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A paper a day

In an effort to read more papers this year, I’m going to read a paper (or something paper-like) each day for the remainder of the year, and post each paper below as I go.

Dec 31

Galanter JM, Gignoux CR, Oh SS, Torgerson D, Pino-Yanes M, Thakur N, et al. Differential methylation between ethnic sub-groups reflects the effect of genetic ancestry and environmental exposures. eLife. doi:10.7554/eLife.20532

Dec 30

Lun ATL, McCarthy DJ, Marioni JC. A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor. F1000Research. 2016. doi:10.12688/f1000research.9501.2

Dec 29

Macia A, Widmann TJ, Heras SR, Ayllon V, Sanchez L, Benkaddour-Boumzaouad M, et al. Engineered LINE-1 retrotransposition in non-dividing human neurons. Genome Research. 2016. doi:10.1101/gr.206805.116

Dec 28

Prabhakaran S, Azizi E, Pe’er D. Dirichlet process mixture model for correcting technical variation in single-cell gene expression data. 2016. Proceedings of The 33rd International Conference on Machine Learning.

Dec 27

Shimada Y, Mohn F, Buhler M. The RNA-induced transcriptional silencing complex targets chromatin exclusively via interacting with nascent transcripts. Genes & Development. 2016. doi:10.1101/gad.292599.116

Dec 26

Lahmy S, Pontier D, Bies-Etheve N, Laudie M, Feng S, Jobet E, et al. Evidence for ARGONAUTE4-DNA interactions in RNA-directed DNA methylation in plants. Genes & Development. 2016. doi:10.1101/gad.289553.116

Dec 25

Gerdes P, Richardson SR, Faulkner GJ. TET enzymes: double agents in the transposable element–host genome conflict. Genome Biology. 2016. doi:10.1186/s13059-016-1124-8

Dec 24

Bright LJ, Chalker DL. One genome’s junk is another’s garbage. eLife. 2016. doi:10.7554/eLife.23447

Dec 23

Rosbash M. Five suggestions for substantial NIH reforms. eLife. 2016. doi:10.7554/eLife.22471

Dec 22

Nelson MG, Linheiro RS, Bergman CM. McClintock: An integrated pipeline for detecting transposable element insertions in whole genome shotgun sequencing data. bioRxiv. 2016. doi:10.1101/095372

Dec 21

Vidalis A, Živković D, Wardenaar R, Roquis D, Tellier A, Johannes F. Methylome evolution in plants. Genome Biology. 2016. doi:10.1186/s13059-016-1127-5

Dec 20

Park K, Kim MY, Vickers M, Park J-S, Hyun Y, Okamoto T, et al. DNA demethylation is initiated in the central cells of Arabidopsis and rice. PNAS. 2016. doi:10.1073/pnas.1619047114

Dec 19

Jaitin DA, Weiner A, Yofe I, Lara-Astiaso D, Keren-Shaul H, David E, et al. Dissecting Immune Circuits by Linking CRISPR-Pooled Screens with Single-Cell RNA-Seq. Cell. 2016. doi:10.1016/j.cell.2016.11.039

Dec 18

Baruzzo G, Hayer KE, Kim EJ, Di Camillo B, FitzGerald GA, Grant GR. Simulation-based comprehensive benchmarking of RNA-seq aligners. Nature Methods. 2016. doi:10.1038/nmeth.4106

Dec 17

Stoiber MH, Quick J, Egan R, Lee JE, Celniker SE, Neely R, et al. De novo Identification of DNA Modifications Enabled by Genome-Guided Nanopore Signal Processing. bioRxiv. 2016. doi:10.1101/094672

Dec 16

Nagano T, Lubling Y, Varnai C, Dudley C, Leung W, Baran Y, et al. Cell cycle dynamics of chromosomal organisation at single-cell resolution. bioRxiv. 2016. doi:10.1101/094466

