4 posts · 1,133 views
Personal views on scientific and societal matters in genomics, bioinformatics and evolutionary biology.
caseybergman
4 posts
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- October 25, 2012
- 02:53 PM
- 346 views
Why You Should Reject the “Rejection Improves Impact” Meme
by caseybergman in I wish you'd made me angry earlier
Over the last two weeks, a meme has been making the rounds in the scientific twittersphere that goes something like “Rejection of a scientific manuscript improves its eventual impact”. This idea is based a recent analysis of patterns of manuscript submission reported in Science by Calcagno et al., which has been actively touted in the [...]... Read more »
Calcagno, V., Demoinet, E., Gollner, K., Guidi, L., Ruths, D., & de Mazancourt, C. (2012) Flows of Research Manuscripts Among Scientific Journals Reveal Hidden Submission Patterns. Science. DOI: 10.1126/science.1227833
- September 9, 2012
- 12:17 PM
- 181 views
On The Neutral Sequence Fallacy
by caseybergman in I wish you'd made me angry earlier
Beginning in the late 1960s, Motoo Kimura overturned over a century of “pan-selectionist” thinking in evolutionary biology by proposing what has come to be called The Neutral Theory of Molecular Evolution. The Neutral Theory in its basic form states that the dynamics of the majority of changes observed at the molecular level are governed by [...]... Read more »
Chin CS, Chuang JH, & Li H. (2005) Genome-wide regulatory complexity in yeast promoters: separation of functionally conserved and neutral sequence. Genome research, 15(2), 205-13. PMID: 15653830
Elnitski L, Hardison RC, Li J, Yang S, Kolbe D, Eswara P, O'Connor MJ, Schwartz S, Miller W, & Chiaromonte F. (2003) Distinguishing regulatory DNA from neutral sites. Genome research, 13(1), 64-72. PMID: 12529307
Lunter G, Ponting CP, & Hein J. (2006) Genome-wide identification of human functional DNA using a neutral indel model. PLoS computational biology, 2(1). PMID: 16410828
Marabotti A, & Facchiano A. (2009) When it comes to homology, bad habits die hard. Trends in biochemical sciences, 34(3), 98-9. PMID: 19181528
Mouse Genome Sequencing Consortium, Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, Agarwal P, Agarwala R, Ainscough R, Alexandersson M.... (2002) Initial sequencing and comparative analysis of the mouse genome. Nature, 420(6915), 520-62. PMID: 12466850
- August 26, 2012
- 02:44 PM
- 327 views
The Logistics of Scientific Growth in the 21st Century
by caseybergman in I wish you'd made me angry earlier
Over the last few months, I’ve noticed an growing number of reports about declining opportunities and increasing pressure for early stage academic researchers (Ph.D. students, post-docs and junior faculty). For example, the Washington Post published an article in early July about trends in the U.S. scientific job market entitled “U.S. pushes for more scientists, but [...]... Read more »
Kealey T. (2000) More is less. Economists and governments lag decades behind Derek Price's thinking. Nature, 405(6784), 279. PMID: 10830939
Sauermann H, & Roach M. (2012) Science PhD career preferences: levels, changes, and advisor encouragement. PloS one, 7(5). PMID: 22567149
- January 28, 2012
- 03:54 PM
- 279 views
A Open Archive of My F1000 Reviews
by caseybergman in I wish you'd made me angry earlier
Following on from a recent conversation with David Stephens on Twitter about my decision to resign from Faculty of 1000, F1000 has clarified their terms for the submission of evaluations and confirmed that it is permissible to “reproduce personal evaluations on institutional & personal blogs if you clearly reference F1000″. @David_S_Bristol @caseybergman You're free to [...]... Read more »
Nelson CE, Hersh BM, & Carroll SB. (2004) The regulatory content of intergenic DNA shapes genome architecture. Genome biology, 5(4). PMID: 15059258
