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Supporting Single Cell RNA-seq Analysis at Harvard - A Community Approach.

Sui SH, Kirchner R, Steinbaugh M, Boswell S, Piper M, Barrera V, Pantano L, Khetani R, Mistry M, Rutherford K, Hutchinson J.

J Biomol Tech. 2019 Dec;30(Suppl):S39.


PHI-base: the pathogen-host interactions database.

Urban M, Cuzick A, Seager J, Wood V, Rutherford K, Venkatesh SY, De Silva N, Martinez MC, Pedro H, Yates AD, Hassani-Pak K, Hammond-Kosack KE.

Nucleic Acids Res. 2020 Jan 8;48(D1):D613-D620. doi: 10.1093/nar/gkz904.


Effects of stocking density during the dry period on dairy cow physiology, metabolism and behaviour.

Fujiwara M, Haskell M, Macrae A, Rutherford K.

J Dairy Res. 2019 Aug;86(3):283-290. doi: 10.1017/S002202991900058X. Epub 2019 Aug 5.


Stress, novel sex genes, and epigenetic reprogramming orchestrate socially controlled sex change.

Todd EV, Ortega-Recalde O, Liu H, Lamm MS, Rutherford KM, Cross H, Black MA, Kardailsky O, Marshall Graves JA, Hore TA, Godwin JR, Gemmell NJ.

Sci Adv. 2019 Jul 10;5(7):eaaw7006. doi: 10.1126/sciadv.aaw7006. eCollection 2019 Jul.


Family therapy approaches for anorexia nervosa.

Fisher CA, Skocic S, Rutherford KA, Hetrick SE.

Cochrane Database Syst Rev. 2019 May 1;5:CD004780. doi: 10.1002/14651858.CD004780.pub4.


Molecular structure of sauropsid β-keratins from tuatara (Sphenodon punctatus).

Parry DAD, Fraser RDB, Alibardi L, Rutherford KM, Gemmell N.

J Struct Biol. 2019 Jul 1;207(1):21-28. doi: 10.1016/j.jsb.2019.04.008. Epub 2019 Apr 9.


Hidden in plain sight: what remains to be discovered in the eukaryotic proteome?

Wood V, Lock A, Harris MA, Rutherford K, Bähler J, Oliver SG.

Open Biol. 2019 Feb 28;9(2):180241. doi: 10.1098/rsob.180241.


Validation and Factor Analysis of the Child and Youth Resilience Measure for Indigenous Australian Boarding School Students.

Langham E, McCalman J, Redman-MacLaren M, Hunter E, Wenitong M, Britton A, Rutherford K, Saunders V, Ungar M, Bainbridge R.

Front Public Health. 2018 Oct 23;6:299. doi: 10.3389/fpubh.2018.00299. eCollection 2018.


PomBase 2018: user-driven reimplementation of the fission yeast database provides rapid and intuitive access to diverse, interconnected information.

Lock A, Rutherford K, Harris MA, Hayles J, Oliver SG, Bähler J, Wood V.

Nucleic Acids Res. 2019 Jan 8;47(D1):D821-D827. doi: 10.1093/nar/gky961.


Family therapy approaches for anorexia nervosa.

Fisher CA, Skocic S, Rutherford KA, Hetrick SE.

Cochrane Database Syst Rev. 2018 Oct 15;10:CD004780. doi: 10.1002/14651858.CD004780.pub3. Update in: Cochrane Database Syst Rev. 2019 May 01;5:CD004780.


Reduced representation sequencing detects only subtle regional structure in a heavily exploited and rapidly recolonizing marine mammal species.

Dussex N, Taylor HR, Stovall WR, Rutherford K, Dodds KG, Clarke SM, Gemmell NJ.

Ecol Evol. 2018 Aug 5;8(17):8736-8749. doi: 10.1002/ece3.4411. eCollection 2018 Sep.


Serine Integrase attP Binding and Specificity.

Li H, Sharp R, Rutherford K, Gupta K, Van Duyne GD.

