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.
Majewski, Ian J., Matthew E. Ritchie, Belinda Phipson, Jason Corbin, Miha Pakusch, Anja Ebert, Meinrad Busslinger et al. “Opposing roles of polycomb repressive complexes in hematopoietic stem and progenitor cells.” Blood 116, no. 5 (2010): 731-739.
Dunn, Timothy W., Yu Mu, Sujatha Narayan, Owen Randlett, Eva A. Naumann, Chao-Tsung Yang, Alexander F. Schier, Jeremy Freeman, Florian Engert, and Misha B. Ahrens. “Brain-wide mapping of neural activity controlling zebrafish exploratory locomotion.” eLife 5 (2016): e12741.
Chowdhury, Saikat, and Ram Rup Sarkar. “Comparison of human cell signaling pathway databases—evolution, drawbacks and challenges.” Database 2015 (2015): bau126.
Janes, Kevin A., H. Christian Reinhardt, and Michael B. Yaffe. “Cytokine-induced signaling networks prioritize dynamic range over signal strength.” Cell 135, no. 2 (2008): 343-354.
Coyle, Scott, and Wendell A. Lim. “Mapping the functional versatility and fragility of Ras GTPase signaling circuits through in vitro network reconstitution.” eLife (2016): e12435.
Wang, Zhong, Mark Gerstein, and Michael Snyder. “RNA-Seq: a revolutionary tool for transcriptomics.” Nature Reviews Genetics 10, no. 1 (2009): 57-63.
Manning, Gerard, Gregory D. Plowman, Tony Hunter, and Sucha Sudarsanam. “Evolution of protein kinase signaling from yeast to man.” Trends in biochemical sciences 27, no. 10 (2002): 514-520.
Whitney, Mike, Edward Rockenstein, Greg Cantin, Tom Knapp, Gregor Zlokarnik, Pam Sanders, Kyle Durick, Frank F. Craig, and Paul A. Negulescu. “A genome-wide functional assay of signal transduction in living mammalian cells.” Nature biotechnology 16, no. 13 (1998): 1329-1333.
Bogdanović, Ozren, Arne H. Smits, Elisa de la Calle Mustienes, Juan J. Tena, Ethan Ford, Ruth Williams, Upeka Senanayake et al. “Active DNA demethylation at enhancers during the vertebrate phylotypic period.” Nature genetics (2016).
Grewal, Savraj S. “Why should cancer biologists care about tRNAs? tRNA synthesis, mRNA translation and the control of growth.” Biochimica et Biophysica Acta (BBA)-Gene Regulatory Mechanisms 1849, no. 7 (2015): 898-907.
Chen, Kelan, Renwick CJ Dobson, Isabelle Lucet, Samuel N. Young, Frederick G. Pearce, Marnie E. Blewitt, and James M. Murphy. “The epigenetic regulator Smchd1 contains a functional GHKL-type ATPase domain.” Biochemical Journal (2016): BCJ20160189.
Gilbert, Luke A., Matthew H. Larson, Leonardo Morsut, Zairan Liu, Gloria A. Brar, Sandra E. Torres, Noam Stern-Ginossar et al. “CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes.” Cell 154, no. 2 (2013): 442-451.
Smith, Donald B., and Kevin S. Johnson. “Single-step purification of polypeptides expressed in Escherichia coli as fusions with glutathione S-transferase.” Gene 67, no. 1 (1988): 31-40.
Miton, Charlotte M., and Nobuhiko Tokuriki. “How mutational epistasis impairs predictability in protein evolution and design.” Protein Science (2016).
Jadwin, Joshua A., Dongmyung Oh, Timothy G. Curran, Mari Ogiue-Ikeda, Lin Jia, Forest M. White, Kazuya Machida, Ji Yu, and Bruce J. Mayer. “Time-resolved multimodal analysis of Src Homology 2 (SH2) domain binding in signaling by receptor tyrosine kinases.” eLife 5 (2016): e11835.
Fraser, Nicholas J., Jian-Wei Liu, Peter D. Mabbitt, Galen J. Correy, Chris W. Coppin, Mathilde Lethier, Matthew A. Perugini et al. “Evolution of Protein Quaternary Structure in Response to Selective Pressure for Increased Thermostability.” Journal of Molecular Biology (2016).
Jeggo, Penny A., Laurence H. Pearl, and Antony M. Carr. “DNA repair, genome stability and cancer: a historical perspective.” Nature Reviews Cancer 16, no. 1 (2016): 35-42.
Croker, Ben A., Hiu Kiu, Marc Pellegrini, Jesse Toe, Simon Preston, Donald Metcalf, Joanne A. O’Donnell et al. “IL-6 promotes acute and chronic inflammatory disease in the absence of SOCS3.” Immunology and cell biology 90, no. 1 (2012): 124-129.
Chen, Sidi, Neville E. Sanjana, Kaijie Zheng, Ophir Shalem, Kyungheon Lee, Xi Shi, David A. Scott et al. “Genome-wide CRISPR screen in a mouse model of tumor growth and metastasis.” Cell 160, no. 6 (2015): 1246-1260.
Müller-Newen, Gerhard. “The cytokine receptor gp130: faithfully promiscuous.” Science Signaling 2003, no. 201 (2003): pe40-pe40.
Greaney, Marie R., Ann E. Privorotskiy, Kristen P. D’Elia, and David Schoppik. “Ocular Motoneuron Pools Develop Along a Dorsoventral Axis in Zebrafish, Danio rerio.” bioRxiv (2016): 049296.
Liongue, Clifford, Tarannum Taznin, and Alister C. Ward. “Signaling via the CytoR/JAK/STAT/SOCS pathway: Emergence during evolution.” Molecular immunology 71 (2016): 166-175.
Tiwari, Ravi P., Wayne G. Reeve, Michael J. Dilworth, and Andrew R. Glenn. “Acid tolerance in Rhizobium meliloti strain WSM419 involves a two-component sensor-regulator system.” Microbiology 142, no. 7 (1996): 1693-1704.
Lopresti, Adrian L., Michael Maes, Garth L. Maker, Sean D. Hood, and Peter D. Drummond. “Curcumin for the treatment of major depression: a randomised, double-blind, placebo controlled study.” Journal of affective disorders 167 (2014): 368-375.
Boulanger, Martin J., Dar-chone Chow, Elena Brevnova, Monika Martick, Gordon Sandford, John Nicholas, and K. Christopher Garcia. “Molecular mechanisms for viral mimicry of a human cytokine: activation of gp130 by HHV-8 interleukin-6.” Journal of molecular biology 335, no. 2 (2004): 641-654.
Cong, Le, F. Ann Ran, David Cox, Shuailiang Lin, Robert Barretto, Naomi Habib, Patrick D. Hsu et al. “Multiplex genome engineering using CRISPR/Cas systems.” Science 339, no. 6121 (2013): 819-823.
Branton, Daniel, David W. Deamer, Andre Marziali, Hagan Bayley, Steven A. Benner, Thomas Butler, Massimiliano Di Ventra et al. “The potential and challenges of nanopore sequencing.” Nature biotechnology 26, no. 10 (2008): 1146-1153.
Gouy, Manolo, Stéphane Guindon, and Olivier Gascuel. “SeaView version 4: a multiplatform graphical user interface for sequence alignment and phylogenetic tree building.” Molecular biology and evolution 27, no. 2 (2010): 221-224.
Kishimoto, Tadamitsu, Shizuo Akira, Masashi Narazaki, and Tetsuya Taga. “Interleukin-6 family of cytokines and gp130.” Blood 86, no. 4 (1995): 1243-1254.