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Items: 1 to 50 of 55

1.

Identification and optimization of PrsA in Bacillus subtilis for improved yield of amylase.

Quesada-Ganuza A, Antelo-Varela M, Mouritzen JC, Bartel J, Becher D, Gjermansen M, Hallin PF, Appel KF, Kilstrup M, Rasmussen MD, Nielsen AK.

Microb Cell Fact. 2019 Sep 17;18(1):158. doi: 10.1186/s12934-019-1203-0.

2.

Review: Milking machine settings, teat condition and milking efficiency in dairy cows.

Odorčić M, Rasmussen MD, Paulrud CO, Bruckmaier RM.

Animal. 2019 Jul;13(S1):s94-s99. doi: 10.1017/S1751731119000417. Review.

PMID:
31280747
3.

Estimating teat canal cross-sectional area to determine the effects of teat-end and mouthpiece chamber vacuum on teat congestion.

Penry JF, Upton J, Mein GA, Rasmussen MD, Ohnstad I, Thompson PD, Reinemann DJ.

J Dairy Sci. 2017 Jan;100(1):821-827. doi: 10.3168/jds.2016-11533. Epub 2016 Nov 9.

4.

Effect of pulsation rest phase duration on teat end congestion.

Upton J, Penry JF, Rasmussen MD, Thompson PD, Reinemann DJ.

J Dairy Sci. 2016 May;99(5):3958-3965. doi: 10.3168/jds.2015-10466.

5.

A comparative encyclopedia of DNA elements in the mouse genome.

Yue F, Cheng Y, Breschi A, Vierstra J, Wu W, Ryba T, Sandstrom R, Ma Z, Davis C, Pope BD, Shen Y, Pervouchine DD, Djebali S, Thurman RE, Kaul R, Rynes E, Kirilusha A, Marinov GK, Williams BA, Trout D, Amrhein H, Fisher-Aylor K, Antoshechkin I, DeSalvo G, See LH, Fastuca M, Drenkow J, Zaleski C, Dobin A, Prieto P, Lagarde J, Bussotti G, Tanzer A, Denas O, Li K, Bender MA, Zhang M, Byron R, Groudine MT, McCleary D, Pham L, Ye Z, Kuan S, Edsall L, Wu YC, Rasmussen MD, Bansal MS, Kellis M, Keller CA, Morrissey CS, Mishra T, Jain D, Dogan N, Harris RS, Cayting P, Kawli T, Boyle AP, Euskirchen G, Kundaje A, Lin S, Lin Y, Jansen C, Malladi VS, Cline MS, Erickson DT, Kirkup VM, Learned K, Sloan CA, Rosenbloom KR, Lacerda de Sousa B, Beal K, Pignatelli M, Flicek P, Lian J, Kahveci T, Lee D, Kent WJ, Ramalho Santos M, Herrero J, Notredame C, Johnson A, Vong S, Lee K, Bates D, Neri F, Diegel M, Canfield T, Sabo PJ, Wilken MS, Reh TA, Giste E, Shafer A, Kutyavin T, Haugen E, Dunn D, Reynolds AP, Neph S, Humbert R, Hansen RS, De Bruijn M, Selleri L, Rudensky A, Josefowicz S, Samstein R, Eichler EE, Orkin SH, Levasseur D, Papayannopoulou T, Chang KH, Skoultchi A, Gosh S, Disteche C, Treuting P, Wang Y, Weiss MJ, Blobel GA, Cao X, Zhong S, Wang T, Good PJ, Lowdon RF, Adams LB, Zhou XQ, Pazin MJ, Feingold EA, Wold B, Taylor J, Mortazavi A, Weissman SM, Stamatoyannopoulos JA, Snyder MP, Guigo R, Gingeras TR, Gilbert DM, Hardison RC, Beer MA, Ren B; Mouse ENCODE Consortium.

Nature. 2014 Nov 20;515(7527):355-64. doi: 10.1038/nature13992.

6.

Short communication: Changes in gait symmetry in healthy and lame dairy cows based on 3-dimensional ground reaction force curves following claw trimming.