J Mol Biol. 2018 Oct 19;430(21):4401-4418. doi: 10.1016/j.jmb.2018.09.007. Epub 2018 Sep 15.


Periparturient Behavior and Physiology: Further Insight Into the Farrowing Process for Primiparous and Multiparous Sows.

Ison SH, Jarvis S, Hall SA, Ashworth CJ, Rutherford KMD.

Front Vet Sci. 2018 Jun 12;5:122. doi: 10.3389/fvets.2018.00122. eCollection 2018.


Survey of dry cow management on UK commercial dairy farms.

Fujiwara M, Haskell MJ, Macrae AI, Rutherford KMD.

Vet Rec. 2018 Sep 8;183(9):297. doi: 10.1136/vr.104755. Epub 2018 Jun 15.


PomBase: The Scientific Resource for Fission Yeast.

Lock A, Rutherford K, Harris MA, Wood V.

Methods Mol Biol. 2018;1757:49-68. doi: 10.1007/978-1-4939-7737-6_4. Review.


Adipose transcriptome analysis provides novel insights into molecular regulation of prolonged fasting in northern elephant seal pups.

Martinez B, Khudyakov J, Rutherford K, Crocker DE, Gemmell N, Ortiz RM.

Physiol Genomics. 2018 Jul 1;50(7):495-503. doi: 10.1152/physiolgenomics.00002.2018. Epub 2018 Apr 6.


De novo draft assembly of the Botrylloides leachii genome provides further insight into tunicate evolution.

Blanchoud S, Rutherford K, Zondag L, Gemmell NJ, Wilson MJ.

Sci Rep. 2018 Apr 3;8(1):5518. doi: 10.1038/s41598-018-23749-w.


Genetic sex assignment in wild populations using genotyping-by-sequencing data: A statistical threshold approach.

Stovall WR, Taylor HR, Black M, Grosser S, Rutherford K, Gemmell NJ.

Mol Ecol Resour. 2018 Mar;18(2):179-190. doi: 10.1111/1755-0998.12767. Epub 2018 Mar 3.


Identification of sex differences in zebrafish (Danio rerio) brains during early sexual differentiation and masculinization using 17α-methyltestoterone.

Lee SLJ, Horsfield JA, Black MA, Rutherford K, Gemmell NJ.

Biol Reprod. 2018 Aug 1;99(2):446-460. doi: 10.1093/biolre/iox175.


Female Mimicry by Sneaker Males Has a Transcriptomic Signature in Both the Brain and the Gonad in a Sex-Changing Fish.

Todd EV, Liu H, Lamm MS, Thomas JT, Rutherford K, Thompson KC, Godwin JR, Gemmell NJ.

Mol Biol Evol. 2018 Jan 1;35(1):225-241. doi: 10.1093/molbev/msx293.


Comparing microbiotas in the upper aerodigestive and lower respiratory tracts of lambs.

Glendinning L, Collie D, Wright S, Rutherford KMD, McLachlan G.

Microbiome. 2017 Oct 27;5(1):145. doi: 10.1186/s40168-017-0364-5.


Analysis of the genome of the New Zealand giant collembolan (Holacanthella duospinosa) sheds light on hexapod evolution.

Wu C, Jordan MD, Newcomb RD, Gemmell NJ, Bank S, Meusemann K, Dearden PK, Duncan EJ, Grosser S, Rutherford K, Gardner PP, Crowhurst RN, Steinwender B, Tooman LK, Stevens MI, Buckley TR.

BMC Genomics. 2017 Oct 17;18(1):795. doi: 10.1186/s12864-017-4197-1.


A systems-level analysis of drug-target-disease associations for drug repositioning.

Rutherford KD, Mazandu GK, Mulder NJ.

Brief Funct Genomics. 2018 Jan 1;17(1):34-41. doi: 10.1093/bfgp/elx015.


Male-female relatedness at specific SNP-linkage groups influences cryptic female choice in Chinook salmon (Oncorhynchus tshawytscha).

Geßner C, Johnson SL, Fisher P, Clarke S, Rutherford K, Symonds J, Gemmell NJ.

