How to read a scientific publication

One skill I think a lot of younger science students lack is the ability to read a paper quickly, dissect all the information and then decide whether the paper is good, bad or somewhere in between. Like many people, I have developed my own method for reading a research article, so I thought I would share it in the hopes of helping others to get through what can sometimes seem like a very daunting task.

  1. Read the title (duh)
    I realise this seems extremely obvious, and you probably did this to choose the paper in the first place. When I’m reading a paper that I really want to understand and remember I write notes on a blank piece of paper about it as I go. So naturally at the top of the page I write the title of the paper. Step 1 done!
  1. Read the abstract
    This gives you the general idea of the paper & what they have done/what you can expect from the paper. This is also the stage at which I decide whether I want to continue reading on.
  1. Read the last paragraph of the introduction
    I usually don’t even bother with the introduction of a paper unless I skim it very quickly. The exception to that is if I don’t know the field and I need a bit of background. But I always read the last paragraph of the intro as it is like a super brief summary of the whole intro, and usually states what question the authors are trying to address. At this stage I go back to my notes page and write down the question I think they are trying to answer/ the hypothesis they are testing.
  1. Skip straight to the figures in the results section
    Here I look at the figures, read the figure legends and write down what I think each of the figures shows. I then read the results section from start to finish to see if the authors and I have reached the same conclusions about the data. This is the best part in my opinion. Sometimes you think the data says exactly what the authors have said it does, sometimes you don’t. At the end of this section, I usually go back to my notes and write what the main points and ideas of the paper are. Sometimes it can be useful to re-draw the important figures in a more basic way- this helps me to wrap my head around some things I don’t get at the time.
  1. Read the methods section
    I tend to do this briefly, but this is often where you you can decide whether the paper is good or not (if you didn’t decide in the results). Here is where you can decide whether their experiments were designed well or not. After reading the methods I like to write down a few points about where they could have improved the study.
  1. Briefly read the discussion and then the conclusions
    I don’t really find the discussion section very helpful, however sometimes it can be interesting to read. The discussion tends to be the most biased part of the paper, and sometimes people make some huge leaps when interpreting their results and putting them in the perspective of the field. Remember when reading the discussion that often the references are there to support their conclusions. If the authors discuss papers that disagree with their results, kudos to them! I still like to read the discussion though. After reading the discussion and conclusion I like to write down the interesting points of the paper, what they showed and how (if possible) the work may relate to my own.
  1. Write your own conclusion about the paper you read
    Here I re-state what I think they were aiming to do and whether they did it. What was new, and what were their limitations in this study? I also write down the questions that I still have about the paper, and if I read the paper again in the future I go back to this notes page and try to answer those questions.
  1. Check if there are any references that you want to follow up on/may be of interest to you.

So that’s how I read my papers when I want to really understand them and take notes. Many people will disagree with this method of reading a paper, but each to their own! Please let me know how you read a paper & if you have any other tips.

366 papers in 2016; looking back on a paper a day

In 2015 at the end of the year myself and a few others though it would be a good idea to read a scientific paper a day in 2016. So on the 1st of Jan 2016 I began this challenge, using the tag #366papers on twitter & listing each paper here on my website. Here are so pros, cons and my thoughts on this challenge:

Pros:

  • You get better at reading scientific papers and digesting them quickly
  • It is interesting, especially if you read widely (which I recommend)
  • It’s a neat challenge if you’re a scientist

Cons:

  • Starts to feel like a chore
  • A paper a day doesn’t leave a lot of time to really understand a paper in depth
  • Some days you want to read 5 papers and others you want to read 0, but that defeats the point of the exercise (I did this anyway)

All in all I wouldn’t do it again & I didn’t even do it properly this time. But I did read 366 papers (more really, but I didn’t list them all). As I was writing my thesis for a large chunk of the year it wasn’t that difficult to hit 366, however some days I just didn’t want to read a paper. I didn’t want to make reading papers feel like something I HAD to do, making it feel like a task, so I didn’t.

In retrospect I think 52 papers a year would be a better better goal. This gives you time to really understand the paper & means you don’t actually have to read one a day, which is not fun on holidays and weekends, or when you’re just flat out. So if you’re thinking of doing a similar challenge in 2017, perhaps think about cutting back to 1 paper a week….. Or try 1 a day, whatever suits you!

December: 366 papers in 2016

Dec 1:

Williams, Adam, Jorge Henao-Mejia, and Richard A. Flavell. “Editing the mouse genome using the CRISPR–Cas9 system.Cold Spring Harbor Protocols 2016, no. 2 (2016): pdb-top087536.

Dec 2:

Nicola, Nicos A., Warren S. Alexander, Douglas J. Hilton, and Ashley P. Ng. “In memoriam: Donald Metcalf (1929-2014)–A historical perspective of his contributions to hematology.Experimental hematology 43, no. 6 (2015): 425-427.

Dec 3:

Westerterp, Marit, Andrew J. Murphy, Mi Wang, Tamara A. Pagler, Yuliya Vengrenyuk, Mojdeh S. Kappus, Darren J. Gorman et al. “Deficiency of ATP-binding cassette transporters A1 and G1 in macrophages increases inflammation and accelerates atherosclerosis in mice.Circulation research 112, no. 11 (2013): 1456-1465.

Dec 4:

Baker, Paul J., Dave Boucher, Damien Bierschenk, Christina Tebartz, Paul G. Whitney, Damian B. D’Silva, Maria C. Tanzer et al. “NLRP3 inflammasome activation downstream of cytoplasmic LPS recognition by both caspase‐4 and caspase‐5.European journal of immunology 45, no. 10 (2015): 2918-2926.

