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EmpiReS: Differential Analysis of Gene Expression and Alternative Splicing [article]

Gergely Csaba, Evi Berchtold, Armin Hadziahmetovic, Markus Gruber, Constantin Ammar, Ralf Zimmer
2020 bioRxiv   pre-print
EmpiRe is a quantitative approach for various kinds of omics data based on fold changes for appropriate features of biological objects.  ...  Therefore, analysis of fold changes is the standard method, but often, a doubly differential analysis of "changes of changes" is required.  ...  MATERIALS AND METHODS The EmpiReS approach and method EmpiRe applied to RNA-seq data MS-EmpiRe (21) is based on an Empirical and Replicate-based, approach, further called EmpiRe, which does not assume  ... 
doi:10.1101/2020.08.23.234237 fatcat:ibi2eug5bzc5pft4ijchbqim6i

Semi-supervised Object Detection with Adaptive Class-Rebalancing Self-Training

Fangyuan Zhang, Tianxiang Pan, Bin Wang
When using only 1% labeled data of MS-COCO, our method achieves 17.02 mAP improvement over the supervised method and 5.32 mAP gains compared with state-of-the-arts.  ...  In this paper, we propose an Adaptive Class-Rebalancing Self-Training (ACRST) with a novel memory module called CropBank to alleviate these imbalances and generate unbiased pseudo-labels.  ...  Then, the new training data {x mix i , y mix i } is generated as follows: where α is a binary mask of c j , and y mix i denotes the new annotations, in which fully occluded instances are removed from the  ... 
doi:10.1609/aaai.v36i3.20234 fatcat:wnaozb5jpjhzviqq4oalul23xu

A practical guide to preclinical systematic review and meta-analysis

Nadia Soliman, Andrew S.C. Rice, Jan Vollert
2020 Pain  
Rice are part of the European Quality In  ...  Acknowledgements The authors thank Dr Emily Sena for her constructive feedback on the manuscript. The work is funded by the BBSRC (grant number BB/M011178/ 1). J. Vollert and A.S.C.  ...  Designed to address a specific research question, SRs use predefined methods to identify, select, and critically appraise all available and relevant literature to answer that question in an unbiased manner  ... 
doi:10.1097/j.pain.0000000000001974 pmid:33449500 fatcat:5efzm4563zbkjk7hrcawrqkkai

Rectified Meta-Learning from Noisy Labels for Robust Image-based Plant Disease Diagnosis [article]

Ruifeng Shi, Deming Zhai, Xianming Liu, Junjun Jiang, Wen Gao
2020 arXiv   pre-print
However, the performance of CNN-based classification approach depends on a large amount of high-quality manually labeled training data, which are inevitably introduced noise on labels in practice, leading  ...  The proposed method enjoys the following merits: i) A rectified meta-learning is designed to pay more attention to unbiased samples, leading to accelerated convergence and improved classification accuracy  ...  Since the selected images are all annotated by professional experts, it can be seen as a clean dataset.  ... 
arXiv:2003.07603v2 fatcat:vmvvu6daqngnxphgbqgv27g3me

Developmental Loci Harbor Clusters of Accelerated Regions That Evolved Independently in Ape Lineages

Dennis Kostka, Alisha K Holloway, Katherine S Pollard, Katja Nowick
2018 Molecular biology and evolution  
We find evidence of GC-biased gene conversion in each ape, but unbiased acceleration consistent with positive selection or loss of constraint is more common in all five lineages.  ...  may have differentially altered expression of a core set of developmental genes across ape evolution.  ...  Our method is based on contrasting a suitably chosen phylogenetic null model with a series of alternative models using likelihood ratio tests (LRTs).  ... 
doi:10.1093/molbev/msy109 pmid:29897475 pmcid:PMC6063267 fatcat:ndunwq4fynfundoefi4jlpfw6a

Developmental loci harbor clusters of accelerated regions that evolved independently in ape lineages [article]