Thorup VM, do Nascimento OF, Skjøth F, Voigt M, Rasmussen MD, Bennedsgaard TW, Ingvartsen KL.

J Dairy Sci. 2014 Dec;97(12):7679-84. doi: 10.3168/jds.2014-8410. Epub 2014 Oct 11.

7.

Genome-wide inference of ancestral recombination graphs.

Rasmussen MD, Hubisz MJ, Gronau I, Siepel A.

PLoS Genet. 2014 May 15;10(5):e1004342. doi: 10.1371/journal.pgen.1004342. eCollection 2014.

8.

Most parsimonious reconciliation in the presence of gene duplication, loss, and deep coalescence using labeled coalescent trees.

Wu YC, Rasmussen MD, Bansal MS, Kellis M.

Genome Res. 2014 Mar;24(3):475-86. doi: 10.1101/gr.161968.113. Epub 2013 Dec 5.

9.

TreeFix: statistically informed gene tree error correction using species trees.

Wu YC, Rasmussen MD, Bansal MS, Kellis M.

Syst Biol. 2013 Jan 1;62(1):110-20. doi: 10.1093/sysbio/sys076. Epub 2012 Sep 4.

10.

Replacing and additive horizontal gene transfer in Streptococcus.

Choi SC, Rasmussen MD, Hubisz MJ, Gronau I, Stanhope MJ, Siepel A.

Mol Biol Evol. 2012 Nov;29(11):3309-20. doi: 10.1093/molbev/mss138. Epub 2012 May 21.

11.

Roles of major facilitator superfamily transporters in phosphate response in Drosophila.

Bergwitz C, Rasmussen MD, DeRobertis C, Wee MJ, Sinha S, Chen HH, Huang J, Perrimon N.

PLoS One. 2012;7(2):e31730. doi: 10.1371/journal.pone.0031730. Epub 2012 Feb 16.

12.

Unified modeling of gene duplication, loss, and coalescence using a locus tree.

Rasmussen MD, Kellis M.

Genome Res. 2012 Apr;22(4):755-65. doi: 10.1101/gr.123901.111. Epub 2012 Jan 23.

13.

A high-resolution map of human evolutionary constraint using 29 mammals.

Lindblad-Toh K, Garber M, Zuk O, Lin MF, Parker BJ, Washietl S, Kheradpour P, Ernst J, Jordan G, Mauceli E, Ward LD, Lowe CB, Holloway AK, Clamp M, Gnerre S, Alföldi J, Beal K, Chang J, Clawson H, Cuff J, Di Palma F, Fitzgerald S, Flicek P, Guttman M, Hubisz MJ, Jaffe DB, Jungreis I, Kent WJ, Kostka D, Lara M, Martins AL, Massingham T, Moltke I, Raney BJ, Rasmussen MD, Robinson J, Stark A, Vilella AJ, Wen J, Xie X, Zody MC; Broad Institute Sequencing Platform and Whole Genome Assembly Team, Baldwin J, Bloom T, Chin CW, Heiman D, Nicol R, Nusbaum C, Young S, Wilkinson J, Worley KC, Kovar CL, Muzny DM, Gibbs RA; Baylor College of Medicine Human Genome Sequencing Center Sequencing Team, Cree A, Dihn HH, Fowler G, Jhangiani S, Joshi V, Lee S, Lewis LR, Nazareth LV, Okwuonu G, Santibanez J, Warren WC, Mardis ER, Weinstock GM, Wilson RK; Genome Institute at Washington University, Delehaunty K, Dooling D, Fronik C, Fulton L, Fulton B, Graves T, Minx P, Sodergren E, Birney E, Margulies EH, Herrero J, Green ED, Haussler D, Siepel A, Goldman N, Pollard KS, Pedersen JS, Lander ES, Kellis M.

Nature. 2011 Oct 12;478(7370):476-82. doi: 10.1038/nature10530.

14.

Evolution at the subgene level: domain rearrangements in the Drosophila phylogeny.

Wu YC, Rasmussen MD, Kellis M.

Mol Biol Evol. 2012 Feb;29(2):689-705. doi: 10.1093/molbev/msr222. Epub 2011 Sep 7.

15.

A Bayesian approach for fast and accurate gene tree reconstruction.