Li R, Ye J, Li S, Wang J, Han Y, Ye C, Wang J, Yang H, Yu J, Wong GK.... (2005) ReAS: Recovery of ancestral sequences for transposable elements from the unassembled reads of a whole genome shotgun. PLoS computational biology, 1(4). PMID: 16184192
Rifkin SA, Houle D, Kim J, & White KP. (2005) A mutation accumulation assay reveals a broad capacity for rapid evolution of gene expression. Nature, 438(7065), 220-3. PMID: 16281035
Denver DR, Morris K, Streelman JT, Kim SK, Lynch M, & Thomas WK. (2005) The transcriptional consequences of mutation and natural selection in Caenorhabditis elegans. Nature genetics, 37(5), 544-8. PMID: 15852004
Caspi A, & Pachter L. (2006) Identification of transposable elements using multiple alignments of related genomes. Genome research, 16(2), 260-70. PMID: 16354754
Simons C, Pheasant M, Makunin IV, & Mattick JS. (2006) Transposon-free regions in mammalian genomes. Genome research, 16(2), 164-72. PMID: 16365385
Wheelan SJ, Scheifele LZ, Martínez-Murillo F, Irizarry RA, & Boeke JD. (2006) Transposon insertion site profiling chip (TIP-chip). Proceedings of the National Academy of Sciences of the United States of America, 103(47), 17632-7. PMID: 17101968
Gabriel A, Dapprich J, Kunkel M, Gresham D, Pratt SC, & Dunham MJ. (2006) Global mapping of transposon location. PLoS genetics, 2(12). PMID: 17173485
Haag-Liautard C, Dorris M, Maside X, Macaskill S, Halligan DL, Houle D, Charlesworth B, & Keightley PD. (2007) Direct estimation of per nucleotide and genomic deleterious mutation rates in Drosophila. Nature, 445(7123), 82-5. PMID: 17203060
Denver DR, Morris K, Lynch M, & Thomas WK. (2004) High mutation rate and predominance of insertions in the Caenorhabditis elegans nuclear genome. Nature, 430(7000), 679-82. PMID: 15295601
Katzourakis A, Pereira V, & Tristem M. (2007) Effects of recombination rate on human endogenous retrovirus fixation and persistence. Journal of virology, 81(19), 10712-7. PMID: 17634225
Giordano J, Ge Y, Gelfand Y, Abrusán G, Benson G, & Warburton PE. (2007) Evolutionary history of mammalian transposons determined by genome-wide defragmentation. PLoS computational biology, 3(7). PMID: 17630829
Schuemie MJ, & Kors JA. (2008) Jane: suggesting journals, finding experts. Bioinformatics (Oxford, England), 24(5), 727-8. PMID: 18227119
Errami M, Wren JD, Hicks JM, & Garner HR. (2007) eTBLAST: a web server to identify expert reviewers, appropriate journals and similar publications. Nucleic acids research, 35(Web Server issue). PMID: 17452348
Pask AJ, Behringer RR, & Renfree MB. (2008) Resurrection of DNA function in vivo from an extinct genome. PloS one, 3(5). PMID: 18493600
Ginsberg J, Mohebbi MH, Patel RS, Brammer L, Smolinski MS, & Brilliant L. (2009) Detecting influenza epidemics using search engine query data. Nature, 457(7232), 1012-4. PMID: 19020500
Taher L, & Ovcharenko I. (2009) Variable locus length in the human genome leads to ascertainment bias in functional inference for non-coding elements. Bioinformatics (Oxford, England), 25(5), 578-84. PMID: 19168912
Bejerano G, Pheasant M, Makunin I, Stephen S, Kent WJ, Mattick JS, & Haussler D. (2004) Ultraconserved elements in the human genome. Science (New York, N.Y.), 304(5675), 1321-5. PMID: 15131266
Hindorff LA, Sethupathy P, Junkins HA, Ramos EM, Mehta JP, Collins FS, & Manolio TA. (2009) Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proceedings of the National Academy of Sciences of the United States of America, 106(23), 9362-7. PMID: 19474294
Thorisson GA, Lancaster O, Free RC, Hastings RK, Sarmah P, Dash D, Brahmachari SK, & Brookes AJ. (2009) HGVbaseG2P: a central genetic association database. Nucleic acids research, 37(Database issue). PMID: 18948288
Tamames J, & de Lorenzo V. (2010) EnvMine: a text-mining system for the automatic extraction of contextual information. BMC bioinformatics, 294. PMID: 20515448
Tamames J, Abellán JJ, Pignatelli M, Camacho A, & Moya A. (2010) Environmental distribution of prokaryotic taxa. BMC microbiology, 85. PMID: 20307274
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