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Tweets on Gen/Transcript/Prote-Omics

Tweets about #genomics OR #transcriptomics OR #proteomics

News by Scientific American

When Will We Learn?
Letters
Dereliction of Duty
The U.S. Congress has not protected health or the environment. Time to make it step up
Income Inequality and Homicide
Where financial disparities are greatest, the murder rate tends to be high
Fixing Wasting Muscles
Scientists edited dogs' genes to correct a common form of muscle dystrophy
Artificial Wood
The synthetic material is both robust and versatile
Flooding the Senses
Visualizing climate catastrophes may spur people to act
Lifelong Learning
Creating artificial intelligence that continues to adapt

XKCD Comic Strip

Tweets by CompGenLabUB

RNA-Seq Blog

Bioinformatics

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A novel method for predicting activity of cis-regulatory modules, based on a diverse training set (Yang, W., Sinha, S.)
signeR: an empirical Bayesian approach to mutational signature discovery (Rosales, R. A., Drummond, R. D., Valieris, R., Dias-Neto, E., da Silva, I. T.)
Multivariate two-part statistics for analysis of correlated mass spectrometry data from multiple biological specimens (Taylor, S. L., Ruhaak, L. R., Weiss, R. H., Kelly, K., Kim, K.)
SiNVICT: ultra-sensitive detection of single nucleotide variants and indels in circulating tumour DNA (Kockan, C., Hach, F., Sarrafi, I., Bell, R. H., McConeghy, B., Beja, K., Haegert, A., Wyatt, A. W., Volik, S. V., Chi, K. N., Collins, C. C., Sahinalp, S. C.)
iRSpot-EL: identify recombination spots with an ensemble learning approach (Liu, B., Wang, S., Long, R., Chou, K.-C.)
Prediction of nucleosome positioning by the incorporation of frequencies and distributions of three different nucleotide segment lengths into a general pseudo k-tuple nucleotide composition (Awazu, A.)
Nanocall: an open source basecaller for Oxford Nanopore sequencing data (David, M., Dursi, L. J., Yao, D., Boutros, P. C., Simpson, J. T.)

PLoS Computational Biology

Measuring uncertainty in human visual segmentation (Jonathan Vacher, Claire Launay, Pascal Mamassian, Ruben Coen-Cagli)
Generalizing biological surround suppression based on center surround similarity via deep neural network models (Xu Pan, Annie DeForge, Odelia Schwartz)
Likelihood-ratio test statistic for the finite-sample case in nonlinear ordinary differential equation models (Christian Tönsing, Bernhard Steiert, Jens Timmer, Clemens Kreutz)
Simulation-based inference for efficient identification of generative models in computational connectomics (Jan Boelts, Philipp Harth, Richard Gao, Daniel Udvary, Felipe Yáñez, Daniel Baum, Hans-Christian Hege, Marcel Oberlaender, Jakob H. Macke)
A platform-independent framework for phenotyping of multiplex tissue imaging data (Mansooreh Ahmadian, Christian Rickert, Angela Minic, Julia Wrobel, Benjamin G. Bitler, Fuyong Xing, Michael Angelo, Elena W. Y. Hsieh, Debashis Ghosh, Kimberly R. Jordan)
Personalized prediction for multiple chronic diseases by developing the multi-task Cox learning model (Shuaijie Zhang, Fan Yang, Lijie Wang, Shucheng Si, Jianmei Zhang, Fuzhong Xue)
Fourteen quick tips for crowdsourcing geographically linked data for public health advocacy (Joshua Atienza, Anjalee Benedict, Lincoln D. Stein, Kashif Pirzada, Cheryl White, Shraddha Pai)
Identifying a developmental transition in honey bees using gene expression data (Bryan C. Daniels, Ying Wang, Robert E. Page Jr, Gro V. Amdam)