Dec 15

Poplin R, Newburger D, Dijamco J, Nguyen N, Loy D, Gross S, et al. Creating a universal SNP and small indel variant caller with deep neural networks. bioRxiv. 2016. doi:10.1101/092890

Dec 14

D’haeseleer P. How does gene expression clustering work? Nature Biotechnology. 2005. doi:10.1038/nbt1205-1499

Dec 13

Halperin E, Stephan DA. SNP imputation in association studies. Nature Biotechnology. 2009. doi:10.1038/nbt0409-349

Dec 12

Charlesworth B, Charlesworth D. Darwin and genetics. Genetics. 2009. doi:10.1534/genetics.109.109991

Dec 11

van Dijk PJ, Ellis THN. The Full Breadth of Mendel’s Genetics. Genetics. 2016. doi:10.1534/genetics.116.196626

Dec 10

Lio C-W, Zhang J, González-Avalos E, Hogan PG, Chang X, Rao A. Tet2 and Tet3 cooperate with B-lineage transcription factors to regulate DNA modification and chromatin accessibility. eLife. 2016. doi:10.7554/eLife.18290

Dec 9

Pawluk A, Amrani N, Zhang Y, Garcia B, Hidalgo-Reyes Y, Lee J, et al. Naturally Occurring Off-Switches for CRISPR-Cas9. Cell. 2016. doi:10.1016/j.cell.2016.11.017

Dec 8

Buckley AR, Standish KA, Bhutani K, Ideker T, Harismendy O, Carter H, et al. Pan-Cancer Analysis Reveals Technical Artifacts in The Cancer Genome Atlas (TCGA) Germline Variant Calls. bioRxiv. 2016. doi:10.1101/092163

Dec 7

Efroni I, Mello A, Nawy T, Ip P-L, Rahni R, DelRose N, et al. Root Regeneration Triggers an Embryo-like Sequence Guided by Hormonal Interactions. Cell. 2016. doi:10.1016/j.cell.2016.04.046

Dec 6

Yang N, MacArthur DG, Gulbin JP, Hahn AG, Beggs AH, Easteal S, et al. ACTN3 genotype is associated with human elite athletic performance. The American Journal of Human Genetics. 2003. doi:10.1086/377590

Dec 5

Noble WS. How does multiple testing correction work? Nature Biotechnology. 2009. doi:10.1038/nbt1209-1135

Dec 4

Williamson CHD, Sanchez A, Vazquez A, Gutman J, Sahl JW. Bacterial genome reduction as a result of short read sequence assembly. bioRxiv. 2016. doi:10.1101/091314

Dec 3

Nattestad M, Chin C-S, Schatz MC. Ribbon: Visualizing complex genome alignments and structural variation. bioRxiv. 2016. doi:10.1101/082123

Dec 2

Carvalho AB, Dupim EG, Goldstein G. Improved assembly of noisy long reads by k-mer validation. Genome Research. 2016. doi:10.1101/gr.209247.116

Dec 1

Lu Z, Hofmeister BT, Vollmers C, DuBois RM, Schmitz RJ. Combining ATAC-seq with nuclei sorting for discovery of cis-regulatory regions in plant genomes. Nucleic Acids Research. 2016. doi:10.1093/nar/gkw1179

Nov 30

Weinreb C, Wolock S, Klein A. SPRING: a kinetic interface for visualizing high dimensional single-cell expression data. bioRxiv. 2016. doi:10.1101/090332

Nov 29

Vergara Z, Sequeira-Mendes J, Morata J, Hénaff E, Peiró R, Costas C, et al. Retrotransposons are specified as DNA replication origins in the gene-poor regions of Arabidopsis heterochromatin. bioRxiv. 2016. doi:10.1101/090183

Nov 28

Wagner A, Regev A, Yosef N. Revealing the vectors of cellular identity with single-cell genomics. 2016. Nature Biotechnology. doi:10.1038/nbt.3711

