Tweets on Gen/Transcript/Prote-Omics
News by Scientific American
The U.S. Congress has not protected health or the environment. Time to make it step up
Where financial disparities are greatest, the murder rate tends to be high
Scientists edited dogs' genes to correct a common form of muscle dystrophy
The synthetic material is both robust and versatile
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
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
Genomic origin and consequence of captive red junglefowl in zoological parks
Yuki Matsuda, Masaki Eda, Shuichi Ito and Tsuyoshi Shimmura
Transcriptome and small RNA sequencings reveal the response of tobacco to aphid infestation
Jiong-Yi Li, Yi-Xuan You, Xiao-Wei Wang, Jian-Ping Chen and Ping Li
X chromosome inactivation across primary human tissues is mostly complete, with significant implications for genetic and clinical studies
Daniel Shriner, Ayo P. Doumatey, Lin Lei, Mateus H. Gouveia, Karlijn A. C. Meeks, Elisabeth F. Heuston, Jie Zhou, Adebowale A. Adeyemo and Charles N. Rotimi
First development of a 100 K SNP array for small yellow croaker and its application in genomic selection for growth and disease resistance
Feng Liu, Rui Wang, Ting Ye, Jiajie Zhu, Dandan Guo, Wei Zhan and Bao Lou
Integration of mRNA and MiRNA analysis reveals the molecular mechanisms of testicular development in newborn and adult sheep
Binpeng Xi, Zengkui Lu, Shengguo Zhao, Rui Zhang, Jianye Li, Xuejiao An and Yaojing Yue
PCR optimization for buccal swab-derived samples: overcoming sporadic inhibition with bovine serum albumin
Stefanie Tietze, Julia Phieler, Sabine Bergmann, Juliane Grimmer, Kathrin Putke, Bastian Joffroy, Yannic Utz, Katrin Hengst, Bianca Heyn, Diana Panhans, Alexander H. Schmidt, Anja Klussmeier and Vinzenz Lange
Plastome comparison and phylogenomic analysis of threatened wild Egyptian Capparis taxa
Norhan Amar, Heba A. M. AbdAlla, Qing-Feng Wang, Mohamed Abd. S. El Zayat, Hager R. Belal, Sheng-Wei Wang, Tao Wan, Mohamed Hamdy Amar and Jun-Nan Wan
RNA-Seq Blog
Bioinformatics
PLoS Computational Biology
GAN-enhanced machine learning and metabolic modeling identify reprogramming in pancreatic cancer
Tahereh Razmpour, Masoud Tabibian, Arman Roohi, Rajib Saha
DSCA-HLAII: A dual-stream cross-attention model for predicting peptide–HLA class II interaction and presentation
Ke Yan, Hongjun Yu, Shutao Chen, Alexey K. Shaytan, Bin Liu, Youyu Wang
CellPredX, a computational framework for cross-data type, cross-sample, and cross-protocol cell type annotation through domain adaptation and deep metric learning
Yan Liu, Yu Xia, He Yan, Long-Chen Shen, Yiheng Zhu, Ji-Peng Qiang, Guo Wei
Coancestry superposed on admixed populations yields measures of relatedness at individual-level resolution
Danfeng Chen, John D. Storey
When predict can also explain: Few-shot prediction to select better neural latents
Kabir V. Dabholkar, Omri Barak
Inverse modeling unveils governing law of mechano-chemical dynamics of epithelial migration
Yuto Kikuchi, Yoshifumi Asakura, Kazuhiro Aoki, Yohei Kondo, Honda Naoki
Gaussian process emulation for exploring complex infectious disease models
Anna M. Langmüller, Kiran A. Chandrasekher, Benjamin C. Haller, Samuel E. Champer, Courtney C. Murdock, Philipp W. Messer
BMC Bioinformatics
SynergyImage: image-based model for drug combinations synergy score prediction
Maryam Mehrabani, Amir Lakizadeh, Alireza Fotuhi Siahpirani and Ali Masoudi-Nejad
Denoising single-cell RNA-seq data with a deep learning-embedded statistical framework
Qinhuan Luo, Yongzhen Yu and Tianying Wang
MCLCBA: multi-view contrastive learning network for RNA methylation site prediction
Honglei Wang, Xuesong Zhang, Yanjing Sun, Zhaoyang Liu and Lin Zhang
SeqForge: a scalable platform for alignment-based searches, motif detection, and sequence curation across meta/genomic datasets
Elijah R. Bring Horvath and Jaclyn M. Winter
AllergenAI: a deep learning model predicting allergenicity based on protein sequence
Jiajia Liu, Surendra S. Negi, Chengyuan Yang, Xiaobo Zhou, Catherine H. Schein, Werner Braun and Pora Kim
Machine learning for genomic prediction of growth traits in aquaculture: a case study of the Australasian snapper (Chrysophrys auratus)
Ze Chen, Julie Blommaert, Yi Mei, Linley Jesson, Maren Wellenreuther and Mengjie Zhang
scMFF: a machine learning framework with multiple feature fusion strategies for cell type identification
Nan Sun, Yu Wang, Xiang Shi, Dengcheng Yang, Rongling Wu and Stephen S.-T. Yau
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
AI can turbocharge scientists’ careers — but limit their scope
Benjamin Thompson, Nick Petrić Howe
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
Long-read structural variant discovery and targeted short read genotyping enables population scale characterization of structural variation in rhesus macaques
Karina Ray, Christina Mulch, Samuel M. Peterson, Sebastian Benjamin, Nathan Gullicksrud, Adam J. Ericsen, Eric J. Vallender, Betsy M. Ferguson, Jeffrey D. Wall and Benjamin N. Bimber
Benchmarking deep learning methods for biologically conserved single-cell integration
Chenxin Yi, Jinyu Cheng, Jiajun Chen, Wanquan Liu, Junwei Liu and Yixue Li
scSpecies: enhancement of network architecture alignment in comparative single-cell studies
Clemens Schächter, Maren Hackenberg, Martin Treppner, Hanne Raum, Joschka Bödecker and Harald Binder
X-LDR: an atlas of linkage disequilibrium across species
Tian-Neng Zhu, Xing Huang, Meng-Yuan Yang, Guo-An Qi, Qi-Xin Zhang, Feng Lin, Wenjing Zhang, Zhe Zhang, Xin Jin, Hou-Feng Zheng, Hai-Ming Xu, Shizhou Yu and Guo-Bo Chen
Cell type-specific inference from bulk RNA-sequencing data by integrating single-cell reference profiles via EPIC-unmix
Chenwei Tang, Quan Sun, Xinyue Zeng, Gang Li, Xiaoyu Yang, Fei Liu, Jinying Zhao, Yin Shen, Boxiang Liu, Jia Wen and Yun Li
Structure-enhanced graph meta learning for few-shot gene regulatory network inference
Weiming Yu, Zhuobin Chen, Yaohua Hu, Jing Qin and Le Ou-Yang