Dennis Kostka, Alisha K. Holloway, Katherine Pollard
2017 biorxiv/medrxiv   pre-print
We find evidence of GC-biased gene conversion in each ape, but unbiased acceleration consistent with positive selection or loss of constraint is more common in all five lineages.  ...  may have differentially altered expression of a core set of developmental genes across ape evolution.  ...  Our method is based on contrasting a suitably chosen phylogenetic null model with a series of alternative models using likelihood ratio tests (LRTs).  ... 
doi:10.1101/226019 fatcat:wf7lgfjp3nhexbzxfncqjxmufq

ProMix: Combating Label Noise via Maximizing Clean Sample Utility [article]

Haobo Wang, Ruixuan Xiao, Yiwen Dong, Lei Feng, Junbo Zhao
2022 arXiv   pre-print
State-of-the-art approaches are based on semi-supervised learning(SSL), which selects small loss examples as clean and then applies SSL techniques for boosted performance.  ...  Based on such a large set of clean data, ProMix improves the best baseline method by +2.67% on CIFAR-10N and +1.61% on CIFAR-100N datasets.  ...  Besides interpolation-based data augmentation, we also employ a masking-based mixed sample data augmentation approach named FMix [Harris et al., 2020] for exploiting local consistency.  ... 
arXiv:2207.10276v2 fatcat:gjxptgkdbjh2tcdghbsm65vkdi

A searchable database of genetic evidence for psychiatric disorders

Thomas Konneker, Todd Barnes, Helena Furberg, Molly Losh, Cynthia M. Bulik, Patrick F. Sullivan
2008 American Journal of Medical Genetics Part B: Neuropsychiatric Genetics  
SLEP is a searchable archive of findings from psychiatric genetics that is freely available on the web for non-commercial use (  ...  This paper describes a new bioinformatic tool for use in psychiatric research, "SLEP" (Sullivan Lab Evidence Project).  ...  The SLEP interface has one tab for each of these query methods.  ... 
doi:10.1002/ajmg.b.30802 pmid:18548508 pmcid:PMC2574546 fatcat:ebcx7dhifje6riqqrrrqbn5phm

Sexually dimorphic gene expression and transcriptome evolution provide mixed evidence for a fast-Z effect in Heliconius

Ana Pinharanda, Marjolaine Rousselle, Simon H. Martin, Joe J. Hanly, John W. Davey, Sujai Kumar, Nicolas Galtier, Chris D. Jiggins
2019 Journal of Evolutionary Biology  
To account for these confounders, we used a Modelling approach to estimate the strength of positive and purifying selection in addition to the Classic approach described above, using the method of Eyre-Walker  ...  We computed (a) the proportion of adaptive nonsynonymous substitutions (α) for both the Classic and the Modelling approaches and (b) ω a and ω na for the Modelling approach. ω a is the per-mutation rate  ... 
doi:10.1111/jeb.13410 pmid:30523653 fatcat:7nb67zniincchi3dekmegs3nva

Normalization of RNA-seq data using factor analysis of control genes or samples

Davide Risso, John Ngai, Terence P Speed, Sandrine Dudoit
2014 Nature Biotechnology  
Our approach leads to more accurate estimates of expression fold-changes and tests of differential expression compared to state-of-the-art normalization methods.  ...  Normalization of RNA-sequencing (RNA-seq) data has proven essential to ensure accurate inference of expression levels.  ...  Upper-quartile normalization based on all genes led to unbiased estimates of log-fold-changes.  ... 
doi:10.1038/nbt.2931 pmid:25150836 pmcid:PMC4404308 fatcat:zfldz6cmdjdtviix6cz77mu2ya

An Empirical Study of UMLS Concept Extraction from Clinical Notes using Boolean Combination Ensembles [article]