Rasmussen MD, Kellis M.

Mol Biol Evol. 2011 Jan;28(1):273-90. doi: 10.1093/molbev/msq189. Epub 2010 Jul 25.

16.

Global transcriptional analysis of Bacillus licheniformis reveals an overlap between heat shock and iron limitation stimulon.

Nielsen AK, Breüner A, Krzystanek M, Andersen JT, Poulsen TA, Olsen PB, Mijakovic I, Rasmussen MD.

J Mol Microbiol Biotechnol. 2010;18(3):162-73. doi: 10.1159/000315457. Epub 2010 Jun 8.

17.

Contributions of the pre- and pro-regions of a Staphylococcus hyicus lipase to secretion of a heterologous protein by Bacillus subtilis.

Kouwen TR, Nielsen AK, Denham EL, Dubois JY, Dorenbos R, Rasmussen MD, Quax WJ, Freudl R, van Dijl JM.

Appl Environ Microbiol. 2010 Feb;76(3):659-69. doi: 10.1128/AEM.01671-09. Epub 2009 Nov 30.

18.

Udder health of cows changing from tie stalls or free stalls with conventional milking to free stalls with either conventional or automatic milking.

Hovinen M, Rasmussen MD, Pyörälä S.

J Dairy Sci. 2009 Aug;92(8):3696-703. doi: 10.3168/jds.2008-1962.

19.

Evolution of pathogenicity and sexual reproduction in eight Candida genomes.

Butler G, Rasmussen MD, Lin MF, Santos MA, Sakthikumar S, Munro CA, Rheinbay E, Grabherr M, Forche A, Reedy JL, Agrafioti I, Arnaud MB, Bates S, Brown AJ, Brunke S, Costanzo MC, Fitzpatrick DA, de Groot PW, Harris D, Hoyer LL, Hube B, Klis FM, Kodira C, Lennard N, Logue ME, Martin R, Neiman AM, Nikolaou E, Quail MA, Quinn J, Santos MC, Schmitzberger FF, Sherlock G, Shah P, Silverstein KA, Skrzypek MS, Soll D, Staggs R, Stansfield I, Stumpf MP, Sudbery PE, Srikantha T, Zeng Q, Berman J, Berriman M, Heitman J, Gow NA, Lorenz MC, Birren BW, Kellis M, Cuomo CA.

Nature. 2009 Jun 4;459(7247):657-62. doi: 10.1038/nature08064.

20.

Performance and scalability of discriminative metrics for comparative gene identification in 12 Drosophila genomes.

Lin MF, Deoras AN, Rasmussen MD, Kellis M.

PLoS Comput Biol. 2008 Apr 18;4(4):e1000067. doi: 10.1371/journal.pcbi.1000067.

21.

Identification of peptides in milk as a result of proteolysis at different levels of somatic cell counts using LC MALDI MS/MS detection.

Wedholm A, Møller HS, Lindmark-Månsson H, Rasmussen MD, Andrén A, Larsen LB.

J Dairy Res. 2008 Feb;75(1):76-83. doi: 10.1017/S0022029907002968. Epub 2008 Jan 29.

PMID:
18226301
22.

A facilitated survey instrument captures significantly more anesthesia events than does traditional voluntary event reporting.

Oken A, Rasmussen MD, Slagle JM, Jain S, Kuykendall T, Ordonez N, Weinger MB.

Anesthesiology. 2007 Dec;107(6):909-22.

PMID:
18043059
23.

Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures.

Stark A, Lin MF, Kheradpour P, Pedersen JS, Parts L, Carlson JW, Crosby MA, Rasmussen MD, Roy S, Deoras AN, Ruby JG, Brennecke J; Harvard FlyBase curators; Berkeley Drosophila Genome Project, Hodges E, Hinrichs AS, Caspi A, Paten B, Park SW, Han MV, Maeder ML, Polansky BJ, Robson BE, Aerts S, van Helden J, Hassan B, Gilbert DG, Eastman DA, Rice M, Weir M, Hahn MW, Park Y, Dewey CN, Pachter L, Kent WJ, Haussler D, Lai EC, Bartel DP, Hannon GJ, Kaufman TC, Eisen MB, Clark AG, Smith D, Celniker SE, Gelbart WM, Kellis M.

