Posts tagged ‘scientific publishing’

Retinal development

  1. Tian C, Zou S, Hu B. Extraocular Source of Oligodendrocytes Contribute to Retinal Myelination and Optokinetic Responses in Zebrafish. Invest Ophthalmol Vis Sci. 2016 Apr 1;57(4):2129-38. doi: 10.1167/iovs.15-17675. PubMed PMID: 27100159.
  2. Riesenberg AN, Brown NL. Cell autonomous and nonautonomous requirements for Delltalike1 during early mouse retinal neurogenesis. Dev Dyn. 2016 Jun;245(6):631-40. doi: 10.1002/dvdy.24402. Epub 2016 Apr 4. PubMed PMID: 26947267; PubMed Central PMCID: PMC4873400.

Scientific Career

  1. Mervis J. BEHIND THE NUMBERS. ‘Employment crisis’ for new Ph.D.s is an illusion. Science. 2016 May 20;352(6288):880. doi: 10.1126/science.352.6288.880. PubMed PMID: 27199396.

Evolution

  1. Karnkowska A, Vacek V, Zubáčová Z, Treitli SC, Petrželková R, Eme L, Novák L, Žárský V, Barlow LD, Herman EK, Soukal P, Hroudová M, Doležal P, Stairs CW, Roger AJ, Eliáš M, Dacks JB, Vlček Č, Hampl V. A Eukaryote without a Mitochondrial Organelle. Curr Biol. 2016 May 23;26(10):1274-84. doi: 10.1016/j.cub.2016.03.053. Epub 2016 May 12. PubMed PMID: 27185558.

Visual behaviour

  1. Orger MB. The Cellular Organization of Zebrafish Visuomotor Circuits. Curr Biol. 2016 May 9;26(9):R377-85. doi: 10.1016/j.cub.2016.03.054. Review. PubMed PMID: 27166700.
  2. Currie SP, Doherty GH, Sillar KT. Deep-brain photoreception links luminance detection to motor output in Xenopus frog tadpoles. Proc Natl Acad Sci U S A. 2016 May 24;113(21):6053-8. doi: 10.1073/pnas.1515516113. Epub 2016 May 10. PubMed PMID: 27166423.

Scientific publishing

  1. Berg JM, Bhalla N, Bourne PE, Chalfie M, Drubin DG, Fraser JS, Greider CW, Hendricks M, Jones C, Kiley R, King S, Kirschner MW, Krumholz HM, Lehmann R, Leptin M, Pulverer B, Rosenzweig B, Spiro JE, Stebbins M, Strasser C, Swaminathan S, Turner P, Vale RD, VijayRaghavan K, Wolberger C. SCIENTIFIC COMMUNITY. Preprints for the life sciences. Science. 2016 May 20;352(6288):899-901. doi: 10.1126/science.aaf9133. PubMed PMID: 27199406.
  2. Sarewitz D. The pressure to publish pushes down quality. Nature. 2016 May 11;533(7602):147. doi: 10.1038/533147a. PubMed PMID: 27172010.

Genome editing

  1. Abudayyeh OO, Gootenberg JS, Konermann S, Joung J, Slaymaker IM, Cox DB, Shmakov S, Makarova KS, Semenova E, Minakhin L, Severinov K, Regev A, Lander ES, Koonin EV, Zhang F. C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector. Science. 2016 Jun 2. pii: aaf5573. [Epub ahead of print] PubMed PMID: 27256883.

Scientific publishing

  1. Gibney E. Open journals that piggyback on arXiv gather momentum. Nature. 2016 Feb 4;530(7588):117-8. PubMed PMID: 26854297.

