and relative reward rates determine adaptive responding in perceptual decision-making (Luis de la Cuesta-Ferrer, Christina Koß, Sarah Starosta, Nils Kasties, Daniel Lengersdorf, Frank Jäkel, Maik C. Stüttgen, )
- Improved detection of microbiome-disease associations via population structure-aware generalized linear mixed effects models (microSLAM) (Miriam Goldman, Chunyu Zhao, Katherine S. Pollard, )
- MaxComp: Predicting single-cell chromatin compartments from 3D chromosome structures (Yuxiang Zhan, Francesco Musella, Frank Alber, )
- Cell-TRACTR: A transformer-based model for end-to-end segmentation and tracking of cells (Owen M. O’Connor, Mary J. Dunlop, )
BMC Bioinformatics
- CRISP: correlation-refined image segmentation process (Jennifer K. Briggs, Erli Jin, Matthew J. Merrins and Richard K. P. Benninger, )
- Gene2role: a role-based gene embedding method for comparative analysis of signed gene regulatory networks (Xin Zeng, Shu Liu, Bowen Liu, Weihang Zhang, Wanzhe Xu, Fujio Toriumi and Kenta Nakai, )
- KF-NIPT: K-mer and fetal fraction-based estimation of chromosomal anomaly from NIPT data (Dongin Kim, Ji Yeon Sohn, Jin Hee Cho, Ji-Hye Choi, Gwi-young Oh and Hyun Goo Woo, )
- scHiCSRS: a self-representation smoothing method with Gaussian mixture model for imputing single cell Hi-C data (Qing Xie, Wang Meng and Shili Lin, )
- GNNs and ensemble models enhance the prediction of new sRNA-mRNA interactions in unseen conditions (Shani Cohen, Lior Rokach and Isana Veksler-Lublinsky, )
- Scmaskgan: masked multi-scale CNN and attention-enhanced GAN for scRNA-seq dropout imputation (You Wu, Li Xu, Xiaohong Cong, Hanxiao Li and Yanli Li, )
- The application of compressed sensing on tumor mutation burden calculation from overlapped pooling sequencing data (Yue Cui, Yi Qiao, Rongming An, Xuan Pan and Jing Tu, )
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
- Electricity-driven enzymatic dynamic kinetic oxidation (Beibei Zhao, Yuanyuan Xu, Qin Zhu, Aokun Liu, Xichao Peng, Tianying Zhang, Lu Yu, Yan Zhang, Xiaoqiang Huang, )
- Taking common medicines might matter for cancer treatment (François-Xavier Mahon, )
- Address academic bullying through structural reform (Steven Bell, )
- The forest space age needs eyes on the ground (Oliver Phillips, Alvaro Duque, Lillian Rodriguez, Irié Casimir Zo-Bi, )
- The diet crazes of the nineteenth century ()
- Global measles eradication goal is urgently needed (David N. Durrheim, Jon K. Andrus, Shahina Tabassum, David Githanga, Mira Kojouharova, Nadia Teleb, )
- Time-management skills I honed as a PhD student now serve me well in industry (Maya Gosztyla, )
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
- AMHY and sex determination in egg-laying mammals (Linda Shearwin-Whyatt, Jane Fenelon, Hongshi Yu, Andrew Major, Zhipeng Qu, Yang Zhou, Keith Shearwin, James Galbraith, Alexander Stuart, David Adelson, Guojie Zhang, Michael Pyne, Stephen Johnston, Craig Smith, Marilyn Renfree and Frank Grützner, )
- Author Correction: Efficient precise knockin with a double cut HDR donor after CRISPR/Cas9-mediated double-stranded DNA cleavage (Jian-Ping Zhang, Xiao-Lan Li, Guo-Hua Li, Wanqiu Chen, Cameron Arakaki, Gary D. Botimer, David Baylink, Lu Zhang, Wei Wen, Ya-Wen Fu, Jing Xu, Noah Chun, Weiping Yuan, Tao Cheng and Xiao-Bing Zhang, )
- Precise measurement of molecular phenotypes with barcode-based CRISPRi systems (Joseph H. Lobel and Nicholas T. Ingolia, )
- Analyzing the relationship of RNA and DNA methylation with gene expression (Shangqian Xie, Darren Hagen, Gabrielle M. Becker, Kimberly M. Davenport, Katie A. Shira, Morgan R. Stegemiller, Jacob W. Thorne, Sarem Khilji, Denise Konetchy, Patricia Villamediana, Brenda M. Murdoch and Stephanie D. McKay, )
- Incorporating scale uncertainty in microbiome and gene expression analysis as an extension of normalization (Michelle Pistner Nixon, Gregory B. Gloor and Justin D. Silverman, )
- A survey of sequence-to-graph mapping algorithms in the pangenome era (Yingbo Cui, Chenchen Peng, Zeyu Xia, Canqun Yang and Yifei Guo, )
- H3K4me3 binding ALFIN-LIKE proteins recruit SWR1 for gene-body deposition of H2A.Z (Linhao Xu, Yafei Wang, Xueying Li, Qin Hu, Vanda Adamkova, Junjie Xu, C. Jake Harris and Israel Ausin, )