Nature. 2007 Nov 8;450(7167):219-32.

24.

Evolution of genes and genomes on the Drosophila phylogeny.

Drosophila 12 Genomes Consortium, Clark AG, Eisen MB, Smith DR, Bergman CM, Oliver B, Markow TA, Kaufman TC, Kellis M, Gelbart W, Iyer VN, Pollard DA, Sackton TB, Larracuente AM, Singh ND, Abad JP, Abt DN, Adryan B, Aguade M, Akashi H, Anderson WW, Aquadro CF, Ardell DH, Arguello R, Artieri CG, Barbash DA, Barker D, Barsanti P, Batterham P, Batzoglou S, Begun D, Bhutkar A, Blanco E, Bosak SA, Bradley RK, Brand AD, Brent MR, Brooks AN, Brown RH, Butlin RK, Caggese C, Calvi BR, Bernardo de Carvalho A, Caspi A, Castrezana S, Celniker SE, Chang JL, Chapple C, Chatterji S, Chinwalla A, Civetta A, Clifton SW, Comeron JM, Costello JC, Coyne JA, Daub J, David RG, Delcher AL, Delehaunty K, Do CB, Ebling H, Edwards K, Eickbush T, Evans JD, Filipski A, Findeiss S, Freyhult E, Fulton L, Fulton R, Garcia AC, Gardiner A, Garfield DA, Garvin BE, Gibson G, Gilbert D, Gnerre S, Godfrey J, Good R, Gotea V, Gravely B, Greenberg AJ, Griffiths-Jones S, Gross S, Guigo R, Gustafson EA, Haerty W, Hahn MW, Halligan DL, Halpern AL, Halter GM, Han MV, Heger A, Hillier L, Hinrichs AS, Holmes I, Hoskins RA, Hubisz MJ, Hultmark D, Huntley MA, Jaffe DB, Jagadeeshan S, Jeck WR, Johnson J, Jones CD, Jordan WC, Karpen GH, Kataoka E, Keightley PD, Kheradpour P, Kirkness EF, Koerich LB, Kristiansen K, Kudrna D, Kulathinal RJ, Kumar S, Kwok R, Lander E, Langley CH, Lapoint R, Lazzaro BP, Lee SJ, Levesque L, Li R, Lin CF, Lin MF, Lindblad-Toh K, Llopart A, Long M, Low L, Lozovsky E, Lu J, Luo M, Machado CA, Makalowski W, Marzo M, Matsuda M, Matzkin L, McAllister B, McBride CS, McKernan B, McKernan K, Mendez-Lago M, Minx P, Mollenhauer MU, Montooth K, Mount SM, Mu X, Myers E, Negre B, Newfeld S, Nielsen R, Noor MA, O'Grady P, Pachter L, Papaceit M, Parisi MJ, Parisi M, Parts L, Pedersen JS, Pesole G, Phillippy AM, Ponting CP, Pop M, Porcelli D, Powell JR, Prohaska S, Pruitt K, Puig M, Quesneville H, Ram KR, Rand D, Rasmussen MD, Reed LK, Reenan R, Reily A, Remington KA, Rieger TT, Ritchie MG, Robin C, Rogers YH, Rohde C, Rozas J, Rubenfield MJ, Ruiz A, Russo S, Salzberg SL, Sanchez-Gracia A, Saranga DJ, Sato H, Schaeffer SW, Schatz MC, Schlenke T, Schwartz R, Segarra C, Singh RS, Sirot L, Sirota M, Sisneros