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Items: 9

1.

The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens.

Zhou N, Jiang Y, Bergquist TR, Lee AJ, Kacsoh BZ, Crocker AW, Lewis KA, Georghiou G, Nguyen HN, Hamid MN, Davis L, Dogan T, Atalay V, Rifaioglu AS, Dalkıran A, Cetin Atalay R, Zhang C, Hurto RL, Freddolino PL, Zhang Y, Bhat P, Supek F, Fernández JM, Gemovic B, Perovic VR, Davidović RS, Sumonja N, Veljkovic N, Asgari E, Mofrad MRK, Profiti G, Savojardo C, Martelli PL, Casadio R, Boecker F, Schoof H, Kahanda I, Thurlby N, McHardy AC, Renaux A, Saidi R, Gough J, Freitas AA, Antczak M, Fabris F, Wass MN, Hou J, Cheng J, Wang Z, Romero AE, Paccanaro A, Yang H, Goldberg T, Zhao C, Holm L, Törönen P, Medlar AJ, Zosa E, Borukhov I, Novikov I, Wilkins A, Lichtarge O, Chi PH, Tseng WC, Linial M, Rose PW, Dessimoz C, Vidulin V, Dzeroski S, Sillitoe I, Das S, Lees JG, Jones DT, Wan C, Cozzetto D, Fa R, Torres M, Warwick Vesztrocy A, Rodriguez JM, Tress ML, Frasca M, Notaro M, Grossi G, Petrini A, Re M, Valentini G, Mesiti M, Roche DB, Reeb J, Ritchie DW, Aridhi S, Alborzi SZ, Devignes MD, Koo DCE, Bonneau R, Gligorijević V, Barot M, Fang H, Toppo S, Lavezzo E, Falda M, Berselli M, Tosatto SCE, Carraro M, Piovesan D, Ur Rehman H, Mao Q, Zhang S, Vucetic S, Black GS, Jo D, Suh E, Dayton JB, Larsen DJ, Omdahl AR, McGuffin LJ, Brackenridge DA, Babbitt PC, Yunes JM, Fontana P, Zhang F, Zhu S, You R, Zhang Z, Dai S, Yao S, Tian W, Cao R, Chandler C, Amezola M, Johnson D, Chang JM, Liao WH, Liu YW, Pascarelli S, Frank Y, Hoehndorf R, Kulmanov M, Boudellioua I, Politano G, Di Carlo S, Benso A, Hakala K, Ginter F, Mehryary F, Kaewphan S, Björne J, Moen H, Tolvanen MEE, Salakoski T, Kihara D, Jain A, Šmuc T, Altenhoff A, Ben-Hur A, Rost B, Brenner SE, Orengo CA, Jeffery CJ, Bosco G, Hogan DA, Martin MJ, O'Donovan C, Mooney SD, Greene CS, Radivojac P, Friedberg I.

Genome Biol. 2019 Nov 19;20(1):244. doi: 10.1186/s13059-019-1835-8.

2.

Synapse maturation by activity-dependent ectodomain shedding of SIRPα.

Toth AB, Terauchi A, Zhang LY, Johnson-Venkatesh EM, Larsen DJ, Sutton MA, Umemori H.

Nat Neurosci. 2013 Oct;16(10):1417-25. doi: 10.1038/nn.3516. Epub 2013 Sep 15.

3.

Promoter element arising from the fusion of standard BioBrick parts.

Yao AI, Fenton TA, Owsley K, Seitzer P, Larsen DJ, Sit H, Lau J, Nair A, Tantiongloc J, Tagkopoulos I, Facciotti MT.

ACS Synth Biol. 2013 Feb 15;2(2):111-20. doi: 10.1021/sb300114d. Epub 2013 Jan 11. Erratum in: ACS Synth Biol. 2013 Jun 21;2(6):351.

PMID:
23656374
4.

A Monte Carlo-based framework enhances the discovery and interpretation of regulatory sequence motifs.

Seitzer P, Wilbanks EG, Larsen DJ, Facciotti MT.

BMC Bioinformatics. 2012 Nov 27;13:317. doi: 10.1186/1471-2105-13-317.

5.

A workflow for genome-wide mapping of archaeal transcription factors with ChIP-seq.

Wilbanks EG, Larsen DJ, Neches RY, Yao AI, Wu CY, Kjolby RA, Facciotti MT.

Nucleic Acids Res. 2012 May;40(10):e74. doi: 10.1093/nar/gks063. Epub 2012 Feb 9.

6.

Large scale physiological readjustment during growth enables rapid, comprehensive and inexpensive systems analysis.

Facciotti MT, Pang WL, Lo FY, Whitehead K, Koide T, Masumura K, Pan M, Kaur A, Larsen DJ, Reiss DJ, Hoang L, Kalisiak E, Northen T, Trauger SA, Siuzdak G, Baliga NS.

BMC Syst Biol. 2010 May 14;4:64. doi: 10.1186/1752-0509-4-64.

7.

Investigation of cholera acquired from the riverine environment in Queensland.

Bourke AT, Cossins YN, Gray BR, Lunney TJ, Rostron NA, Holmes RV, Griggs ER, Larsen DJ, Kelk VR.

Med J Aust. 1986 Mar 3;144(5):229-34.

PMID:
3587092
8.

Analytical methods used in a study of coke oven effluent.

Schulte KA, Larsen DJ, Hornung RW, Crable JV.

Am Ind Hyg Assoc J. 1975 Feb;36(2):131-9.

PMID:
1146677
9.

The quantitative dermination of quartz in coal dust by infrared spectroscopy.

Larsen DJ, Von Doenhoff LJ, Crable JV.

Am Ind Hyg Assoc J. 1972 Jun;33(6):367-72. No abstract available.

PMID:
4346787

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