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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

Bacterial clustering amplifies the reshaping of eutrophic plumes around marine particles: A hybrid data-driven model (George E. Kapellos, Hermann J. Eberl, Nicolas Kalogerakis, Patrick S. Doyle, Christakis A. Paraskeva)
Differential quantification of alternative splicing events on spliced pangenome graphs (Simone Ciccolella, Davide Cozzi, Gianluca Della Vedova, Stephen Njuguna Kuria, Paola Bonizzoni, Luca Denti)
Preserving friendships in school contacts: An algorithm to construct synthetic temporal networks for epidemic modelling (Lucille Calmon, Elisabetta Colosi, Giulia Bassignana, Alain Barrat, Vittoria Colizza)
Federated privacy-protected meta- and mega-omics data analysis in multi-center studies with a fully open-source analytic platform (Xavier Escriba-Montagut, Yannick Marcon, Augusto Anguita-Ruiz, Demetris Avraam, Jose Urquiza, Andrei S. Morgan, Rebecca C. Wilson, Paul Burton, Juan R. Gonzalez)
Oscillatory dynamics of Rac1 activity in Dictyostelium discoideum amoebae (Marko Šoštar, Maja Marinović, Vedrana Filić, Nenad Pavin, Igor Weber)
Dose-dependent interaction of parasites with tiers of host defense predicts “wormholes” that prolong infection at intermediate inoculum sizes (Andrea L. Graham, Roland R. Regoes)
Large scale paired antibody language models (Henry Kenlay, Frédéric A. Dreyer, Aleksandr Kovaltsuk, Dom Miketa, Douglas Pires, Charlotte M. Deane)
OneNet—One network to rule them all: Consensus network inference from microbiome data (Camille Champion, Raphaëlle Momal, Emmanuelle Le Chatelier, Mathilde Sola, Mahendra Mariadassou, Magali Berland)

BMC Bioinformatics

MTAF–DTA: multi-type attention fusion network for drug–target affinity prediction (Jinghong Sun, Han Wang, Jia Mi, Jing Wan and Jingyang Gao)
Correction: Maptcha: an efficient parallel workflow for hybrid genome scaffolding (Oieswarya Bhowmik, Tazin Rahman and Ananth Kalyanaraman)
Pheno-Ranker: a toolkit for comparison of phenotypic data stored in GA4GH standards and beyond (Ivo C. Leist, María Rivas-Torrubia, Marta E. Alarcón-Riquelme, Guillermo Barturen, PRECISESADS Clinical Consortium, Ivo G. Gut and Manuel Rueda)
Managing false positives during detection of pathogen sequences in shotgun metagenomics datasets (Lauren M. Bradford, Catherine Carrillo and Alex Wong)
The evaluation of transcription factor binding site prediction tools in human and Arabidopsis genomes (Dinithi V. Wanniarachchi, Sameera Viswakula and Anushka M. Wickramasuriya)
Single-character insertion–deletion model preserves long indels in ancestral sequence reconstruction (Gholamhossein Jowkar, Jūlija Pečerska, Manuel Gil and Maria Anisimova)
A novel phenotype imputation method with copula model (Jianjun Zhang, Jane Zizhen Zhao, Samantha Gonzales, Xuexia Wang and Qiuying Sha)
Enhanced prediction of hemolytic activity in antimicrobial peptides using deep learning-based sequence analysis (Ibrahim Abdelbaky, Mohamed Elhakeem, Hilal Tayara, Elsayed Badr and Mustafa Abdul Salam)