NB, Smith CD, Smith TF, Spieth J, Stage DE, Stark A, Stephan W, Strausberg RL, Strempel S, Sturgill D, Sutton G, Sutton GG, Tao W, Teichmann S, Tobari YN, Tomimura Y, Tsolas JM, Valente VL, Venter E, Venter JC, Vicario S, Vieira FG, Vilella AJ, Villasante A, Walenz B, Wang J, Wasserman M, Watts T, Wilson D, Wilson RK, Wing RA, Wolfner MF, Wong A, Wong GK, Wu CI, Wu G, Yamamoto D, Yang HP, Yang SP, Yorke JA, Yoshida K, Zdobnov E, Zhang P, Zhang Y, Zimin AV, Baldwin J, Abdouelleil A, Abdulkadir J, Abebe A, Abera B, Abreu J, Acer SC, Aftuck L, Alexander A, An P, Anderson E, Anderson S, Arachi H, Azer M, Bachantsang P, Barry A, Bayul T, Berlin A, Bessette D, Bloom T, Blye J, Boguslavskiy L, Bonnet C, Boukhgalter B, Bourzgui I, Brown A, Cahill P, Channer S, Cheshatsang Y, Chuda L, Citroen M, Collymore A, Cooke P, Costello M, D'Aco K, Daza R, De Haan G, DeGray S, DeMaso C, Dhargay N, Dooley K, Dooley E, Doricent M, Dorje P, Dorjee K, Dupes A, Elong R, Falk J, Farina A, Faro S, Ferguson D, Fisher S, Foley CD, Franke A, Friedrich D, Gadbois L, Gearin G, Gearin CR, Giannoukos G, Goode T, Graham J, Grandbois E, Grewal S, Gyaltsen K, Hafez N, Hagos B, Hall J, Henson C, Hollinger A, Honan T, Huard MD, Hughes L, Hurhula B, Husby ME, Kamat A, Kanga B, Kashin S, Khazanovich D, Kisner P, Lance K, Lara M, Lee W, Lennon N, Letendre F, LeVine R, Lipovsky A, Liu X, Liu J, Liu S, Lokyitsang T, Lokyitsang Y, Lubonja R, Lui A, MacDonald P, Magnisalis V, Maru K, Matthews C, McCusker W, McDonough S, Mehta T, Meldrim J, Meneus L, Mihai O, Mihalev A, Mihova T, Mittelman R, Mlenga V, Montmayeur A, Mulrain L, Navidi A, Naylor J, Negash T, Nguyen T, Nguyen N, Nicol R, Norbu C, Norbu N, Novod N, O'Neill B, Osman S, Markiewicz E, Oyono OL, Patti C, Phunkhang P, Pierre F, Priest M, Raghuraman S, Rege F, Reyes R, Rise C, Rogov P, Ross K, Ryan E, Settipalli S, Shea T, Sherpa N, Shi L, Shih D, Sparrow T, Spaulding J, Stalker J, Stange-Thomann N, Stavropoulos S, Stone C, Strader C, Tesfaye S, Thomson T, Thoulutsang Y, Thoulutsang D, Topham K, Topping I, Tsamla T, Vassiliev H, Vo A, Wangchuk T, Wangdi T, Weiand M, Wilkinson J, Wilson A, Yadav S, Young G, Yu Q, Zembek L, Zhong D, Zimmer A, Zwirko Z, Jaffe DB, Alvarez P, Brockman W, Butler J, Chin C, Gnerre S, Grabherr M, Kleber M, Mauceli E, MacCallum I.