Genome editing

  1. Wu B, Luo L, Gao XJ. Cas9-triggered chain ablation of cas9 as a gene drive brake. Nat Biotechnol. 2016 Feb 5;34(2):137-8. doi: 10.1038/nbt.3444. PubMed PMID: 26849513.
  2. Alphey L. Can CRISPR-Cas9 gene drives curb malaria? Nat Biotechnol. 2016 Feb 5;34(2):149-50. doi: 10.1038/nbt.3473. PubMed PMID: 26849518.
  3. Rajagopal N, Srinivasan S, Kooshesh K, Guo Y, Edwards MD, Banerjee B, Syed T, Emons BJ, Gifford DK, Sherwood RI. High-throughput mapping of regulatory DNA. Nat Biotechnol. 2016 Feb;34(2):167-74. doi: 10.1038/nbt.3468. Epub 2016 Jan 25. PubMed PMID: 26807528.
  4. Korkmaz G, Lopes R, Ugalde AP, Nevedomskaya E, Han R, Myacheva K, Zwart W, Elkon R, Agami R. Functional genetic screens for enhancer elements in the human genome using CRISPR-Cas9. Nat Biotechnol. 2016 Feb;34(2):192-8. doi: 10.1038/nbt.3450. Epub 2016 Jan 11. PubMed PMID: 26751173.
  5. Zhou Y, Wei W. Mapping regulatory elements. Nat Biotechnol. 2016 Feb 5;34(2):151-2. doi: 10.1038/nbt.3477. PubMed PMID: 26849519.
  6. Doench JG, Fusi N, Sullender M, Hegde M, Vaimberg EW, Donovan KF, Smith I, Tothova Z, Wilen C, Orchard R, Virgin HW, Listgarten J, Root DE. Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9. Nat Biotechnol. 2016 Feb;34(2):184-91. doi: 10.1038/nbt.3437. Epub 2016 Jan 18. PubMed PMID: 26780180; PubMed Central PMCID: PMC4744125.
  7. Farasat I, Salis HM. A Biophysical Model of CRISPR/Cas9 Activity for Rational Design of Genome Editing and Gene Regulation. PLoS Comput Biol. 2016 Jan 29;12(1):e1004724. doi: 10.1371/journal.pcbi.1004724. eCollection 2016 Jan. PubMed PMID: 26824432; PubMed Central PMCID: PMC4732943.

Neuroscience

  1. Fuzik J, Zeisel A, Máté Z, Calvigioni D, Yanagawa Y, Szabó G, Linnarsson S, Harkany T. Integration of electrophysiological recordings with single-cell RNA-seq data identifies neuronal subtypes. Nat Biotechnol. 2016 Feb;34(2):175-83. doi: 10.1038/nbt.3443. Epub 2015 Dec 21. PubMed PMID: 26689544.
  2. Cadwell CR, Palasantza A, Jiang X, Berens P, Deng Q, Yilmaz M, Reimer J, Shen S, Bethge M, Tolias KF, Sandberg R, Tolias AS. Electrophysiological, transcriptomic and morphologic profiling of single neurons using Patch-seq. Nat Biotechnol. 2016 Feb;34(2):199-203. doi: 10.1038/nbt.3445. Epub 2015 Dec 21. PubMed PMID: 26689543.

Disease

  1. Mlakar J, Korva M, Tul N, Popović M, Poljšak-Prijatelj M, Mraz J, Kolenc M, Resman Rus K, Vesnaver Vipotnik T, Fabjan Vodušek V, Vizjak A, Pižem J, Petrovec M, Avšič Županc T. Zika Virus Associated with Microcephaly. N Engl J Med. 2016 Feb 10. [Epub ahead of print] PubMed PMID: 26862926.

ESLI

  1. Baker M. Biotech giant publishes failures to confirm high-profile science. Nature. 2016 Feb 11;530(7589):141. doi: 10.1038/nature.2016.19269. PubMed PMID: 26863961.