Dec 5:

Kershaw, Nadia J., James M. Murphy, Nicholas PD Liau, Leila N. Varghese, Artem Laktyushin, Eden L. Whitlock, Isabelle S. Lucet, Nicos A. Nicola, and Jeffrey J. Babon. “SOCS3 binds specific receptor–JAK complexes to control cytokine signaling by direct kinase inhibition.Nature structural & molecular biology 20, no. 4 (2013): 469-476.

Dec 6:

Jenkins, Misty R., Jesse A. Rudd-Schmidt, Jamie A. Lopez, Kelly M. Ramsbottom, Stuart I. Mannering, Daniel M. Andrews, Ilia Voskoboinik, and Joseph A. Trapani. “Failed CTL/NK cell killing and cytokine hypersecretion are directly linked through prolonged synapse time.The Journal of experimental medicine 212, no. 3 (2015): 307-317.

Dec 7:

Berry, Richard, Stephen J. Headey, Melissa J. Call, James McCluskey, Clive A. Tregaskes, Jim Kaufman, Ruide Koh, Martin J. Scanlon, Matthew E. Call, and Jamie Rossjohn. “Structure of the Chicken CD3ϵδ/γ Heterodimer and Its Assembly with the αβT Cell Receptor.Journal of Biological Chemistry 289, no. 12 (2014): 8240-8251.

Dec 8:

Ernst, Christina, Jeremy Pike, Sarah J. Aitken, Hannah K. Long, Nils Eling, Lovorka Stojic, Michelle C. Ward et al. “Successful transmission and transcriptional deployment of a human chromosome via mouse male meiosis.eLife 5 (2016): e20235.

Dec 9:

Gibson, Daniel G., Hamilton O. Smith, Clyde A. Hutchison III, J. Craig Venter, and Chuck Merryman. “Chemical synthesis of the mouse mitochondrial genome.” nature methods 7, no. 11 (2010): 901-903.

Dec 10:

Bank, Claudia, Sebastian Matuszewski, Ryan T. Hietpas, and Jeffrey D. Jensen. “On the (un-) predictability of a large intragenic fitness landscape.bioRxiv (2016): 048769.

Dec 11:

Rosenfeld, Lior, Michael Heyne, Julia M. Shifman, and Niv Papo. “Protein Engineering by Combined Computational and In Vitro Evolution Approaches.Trends in biochemical sciences 41, no. 5 (2016): 421-433.

Dec 12:

Rost, Fabian, Aida Rodrigo Albors, Vladimir Mazurov, Lutz Brusch, Andreas Deutsch, Elly M. Tanaka, and Osvaldo Chara. “Accelerated cell divisions drive the outgrowth of the regenerating spinal cord in axolotls.eLife 5 (2016): e20357.

Dec 13:

Suto, Nobuyoshi, Amanda Laque, Genna L. De Ness, Grant E. Wagner, Debbie Watry, Tony Kerr, Eisuke Koya, Mark R. Mayford, Bruce T. Hope, and Friedbert Weiss. “Distinct memory engrams in the infralimbic cortex of rats control opposing environmental actions on a learned behavior.eLife 5 (2016): e21920.

Dec 14:

Alcock, Felicity, Phillip J. Stansfeld, Hajra Basit, Johann Habersetzer, Matthew AB Baker, Tracy Palmer, Mark I. Wallace, and Ben C. Berks. “Assembling the Tat protein translocase.eLife 5 (2016): e20718.

Dec 15:

Wells, Michael F., Max R. Salick, Ole Wiskow, Daniel J. Ho, Kathleen A. Worringer, Robert J. Ihry, Sravya Kommineni et al. “Genetic ablation of AXL does not protect human neural progenitor cells and cerebral organoids from Zika virus infection.Cell Stem Cell 19, no. 6 (2016): 703-708.

Dec 16:

Hutchison, Clyde A., Ray-Yuan Chuang, Vladimir N. Noskov, Nacyra Assad-Garcia, Thomas J. Deerinck, Mark H. Ellisman, John Gill et al. “Design and synthesis of a minimal bacterial genome.Science 351, no. 6280 (2016): aad6253.

Dec 17:

Telenti, Amalio, Levi CT Pierce, William H. Biggs, Julia di Iulio, Emily HM Wong, Martin M. Fabani, Ewen F. Kirkness et al. “Deep sequencing of 10,000 human genomes.Proceedings of the National Academy of Sciences (2016): 201613365.

Dec 18:

Zahn, Laura M., P. Mickey Williams, Jeremy P. Segal, Itay Tirosh, Benjamin Izar, Sanjay M. Prakadan, Marc H. Wadsworth II et al. “Single-cell expression profiles of melanoma.Science 183 (2016): 185.

Dec 19:

Telenti, Amalio, Brad A. Perkins, and J. Craig Venter. “Dynamics of an aging genome.Cell Metabolism 23, no. 6 (2016): 949-950.

Dec 20:

Vinson, Valda, Denes Hnisz, Abraham S. Weintraub, Daniel S. Day, Anne-Laure Valton, Rasmus O. Bak, Charles H. Li et al. “A proton pump in action.Science 351, no. 6280 (2016): 1411-1413.

Dec 21:

Tabebordbar, Mohammadsharif, Kexian Zhu, Jason KW Cheng, Wei Leong Chew, Jeffrey J. Widrick, Winston X. Yan, Claire Maesner et al. “In vivo gene editing in dystrophic mouse muscle and muscle stem cells.” Science 351, no. 6271 (2016): 407-411.

Dec 22:

Session, Adam M., Yoshinobu Uno, Taejoon Kwon, Jarrod A. Chapman, Atsushi Toyoda, Shuji Takahashi, Akimasa Fukui et al. “Genome evolution in the allotetraploid frog Xenopus laevis.Nature 538, no. 7625 (2016): 336-343.

