As one of my 2016 scientific resolutions I will be reading one paper every day of the year and posting each here (hopefully) daily. Along with me, Natalie Matosin, Martin Engel and Lauren Drogos will also be doing the same and likewise posting each paper on their respective blogs. You can also follow the three of us and the others who are joining us using the tag #366papers on twitter. Also find Dr Lauren Drogos here, Dr Natalie Matosin here and find Dr Martin Engel here.
Wilson, Christopher GM, Thomas J. Magliery, and Lynne Regan. “Detecting protein-protein interactions with GFP-fragment reassembly.” Nature methods 1, no. 3 (2004): 255-262.
Gerlier, Denis, and Nicole Thomasset. “Use of MTT colorimetric assay to measure cell activation.” Journal of immunological methods 94, no. 1-2 (1986): 57-63.
Quail, Michael A., Iwanka Kozarewa, Frances Smith, Aylwyn Scally, Philip J. Stephens, Richard Durbin, Harold Swerdlow, and Daniel J. Turner. “A large genome center’s improvements to the Illumina sequencing system.” Nature methods 5, no. 12 (2008): 1005-1010.
Bonnici, Vincenzo, and Vincenzo Manca. “Informational laws of genome structures.” Scientific Reports 6 (2016): 28840.
Wang, J., E. Santiago, and A. Caballero. “Prediction and estimation of effective population size.” Heredity (2016).
Zhou, Honglin, Min Xu, Qian Huang, Adam T. Gates, Xiaohua D. Zhang, John C. Castle, Erica Stec et al. “Genome-scale RNAi screen for host factors required for HIV replication.” Cell host & microbe 4, no. 5 (2008): 495-504.
Luo, Ji, Michael J. Emanuele, Danan Li, Chad J. Creighton, Michael R. Schlabach, Thomas F. Westbrook, Kwok-Kin Wong, and Stephen J. Elledge. “A genome-wide RNAi screen identifies multiple synthetic lethal interactions with the Ras oncogene.” Cell 137, no. 5 (2009): 835-848.
Mohseni, Morvarid, Jianlong Sun, Allison Lau, Stephen Curtis, Jeffrey Goldsmith, Victor L. Fox, Chongjuan Wei et al. “A genetic screen identifies an LKB1–MARK signalling axis controlling the Hippo–YAP pathway.” Nature cell biology 16, no. 1 (2014): 108-117.
Hoi, Charlene SL, Wenjun Xiong, and Ilaria Rebay. “Retinal Axon Guidance Requires Integration of Eya and the JAK/STAT Pathway into Phosphotyrosine-Based Signaling Circuitries in Drosophila.” Genetics (2016): genetics-115.
Stark, George R., and James E. Darnell. “The JAK-STAT pathway at twenty.” Immunity 36, no. 4 (2012): 503-514.
Thorvaldsdóttir, Helga, James T. Robinson, and Jill P. Mesirov. “Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration.” Briefings in bioinformatics 14, no. 2 (2013): 178-192.
Krzywinski, Martin, Jacqueline Schein, Inanc Birol, Joseph Connors, Randy Gascoyne, Doug Horsman, Steven J. Jones, and Marco A. Marra. “Circos: an information aesthetic for comparative genomics.” Genome research 19, no. 9 (2009): 1639-1645.
Marguerat, Samuel, and Jürg Bähler. “RNA-seq: from technology to biology.” Cellular and molecular life sciences 67, no. 4 (2010): 569-579.
Cirulli, Elizabeth T., Brittany N. Lasseigne, Slavé Petrovski, Peter C. Sapp, Patrick A. Dion, Claire S. Leblond, Julien Couthouis et al. “Exome sequencing in amyotrophic lateral sclerosis identifies risk genes and pathways.” Science 347, no. 6229 (2015): 1436-1441.
Loman, Nicholas J., and Mick Watson. “Successful test launch for nanopore sequencing.” Nature methods 12, no. 4 (2015): 303-304.
Robert, Christelle, and Mick Watson. “Errors in RNA-Seq quantification affect genes of relevance to human disease.” Genome biology 16, no. 1 (2015): 1.
Uyeda, Josef C., Daniel S. Caetano, and Matthew W. Pennell. “Comparative analysis of principal components can be misleading.” Systematic biology (2015): syv019.
Sakakibara, Daisuke, Atsuko Sasaki, Teppei Ikeya, Junpei Hamatsu, Tomomi Hanashima, Masaki Mishima, Masatoshi Yoshimasu et al. “Protein structure determination in living cells by in-cell NMR spectroscopy.” Nature 458, no. 7234 (2009): 102-105
Law, Charity W., Yunshun Chen, Wei Shi, and Gordon K. Smyth. “Voom: precision weights unlock linear model analysis tools for RNA-seq read counts.” Genome biology 15, no. 2 (2014): 1.
Shalem, Ophir, Neville E. Sanjana, and Feng Zhang. “High-throughput functional genomics using CRISPR-Cas9.” Nature Reviews Genetics 16, no. 5 (2015): 299-311.
Jones, Bryony. “Chromosome biology: Diverse evolution of sex chromosomes in flies.” Nature Reviews Genetics 16, no. 6 (2015): 316-317.
Wright, Jason B., and Neville E. Sanjana. “CRISPR Screens to Discover Functional Noncoding Elements.” Trends in Genetics (2016)
Trenker, R., M. J. Call, and M. E. Call. “Progress and prospects for structural studies of transmembrane interactions in single-spanning receptors.” Current opinion in structural biology 39 (2016): 115.
Lee, Michael J., and Michael B. Yaffe. “Protein regulation in signal transduction.” Cold Spring Harbor perspectives in biology 8, no. 6 (2016): a005918.
Yaffe, Michael B. “How to “cell” a genomic or proteomic screen.” Science signaling 1, no. 47 (2008): eg9-eg9.
Yaffe, Michael B., and Nancy R. Gough. “Leveraging signaling research to understand and treat disease.” Sci. Signal. 9, no. 421 (2016): eg4-eg4.
Roberts, Kathryn G., Yongjin Li, Debbie Payne-Turner, Richard C. Harvey, Yung-Li Yang, Deqing Pei, Kelly McCastlain et al. “Targetable kinase-activating lesions in Ph-like acute lymphoblastic leukemia.” New England journal of medicine 371, no. 11 (2014): 1005-1015.
Zhang, Xiaotian, Jianzhong Su, Mira Jeong, Myunggon Ko, Yun Huang, Hyun Jung Park, Anna Guzman et al. “DNMT3A and TET2 compete and cooperate to repress lineage-specific transcription factors in hematopoietic stem cells.” Nature Genetics (2016).
Weinstein, John N., Eric A. Collisson, Gordon B. Mills, Kenna R. Mills Shaw, Brad A. Ozenberger, Kyle Ellrott, Ilya Shmulevich, Chris Sander, Joshua M. Stuart, and Cancer Genome Atlas Research Network. “The cancer genome atlas pan-cancer analysis project.” Nature genetics 45, no. 10 (2013): 1113-1120.
Lawrence, Michael S., Petar Stojanov, Paz Polak, Gregory V. Kryukov, Kristian Cibulskis, Andrey Sivachenko, Scott L. Carter et al. “Mutational heterogeneity in cancer and the search for new cancer-associated genes.” Nature 499, no. 7457 (2013): 214-218.