Searching journal content for articles similar to Setakis et al. 16 (2): 290.

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Method: Debiased personalized gene coexpression networks for population-scale scRNA-seq data
- Shan Lu and
- Sunduz Keles
Genome Res. June 9, 2023 gr.277363.122; Published in Advance June 9, 2023, doi:10.1101/gr.277363.122
....74 across the modules, 68% higher than the second best method SCT.Pearson. Dozer is robust against sequencing depth differences of the scRNA-seq datasets In large-scale scRNA-seq studies, data are typically generated in separate batches due to logistical constraints, e.g., at different times, laboratories...
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Resource: Genome variation and population structure among 1142 mosquitoes of the African malaria vector species Anopheles gambiae and Anopheles coluzzii
- The Anopheles gambiae 1000 Genomes Consortium
Genome Res. October 2020 30: 1533-1546; Published in Advance September 28, 2020, doi:10.1101/gr.262790.120
...of potential mates for an individual and can be viewed as a measurement of how genetic differentiation between populations correlates with the geographical distance between them (isolation by distance). We used Rousset's method for estimating neighborhood size based on a regression of normalized FST against...
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Method: Detecting differential growth of microbial populations with Gaussian process regression
- Peter D. Tonner,
- Cynthia L. Darnell,
- Barbara E. Engelhardt,
- and Amy K. Schmid
Genome Res. February 2017 27: 320-333; Published in Advance November 18, 2016, doi:10.1101/gr.210286.116
...regression and primary growth models (Gompertz, population logistic, Schnute, and Richards) on microbial growth data under standard conditions. (B) Logarithm of mean squared error (MSE) for primary growth models compared with GP regression on microbial population growth under standard conditions. Bars...
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Method: Revealing the genetic structure of a trait by sequencing a population under selection
- Leopold Parts,
- Francisco A. Cubillos,
- Jonas Warringer,
- Kanika Jain,
- Francisco Salinas,
- Suzannah J. Bumpstead,
- Mikael Molin,
- Amin Zia,
- Jared T. Simpson,
- Michael A. Quail,
- Alan Moses,
- Edward J. Louis,
- Richard Durbin,
- and Gianni Liti
Genome Res. July 2011 21: 1131-1138; Published in Advance March 21, 2011, doi:10.1101/gr.116731.110
...www..org Parts et al. on average in a set of 96 F1 segregants genotyped at ;200 evenly spaced loci (Cubillos et al. 2011). Changes in population allele frequency in response to heat selection indicate protective alleles To identify the alleles underlying variation in high temperature tolerance, we...
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Research: Decoding the function of bivalent chromatin in development and cancer
- Dhirendra Kumar,
- Senthilkumar Cinghu,
- Andrew J. Oldfield,
- Pengyi Yang,
- and Raja Jothi
Genome Res. December 2021 31: 2170-2184; Published in Advance October 19, 2021, doi:10.1101/gr.275736.121
...plots showing the distribution of CpG dinucleotide frequency at promoters (±500 bp of TSS) of genes within each the four classes defined in Figure 2B. (E) Statistics summarizing the performance of the multinomial logistic regression-based machine learning method for predicting chromatin state of mouse...
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Research: Genome specialization and decay of the strangles pathogen, Streptococcus equi, is driven by persistent infection
- Simon R. Harris,
- Carl Robinson,
- Karen F. Steward,
- Katy S. Webb,
- Romain Paillot,
- Julian Parkhill,
- Matthew T.G. Holden,
- and Andrew S. Waller
Genome Res. September 2015 25: 1360-1371; Published in Advance July 9, 2015, doi:10.1101/gr.189803.115
...to persistent isolates against those leading to isolates from acute infection (Supplemental Fig. 6a). We found a significant difference (P = 0.0004) in rates between the two populations, with persistent isolates exhibiting a significantly increased rate. A linear regression of substitution rate against time...
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Method: An integrated metagenomics pipeline for strain profiling reveals novel patterns of bacterial transmission and biogeography
- Stephen Nayfach,
- Beltran Rodriguez-Mueller,
- Nandita Garud,
- and Katherine S. Pollard
Genome Res. November 2016 26: 1612-1625; Published in Advance October 18, 2016, doi:10.1101/gr.201863.115
...indicates whether a strain of the species was transmitted from themother (y = 1) or not (y = 0) at 12mo. The curve is a logistic regression fitted to data points. (F) Histograms indicate the distribution of relative abundance at 4 d for strains that were transmitted and not transmitted from an infant...