Dec 23:

Chavez, Alejandro, Marcelle Tuttle, Benjamin W. Pruitt, Ben Ewen-Campen, Raj Chari, Dmitry Ter-Ovanesyan, Sabina J. Haque et al. “Comparative Analysis of Cas9 Activators Across Multiple Species.” (2016).

Dec 24:

Zhirnov, Victor, Reza M. Zadegan, Gurtej S. Sandhu, George M. Church, and William L. Hughes. “Nucleic acid memory.” Nature materials 15, no. 4 (2016): 366-370.

Dec 25:

Ostrov, Nili, Matthieu Landon, Marc Guell, Gleb Kuznetsov, Jun Teramoto, Natalie Cervantes, Minerva Zhou et al. “Design, synthesis, and testing toward a 57-codon genome.Science 353, no. 6301 (2016): 819-822.

Dec 26:

Shipman, Seth L., Jeff Nivala, Jeffrey D. Macklis, and George M. Church. “Molecular recordings by directed CRISPR spacer acquisition.Science (2016): aaf1175.

Dec 27:

Stranges, P. Benjamin, Mirkó Palla, Sergey Kalachikov, Jeff Nivala, Michael Dorwart, Shiv Kumar, Mintu Porel et al. “Design and characterization of a nanopore-coupled polymerase for single-molecule DNA sequencing by synthesis on an electrode array.Proceedings of the National Academy of Sciences 113, no. 44 (2016): E6749-E6756.

Dec 28:

Fuller, Carl W., Shiv Kumar, Mintu Porel, Minchen Chien, Arek Bibillo, P. Benjamin Stranges, Michael Dorwart et al. “Real-time single-molecule electronic DNA sequencing by synthesis using polymer-tagged nucleotides on a nanopore array.Proceedings of the National Academy of Sciences 113, no. 19 (2016): 5233-5238.

Dec 29:

Deamer, David, Mark Akeson, and Daniel Branton. “Three decades of nanopore sequencing.Nature biotechnology 34, no. 5 (2016): 518-524.

Dec 30:

Kasianowicz, John J., and Sergey M. Bezrukov. “On’three decades of nanopore sequencing’.” Nature biotechnology 34, no. 5 (2016): 481-482.

Dec 31:

van Gent, Dik C., and Roland Kanaar. “Exploiting DNA repair defects for novel cancer therapies.Molecular Biology of the Cell 27, no. 14 (2016): 2145-2148.

 

November: 366 papers in 2016

Nov 1:

Lander, L. J., and T. R. Parkin. “Counterexample to Euler’s conjecture on sums of like powers.Bulletin of the American Mathematical Society 72, no. 6 (1966): 1079.

Nov 2:

Coffey, Michael J., Brad E. Sleebs, Alessandro D. Uboldi, Alexandra Garnham, Magdalena Franco, Nicole D. Marino, Michael W. Panas et al. “An aspartyl protease defines a novel pathway for export of Toxoplasma proteins into the host cell.Elife 4 (2015): e10809.

Nov 3:

Boddey, Justin A., and Alan F. Cowman. “Plasmodium nesting: remaking the erythrocyte from the inside out.Annual review of microbiology 67 (2013): 243-269.

Nov 4:

Wang, Lei, and Peter G. Schultz. “Expanding the genetic code.” Angewandte chemie international edition 44, no. 1 (2005): 34-66.

Nov 5:

Sinkins, Steven P., and Fred Gould. “Gene drive systems for insect disease vectors.Nature Reviews Genetics 7, no. 6 (2006): 427-435.

Nov 6:

Gantz, Valentino M., Nijole Jasinskiene, Olga Tatarenkova, Aniko Fazekas, Vanessa M. Macias, Ethan Bier, and Anthony A. James. “Highly efficient Cas9-mediated gene drive for population modification of the malaria vector mosquito Anopheles stephensi.Proceedings of the National Academy of Sciences 112, no. 49 (2015): E6736-E6743.

Nov 7:

Ushiki, Takashi, Nicholas D. Huntington, Stefan P. Glaser, Hiu Kiu, Angela Georgiou, Jian-Guo Zhang, Donald Metcalf, Nicos A. Nicola, Andrew W. Roberts, and Warren S. Alexander. “Rapid Inflammation in Mice Lacking Both SOCS1 and SOCS3 in Hematopoietic Cells.PloS one 11, no. 9 (2016): e0162111.

Nov 8:

Teckchandani, Anjali, and Jonathan A. Cooper. “The ubiquitin-proteasome system regulates focal adhesions at the leading edge of migrating cells.eLife 5 (2016): e17440.

Nov 9:

Datlinger, Paul, Christian Schmidl, Andre F. Rendeiro, Peter Traxler, Johanna Klughammer, Linda Schuster, and Christoph Bock. “Pooled CRISPR screening with single-cell transcriptome read-out.bioRxiv (2016): 083774.

Nov 10:

Rautela, Jai, and Nicholas D. Huntington. “IL-15 signaling in NK cell cancer immunotherapy.” Current Opinion in Immunology 44 (2017): 1-6.

Nov 11:

Babon, Jeffrey J., Leila N. Varghese, and Nicos A. Nicola. “Inhibition of IL-6 family cytokines by SOCS3.” In Seminars in immunology, vol. 26, no. 1, pp. 13-19. Academic Press, 2014.

Nov 12:

Tan, Jenille M., and Scott E. Martin. “Exploring arrayed synthetic CRISPR for functional genomic screening.Cancer Research 76, no. 14 Supplement (2016): 73-73.

Nov 13:

Morozova, Olena, and Marco A. Marra. “Applications of next-generation sequencing technologies in functional genomics.Genomics 92, no. 5 (2008): 255-264.

Nov 14:

Gao, Jianjiong, James Lindsay, Stuart Watt, Istemi Bahceci, Pieter Lukasse, Adam Abeshouse, Hsiao-Wei Chen et al. “The cBioPortal for cancer genomics and its application in precision oncology.Cancer Research 76, no. 14 Supplement (2016): 5277-5277.