Nature. 2007 Nov 8;450(7167):203-18.

PMID:
17994087
25.
26.

Neighborhoods and obesity in older adults: the Baltimore Memory Study.

Glass TA, Rasmussen MD, Schwartz BS.

Am J Prev Med. 2006 Dec;31(6):455-63.

27.

Influence of air intake on the concentration of free fatty acids and vacuum fluctuations during automatic milking.

Rasmussen MD, Wiking L, Bjerring M, Larsen HC.

J Dairy Sci. 2006 Dec;89(12):4596-605.

28.

A model for detection of individual cow mastitis based on an indicator measured in milk.

Chagunda MG, Friggens NC, Rasmussen MD, Larsen T.

J Dairy Sci. 2006 Aug;89(8):2980-98.

29.
30.

Visual scoring of clots in foremilk.

Rasmussen MD.

J Dairy Res. 2005 Nov;72(4):406-14.

PMID:
16223455
31.

Visual scoring of milk mixed with blood.

Rasmussen MD, Bjerring M.

J Dairy Res. 2005 Aug;72(3):257-63.

PMID:
16174354
32.

Changes in freezing point of blood and milk during dehydration and rehydration in lactating cows.

Bjerg M, Rasmussen MD, Nielsen MO.

J Dairy Sci. 2005 Sep;88(9):3174-85.

33.
34.

Structure of a Bacillus halmapalus family 13 alpha-amylase, BHA, in complex with an acarbose-derived nonasaccharide at 2.1 A resolution.

Davies GJ, Brzozowski AM, Dauter Z, Rasmussen MD, Borchert TV, Wilson KS.

Acta Crystallogr D Biol Crystallogr. 2005 Feb;61(Pt 2):190-3. Epub 2005 Jan 19.

PMID:
15681870
35.

Complete genome sequence of the industrial bacterium Bacillus licheniformis and comparisons with closely related Bacillus species.

Rey MW, Ramaiya P, Nelson BA, Brody-Karpin SD, Zaretsky EJ, Tang M, Lopez de Leon A, Xiang H, Gusti V, Clausen IG, Olsen PB, Rasmussen MD, Andersen JT, Jørgensen PL, Larsen TS, Sorokin A, Bolotin A, Lapidus A, Galleron N, Ehrlich SD, Berka RM.

Genome Biol. 2004;5(10):R77. Epub 2004 Sep 13.

36.

Physical properties of mammary secretions in relation to chemical changes during transition from colostrum to milk.

Madsen BD, Rasmussen MD, Nielsen MO, Wiking L, Larsen LB.

J Dairy Res. 2004 Aug;71(3):263-72.

PMID:
15354571
37.
38.

Adsorption of O2 and oxidation of CO at Au nanoparticles supported by TiO2(110).

Molina LM, Rasmussen MD, Hammer B.

J Chem Phys. 2004 Apr 22;120(16):7673-80. Erratum in: J Chem Phys. 2005 Jul 8;123(2):029903.

PMID:
15267678
39.

How teat canal keratin depends on the length and diameter of the teat canal in dairy cows.

Paulrud CO, Rasmussen MD.

J Dairy Res. 2004 May;71(2):253-5. No abstract available.

PMID:
15190955
40.

Short-term impact of Experience Corps participation on children and schools: results from a pilot randomized trial.

Rebok GW, Carlson MC, Glass TA, McGill S, Hill J, Wasik BA, Ialongo N, Frick KD, Fried LP, Rasmussen MD.

J Urban Health. 2004 Mar;81(1):79-93.

41.

wCLUTO: a Web-enabled clustering toolkit.

Rasmussen MD, Deshpande MS, Karypis G, Johnson J, Crow JA, Retzel EF.

Plant Physiol. 2003 Oct;133(2):510-6.

42.

Milk quality on Danish farms with automatic milking systems.

Rasmussen MD, Bjerring M, Justesen P, Jepsen L.

J Dairy Sci. 2002 Nov;85(11):2869-78.

43.

Cytotoxic potential of industrial strains of Bacillus sp.

Pedersen PB, Bjørnvad ME, Rasmussen MD, Petersen JN.

Regul Toxicol Pharmacol. 2002 Oct;36(2):155-61.

PMID:
12460750
44.

Growth factor treatment enhances vestibular hair cell renewal and results in improved vestibular function.

Kopke RD, Jackson RL, Li G, Rasmussen MD, Hoffer ME, Frenz DA, Costello M, Schultheiss P, Van De Water TR.

Proc Natl Acad Sci U S A. 2001 May 8;98(10):5886-91. Epub 2001 May 1.

46.
47.

Pressure in the teat cistern and the mouth of the calf during suckling.

Rasmussen MD, Mayntz M.

J Dairy Res. 1998 Nov;65(4):685-92. No abstract available.

PMID:
9839217
48.

Milking performance and udder health of cows milked with two different liners.

Rasmussen MD, Frimer ES, Kaartinen L, Jensen NE.

J Dairy Res. 1998 Aug;65(3):353-63.

PMID:
9718489
49.

Reverse pressure gradients across the teat canal related to machine milking.

Rasmussen MD, Frimer ES, Decker EL.

J Dairy Sci. 1994 Apr;77(4):984-93.

50.

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