Nov 27

http://genomestake.blogspot.com.au/2016/11/thirty-fifth-take-is-what-ails-us.html

Nov 26

Gasch AP, Hose J, Newton MA, Sardi M, Yong M, Wang Z. Further support for aneuploidy tolerance in wild yeast and effects of dosage compensation on gene copy-number evolution. eLife. 2016. doi:10.7554/eLife.14409

Nov 25

Li Z, Wang S, Cheng J, Su C, Zhong S, Liu Q, et al. Intron Lariat RNA Inhibits MicroRNA Biogenesis by Sequestering the Dicing Complex in Arabidopsis. Mittelsten Scheid O, editor. PLoS Genetics. 2016. doi:10.1371/journal.pgen.1006422

Nov 24

la Rica de L, Deniz Ö, Cheng KCL, Todd CD, Cruz C, Houseley J, et al. TET-dependent regulation of retrotransposable elements in mouse embryonic stem cells. Genome Biology. 2016. doi:10.1186/s13059-016-1096-8

Nov 23

Stegle O, Teichmann SA, Marioni JC. Computational and analytical challenges in single-cell transcriptomics. Nature Reviews Genetics. 2015. doi:10.1038/nrg3833

Nov 22

Chuong EB, Elde NC, Feschotte C. Regulatory activities of transposable elements: from conflicts to benefits. 2016. Nature Reviews Genetics. doi:10.1038/nrg.2016.139

Nov 21

Tirosh I, Venteicher AS, Hebert C, Escalante LE, Patel AP, Yizhak K, et al. Single-cell RNA-seq supports a developmental hierarchy in human oligodendroglioma. 2016. Nature. doi:10.1038/nature20123

Nov 20

Sulak M, Fong L, Mika K, Chigurupati S, Yon L, Mongan NP, et al. TP53 copy number expansion is associated with the evolution of increased body size and an enhanced DNA damage response in elephants. 2016. eLife. doi:10.7554/eLife.11994

Nov 19

L Lun AT, Bach K, Marioni JC. Pooling across cells to normalize single-cell RNA sequencing data with many zero counts. Genome Biology. 2016. doi:10.1186/s13059-016-0947-7

Nov 18

Barau J, Teissandier A, Zamudio N, Roy S, Nalesso V, Hérault Y, et al. The DNA methyltransferase DNMT3C protects male germ cells from transposon activity. Science. 2016. doi:10.1126/science.aah5143

Nov 17

Molinaro AM, Pearson BJ. In silico lineage tracing through single cell transcriptomics identifies a neural stem cell population in planarians. Genome Biology. 2016. doi:10.1186/s13059-016-0937-9

Nov 16

Ntranos V, Kamath GM, Zhang JM, Pachter L, Tse DN. Fast and accurate single-cell RNA-seq analysis by clustering of transcript-compatibility counts. Genome Biology. 2016. doi:10.1186/s13059-016-0970-8

Nov 15

Li S, Yamada M, Han X, Ohler U, Benfey PN. High-Resolution Expression Map of the Arabidopsis Root Reveals Alternative Splicing and lincRNA Regulation. Dev Cell. 2016. doi:10.1016/j.devcel.2016.10.012

Nov 14

Korthauer KD, Chu L-F, Newton MA, Li Y, Thomson J, Stewart R, et al. A statistical approach for identifying differential distributions in single-cell RNA-seq experiments. Genome Biology. 2016. doi:10.1186/s13059-016-1077-y

Nov 13

Bendall SC, Davis KL, Amir E-AD, Tadmor MD, Simonds EF, Chen TJ, et al. Single-cell trajectory detection uncovers progression and regulatory coordination in human B cell development. Cell. 2014. doi:10.1016/j.cell.2014.04.005

Nov 12

Ding B, Zheng L, Zhu Y, Li N, Jia H, Ai R, et al. Normalization and noise reduction for single cell RNA-seq experiments. Bioinformatics. 2015. doi:10.1093/bioinformatics/btv122