Nov 15:

Ulitsky, Igor. “Evolution to the rescue: using comparative genomics to understand long non-coding RNAs.Nature Reviews Genetics 17, no. 10 (2016): 601-614.

Nov 16:

Pang, Swee Heng Milon, Martina Minnich, Pradnya Gangatirkar, Zhen Zheng, Anja Ebert, Guangchun Song, R. A. Dickins et al. “PU. 1 cooperates with IRF4 and IRF8 to suppress pre-B-cell leukemia.Leukemia (2016).

Nov 17:

Babon, Jeffrey J., Jennifer K. Sabo, Alfreda Soetopo, Shenggen Yao, Michael F. Bailey, Jian-Guo Zhang, Nicos A. Nicola, and Raymond S. Norton. “The SOCS box domain of SOCS3: structure and interaction with the elonginBC-cullin5 ubiquitin ligase.Journal of molecular biology 381, no. 4 (2008): 928-940.

Nov 18:

Babon, Jeffrey J., Nicholas PD Liau, and Nadia J. Kershaw. “JAK1 Takes a FERM Hold of Type II Cytokine Receptors.Structure 24, no. 6 (2016): 840-842.

Nov 19:

Adzhubei, Ivan A., Steffen Schmidt, Leonid Peshkin, Vasily E. Ramensky, Anna Gerasimova, Peer Bork, Alexey S. Kondrashov, and Shamil R. Sunyaev. “A method and server for predicting damaging missense mutations.” Nature methods 7, no. 4 (2010): 248-249.

Nov 20:

Rusk, Nicole. “Genomics: CRISPR gain-of-function screens.Nature methods 12, no. 2 (2015): 102-103.

Nov 21:

Gibson, Daniel G., Gwynedd A. Benders, Cynthia Andrews-Pfannkoch, Evgeniya A. Denisova, Holly Baden-Tillson, Jayshree Zaveri, Timothy B. Stockwell et al. “Complete chemical synthesis, assembly, and cloning of a Mycoplasma genitalium genome.science 319, no. 5867 (2008): 1215-1220.

Nov 22:

Biggin, M. D., T. J. Gibson, and G. F. Hong. “Buffer gradient gels and 35S label as an aid to rapid DNA sequence determination.” Proceedings of the National Academy of Sciences 80, no. 13 (1983): 3963-3965.

Nov 23:

Gibson, Daniel G., Hamilton O. Smith, Clyde A. Hutchison III, J. Craig Venter, and Chuck Merryman. “Chemical synthesis of the mouse mitochondrial genome.nature methods 7, no. 11 (2010): 901-903.

Nov 24:

Gibson, Daniel G. “Enzymatic assembly of overlapping DNA fragments.Methods Enzymol 498 (2011): 349-361.

Nov 25:

Upper, Dennis. “THE UNSUCCESSFUL SELF‐TREATMENT OF A CASE OF “WRITER’S BLOCK” 1.” Journal of applied behavior analysis 7, no. 3 (1974): 497-497.

Nov 26:

A comprehensive overview of chemical-free consumer products Alexander F. G. Goldberg

Nov 27:

Stojković, Biljana, Ahmed Sayadi, Mirko Đorđević, Jelena Jović, Uroš Savković, and Göran Arnqvist. “Divergent evolution of life span associated with mitochondrial DNA evolution.Evolution (2016).

Nov 28:

Rothberg, Bonnie E. Gould, and Jonathan M. Rothberg. “Massively Parallel (“Next-Generation”) DNA Sequencing.” Clinical chemistry 61, no. 7 (2015): 997-998.

Nov 29:

Chinwalla, Asif T., Lisa L. Cook, Kimberly D. Delehaunty, Ginger A. Fewell, Lucinda A. Fulton, Robert S. Fulton, Tina A. Graves et al. “Initial sequencing and comparative analysis of the mouse genome.Nature 420, no. 6915 (2002): 520-562.

Nov 30:

Wasserman, Wyeth W., Michael Palumbo, William Thompson, James W. Fickett, and Charles E. Lawrence. “Human-mouse genome comparisons to locate regulatory sites.Nature genetics 26, no. 2 (2000): 225-228.

 

 

 

October: 366 papers in 2016

Oct 1:

Mallon, John, and Scott Bailey. “A molecular arms race: new insights into anti-CRISPR mechanisms.Nature Structural & Molecular Biology 23, no. 9 (2016): 765-766.

Oct 2:

Lagarde, Julien, Barbara Uszczynska-Ratajczak, Javier Santoyo-Lopez, Jose Manuel Gonzalez, Electra Tapanari, Jonathan M. Mudge, Charles A. Steward et al. “Extension of human lncRNA transcripts by RACE coupled with long-read high-throughput sequencing (RACE-Seq).Nature communications 7 (2016).

Oct 3:

Fan, Chenguang, Kevan Ip, and Dieter Söll. “Expanding the genetic code of Escherichia coli with phosphotyrosine.FEBS letters 590, no. 17 (2016): 3040-3047.

Oct 4:

Lajoie, M. J., D. Söll, and G. M. Church. “Overcoming challenges in engineering the genetic code.Journal of molecular biology 428, no. 5 (2016): 1004-1021.

Oct 5:

Jewett, Michael C., and Vincent Noireaux. “Synthetic biology: Tailor-made genetic codes.” Nature chemistry 8, no. 4 (2016): 291-292.

Oct 6:

Qiu, Jing, Jamie McQueen, Bilada Bilican, Owen Dando, Dario Magnani, Karolina Punovuori, Bhuvaneish T. Selvaraj et al. “Evidence for evolutionary divergence of activity-dependent gene expression in developing neurons.” eLife 5 (2016): e20337.

