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
- Genomic variants associated with type 2 diabetes mellitus among Filipinos (Eva Maria C. Cutiongco-de la Paz, Jose B. Nevado Jr., Elizabeth T. Paz-Pacheco, Gabriel V. Jasul Jr., Aimee Yvonne Criselle L. Aman, Mark David G. Francisco, )
- From meta-analysis to Mendelian randomization: Unidirectional perspectives on the association of glaucoma with depression and anxiety (Jie Deng, YuHui Qin, )
- Prediction of virus-host associations using protein language models and multiple instance learning (Dan Liu, Francesca Young, Kieran D. Lamb, David L. Robertson, Ke Yuan, )
- Cell type-specific weighting-factors to solve solid organs-specific limitations of single cell RNA-sequencing (Kengo Tejima, Satoshi Kozawa, Thomas N. Sato, )
- Rapid prediction of key residues for foldability by machine learning model enables the design of highly functional libraries with hyperstable constrained peptide scaffolds (Fei Cai, Yuehua Wei, Daniel Kirchhofer, Andrew Chang, Yingnan Zhang, )
- No association between genetically predicted vitamin D levels and Parkinson’s disease (Zihao Wang, Huan Xia, Yunfa Ding, Ranran Lu, Xinling Yang, )
- Integrative omics analysis identifies biomarkers of septic cardiomyopathy (Kexin Cai, Yuqing Luo, Hongyin Chen, Yanfang Dong, Yunyun Su, Chen Lin, Chuanqi Cai, Yikbin Shi, Siming Lin, Guili Lian, Zhihong Lin, Shaodan Feng, )
BMC Genomics
- New genomic resources inform transcriptomic responses to heavy metal toxins in the common Eastern bumble bee Bombus impatiens (Amy L. Toth, Christopher D. R. Wyatt, Rick E. Masonbrink, Katherine S. Geist, Ryan Fortune, Sarah B. Scott, Emeline Favreau, Sandra M. Rehan, Seirian Sumner, Mary M. Gardiner and Frances S. Sivakoff, )
- Correction: Identification of structural variation related to spawn capability of Penaeus vannamei (Yongyu Huang, Hao Wang, Shengyu Xu, Jinli Liu, Qifan Zeng, Jingjie Hu and Zhenmin Bao, )
- Effects of exogenous melatonin on drought stress in celery (Apium graveolens L.): unraveling the modulation of chlorophyll and glucose metabolism pathways (Jiageng Du, Weilong Li, Zhuo Wang, Zhiheng Chen, Chao Wang, Wei Lu, Aisheng Xiong, Guofei Tan, Yangxia Zheng and Mengyao Li, )
- Transcriptome-wide identification and analysis reveals m6A regulation of metabolic reprogramming in shrimp (Marsupenaeus japonicus) under virus infection (Xumei Sun, Yu-Lei Chen, Fan Xin and Siyuan Zhang, )
- Correction: ProbC: joint modeling of epigenome and transcriptome effects in 3D genome (Emre Sefer, )
- Comparative transcriptomic and hormonal analyses reveal potential regulation networks of adventitious root formation in Metasequoia glyptostroboides Hu et Cheng (Yuping Xiong, Xiaohong Chen, Junyu Liu, Yuan Li, Zhan Bian, Xinhua Zhang, Songjun Zeng, Jaime A. Teixeira da Silva and Guohua Ma, )
- qGO: a novel method for quantifying the diversity of mitochondrial genome organization (Haihe Shi, Shuai Yang, Meicai Wei and Gengyun Niu, )
RNA-Seq Blog
- Single-cell RNA sequencing reveals how marine worms regenerate lost body parts ()
- Single-cell RNA sequencing reveals immune dysfunction increases cancer risk in obese populations ()
- scPair – Boosting single cell multimodal analysis by leveraging implicit feature selection and single cell atlases ()
- AI tool ‘sees’ cancer gene expression in biopsy images ()
- Lexogen launches streamlined, large-scale RNA-Seq service for blood samples ()
- Transcriptome-wide analysis of the 5′ Cap status of RNA and RNA sequencing ()
- Concurrent DNA and RNA sequencing detect more actionable variants in NSCLC ()
- Deciphering gene expression patterns using large-scale transcriptomic data ()
Bioinformatics
- Pf-HaploAtlas: an interactive web app for spatiotemporal analysis of P. falciparum genes ()
- Gene count estimation with pytximport enables reproducible analysis of bulk RNA sequencing data in Python ()
- MMOSurv: Meta-learning for few-shot survival analysis with multi-omics data ()
- Micro-DeMix: a mixture beta-multinomial model for investigating the heterogeneity of the stool microbiome compositions ()
- PhosX: data-driven kinase activity inference from phosphoproteomics experiments ()
- DrugRepPT: a deep pre-training and fine-tuning framework for drug repositioning based on drug’s expression perturbation and treatment effectiveness ()
- Mutual information for detecting multi-class biomarkers when integrating multiple bulk or single-cell transcriptomic studies ()
PLoS Computational Biology
- Learning patterns of HIV-1 resistance to broadly neutralizing antibodies with reduced subtype bias using multi-task learning (Aime Bienfait Igiraneza, Panagiota Zacharopoulou, Robert Hinch, Chris Wymant, Lucie Abeler-Dörner, John Frater, Christophe Fraser, )