Nov 11

Grün D, van Oudenaarden A. Design and Analysis of Single-Cell Sequencing Experiments. Cell. 2015. doi:10.1016/j.cell.2015.10.039

Nov 10

Buenrostro JD, Giresi PG, Zaba LC, Chang HY, Greenleaf WJ. Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nature Methods. 2013. doi:10.1038/nmeth.2688

Nov 9

Buettner F, Natarajan KN, Casale FP, Proserpio V, Scialdone A, Theis FJ, et al. Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells. Nature Biotechnology. 2015. doi:10.1038/nbt.3102

Nov 8

Satgé C, Moreau S, Sallet E, Lefort G, Auriac M-C, Remblière C, et al. Reprogramming of DNA methylation is critical for nodule development in Medicago truncatula. Nature Plants. doi:10.1038/nplants.2016.166

Nov 7

Kolodziejczyk AA, Kim JK, Svensson V, Marioni JC, Teichmann SA. The Technology and Biology of Single-Cell RNA Sequencing. Molecular Cell. 2015. doi:10.1016/j.molcel.2015.04.005

Nov 6

Svensson V, Natarajan KN, Ly L-H, Miragaia RJ, Labalette C, Macaulay IC, et al. Power Analysis of Single Cell RNA‐Sequencing Experiments. bioRxiv. 2016. doi:10.1101/073692

Nov 5

Bacher R, Kendziorski C. Design and computational analysis of single-cell RNA-sequencing experiments. Genome Biology. 2016. doi:10.1186/s13059-016-0927-y

Nov 4

Song L, Huang S-SC, Wise A, Castanon R, Nery JR, Chen H, et al. A transcription factor hierarchy defines an environmental stress response network. Science. 2016. doi:10.1126/science.aag1550

Nov 3

Liu S, Trapnell C. Single-cell transcriptome sequencing: recent advances and remaining challenges. F1000Res. 2016, doi:10.12688/f1000research.7223.1

Nov 2

Wattenberg M, Viégas F, Johnson I. How to Use t-SNE Effectively. 2016. http://distill.pub/2016/misread-tsne/

Nov 1

Faridani OR, Abdullayev I, Hagemann-Jensen M, Schell JP, Lanner F, Sandberg R. Single-cell sequencing of the small-RNA transcriptome. Nat Biotech. 2016. doi:10.1038/nbt.3701

Oct 31

Olsson A, Venkatasubramanian M, Chaudhri VK, Aronow BJ, Salomonis N, Singh H, et al. Single-cell analysis of mixed-lineage states leading to a binary cell fate choice. Nature. 2016. doi:10.1038/nature19348

Oct 30

Yi X, Dean AM. Phenotypic plasticity as an adaptation to a functional trade-off. eLife. doi:10.7554/eLife.19307

Oct 29

Efroni I, Birnbaum KD. The potential of single-cell profiling in plants. Genome Biology. 2016. doi:10.1186/s13059-016-0931-2

Oct 28

Trizzino M, Park Y, Holsbach-Beltrame M, Aracena K, Mika K, Caliskan M, et al. Transposable element exaptation is the primary source of novelty in the primate gene regulatory landscape. bioRxiv. 2016. doi:10.1101/083980

Oct 27

Lockton S, Gaut BS. The evolution of transposable elements in natural populations of self-fertilizing Arabidopsis thaliana and its outcrossing relative Arabidopsis lyrata. BMC Evolutionary Biology. 2010. doi:10.1186/1471-2148-10-10

Oct 26

Freeling M, Lyons E, Pedersen B, Alam M, Ming R, Lisch D. Many or most genes in Arabidopsis transposed after the origin of the order Brassicales. Genome Research. 2008. doi:10.1101/gr.081026.108

Oct 25

Lynch M, Ackerman MS, Gout J-F, Long H, Sung W, Thomas WK, et al. Genetic drift, selection and the evolution of the mutation rate. Nature Reviews Genetics. 2016. doi:10.1038/nrg.2016.104