Stem cells

  1. Chakradhar S. An eye to the future: Researchers debate best path for stem cell-derived therapies. Nat Med. 2016 Feb 4;22(2):116-9. doi: 10.1038/nm0216-116. PubMed PMID: 26845400.
  2. Scognamiglio R, Cabezas-Wallscheid N, Thier MC, Altamura S, Reyes A, Prendergast ÁM, Baumgärtner D, Carnevalli LS, Atzberger A, Haas S, von Paleske L, Boroviak T, Wörsdörfer P, Essers MA, Kloz U, Eisenman RN, Edenhofer F, Bertone P, Huber W, van der Hoeven F, Smith A, Trumpp A. Myc Depletion Induces a Pluripotent Dormant State Mimicking Diapause. Cell. 2016 Feb 11;164(4):668-80. doi: 10.1016/j.cell.2015.12.033. PubMed PMID: 26871632.

Systems Biology

  1. Yang X, Coulombe-Huntington J, Kang S, Sheynkman GM, Hao T, Richardson A, Sun S, Yang F, Shen YA, Murray RR, Spirohn K, Begg BE, Duran-Frigola M, MacWilliams A, Pevzner SJ, Zhong Q, Trigg SA, Tam S, Ghamsari L, Sahni N, Yi S, Rodriguez MD, Balcha D, Tan G, Costanzo M, Andrews B, Boone C, Zhou XJ, Salehi-Ashtiani K, Charloteaux B, Chen AA, Calderwood MA, Aloy P, Roth FP, Hill DE, Iakoucheva LM, Xia Y, Vidal M. Widespread Expansion of Protein Interaction Capabilities by Alternative Splicing. Cell. 2016 Feb 11;164(4):805-17. doi: 10.1016/j.cell.2016.01.029. PubMed PMID: 26871637.
  2. Morsut L, Roybal KT, Xiong X, Gordley RM, Coyle SM, Thomson M, Lim WA. Engineering Customized Cell Sensing and Response Behaviors Using Synthetic Notch Receptors. Cell. 2016 Feb 11;164(4):780-91. doi: 10.1016/j.cell.2016.01.012. Epub 2016 Jan 28. PubMed PMID: 26830878; PubMed Central PMCID: PMC4752866.
  3. Tsiairis CD, Aulehla A. Self-Organization of Embryonic Genetic Oscillators into Spatiotemporal Wave Patterns. Cell. 2016 Feb 11;164(4):656-67. doi: 10.1016/j.cell.2016.01.028. PubMed PMID: 26871631.
  4. Sylwestrak EL, Rajasethupathy P, Wright MA, Jaffe A, Deisseroth K. Multiplexed Intact-Tissue Transcriptional Analysis at Cellular Resolution. Cell. 2016 Feb 11;164(4):792-804. doi: 10.1016/j.cell.2016.01.038. PubMed PMID: 26871636.

Development

  1. Tsiairis CD, Aulehla A. Self-Organization of Embryonic Genetic Oscillators into Spatiotemporal Wave Patterns. Cell. 2016 Feb 11;164(4):656-67. doi: 10.1016/j.cell.2016.01.028. PubMed PMID: 26871631.

Genomics

  1. Venter’s New Goal: World’s Largest Sequencing Operation
  2. Clinical Whole Genome Sequencing: Not Quite Ready for Prime Time?

Genetics

  1. Vanderperre B, Lucier JF, Bissonnette C, Motard J, Tremblay G, Vanderperre S, Wisztorski M, Salzet M, Boisvert FM, Roucou X. Direct detection of alternative open reading frames translation products in human significantly expands the proteome. PLoS One. 2013 Aug 12;8(8):e70698. doi: 10.1371/journal.pone.0070698. eCollection 2013. PubMed PMID: 23950983; PubMed Central PMCID: PMC3741303.

Stem cells

  1. Acid-bath stem-cell study under investigation.

Genome-editing

  1. Tebas P, Stein D, Tang WW, Frank I, Wang SQ, Lee G, Spratt SK, Surosky RT, Giedlin MA, Nichol G, Holmes MC, Gregory PD, Ando DG, Kalos M, Collman RG, Binder-Scholl G, Plesa G, Hwang WT, Levine BL, June CH. Gene editing of CCR5 in autologous CD4 T cells of persons infected with HIV. N Engl J Med. 2014 Mar 6;370(10):901-10. doi: 10.1056/NEJMoa1300662. PubMed PMID: 24597865.
    • Editorial commentary: Kay MA, Walker BD. Engineering cellular resistance to HIV. N Engl J Med. 2014
      Mar 6;370(10):968-9. doi: 10.1056/NEJMe1400593. PubMed PMID: 24597871.
    • News coverage: Editing Genes May Make Cells Resist HIV.

