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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

Therapeutic dose prediction of α5-GABA receptor modulation from simulated EEG of depression severity (Alexandre Guet-McCreight, Frank Mazza, Thomas D. Prevot, Etienne Sibille, Etay Hay)
The Burr distribution as a model for the delay between key events in an individual’s infection history (Nyall Jamieson, Christiana Charalambous, David M. Schultz, Ian Hall)
Cancer molecular subtyping using limited multi-omics data with missingness (Yongqi Bu, Jiaxuan Liang, Zhen Li, Jianbo Wang, Jun Wang, Guoxian Yu)
Deciphering regulatory architectures of bacterial promoters from synthetic expression patterns (Rosalind Wenshan Pan, Tom Röschinger, Kian Faizi, Hernan G. Garcia, Rob Phillips)
Computational Analysis of MDR1 Variants Predicts Effect on Cancer Cells via their Effect on mRNA Folding (Tal Gutman, Tamir Tuller)
Properties of winning Iterated Prisoner’s Dilemma strategies (Nikoleta E. Glynatsi, Vincent Knight, Marc Harper)
Estimating the distribution of parameters in differential equations with repeated cross-sectional data (Hyeontae Jo, Sung Woong Cho, Hyung Ju Hwang)
Estimating the time-varying effective reproduction number via Cycle Threshold-based Transformer (Xin-Yu Zhang, Lan-Lan Yu, Wei-Yi Wang, Gui-Quan Sun, Jian-Cheng Lv, Tao Zhou, Quan-Hui Liu)

BMC Bioinformatics

AEGAN-Pathifier: a data augmentation method to improve cancer classification for imbalanced gene expression data (Qiaosheng Zhang, Yalong Wei, Jie Hou, Hongpeng Li and Zhaoman Zhong)
Deep learning-based metabolomics data study of prostate cancer (Liqiang Sun, Xiaojing Fan, Yunwei Zhao, Qi Zhang and Mingyang Jiang)
An effective heuristic for developing hybrid feature selection in high dimensional and low sample size datasets (Hyunseok Shin and Sejong Oh)
Optimizing sequence data analysis using convolution neural network for the prediction of CNV bait positions (Zoltán Maróti, Peter Juma Ochieng, József Dombi, Miklós Krész and Tibor Kalmár)
scEGOT: single-cell trajectory inference framework based on entropic Gaussian mixture optimal transport (Toshiaki Yachimura, Hanbo Wang, Yusuke Imoto, Momoko Yoshida, Sohei Tasaki, Yoji Kojima, Yukihiro Yabuta, Mitinori Saitou and Yasuaki Hiraoka)
MISDP: multi-task fusion visit interval for sequential diagnosis prediction (Shengrong Zhu, Ruijia Yang, Zifeng Pan, Xuan Tian and Hong Ji)
Prediction of miRNA-disease associations based on PCA and cascade forest (Chuanlei Zhang, Yubo Li, Yinglun Dong, Wei Chen and Changqing Yu)
Piikun: an information theoretic toolkit for analysis and visualization of species delimitation metric space (Jeet Sukumaran and Marina Meila)