Oct 24

di Iulio J, Bartha I, Wong E, Yu H-C, Hicks M, Shah N, et al. The human functional genome defined by genetic diversity. bioRxiv. 2016. doi:10.1101/082362

Oct 23

Greaves IK, Eichten SR, Groszmann M, Wang A, Ying H, Peacock WJ, et al. Twenty-four–nucleotide siRNAs produce heritable trans-chromosomal methylation in F1 Arabidopsis hybrids. PNAS. 2016. doi:10.1073/pnas.1613623113

Oct 22

Watson JM, Platzer A, Kazda A, Akimcheva S, Valuchova S, Nizhynska V, et al. Germline replications and somatic mutation accumulation are independent of vegetative life span in Arabidopsis. PNAS. 2016. doi:10.1073/pnas.1609686113

Oct 21

Schmidt F, Gasparoni N, Gasparoni G, Gianmoena K, Cadenas C, Polansky JK, et al. Combining transcription factor binding affinities with open-chromatin data for accurate gene expression prediction. bioRxiv. 2016. doi:10.1101/081935

Oct 20

Huff JT, Zilberman D, Roy SW. Mechanism for DNA transposons to generate introns on genomic scales. Nature. doi:10.1038/nature20110

Oct 19

Schalk C, Drevensek S, Kramdi A, Kassam M, Ahmed I, Cognat V, et al. DNA DAMAGE BINDING PROTEIN2 Shapes the DNA Methylation Landscape. The Plant Cell. 2016. doi:10.1105/tpc.16.00474

Oct 18

Hikabe O, Hamazaki N, Nagamatsu G, Obata Y, Hirao Y, Hamada N, et al. Reconstitution in vitro of the entire cycle of the mouse female germ line. Nature. 2016. doi:10.1038/nature20104

Oct 17

Pietzenuk B, Markus C, Gaubert H, Bagwan N, Merotto A, Bucher E, et al. Recurrent evolution of heat-responsiveness in Brassicaceae COPIA elements. Genome Biology. 2016. doi:10.1186/s13059-016-1072-3

Oct 16

D’haeseleer P. How does DNA sequence motif discovery work? Nature Biotechnology. 2006. doi:10.1038/nbt0806-959

Oct 15

Trapnell C, Salzberg SL. How to map billions of short reads onto genomes. Nature Biotechnology. 2009. doi:10.1038/nbt0509-455

Oct 14

Do CB, Batzoglou S. What is the expectation maximization algorithm? Nature Biotechnology. 2008. doi:10.1038/nbt1406

Oct 13

D’haeseleer P. What are DNA sequence motifs? Nature Biotechnology. 2006. doi:10.1038/nbt0406-423

Oct 12

Novikova PY, Hohmann N, Nizhynska V, Tsuchimatsu T, Ali J, Muir G, et al. Sequencing of the genus Arabidopsis identifies a complex history of nonbifurcating speciation and abundant trans-specific polymorphism. Nat Gen. 2016. doi:10.1038/ng.3617

Oct 11

Urban JM, Bliss J, Lawrence CE, Gerbi SA. Sequencing ultra-long DNA molecules with the Oxford Nanopore MinION. bioRxiv. 2015. doi:10.1101/019281

Oct 10

Bousios A, Gaut BS, Darzentas N. Considerations and complications of mapping small RNA libraries to transposable elements. bioRxiv. 2016. doi:10.1101/079749

Oct 9

McLeay RC, Lesluyes T, Cuellar Partida G, Bailey TL. Genome-wide in silico prediction of gene expression. Bioinformatics. 2012. doi:10.1093/bioinformatics/bts529

Oct 8

Cheng C, Gerstein M. Modeling the relative relationship of transcription factor binding and histone modifications to gene expression levels in mouse embryonic stem cells. Nucleic Acids Research. 2012. doi:10.1093/nar/gkr752