Oct 7:

Venter, J. Craig, Mark D. Adams, Eugene W. Myers, Peter W. Li, Richard J. Mural, Granger G. Sutton, Hamilton O. Smith et al. “The sequence of the human genome.science 291, no. 5507 (2001): 1304-1351.

Oct 8:

Roby, Justin Alexander, Brian C. Keller, Hilario J. Ramos, Michael S. Diamond, and Michael J. Gale. “The JAK/STAT signaling cascades of multiple cytokines are dysregulated during West Nile virus infection.The Journal of Immunology 196, no. 1 Supplement (2016): 217-38.

Oct 9:

Yang, Hairu, and Dan Hultmark. “JAK/STAT and insulin signaling in Drosophila muscles regulate cellular immune responses against parasitoid wasp infection.” (2016).

Oct 10:

Seldon, Crystal S., Lauren E. Colbert, William A. Hall, Sarah B. Fisher, David S. Yu, and Jerome C. Landry. “Chromodomain-helicase-DNA binding protein 5, 7 and pronecrotic mixed lineage kinase domain-like protein serve as potential prognostic biomarkers in patients with resected pancreatic adenocarcinomas.” World journal of gastrointestinal oncology 8, no. 4 (2016): 358.

Oct 11:

Kusano, Seisuke, Mutsuko Kukimoto‐Niino, Nobumasa Hino, Noboru Ohsawa, Masashi Ikutani, Satoshi Takaki, Kensaku Sakamoto et al. “Structural basis of interleukin‐5 dimer recognition by its α receptor.Protein Science 21, no. 6 (2012): 850-864.

Oct 12:

Ernst, Matthias, and Tracy L. Putoczki. “Molecular Pathways: IL11 as a Tumor-Promoting Cytokine—Translational Implications for Cancers.Clinical Cancer Research 20, no. 22 (2014): 5579-5588.

Oct 13:

Robinson, Mark D., Davis J. McCarthy, and Gordon K. Smyth. “edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.Bioinformatics 26, no. 1 (2010): 139-140.

Oct 14:

Babon, Jeffrey J., Jennifer K. Sabo, Jian-Guo Zhang, Nicos A. Nicola, and Raymond S. Norton. “The SOCS box encodes a hierarchy of affinities for Cullin5: implications for ubiquitin ligase formation and cytokine signalling suppression.Journal of molecular biology 387, no. 1 (2009): 162-174.

Oct 15:

Owen, Dianne, and L. C. Kühn. “Noncoding 3’sequences of the transferrin receptor gene are required for mRNA regulation by iron.” The EMBO Journal 6, no. 5 (1987): 1287.

Oct 16:

Privalov, Petkr L., Pedro L. Mateo, Nikolai N. Khechinashvili, Valentin M. Stepanov, and Lyudmila P. Revina. “Comparative thermodynamic study of pepsinogen and pepsin structure.Journal of molecular biology 152, no. 2 (1981): 445-464.

Oct 17:

Abad‐Zapatero, Cele, Timothy J. Rydel, and John Erickson. “Revised 2.3 Å structure of porcine pepsin: evidence for a flexible subdomain.Proteins: Structure, Function, and Bioinformatics 8, no. 1 (1990): 62-81.

Oct 18:

Turpin, David H. “Effects of inorganic N availability on algal photosynthesis and carbon metabolism.” Journal of Phycology 27, no. 1 (1991): 14-20.

Oct 19:

Peisker, M. “Models of carbon metabolism in C3‐C4 intermediate plants as applied to the evolution of C4 photosynthesis.Plant, Cell & Environment 9, no. 8 (1986): 627-635.

Oct 20:

Kanyenda, Limbikani J., Guiseppe Verdile, Ralph Martins, Bruno P. Meloni, Joanne Chieng, Francis Mastaglia, Simon M. Laws, Ryan S. Anderton, and Sherif Boulos. “Is cholesterol and amyloid-β stress induced CD147 expression a protective response? Evidence that extracellular cyclophilin a mediated neuroprotection is reliant on CD147.” Journal of Alzheimer’s Disease 39, no. 3 (2014): 545-556.

Oct 21:

Meloni, Bruno P., Laura M. Brookes, Vince W. Clark, Jane L. Cross, Adam B. Edwards, Ryan S. Anderton, Richard M. Hopkins, Katrin Hoffmann, and Neville W. Knuckey. “Poly-arginine and arginine-rich peptides are neuroprotective in stroke models.” Journal of Cerebral Blood Flow & Metabolism 35, no. 6 (2015): 993-1004.

Oct 22:

Allegre, Claude J., and Stephen H. Schneider. “The evolution of the Earth.Scientific American 271 (1994): 44-51.

Oct 23:

Margulis, Lynn. “Symbiosis in cell evolution: Life and its environment on the early earth.” (1981).

Oct 24:

Li, Ming O., and Alexander Y. Rudensky. “T cell receptor signalling in the control of regulatory T cell differentiation and function.Nature Reviews Immunology 16, no. 4 (2016): 220-233.

Oct 25:

Takeuchi, Osamu. “Posttranscriptional Regulation of Cytokine mRNA Controls the Initiation and Resolution of Inflammation.Chronic Inflammation: Mechanisms and Regulation (2016): 319.

Oct 26:

Haskett, Timothy L., Jason J. Terpolilli, Amanuel Bekuma, Graham W. O’Hara, John T. Sullivan, Penghao Wang, Clive W. Ronson, and Joshua P. Ramsay. “Assembly and transfer of tripartite integrative and conjugative genetic elements.Proceedings of the National Academy of Sciences (2016): 201613358.

Oct 27:

Bombicz, Petra. “X-ray crystallography.” Crystallography Reviews 22, no. 1 (2016): 79-81.