BMC Genomics

Predicting lncRNA-protein interactions using a hybrid deep learning model with dinucleotide-codon fusion feature encoding (Li Tan, Li Mengshan, Fu Yu, Li Yelin, Zhu Jihong and Guan Lixin)
EDCLoc: a prediction model for mRNA subcellular localization using improved focal loss to address multi-label class imbalance (Yu Deng, Jianhua Jia and Mengyue Yi)
LCRAnnotationsDB: a database of low complexity regions functional and structural annotations (Joanna Ziemska-Legiecka, Patryk Jarnot, Sylwia Szymańska, Dagmara Błaszczyk, Alicja Staśczak, Hanna Langer-Macioł, Kinga Lucińska, Karolina Widzisz, Aleksandra Janas, Hanna Słowik, Wiktoria Śliwińska, Aleksandra Gruca and Marcin Grynberg)
RNA profiles differ between small and large extracellular vesicle subsets isolated from porcine seminal plasma (Isabel Barranco, Carmen Almiñana, Ana Parra, Pablo Martínez-Diaz, Xiomara Lucas, Stefan Bauersachs and Jordi Roca)
Evidence of an emerging triple-reassortant H3N3 avian influenza virus in China (Lei He, Yuhao Zhang, Kaixin Si, Chuan Yu, Ke Shang, Zuhua Yu, Ying Wei, Chunhai Ding, Subir Sarker and Songbiao Chen)
Comparative genomics of Fervidobacterium: a new phylogenomic landscape of these wide-spread thermophilic anaerobes (Rubén Javier-López, Natia Geliashvili and Nils-Kåre Birkeland)
Polygenic response to selection by transgenic Bt-expressing crops in wild Helicoverpa zea and characterization of a major effect locus (Katherine L. Taylor, Jane Quackenbush, Cara Lamberty, Kelly A. Hamby and Megan L. Fritz)
The complete chloroplast genomes and comparative study of the two tung trees of Vernicia (Euphorbiaceae) (Zhenzhou Chu, Yuwei Wang, Jianjun Yang, Gulbar Yisilam, Jialei Li and Xinmin Tian)

Genome Biology

Descart: a method for detecting spatial chromatin accessibility patterns with inter-cellular correlations (Xiaoyang Chen, Keyi Li, Xiaoqing Wu, Zhen Li, Qun Jiang, Xuejian Cui, Zijing Gao, Yanhong Wu and Rui Jiang)
vmrseq: probabilistic modeling of single-cell methylation heterogeneity (Ning Shen and Keegan Korthauer)
Chromatin-based memory as a self-stabilizing influence on cell identity (Charles C. Bell, Geoffrey J. Faulkner and Omer Gilan)
Multi-omics approaches reveal that diffuse midline gliomas present altered DNA replication and are susceptible to replication stress therapy (Anastasia E. Hains, Kashish Chetal, Tsunetoshi Nakatani, Joana G. Marques, Andreas Ettinger, Carlos A. O. Biagi Junior, Adriana Gonzalez-Sandoval, Renjitha Pillai, Mariella G. Filbin, Maria-Elena Torres-Padilla, Ruslan I. Sadreyev and Capucine Van Rechem)
TEMPTED: time-informed dimensionality reduction for longitudinal microbiome studies (Pixu Shi, Cameron Martino, Rungang Han, Stefan Janssen, Gregory Buck, Myrna Serrano, Kouros Owzar, Rob Knight, Liat Shenhav and Anru R. Zhang)
Systematic evaluation of methylation-based cell type deconvolution methods for plasma cell-free DNA (Tongyue Sun, Jinqi Yuan, Yacheng Zhu, Jingqi Li, Shen Yang, Junpeng Zhou, Xinzhou Ge, Susu Qu, Wei Li, Jingyi Jessica Li and Yumei Li)
GenomeDelta: detecting recent transposable element invasions without repeat library (Riccardo Pianezza, Anna Haider and Robert Kofler)
SQUiD: ultra-secure storage and analysis of genetic data for the advancement of precision medicine (Jacob Blindenbach, Jiayi Kang, Seungwan Hong, Caline Karam, Thomas Lehner and Gamze Gürsoy)

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

The case for Latin to communicate science
Chinese rice actually tastes ever more nice (Lin Lu, Xianqiao Hu, Mingxue Chen, Peisong Hu)
One way to find mental-health support when professional help is not available (Madhurima Ghosh, Biswa Prasun Chatterji)
To solve the global wildfire crisis, don’t just focus on flames (Cathelijne Stoof, Marc Castellnou Ribau, Peter F. Moore, Georgios Boustras)
Apply the legal ‘true malice’ principle to protect research-misconduct sleuths (Gengyan Tang)
2025 must be the year when the rules of global finance are reformed
How AI is unlocking ancient texts — and could rewrite history (Jo Marchant)
Of your own device (Victoria Chvatal)

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)

Page last modified on Monday 16 of October, 2017 20:53:40 CEST

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