Oct 7

Miska EA, Ferguson-Smith AC. Transgenerational inheritance: Models and mechanisms of non–DNA sequence–based inheritance. Science. 2016. doi:10.1126/science.aaf4945

Oct 6

Ito H, Yoshida T, Tsukahara S, Kawabe A. Evolution of the ONSEN retrotransposon family activated upon heat stress in Brassicaceae. Gene. 2013. doi:10.1016/j.gene.2013.01.034

Oct 5

Budden DM, Hurley DG, Crampin EJ. Predictive modelling of gene expression from transcriptional regulatory elements. Briefings in Bioinformatics. 2015. doi:10.1093/bib/bbu034

Oct 4

Matsunaga W, Ohama N, Tanabe N, Masuta Y, Masuda S, Mitani N, et al. A small RNA mediated regulation of a stress-activated retrotransposon and the tissue specific transposition during the reproductive period in Arabidopsis. Front Plant Sci. 2015. doi:10.3389/fpls.2015.00048

Oct 3

Larivière V, Costas R. How Many Is Too Many? On the Relationship between Research Productivity and Impact. PLoS ONE. 2016. doi:10.1371/journal.pone.0162709

Oct 2

Kingsford C, Salzberg SL. What are decision trees? Nature Biotechnology. 2008. doi:10.1038/nbt0908-1011

Oct 1

Olah C, Carter S. Attention and Augmented Recurrent Neural Networks. 2016. http://distill.pub/2016/augmented-rnns/

Sep 30

Cavrak VV, Lettner N, Jamge S, Kosarewicz A, Bayer LM, Mittelsten Scheid O. How a Retrotransposon Exploits the Plant’s Heat Stress Response for Its Activation. PLoS Genetics. 2014. doi:10.1371/journal.pgen.1004115

Sep 29

Brzezinka K, Altmann S, Czesnick H, Nicolas P, Gorka M, Benke E, et al. Arabidopsis FORGETTER1 mediates stress-induced chromatin memory through nucleosome remodeling. eLife. 2016. doi:10.7554/eLife.17061

Sep 28

Herman JJ, Sultan SE. DNA methylation mediates genetic variation for adaptive transgenerational plasticity. Proceedings of the Royal Society of London B: Biological Sciences. 2016. doi:10.1098/rspb.2016.0988

Sep 27

Burkart-Waco D, Ngo K, Dilkes B, Josefsson C, Comai L. Early disruption of maternal-zygotic interaction and activation of defense-like responses in Arabidopsis interspecific crosses. The Plant Cell; 2013. doi:10.1105/tpc.112.108258

Sep 26

Burkart-Waco D, Ngo K, Lieberman M, Comai L. Perturbation of parentally biased gene expression during interspecific hybridization. PLoS ONE. 2015. doi:10.1371/journal.pone.0117293

Sep 25

Eddy SR. What is dynamic programming? Nature Biotechnology. 2004. doi:10.1038/nbt0704-909

Sep 24

Malaspinas A-S, Westaway MC, Muller C, Sousa VC, Lao O, Alves I, et al. A genomic history of Aboriginal Australia. Nature. 2016. doi:10.1038/nature18299

Sep 23

Wulfridge P, Langmead B, Feinberg AP, Hansen K. Choice of reference genome can introduce massive bias in bisulfite sequencing data. bioRxiv. 2016. doi:10.1101/076844

Sep 22

Yang G, Nagel DH, Feschotte C, Hancock CN, Wessler SR. Tuned for Transposition: Molecular Determinants Underlying the Hyperactivity of a Stowaway MITE. Science. 2009. doi:10.1126/science.1175688

Sep 21

Libbrecht MW, Noble WS. Machine learning applications in genetics and genomics. Nature Reviews Genetics. 2015. doi:10.1038/nrg3920