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Research: Genetic and environmental exposures constrain epigenetic drift over the human life course
- Sonia Shah,
- Allan F. McRae,
- Riccardo E. Marioni,
- Sarah E. Harris,
- Jude Gibson,
- Anjali K. Henders,
- Paul Redmond,
- Simon R. Cox,
- Alison Pattie,
- Janie Corley,
- Lee Murphy,
- Nicholas G. Martin,
- Grant W. Montgomery,
- John M. Starr,
- Naomi R. Wray,
- Ian J. Deary,
- and Peter M. Visscher
Genome Res. November 2014 24: 1725-1733; Published in Advance September 23, 2014, doi:10.1101/gr.176933.114
...strongly enriched for high heritability. Our results show that a large number of CpGs across the genome, as a result of environmental and/or genetic constraints, have stable DNAm variation over the human lifetime. Moreover, at a number of CpGs, most variation in the population is due to genetic factors...
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Resource: A DNA methylation fingerprint of 1628 human samples
- Agustin F. Fernandez,
- Yassen Assenov,
- Jose Ignacio Martin-Subero,
- Balazs Balint,
- Reiner Siebert,
- Hiroaki Taniguchi,
- Hiroyuki Yamamoto,
- Manuel Hidalgo,
- Aik-Choon Tan,
- Oliver Galm,
- Isidre Ferrer,
- Montse Sanchez-Cespedes,
- Alberto Villanueva,
- Javier Carmona,
- Jose V. Sanchez-Mut,
- Maria Berdasco,
- Victor Moreno,
- Gabriel Capella,
- David Monk,
- Esteban Ballestar,
- Santiago Ropero,
- Ramon Martinez,
- Marta Sanchez-Carbayo,
- Felipe Prosper,
- Xabier Agirre,
- Mario F. Fraga,
- Osvaldo Graña,
- Luis Perez-Jurado,
- Jaume Mora,
- Susana Puig,
- Jaime Prat,
- Lina Badimon,
- Annibale A. Puca,
- Stephen J. Meltzer,
- Thomas Lengauer,
- John Bridgewater,
- Christoph Bock,
- and Manel Esteller
Genome Res. February 2012 22: 407-419; Published in Advance May 25, 2011, doi:10.1101/gr.119867.110
...landscapes obtained with those from the aforementioned human malignancy collection where the original tissue type was known. We were able to assign a given tumor type for these CUPs in 69% (29 of 42) of cases using L1-regularized logistic regression with misclassification (R, version 2.10) to create...
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RESOURCE: A resource for the simultaneous high-resolution mapping of multiple quantitative trait loci in rats: The NIH heterogeneous stock
- Martina Johannesson,
- Regina Lopez-Aumatell,
- Pernilla Stridh,
- Margarita Diez,
- Jonatan Tuncel,
- Gloria Blázquez,
- Esther Martinez-Membrives,
- Toni Cañete,
- Elia Vicens-Costa,
- Delyth Graham,
- Richard R. Copley,
- Polinka Hernandez-Pliego,
- Amennai D. Beyeen,
- Johan Öckinger,
- Cristina Fernández-Santamaría,
- Percio S. Gulko,
- Max Brenner,
- Adolf Tobeña,
- Marc Guitart-Masip,
- Lydia Giménez-Llort,
- Anna Dominiczak,
- Rikard Holmdahl,
- Dominique Gauguier,
- Tomas Olsson,
- Richard Mott,
- William Valdar,
- Eva E. Redei,
- Alberto Fernández-Teruel,
- and Jonathan Flint
Genome Res. January 2009 19: 150-158; Published in Advance October 29, 2008, doi:10.1101/gr.081497.108
...haplotype composition along chromosome 5 using a combination of hierarchical binomial logistic regression and the multipoint haplotype reconstruction method HAPPY ( Mott et al. 2000 ). HAPPY estimates the expected proportion of each founder haplotype between each consecutive pair of markers (marker interval...

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