Philosophy

How Academia and Publishing are Destroying Scientific Innovation: A Conversation with Sydney Brenner

Medicine

  1. Flannick J, Thorleifsson G, Beer NL, Jacobs SB, Grarup N, Burtt NP, Mahajan A, Fuchsberger C, Atzmon G, Benediktsson R, Blangero J, Bowden DW, Brandslund I, Brosnan J, Burslem F, Chambers J, Cho YS, Christensen C, Douglas DA, Duggirala R, Dymek Z, Farjoun Y, Fennell T, Fontanillas P, Forsén T, Gabriel S, Glaser B, Gudbjartsson DF, Hanis C, Hansen T, Hreidarsson AB, Hveem K, Ingelsson E, Isomaa  B, Johansson S, Jørgensen T, Jørgensen ME, Kathiresan S, Kong A, Kooner J, Kravic J, Laakso M, Lee JY, Lind L, Lindgren CM, Linneberg A, Masson G, Meitinger T, Mohlke KL, Molven A, Morris AP, Potluri S, Rauramaa R, Ribel-Madsen R, Richard AM, Rolph T, Salomaa V, Segrè AV, Skärstrand H, Steinthorsdottir V, Stringham HM, Sulem P, Tai ES, Teo YY, Teslovich T, Thorsteinsdottir U, Trimmer JK, Tuomi T, Tuomilehto J, Vaziri-Sani F, Voight BF, Wilson JG, Boehnke M, McCarthy MI, Njølstad PR, Pedersen O, Groop L, Cox DR, Stefansson K, Altshuler D. Loss-of-function mutations in SLC30A8 protect against type 2 diabetes. Nat Genet. 2014 Mar 2. doi: 10.1038/ng.2915. [Epub ahead of print] PubMed PMID: 24584071.
  2. Mapstone M, Cheema AK, Fiandaca MS, Zhong X, Mhyre TR, Macarthur LH, Hall WJ, Fisher SG, Peterson DR, Haley JM, Nazar MD, Rich SA, Berlau DJ, Peltz CB, Tan MT, Kawas CH, Federoff HJ. Plasma phospholipids identify antecedent memory impairment in older adults. Nat Med. 2014 Mar 9. doi: 10.1038/nm.3466. [Epub ahead of print]
    PubMed PMID: 24608097.

Imaging

  1. Foldscope: Origami-based paper microscope

Zebrafish

  1. Cressey D. Fish-kill method questioned. Nature. 2014 Feb 27;506(7489):419-20. doi: 10.1038/506419a. PubMed PMID: 24572404.

 

Eye disease

  1. Fernandez de Castro J, Scott PA, Fransen JW, Demas J, Demarco PJ, Kaplan HJ, McCall MA. Cone Photoreceptors Develop Normally in the Absence of Functional Rod Photoreceptors in a Transgenic Swine Model of Retinitis Pigmentosa. Invest Ophthalmol Vis Sci. 2014 Mar 11. pii: iovs.13-13724v1. doi: 10.1167/iovs.13-13724. [Epub ahead of print] PubMed PMID: 24618325.

Vision

  1. Partridge JC, Douglas RH, Marshall NJ, Chung WS, Jordan TM, Wagner HJ. Reflecting optics in the diverticular eye of a deep-sea barreleye fish (Rhynchohyalus natalensis). Proc Biol Sci. 2014 Mar 19;281(1782):20133223. doi: 10.1098/rspb.2013.3223. Print 2014. PubMed PMID: 24648222.