Sep 20

Huang X, Yang S, Gong J, Zhao Q, Feng Q, Zhan Q, et al. Genomic architecture of heterosis for yield traits in rice. Nature. 2016. doi:10.1038/nature19760

Sep 19

Compeau PEC, Pevzner PA, Tesler G. How to apply de Bruijn graphs to genome assembly. Nature Biotechnology. 2011. doi:10.1038/nbt.2023

Sep 18

Price MN, Wetmore KM, Waters RJ, Callaghan M, Ray J, Kuehl JV, et al. Deep Annotation of Protein Function across Diverse Bacteria from Mutant Phenotypes. bioRxiv. 2016. doi:10.1101/072470

Sep 17

Eddy SR. What is a hidden Markov model? Nature Biotechnology. 2004. doi:10.1038/nbt1004-1315

Sep 16

Krogh A. What are artificial neural networks? Nature Biotechnology. 2008. doi:10.1038/nbt1386

Sep 15

Noble WS. What is a support vector machine? Nature Biotechnology. 2006. doi:10.1038/nbt1206-1565

Sep 14

Chen J, Wrightsman T, Wessler SR, Stajich JE. RelocaTE2: a high resolution transposable element polymorphism mapping tool for population resequencing. PeerJ Preprints. 2016. doi:10.7287/peerj.preprints.2447v1

Sep 13

Baker M, Why scientists must share their research code. Nature. 2016. doi:10.1038/nature.2016.20504

Sep 12

Sindi SS, Önal S, Peng LC, Wu H-T, Raphael BJ. An integrative probabilistic model for identification of structural variation in sequencing data. Genome Biology. 2012. doi:10.1186/gb-2012-13-3-r22

Sep 11

Spies N, Weng Z, Bishara A, McDaniel J, Catoe D, Zook JM, et al. Genome-wide reconstruction of complex structural variants using read clouds. bioRxiv. 2016. doi:10.1101/074518

Sep 10

Li X, Kim Y, Tsang EK, Davis JR, Damani FN, Chiang C, et al. The impact of rare variation on gene expression across tissues. bioRxiv. 2016. doi:10.1101/074443

Sep 9

Peng RD. Reproducible Research in Computational Science. Science. 2011. doi:10.1126/science.1213847

Sep 8

http://simplystatistics.org/open%20science/2016/09/07/interview-with-a-data-sucker/

Sep 7

Kover PX, Valdar W, Trakalo J, Scarcelli N, Ehrenreich IM, Purugganan MD, et al. A Multiparent Advanced Generation Inter-Cross to Fine-Map Quantitative Traits in Arabidopsis thaliana. PLoS Genet. 2009. doi:10.1371/journal.pgen.1000551

Sep 6

Geman D, Geman S. Opinion: Science in the age of selfies. PNAS. 2016. doi:10.1073/pnas.1609793113

Sep 5

Muñoz-Gómez SA, Roger AJ. Leaving negative ancestors behind. eLife. 2016. doi:10.7554/eLife.20061

Sep 4

Altman N, Krzywinski M. Points of significance: Sources of variation. Nat Meth. 2015. doi:10.1038/nmeth.3224

Sep 3

Blainey P, Krzywinski M, Altman N. Points of Significance: Replication. Nat Meth. 2014. doi:10.1038/nmeth.3091

Sep 2

Wilson G, Bryan J, Cranston K, Kitzes J, Nederbragt L, Teal TK. Good Enough Practices in Scientific Computing. arXiv. 2016. arXiv:1609.00037

Sep 1

Harris EY, Ounit R, Lonardi S. BRAT-nova: fast and accurate mapping of bisulfite-treated reads. Bioinformatics. 2016. doi:10.1093/bioinformatics/btw226

Aug 31

Schnorrenberg S, Grotjohann T, Vorbrüggen G, Herzig A, Hell SW, Jakobs S. In vivo super-resolution RESOLFT microscopy of Drosophila melanogaster. eLife. 2016. doi:10.7554/eLife.15567