Oct 28:

Shen, Jian-Ren. “Crystallography: Resolution beyond the diffraction limit.” Nature 530, no. 7589 (2016): 168-169.

Oct 29:

Bedi, Rajiv K., Chandan Patel, Vandana Mishra, Huogen Xiao, Rickey Y. Yada, and Prasenjit Bhaumik. “Understanding the structural basis of substrate recognition by Plasmodium falciparum plasmepsin V to aid in the design of potent inhibitors.” Scientific Reports 6 (2016).

Oct 30:

Orlenko, Alena, Russell A. Hermansen, and David A. Liberles. “Flux Control in Glycolysis Varies Across the Tree of Life.” Journal of molecular evolution 82, no. 2-3 (2016): 146-161.

Oct 31:

Havird, Justin C., and Daniel B. Sloan. “The roles of mutation, selection, and expression in determining relative rates of evolution in mitochondrial vs. nuclear genomes.” Molecular Biology and Evolution (2016): msw185.

 

September: 366 papers in 2016

Sept 1:

Schindler, Christian, David E. Levy, and Thomas Decker. “JAK-STAT signaling: from interferons to cytokines.” Journal of Biological Chemistry 282, no. 28 (2007): 20059-20063.

Sept 2:

Breems, Dimitri A., Wim LJ Van Putten, Georgine E. De Greef, Shama L. Van Zelderen-Bhola, Klasien BJ Gerssen-Schoorl, Clemens HM Mellink, Aggie Nieuwint et al. “Monosomal karyotype in acute myeloid leukemia: a better indicator of poor prognosis than a complex karyotype.Journal of Clinical Oncology 26, no. 29 (2008): 4791-4797.

Sept 3:

Stevenson, Brian J., Nelson Rhodes, Beverly Errede, and George F. Sprague. “Constitutive mutants of the protein kinase STE11 activate the yeast pheromone response pathway in the absence of the G protein.Genes & development 6, no. 7 (1992): 1293-1304.

Sept 4:

Armstrong, John B., Julius Adler, and Margaret M. Dahl. “Nonchemotactic mutants of Escherichia coli.Journal of bacteriology 93, no. 1 (1967): 390-398.

Sept 5:

Armstrong, John B., and Julius Adler. “Genetics of motility in Escherichia coli: complementation of paralyzed mutants.Genetics 56, no. 3 (1967): 363.

Sept 6:

Horvitz, H. Robert, and John E. Sulston. “Isolation and genetic characterization of cell-lineage mutants of the nematode Caenorhabditis elegans.” Genetics 96, no. 2 (1980): 435-454.

Sept 7:

Dickson, B., F. Sprenger, and E. Hafen. “Prepattern in the developing Drosophila eye revealed by an activated torso–sevenless chimeric receptor.Genes & Development 6, no. 12a (1992): 2327-2339.

Sept 8:

Jinek, Martin, Alexandra East, Aaron Cheng, Steven Lin, Enbo Ma, and Jennifer Doudna. “RNA-programmed genome editing in human cells.elife 2 (2013): e00471.

Sept 9:

Larson, Matthew H., Luke A. Gilbert, Xiaowo Wang, Wendell A. Lim, Jonathan S. Weissman, and Lei S. Qi. “CRISPR interference (CRISPRi) for sequence-specific control of gene expression.” Nature protocols 8, no. 11 (2013): 2180-2196.

Sept 10:

Bedell, Victoria M., Stephanie E. Westcot, and Stephen C. Ekker. “Lessons from morpholino-based screening in zebrafish.Briefings in functional genomics (2011): elr021.

Sept 11:

Sessions, Allen, Ellen Burke, Gernot Presting, George Aux, John McElver, David Patton, Bob Dietrich et al. “A high-throughput Arabidopsis reverse genetics system.The Plant Cell 14, no. 12 (2002): 2985-2994.

Sept 12:

Krebs, Danielle L., Donald Metcalf, Tobias D. Merson, Anne K. Voss, Tim Thomas, Jian-Guo Zhang, Steven Rakar et al. “Development of hydrocephalus in mice lacking SOCS7.” Proceedings of the National Academy of Sciences of the United States of America 101, no. 43 (2004): 15446-15451.

Sept 13:

Bao, Riyue, Lei Huang, Jorge Andrade, Wei Tan, Warren A. Kibbe, Hongmei Jiang, and Gang Feng. “Review of current methods, applications, and data management for the bioinformatics analysis of whole exome sequencing.” Cancer informatics (2014): 67-83.

Sept 14:

Starr, Robyn, Donald Metcalf, Andrew G. Elefanty, Marta Brysha, Tracy A. Willson, Nicos A. Nicola, Douglas J. Hilton, and Warren S. Alexander. “Liver degeneration and lymphoid deficiencies in mice lacking suppressor of cytokine signaling-1.Proceedings of the National Academy of Sciences 95, no. 24 (1998): 14395-14399.

Sept 15:

Eshel, Ilan. “Selection on sex ratio and the evolution of sex determination.” Heredity 34, no. 3 (1975): 351-361.

Sept 16:

Pinker, Steven. “How the mind works.” Annals of the New York Academy of Sciences 882, no. 1 (1999): 119-127.

Sept 17:

Babon, Jeffrey J., Isabelle S. Lucet, James M. Murphy, Nicos A. Nicola, and Leila N. Varghese. “The molecular regulation of Janus kinase (JAK) activation.Biochemical Journal 462, no. 1 (2014): 1-13.

Sept 18:

Xu, Yibin, Nadia J. Kershaw, Cindy S. Luo, Priscilla Soo, Michael J. Pocock, Peter E. Czabotar, Douglas J. Hilton, Nicos A. Nicola, Thomas PJ Garrett, and Jian-Guo Zhang. “Crystal Structure of the Entire Ectodomain of gp130 INSIGHTS INTO THE MOLECULAR ASSEMBLY OF THE TALL CYTOKINE RECEPTOR COMPLEXES.” Journal of Biological Chemistry 285, no. 28 (2010): 21214-21218.