BMC Bioinformatics

An optimal variant to gene distance window derived from an empirical definition of cis and trans protein QTLs (Eric B. Fauman and Craig Hyde)
Sparse sliced inverse regression for high dimensional data analysis (Haileab Hilafu and Sandra E. Safo)
HGGA: hierarchical guided genome assembler (Riku Walve and Leena Salmela)
SPINNAKER: an R-based tool to highlight key RNA interactions in complex biological networks (Paola Paci and Giulia Fiscon)
RSNET: inferring gene regulatory networks by a redundancy silencing and network enhancement technique (Xiaohan Jiang and Xiujun Zhang)
CircMiMi: a stand-alone software for constructing circular RNA-microRNA-mRNA interactions across species (Tai-Wei Chiang, Te-Lun Mai and Trees-Juen Chuang)
A novel approach to predicting the synergy of anti-cancer drug combinations using document-based feature extraction (Yongsun Shim, Munhwan Lee, Pil-Jong Kim and Hong-Gee Kim)
A deep learning approach for orphan gene identification in moso bamboo (Phyllostachys edulis) based on the CNN + Transformer model (Xiaodan Zhang, Jinxiang Xuan, Chensong Yao, Qijuan Gao, Lianglong Wang, Xiu Jin and Shaowen Li)

BMC Genomics

Identification of novel key regulatory lncRNAs in gastric adenocarcinoma (Houri Razavi and Ali Katanforosh)
Association between high immune activity and worse prognosis in uveal melanoma and low-grade glioma in TCGA transcriptomic data (Hitoshi Matsuo, Takashi Kamatani, Yu Hamba, Keith A. Boroevich and Tatsuhiko Tsunoda)
Small RNA sequencing and bioinformatics analysis of RAW264.7-derived exosomes after Mycobacterium Bovis Bacillus Calmette-Guérin infection (Xuehua Zhan, Wenqi Yuan, Yueyong Zhou, Rong Ma and Zhaohui Ge)
Evolution and dispersal of mitochondrial DNA haplogroup U5 in Northern Europe: insights from an unsupervised learning approach to phylogeography (Dana Kristjansson, Jon Bohlin, Truc Trung Nguyen, Astanand Jugessur and Theodore G. Schurr)
Genomic features of the polyphagous cotton leafworm Spodoptera littoralis (Chao Wu, Lei Zhang, Bo Liu, Bojia Gao, Cong Huang, Ji Zhang, Minghui Jin, Hanyue Wang, Yan Peng, Annabel Rice, Esmat Hegazi, Kenneth Wilson, Pengjun Xu and Yutao Xiao)
Identification of condition-specific regulatory mechanisms in normal and cancerous human lung tissue (Yuqing Hang, Josh Burns, Benjamin T. Shealy, Rini Pauly, Stephen P. Ficklin and Frank A. Feltus)
Optimized Cas9:sgRNA delivery efficiently generates biallelic MSTN knockout sheep without affecting meat quality (Shiwei Zhou, Peter Kalds, Qi Luo, Kexin Sun, Xiaoe Zhao, Yawei Gao, Bei Cai, Shuhong Huang, Qifang Kou, Bjoern Petersen, Yulin Chen, Baohua Ma and Xiaolong Wang)
Modulation of the Drosophila transcriptome by developmental exposure to alcohol (Tatiana V. Morozova, Vijay Shankar, Rebecca A. MacPherson, Trudy F. C. Mackay and Robert R. H. Anholt)