- Co-contraction embodies uncertainty: An optimal feedforward strategy for robust motor control (Bastien Berret, Dorian Verdel, Etienne Burdet, Frédéric Jean, )
- A framework for counterfactual analysis, strategy evaluation, and control of epidemics using reproduction number estimates (Baike She, Rebecca Lee Smith, Ian Pytlarz, Shreyas Sundaram, Philip E. Paré, )
- Upstream open reading frames may contain hundreds of novel human exons (Hyun Joo Ji, Steven L. Salzberg, )
- Prediction of virus-host associations using protein language models and multiple instance learning (Dan Liu, Francesca Young, Kieran D. Lamb, David L. Robertson, Ke Yuan, )
- Efficient modelling of infectious diseases in wildlife: A case study of bovine tuberculosis in wild badgers (Evandro Konzen, Richard J. Delahay, Dave J. Hodgson, Robbie A. McDonald, Ellen Brooks Pollock, Simon E. F. Spencer, Trevelyan J. McKinley, )
- Reward Bases: A simple mechanism for adaptive acquisition of multiple reward types (Beren Millidge, Yuhang Song, Armin Lak, Mark E. Walton, Rafal Bogacz, )
BMC Bioinformatics
- Conformal novelty detection for multiple metabolic networks (Ariane Marandon, Tabea Rebafka, Nataliya Sokolovska and Hédi Soula, )
- Rare copy number variant analysis in case–control studies using snp array data: a scalable and automated data analysis pipeline (Haydee Artaza, Ksenia Lavrichenko, Anette S. B. Wolff, Ellen C. Røyrvik, Marc Vaudel and Stefan Johansson, )
- Mining contextually meaningful subgraphs from a vertex-attributed graph (Riyad Hakim and Saeed Salem, )
- Robust double machine learning model with application to omics data (Xuqing Wang, Yahang Liu, Guoyou Qin and Yongfu Yu, )
- A mapping-free natural language processing-based technique for sequence search in nanopore long-reads (Tomasz Strzoda, Lourdes Cruz-Garcia, Mustafa Najim, Christophe Badie and Joanna Polanska, )
- Closha 2.0: a bio-workflow design system for massive genome data analysis on high performance cluster infrastructure (Gunhwan Ko, Pan-Gyu Kim, Byung-Ha Yoon, JaeHee Kim, Wangho Song, IkSu Byeon, JongCheol Yoon, Byungwook Lee and Young-Kuk Kim, )
- DeepBP: Ensemble deep learning strategy for bioactive peptide prediction (Ming Zhang, Jianren Zhou, Xiaohua Wang, Xun Wang and Fang Ge, )
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
- Setting the stage for using AI in language tasks 50 years ago ()
- ‘Heroic interference’ should not be the endgame of coral-reef restoration (Mikhail Matz, )
- Communicate the risk as well as the promise of weight-loss drugs (Bo Li, Yu Li, Zhihe Zhao, Longjiang Li, )
- Nobel-prizewinning economics research says don’t dismantle DEI initiatives (Afsaneh Shirani, )
- Words won’t reduce the impact of conflict on nature — what’s needed is action (Christopher P. Dunn, Brendan Mackey, Kathryn Gwiazdon, )
- How the world will weather Trump’s withdrawal from global agreements (David G. Victor, )
- Leon Cooper obituary: Nobel laureate who developed theory of superconductivity (Georgina Ferry, )
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
- VI-VS: calibrated identification of feature dependencies in single-cell multiomics (Pierre Boyeau, Stephen Bates, Can Ergen, Michael I. Jordan and Nir Yosef, )
- Cohesin distribution alone predicts chromatin organization in yeast via conserved-current loop extrusion (Tianyu Yuan, Hao Yan, Kevin C. Li, Ivan Surovtsev, Megan C. King and Simon G. J. Mochrie, )
- Adenine base editors induce off-target structure variations in mouse embryos and primary human T cells (Leilei Wu, Shutan Jiang, Meisong Shi, Tanglong Yuan, Yaqin Li, Pinzheng Huang, Yingqi Li, Erwei Zuo, Changyang Zhou and Yidi Sun, )
- IAMSAM: image-based analysis of molecular signatures using the Segment Anything Model (Dongjoo Lee, Jeongbin Park, Seungho Cook, Seongjin Yoo, Daeseung Lee and Hongyoon Choi, )
- SpottedPy quantifies relationships between spatial transcriptomic hotspots and uncovers environmental cues of epithelial-mesenchymal plasticity in breast cancer (Eloise Withnell and Maria Secrier, )
- CaClust: linking genotype to transcriptional heterogeneity of follicular lymphoma using BCR and exomic variants (Kazimierz Oksza-Orzechowski, Edwin Quinten, Shadi Shafighi, Szymon M. Kiełbasa, Hugo W. van Kessel, Ruben A. L. de Groen, Joost S. P. Vermaat, Julieta H. Sepúlveda Yáñez, Marcelo A. Navarrete, Hendrik Veelken, Cornelis A. M. van Bergen and Ewa Szczurek, )
- TDFPS-Designer: an efficient toolkit for barcode design and selection in nanopore sequencing (Junhai Qi, Zhengyi Li, Yao-zhong Zhang, Guojun Li, Xin Gao and Renmin Han, )