Greg M. Silverman, Raymond L. Finzel, Michael V. Heinz, Jake Vasilakes, Jacob C. Solinsky, Reed McEwan, Benjamin C. Knoll, Christopher J. Tignanelli, Hongfang Liu, Hua Xu, Xiaoqian Jiang, Genevieve B. Melton (+1 others)
2021 arXiv   pre-print
Use of an approximate grid-search can help optimize the precision-recall tradeoff and can provide a set of heuristics for choosing an optimal set of ensembles.  ...  We used three corpora annotated for UMLS concepts: 2010 i2b2 VA challenge set (31,161 annotations), Multi-source Integrated Platform for Answering Clinical Questions (MiPACQ) corpus (17,457 annotations  ...  Acknowledgements We would like to thank Jen Morgan, Angel Helget, and George Konstantinides for their help with annotating clinical data.  ... 
arXiv:2108.02255v1 fatcat:2jjsp5wuovfrbo3rqvb4ui4zo4

Whole-genome sequence–based analysis of high-density lipoprotein cholesterol

Alanna C Morrison, Arend Voorman, Andrew D Johnson, Xiaoming Liu, Jin Yu, Alexander Li, Donna Muzny, Fuli Yu, Kenneth Rice, Chengsong Zhu, Joshua Bis, Gerardo Heiss (+5 others)
2013 Nature Genetics  
We describe initial steps for interrogating whole genome sequence (WGS) data to characterize the genetic architecture of a complex trait, such as high density lipoprotein cholesterol (HDL-C).  ...  We estimate that common variation contributes more to HDL-C heritability than rare variation, and Users may view, print, copy, download and text and data-mine the content in such documents, for the purposes  ...  The authors thank the staff and participants of the ARIC study for their important contributions.  ... 
doi:10.1038/ng.2671 pmid:23770607 pmcid:PMC4030301 fatcat:zy25yflahjgl3dgwxwxobhl2g4

Gene set enrichment analysis for genome-wide DNA methylation data [article]

Jovana Maksimovic, Alicia Oshlack, Belinda Phipson
2020 bioRxiv   pre-print
Benchmarking analyses demonstrate GOmeth outperforms other approaches and GOregion is the first method for gene set testing of differentially methylated regions.  ...  GOmeth and GOregion are new methods for performing unbiased gene set testing following differential methylation analysis.  ...  Acknowledgements We would like to acknowledge Peter Langfelder for providing detailed code and simulations which helped us to discover and correct for multi-gene bias in our testing framework.  ... 
doi:10.1101/2020.08.24.265702 fatcat:ffujpnffgfbq7eyg27jnzzkg7y

Digital transcriptome profiling using selective hexamer priming for cDNA synthesis

Christopher D Armour, John C Castle, Ronghua Chen, Tomas Babak, Patrick Loerch, Stuart Jackson, Jyoti K Shah, John Dey, Carol A Rohl, Jason M Johnson, Christopher K Raymond
2009 Nature Methods  
In eukaryotic cells, mRNA selection has been a central feature of the most widely used methods for ultrahigh-throughput sequencing 1,2 .  ...  This method is based on the empirical observation that heptamer and hexamer sequences are capable of sequence-specific priming of cDNA synthesis, whereas pentamers are not 5 .  ...  Moreover, priming specificity can be refined by combining empirical data with computational selection for NSR hexamer design.  ... 
doi:10.1038/nmeth.1360 pmid:19668204 fatcat:6ezh4mjlsvabnhpkfiuxl6bzfi

Methods and results from the genome-wide association group at GAW20

Xuexia Wang, Felix Boekstegers, Regina Brinster
2018 BMC Genetics  
A real or a simulated data set based on the Genetics of Lipid Lowering Drugs and Diet Network (GOLDN) study was employed by different methods.  ...  The GWAS group contributions focused on topics such as association tests, phenotype imputation, and application of empirical kinships. The goals of the GWAS group contributions were varied.  ...  For a fixed genotyping budget, population-based design is often the most powerful study design [51] .  ... 
doi:10.1186/s12863-018-0649-0 pmid:30255814 pmcid:PMC6157187 fatcat:2icfq7ugxzbbtajz2pgm4ucruq
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