BMC Genomics

Correction: Genome-wide association study identifies key quantitative trait loci (QTL) for fruit morphometric traits in avocado (Persea spp.) (Jin Li, Shamseldeen Eltaher, Barbie Freeman, Sukhwinder Singh and Gul Shad Ali)
Alternative splicing induces sample-level variation in gene–gene correlations (Yihao Lu, Brandon L. Pierce, Pei Wang, Fan Yang and Lin S. Chen)
Unveiling genetic insights: Array-CGH and WES discoveries in a cohort of 122 children with essential autism spectrum disorder (Paola Granata, Alessandra Zito, Dario Cocciadiferro, Antonio Novelli, Chiara Pessina, Tommaso Mazza, Matteo Ferri, Paolo Piccinelli, Chiara Luoni, Cristiano Termine, Mauro Fasano and Rosario Casalone)
Exploring the forensic effectiveness and population genetic differentiation in Guizhou Miao and Bouyei group by the self-constructed panel of X chromosomal multi-insertion/deletions (Xiaolan Huang, Changyun Gu, Qianchong Ran, Li Chen, Shunyi Tian, Min Zhong, Zheng Ren, Qiyan Wang, Meiqing Yang, Jingyan Ji, Wen Wan, Jiang Huang, Hongling Zhang and Xiaoye Jin)
Examination of homozygosity runs and selection signatures in native goat breeds of Henan, China (Weifeng Peng, Yiyuan Zhang, Lei Gao, Shuping Wang, Mengting Liu, Enrui Sun, Kaixin Lu, Yunxia Zhang, Bing Li, Guoyin Li, Jingya Cao and Mingsheng Yang)
Insights into the transcriptomic responses of silver-lipped pearl oysters Pinctada maxima exposed to a simulated large-scale seismic survey (Cecile Dang, Anita A. Severn-Ellis, Philipp Bayer, Nicole Anderson, Hosna Gholipour-Kanani, Jacqueline Batley, Robert D. McCauley, Ryan D. Day, Jayson M. Semmens, Conrad Speed, Mark G. Meekan and Miles J.G. Parsons)
Immunomodulatory dynamics in the porcine myometrium: global transcriptome analysis, including the effects of PPARγ ligands (Aleksandra Kurzynska, Karol Mierzejewski, Monika Golubska, Jan Pawel Jastrzebski and Iwona Bogacka)
Genome-wide association and transcriptomic analysis and the identification of growth-related genes in Macrobrachium nipponense (Zijian Gao, Wenyi Zhang, Sufei Jiang, Hui Qiao, Yiwei Xiong, Shubo Jin and Hongtuo Fu)

Genome Biology

Systemic evaluation of various CRISPR/Cas13 orthologs for knockdown of targeted transcripts in plants (Lu Yu, Jiawei Zou, Amjad Hussain, Ruoyu Jia, Yibo Fan, Jinhang Liu, Xinhui Nie, Xianlong Zhang and Shuangxia Jin)
Chromatin loops gather targets of upstream regulators together for efficient gene transcription regulation during vernalization in wheat (Yanyan Liu, Xintong Xu, Chao He, Liujie Jin, Ziru Zhou, Jie Gao, Minrong Guo, Xin Wang, Chuanye Chen, Mohammed H. Ayaad, Xingwang Li and Wenhao Yan)
EpiCHAOS: a metric to quantify epigenomic heterogeneity in single-cell data (Katherine Kelly, Michael Scherer, Martina Maria Braun, Pavlo Lutsik and Christoph Plass)
MoCHI: neural networks to fit interpretable models and quantify energies, energetic couplings, epistasis, and allostery from deep mutational scanning data (Andre J. Faure and Ben Lehner)
HTAD: a human-in-the-loop framework for supervised chromatin domain detection (Wei Shen, Ping Zhang, Yiwei Jiang, Hailin Tao, Zhike Zi and Li Li)
Genetic-by-age interaction analyses on complex traits in UK Biobank and their potential to identify effects on longitudinal trait change (Thomas W. Winkler, Simon Wiegrebe, Janina M. Herold, Klaus J. Stark, Helmut Küchenhoff and Iris M. Heid)
Hierarchical annotation of eQTLs by H-eQTL enables identification of genes with cell type-divergent regulation (Pawel F. Przytycki and Katherine S. Pollard)
Publisher Correction: Tagging large CNV blocks in wheat boosts digitalization of germplasm resources by ultra-low-coverage sequencing (Jianxia Niu, Wenxi Wang, Zihao Wang, Zhe Chen, Xiaoyu Zhang, Zhen Qin, Lingfeng Miao, Zhengzhao Yang, Chaojie Xie, Mingming Xin, Huiru Peng, Yingyin Yao, Jie Liu, Zhongfu Ni, Qixin Sun and Weilong Guo)

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

Aromatic ring-opening metathesis (Valeriia Hutskalova, Christof Sparr)
Skin autonomous antibody production regulates host-microbiota interactions (Inta Gribonika, Victor I. Band, Liang Chi, Paula Juliana Perez-Chaparro, Verena M. Link, Eduard Ansaldo, Cihan Oguz, Djenet Bousbaine, Michael A. Fischbach, Yasmine Belkaid)
Structures and mechanism of condensation in nonribosomal peptide synthesis (Angelos Pistofidis, Pengchen Ma, Zihao Li, Kim Munro, K. N. Houk, T. Martin Schmeing)
The structure of apolipoprotein B100 from human low-density lipoprotein (Zachary T. Berndsen, C. Keith Cassidy)
I help researchers to measure methane at a local level so that we can make global changes (Oscar Allan)
How provinces and cities can sustain US–China climate cooperation (Fan Dai, Jerry Brown, Zhenhua Xie, Yi Wang, Peng Gong)
The contentious genius who made black holes real (Davide Castelvecchi)
Great power and great responsibility: how consciousness changes the world (Alan C. Love)

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)

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