Sept 19:

Wong, Gordon G., and Steven C. Clark. “Multiple actions of interleukin 6 within a cytokine network.Immunology today 9, no. 5 (1988): 137-139.

Sept 20:

Dietrich, W. F., J. Miller, R. Steen, M. A. Merchant, D. DamronBoles, Z. Husain, R. Dredge et al. “A Comprehensive Genetic-Map of the Mouse Genome (Vol 380, Pg 149, 1996).” Nature 381, no. 6578 (1996): 172-172.

Sept 21:

Levy, David E., D. S. Kessler, Richard Pine, and J. E. Darnell. “Cytoplasmic activation of ISGF3, the positive regulator of interferon-alpha-stimulated transcription, reconstituted in vitro.Genes & Development 3, no. 9 (1989): 1362-1371.

Sept 22:

Levy, David E., Daniel S. Kessler, Richard Pine, Nancy Reich, and J. E. Darnell. “Interferon-induced nuclear factors that bind a shared promoter element correlate with positive and negative transcriptional control.Genes & development 2, no. 4 (1988): 383-393.

Sept 23:

Li, Heng, and Richard Durbin. “Fast and accurate short read alignment with Burrows–Wheeler transform.Bioinformatics 25, no. 14 (2009): 1754-1760.

Sept 24:

Zamore, Phillip D., Thomas Tuschl, Phillip A. Sharp, and David P. Bartel. “RNAi: double-stranded RNA directs the ATP-dependent cleavage of mRNA at 21 to 23 nucleotide intervals.Cell 101, no. 1 (2000): 25-33.

Sept 25:

Porebski, Benjamin T., Shani Keleher, Jeffrey J. Hollins, Adrian A. Nickson, Emilia M. Marijanovic, Natalie A. Borg, Mauricio GS Costa et al. “Smoothing a rugged protein folding landscape by sequence-based redesign.Scientific Reports 6 (2016): 33958.

Sept 26:

Jafree, Daniyal J., Katharine Whitehurst, and Shivanchan Rajmohan. “How to approach supervisors for research opportunities.Annals of Medicine and Surgery (2016).

Sept 27:

Shendure, Jay. “Human genomics: A deep dive into genetic variation.Nature 536, no. 7616 (2016): 277-278.

Sept 28:

Pinker, Steven. “How the mind works.” Annals of the New York Academy of Sciences 882,

Sept 29:

Sørensen, Henrik Toft. “I-determinants for a successful PhD or postdoctoral outcome.Clinical Epidemiology 8 (2016): 297.

Sept 30:

Isaacs, Alick, and Jean Lindenmann. “Virus interference. I. The interferon.” Proceedings of the Royal Society of London B: Biological Sciences 147, no. 927 (1957): 258-267.

 

August: 366 papers in 2016

As one of my 2016 scientific resolutions I will be reading one paper every day of the year and posting each here (hopefully) daily.

 

Aug 1:

Yaffe, Michael B. “Reproducibility in science.” Sci. Signal. 8, no. 371 (2015): eg5-eg5.

Aug 2:

Naegle, Kristen, Nancy R. Gough, and Michael B. Yaffe. “Criteria for biological reproducibility: what does” n” mean?.Science signaling 8, no. 371 (2015): fs7.

Aug 3:

Parnas, Oren, Marko Jovanovic, Thomas M. Eisenhaure, Rebecca H. Herbst, Atray Dixit, Chun Jimmie Ye, Dariusz Przybylski et al. “A genome-wide CRISPR screen in primary immune cells to dissect regulatory networks.” Cell 162, no. 3 (2015): 675-686.

Aug 4:

Evers, Bastiaan, Katarzyna Jastrzebski, Jeroen PM Heijmans, Wipawadee Grernrum, Roderick L. Beijersbergen, and Rene Bernards. “CRISPR knockout screening outperforms shRNA and CRISPRi in identifying essential genes.Nature biotechnology (2016).

Aug 5:

Housden, Benjamin E., and Norbert Perrimon. “Comparing CRISPR and RNAi-based screening technologies.Nature Biotechnology 34, no. 6 (2016): 621-623.

Aug 6:

Qi, Xiaolong, Jiwei Zhang, Yongzhao Zhao, Tao Chen, Yi Xiang, Jialiang Hui, Danxian Cai et al. “The applications of CRISPR screen in functional genomics.” Briefings in Functional Genomics (2016): elw020.

Aug 7:

Vickers, Claudia E. “The minimal genome comes of age.” Nature Biotechnology 34, no. 6 (2016): 623-624.

Aug 8:

Nam, Jae-Yong, Nayoung KD Kim, Sang Cheol Kim, Je-Gun Joung, Ruibin Xi, Semin Lee, Peter J. Park, and Woong-Yang Park. “Evaluation of somatic copy number estimation tools for whole-exome sequencing data.Briefings in bioinformatics 17, no. 2 (2016): 185-192.

Aug 9:

Belkadi, Aziz, Alexandre Bolze, Yuval Itan, Aurelie Cobat, Quentin B. Vincent, Alexander Antipenko, Lei Shang, Bertrand Boisson, Jean-Laurent Casanova, and Laurent Abel. “Whole-genome sequencing is more powerful than whole-exome sequencing for detecting exome variants.Proceedings of the National Academy of Sciences 112, no. 17 (2015): 5473-5478.

Aug 10:

Law, Charity W., Monther Alhamdoosh, Shian Su, Gordon K. Smyth, and Matthew E. Ritchie. “RNA-seq analysis is easy as 1-2-3 with limma, Glimma and edgeR.F1000Research 5 (2016).