Aug 30

Martin AR, Gignoux CR, Walters RK, Wojcik GL, Gravel S, Daly MJ, et al. Population genetic history and polygenic risk biases in 1000 Genomes populations. bioRxiv. 2016. doi:10.1101/070797

Aug 29

Wright SI, Gaut BS. Molecular population genetics and the search for adaptive evolution in plants. Molecular Biology and Evolution. 2005. doi:10.1093/molbev/msi035

Aug 28

Maumus F, Quesneville H. Ancestral repeats have shaped epigenome and genome composition for millions of years in Arabidopsis thaliana. Nature Communications. 2014. doi:10.1038/ncomms5104

Aug 27

Takuno S, Ran J-H, Gaut BS. Evolutionary patterns of genic DNA methylation vary across land plants. Nature Plants. 2016. doi:10.1038/nplants.2015.222

Aug 26

http://simplystatistics.org/2016/08/24/replication-crisis/

Aug 25

Altman DG, Bland JM. How to obtain the confidence interval from a P value. BMJ. 2011. doi:10.1136/bmj.d2090

Aug 24

Hollister JD, Gaut BS. Epigenetic silencing of transposable elements: a trade-off between reduced transposition and deleterious effects on neighboring gene expression. Genome Research. 2009. doi:10.1101/gr.091678.109

Aug 23

Cano-Rodriguez D, Gjaltema RAF, Jilderda LJ, Jellema P, Dokter-Fokkens J, Ruiters MHJ, et al. Writing of H3K4Me3 overcomes epigenetic silencing in a sustained but context-dependent manner. Nature Communications. 2016. doi:10.1038/ncomms12284

Aug 22

Yang D-L, Zhang G, Tang K, Li J, Yang L, Huang H, et al. Dicer-independent RNA-directed DNA methylation in Arabidopsis. Cell Res. 2016. doi:10.1038/cr.2015.145

Aug 21

Walley JW, Sartor RC, Shen Z, Schmitz RJ, Wu KJ, Urich MA, et al. Integration of omic networks in a developmental atlas of maize. Science. 2016. doi:10.1126/science.aag1125

Aug 20

Elyashiv E, Sattath S, Hu TT, Strutsovsky A, McVicker G, Andolfatto P, et al. A Genomic Map of the Effects of Linked Selection in Drosophila. PLoS Genetics. 2016. doi:10.1371/journal.pgen.1006130

Aug 19

Keren L, Hausser J, Lotan-Pompan M, Vainberg Slutskin I, Alisar H, Kaminski S, et al. Massively Parallel Interrogation of the Effects of Gene Expression Levels on Fitness. Cell. 2016. doi:10.1016/j.cell.2016.07.024

Aug 18

Wei B, Liu H, Liu X, Xiao Q, Wang Y, Zhang J, et al. Genome-wide characterization of non-reference transposons in crops suggests non-random insertion. BMC Genomics. doi:10.1186/s12864-016-2847-3

Aug 17

Weir W, Capewell P, Foth B, Clucas C, Pountain A, Steketee P, et al. Population genomics reveals the origin and asexual evolution of human infective trypanosomes. eLife. 2016. doi:10.7554/eLife.11473

Aug 16

Altman N, Krzywinski M. Points of Significance: Association, correlation and causation. Nat Meth. doi:10.1038/nmeth.3587

Aug 15

Altman N, Krzywinski M. Points of Significance: Simple linear regression. Nat Meth. doi:10.1038/nmeth.3627

Aug 14

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Related: http://www.michaeleisen.org/blog/?p=1733

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Interesting or important points:

An as yet entirely unexplored possibility is the prospect that transcriptional memory might be underpinned by changes in mRNA stability rather than transcription.

I think certain RNA modifications have been shown to be induced by stress (at least in yeast), perhaps they play a role in modifying mRNA stability to facilitate stress memory.