Genome Biology

TT-Mars: structural variants assessment based on haplotype-resolved assemblies (Jianzhi Yang and Mark J.P. Chaisson)
Enhancer transcription detected in the nascent transcriptomic landscape of bread wheat (Yilin Xie, Yan Chen, Zijuan Li, Jiafu Zhu, Min Liu, Yijing Zhang and Zhicheng Dong)
Systematic evaluation of colorectal cancer organoid system by single-cell RNA-Seq analysis (Rui Wang, Yunuo Mao, Wendong Wang, Xin Zhou, Wei Wang, Shuai Gao, Jingyun Li, Lu Wen, Wei Fu and Fuchou Tang)
DeepRepeat: direct quantification of short tandem repeats on signal data from nanopore sequencing (Li Fang, Qian Liu, Alex Mas Monteys, Pedro Gonzalez-Alegre, Beverly L. Davidson and Kai Wang)
Author Correction: Mutational signatures reveal the role of RAD52 in p53-independent p21-driven genomic instability (Panagiotis Galanos, George Pappas, Alexander Polyzos, Athanassios Kotsinas, Ioanna Svolaki, Nickolaos N. Giakoumakis, Christina Glytsou, Ioannis S. Pateras, Umakanta Swain, Vassilis L. Souliotis, Alexandros G. Georgakilas, Nicholas Geacintov, Luca Scorran)
Comprehensive enhancer-target gene assignments improve gene set level interpretation of genome-wide regulatory data (Tingting Qin, Christopher Lee, Shiting Li, Raymond G. Cavalcante, Peter Orchard, Heming Yao, Hanrui Zhang, Shuze Wang, Snehal Patil, Alan P. Boyle and Maureen A. Sartor)
Author Correction: scINSIGHT for interpreting single-cell gene expression from biologically heterogeneous data (Kun Qian, Shiwei Fu, Hongwei Li and Wei Vivian Li)
Predicting RNA splicing from DNA sequence using Pangolin (Tony Zeng and Yang I Li)

PLoS ONE

Alteration of Antiviral Signalling by Single Nucleotide Polymorphisms (SNPs) of Mitochondrial Antiviral Signalling Protein (MAVS) (Fei Xing et al.)
Genome Analysis of Listeria monocytogenes Sequence Type 8 Strains Persisting in Salmon and Poultry Processing Environments and Comparison with Related Strains (Annette Fagerlund et al.)
Transcriptome Profiling of Two Asparagus Bean (Vigna unguiculata subsp. sesquipedalis) Cultivars Differing in Chilling Tolerance under Cold Stress (Huaqiang Tan et al.)
A Human "eFP" Browser for Generating Gene Expression Anatograms (Rohan V. Patel et al.)
Population Structure and Antimicrobial Resistance Profiles of Streptococcus suis Serotype 2 Sequence Type 25 Strains (Taryn B. T. Athey et al.)
Analysis of the Phialocephala subalpina Transcriptome during Colonization of Its Host Plant Picea abies (Vanessa Reininger et al.)
Proteomic Analysis of the Secretome of Cellulomonas fimi ATCC 484 and Cellulomonas flavigena ATCC 482 (Warren W. Wakarchuk et al.)
First Microsatellite Markers Developed from Cupuassu ESTs: Application in Diversity Analysis and Cross-Species Transferability to Cacao (Lucas Ferraz dos Santos et al.)

CompGen Posts at FaceBook

Nature

Publisher Correction: Distinguishing externally from saccade-induced motion in visual cortex (Satoru K. Miura, Massimo Scanziani)
Violent conservation, and your brain on magic: Books in brief (Andrew Robinson)
Publisher Correction: A brainstem map for visceral sensations (Chen Ran, Jack C. Boettcher, Judith A. Kaye, Catherine E. Gallori, Stephen D. Liberles)
Soaring energy costs mean we are using less — but for how long? (Heidi Ledford)
Conflict resolution (Holly Schofield)
Charge dropped against New Zealand science agency after deadly volcano eruption (Dyani Lewis)
Surprise! The UK is spending way more on research than it thought (Holly Else)
Should AI have a role in assessing research quality? (Dalmeet Singh Chawla)

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.)
TCR-like antibodies tackle celiac disease (Williams, I.)

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)
BIN1 modulation in vivo rescues dynamin-related myopathy [Medical Sciences] (Valentina Maria Lionello, Christine Kretz, Evelina Edelweiss, Corinne Crucifix, Raquel Gomez–Oca, Nadia Messaddeq, Suzie Buono, Pascale Koebel, Xenia Massana Munoz, Nadege Diedhiou, Belinda S. Cowling, Marc Bitoun, Jocelyn Laporte)

The original document is available at https://compgen.bio.ub.edu/CompGenOld/News