Aug 11:

Schurch, Nicholas J., Pietá Schofield, Marek Gierliński, Christian Cole, Alexander Sherstnev, Vijender Singh, Nicola Wrobel et al. “How many biological replicates are needed in an RNA-seq experiment and which differential expression tool should you use?.” RNA 22, no. 6 (2016): 839-851.

Aug 12:

Delconte, Rebecca B., Tatiana B. Kolesnik, Laura F. Dagley, Jai Rautela, Wei Shi, Eva M. Putz, Kimberley Stannard et al. “CIS is a potent checkpoint in NK cell-mediated tumor immunity.Nature immunology (2016).

Aug 13:

Gamon, L. F., J. M. White, and U. Wille. “Oxidative damage of aromatic dipeptides by the environmental oxidants NO 2˙ and O 3.Organic & biomolecular chemistry 12, no. 41 (2014): 8280-8287.

Aug 14:

Cerami, Ethan, Jianjiong Gao, Ugur Dogrusoz, Benjamin E. Gross, Selcuk Onur Sumer, Bülent Arman Aksoy, Anders Jacobsen et al. “The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data.Cancer discovery 2, no. 5 (2012): 401-404.

Aug 15:

Pham, Thu-Hang, Julia Minderjahn, Christian Schmidl, Helen Hoffmeister, Sandra Schmidhofer, Wei Chen, Gernot Längst, Christopher Benner, and Michael Rehli. “Mechanisms of in vivo binding site selection of the hematopoietic master transcription factor PU. 1.Nucleic acids research (2013): gkt355.

Aug 16:

Nakamura, Tetsuya, Andrew R. Gehrke, Justin Lemberg, Julie Szymaszek, and Neil H. Shubin. “Digits and fin rays share common developmental histories.” Nature (2016).

Aug 17:

de Graaf, Carolyn A., Jarny Choi, Tracey M. Baldwin, Jessica E. Bolden, Kirsten A. Fairfax, Aaron J. Robinson, Christine Biben et al. “Haemopedia: An Expression Atlas of Murine Hematopoietic Cells.Stem Cell Reports (2016).

Aug 18:

Dobin, Alexander, Carrie A. Davis, Felix Schlesinger, Jorg Drenkow, Chris Zaleski, Sonali Jha, Philippe Batut, Mark Chaisson, and Thomas R. Gingeras. “STAR: ultrafast universal RNA-seq aligner.Bioinformatics 29, no. 1 (2013): 15-21.

Aug 19:

Muniz, João RC, Kunde Guo, Nadia J. Kershaw, Vikram Ayinampudi, Frank von Delft, Jeffrey J. Babon, and Alex N. Bullock. “Molecular architecture of the ankyrin SOCS box family of Cul5-dependent E3 ubiquitin ligases.Journal of molecular biology 425, no. 17 (2013): 3166-3177.

Aug 20:

Guillerey, Camille, Nicholas D. Huntington, and Mark J. Smyth. “Targeting natural killer cells in cancer immunotherapy.Nature Immunology 17, no. 9 (2016): 1025-1036.

Aug 21:

Masuda, Kazuya, and Tadamitsu Kishimoto. “CD5: A New Partner for IL-6.” Immunity 44, no. 4 (2016): 720-722.

Aug 22:

Moss-Racusin, Corinne A., Jojanneke van der Toorn, John F. Dovidio, Victoria L. Brescoll, Mark J. Graham, and Jo Handelsman. “A “Scientific Diversity” Intervention to Reduce Gender Bias in a Sample of Life Scientists.CBE-Life Sciences Education 15, no. 3 (2016): ar29.

Aug 23:

Obenauer, John C., Lewis C. Cantley, and Michael B. Yaffe. “Scansite 2.0: Proteome-wide prediction of cell signaling interactions using short sequence motifs.Nucleic acids research 31, no. 13 (2003): 3635-3641.

Aug 24:

Chen, Chang-Zheng, Ling Li, Harvey F. Lodish, and David P. Bartel. “MicroRNAs modulate hematopoietic lineage differentiation.science 303, no. 5654 (2004): 83-86.

Aug 25:

Mueckler, Mike, Carla Caruso, Stephen A. Baldwin, Maria Panico, Ian Blench, Howard R. Morris, W. Jeffrey Allard, Gustav E. Lienhard, and Harvey F. Lodish. “Sequence and structure of a human glucose transporter.Science 229, no. 4717 (1985): 941-945.

Aug 26:

Lodish, Harvey F. “Accommodating family life: mentoring future female faculty members.Trends in cell biology 25, no. 3 (2015): 109-111.

Aug 27:

de Koning-Ward, Tania F., Paul R. Gilson, and Brendan S. Crabb. “Advances in molecular genetic systems in malaria.” Nature Reviews Microbiology 13, no. 6 (2015): 373-387.

Aug 28:

Koonin, Eugene V., and Mart Krupovic. “Evolution of adaptive immunity from transposable elements combined with innate immune systems.” Nature Reviews Genetics 16, no. 3 (2015): 184-192.

Aug 29:

Sulonen, Anna-Maija, Pekka Ellonen, Henrikki Almusa, Maija Lepistö, Samuli Eldfors, Sari Hannula, Timo Miettinen et al. “Comparison of solution-based exome capture methods for next generation sequencing.” Genome biology 12, no. 9 (2011): 1.

Aug 30:

Hodge, David R., Elaine M. Hurt, and William L. Farrar. “The role of IL-6 and STAT3 in inflammation and cancer.” European journal of cancer 41, no. 16 (2005): 2502-2512.

Aug 31:

Shuai, Ke, and Bin Liu. “Regulation of JAK–STAT signalling in the immune system.Nature Reviews Immunology 3, no. 11 (2003): 900-911.