Evolution

  1. Gassmann AJ, Petzold-Maxwell JL, Clifton EH, Dunbar MW, Hoffmann AM, Ingber DA, Keweshan RS. Field-evolved resistance by western corn rootworm to multiple Bacillus thuringiensis toxins in transgenic maize. Proc Natl Acad Sci U S A. 2014 Mar 17. [Epub ahead of print] PubMed PMID: 24639498.

Neuroscience

  1. Bushdid C, Magnasco MO, Vosshall LB, Keller A. Humans can discriminate more than 1 trillion olfactory stimuli. Science. 2014 Mar 21;343(6177):1370-2. doi: 10.1126/science.1249168. PubMed PMID: 24653035.

Nature Special Issue on “The Future of Publishing

Neuroscience

  1. Horikawa T, Tamaki M, Miyawaki Y, Kamitani Y. Neural Decoding of Visual Imagery During Sleep. Science. 2013 Apr 4. [Epub ahead of print] PubMed PMID: 23558170.
  2. Chung K, Wallace J, Kim SY, Kalyanasundaram S, Andalman AS, Davidson TJ, Mirzabekov JJ, Zalocusky KA, Mattis J, Denisin AK, Pak S, Bernstein H, Ramakrishnan C, Grosenick L, Gradinaru V, Deisseroth K. Structural and molecular interrogation of intact biological systems. Nature. 2013 Apr 10. doi: 10.1038/nature12107. [Epub ahead of print]
    • A new way of clearing tissue for imaging!
    • Commentary: Shen H. See-through brains clarify connections. Nature. 2013 Apr 11;496(7444):151. doi: 10.1038/496151a. PubMed PMID: 23579658.
    • From the New York Times: Brains as Clear as Jell-O for Scientists to Explore

Genomics

Zebrafish genome sequencing

  1. Howe K, et al. The zebrafish reference genome sequence and its relationship to the human genome. Nature. 2013 Apr 17. doi: 10.1038/nature12111. [Epub ahead of print] PubMed PMID: 23594743.
  2. Schier AF. Genomics: Zebrafish earns its stripes. Nature. 2013 Apr 17. doi: 10.1038/nature12094. [Epub ahead of print] PubMed PMID: 23594741.
  3. Kettleborough RN, Busch-Nentwich EM, Harvey SA, Dooley CM, de Bruijn E, van Eeden F, Sealy I, White RJ, Herd C, Nijman IJ, Fényes F, Mehroke S, Scahill C, Gibbons R, Wali N, Carruthers S, Hall A, Yen J, Cuppen E, Stemple DL. A
    systematic genome-wide analysis of zebrafish protein-coding gene function. Nature. 2013 Apr 17. doi: 10.1038/nature11992. [Epub ahead of print] PubMed PMID: 23594742.

 

Just come across these two great TED talks by Ben Goldacre that talks about how the information in scientific literature can be distorted and why not all information that is essential for medical advance can be found in the literature. It is really a flaw in the research system and human nature that positive and new findings will (preferentially) be rewarded. This has suppressed the appearance of negative findings and solid repeats that would validate ideas that would benefit human kinds. The reason behind this is partially because the scientists who conducted these kinds of studies will often be labeled non-productive (productive = getting positive findings) and non-innovative. Is there a solution to that?

 

I have been paying attention to the ongoing discussion on open access to scientific research in the news media and have collected a number of interesting articles.  Here I will keep a record of a few interesting ones

2012-11-08 From the Guardian: “Open Access: ‘we no longer need expensive publishing networks‘”

2012-06-19 From the New Scientist: “Set science free from publishers’ paywalls

2012-04-17 From the Harvard Faculty Advisory Council Memorandum on Journal Pricing: “Major Periodical Subscriptions Cannot Be Sustained

I once wrote about the difficulty in getting access to the research papers here and I had to ask my friends from my home country to download that for me. The expensive journal subscription is obviously one reason that caused the problem. Obviously publishing in high-quality, open access journals with publisher like PLOS and BMC can be a good solution. However for many practical reasons, i.e. to survive and be recognized, scientists often do not act what they advocate is good. Let’s hope the field can wise up and treasure what is actually important to us.