Proc Biol Sci. 2017 Jul 26;284(1859). pii: 20170853. doi: 10.1098/rspb.2017.0853.


Histological and transcriptomic effects of 17α-methyltestosterone on zebrafish gonad development.

Lee SLJ, Horsfield JA, Black MA, Rutherford K, Fisher A, Gemmell NJ.

BMC Genomics. 2017 Jul 24;18(1):557. doi: 10.1186/s12864-017-3915-z.


The Use of Text Messaging to Improve the Hospital-to-Community Transition in Acute Coronary Syndrome Patients (Txt2Prevent): Intervention Development and Pilot Randomized Controlled Trial Protocol.

Ross ES, Sakakibara BM, Mackay MH, Whitehurst DG, Singer J, Toma M, Corbett KK, Van Spall HG, Rutherford K, Gheorghiu B, Code J, Lear SA.

JMIR Res Protoc. 2017 May 23;6(5):e91. doi: 10.2196/resprot.6968.


Measuring Assessment Quality With an Assessment Utility Rubric for Medical Education.

Colbert-Getz JM, Ryan M, Hennessey E, Lindeman B, Pitts B, Rutherford KA, Schwengel D, Sozio SM, George J, Jung J.

MedEdPORTAL. 2017 May 24;13:10588. doi: 10.15766/mep_2374-8265.10588.


Large-scale data-driven integrative framework for extracting essential targets and processes from disease-associated gene data sets.

Mazandu GK, Chimusa ER, Rutherford K, Zekeng EG, Gebremariam ZZ, Onifade MY, Mulder NJ.

Brief Bioinform. 2018 Nov 27;19(6):1141-1152. doi: 10.1093/bib/bbx052.


Patterns and trends in long-term opioid use for non-cancer pain in British Columbia, 2005-2012.

Smolina K, Gladstone EJ, Rutherford K, Morgan SG.

Can J Public Health. 2016 Dec 27;107(4-5):e404-e409. doi: 10.17269/cjph.107.5413.


A Review of Pain Assessment in Pigs.

Ison SH, Clutton RE, Di Giminiani P, Rutherford KM.

Front Vet Sci. 2016 Nov 28;3:108. eCollection 2016. Review.


PHI-base: a new interface and further additions for the multi-species pathogen-host interactions database.

Urban M, Cuzick A, Rutherford K, Irvine A, Pedro H, Pant R, Sadanadan V, Khamari L, Billal S, Mohanty S, Hammond-Kosack KE.

Nucleic Acids Res. 2017 Jan 4;45(D1):D604-D610. doi: 10.1093/nar/gkw1089. Epub 2016 Dec 3.


The identification of potential behavioural indicators of pain in periparturient sows.

Ison SH, Jarvis S, Rutherford KM.

Res Vet Sci. 2016 Dec;109:114-120. doi: 10.1016/j.rvsc.2016.10.002. Epub 2016 Oct 6.


Discovery of an expanded set of avian leucosis subgroup E proviruses in chickens using Vermillion, a novel sequence capture and analysis pipeline.

Rutherford K, Meehan CJ, Langille MG, Tyack SG, McKay JC, McLean NL, Benkel K, Beiko RG, Benkel B.

Poult Sci. 2017 May;96(5):1516. doi: 10.3382/ps/pew404. Epub 2016 Oct 19. No abstract available.


Epigenetics and developmental programming of welfare and production traits in farm animals.

Sinclair KD, Rutherford KM, Wallace JM, Brameld JM, Stöger R, Alberio R, Sweetman D, Gardner DS, Perry VE, Adam CL, Ashworth CJ, Robinson JE, Dwyer CM.

Reprod Fertil Dev. 2016 Jul 21. doi: 10.1071/RD16102. [Epub ahead of print]


The ethics of conducting molecular autopsies in cases of sudden death in the young.

McGuire AL, Moore Q, Majumder M, Walkiewicz M, Eng CM, Belmont JW, Nassef S, Darilek S, Rutherford K, Pereira S, Scherer SE, Sutton VR, Wolf D, Gibbs RA, Kahn R, Sanchez LA; Molecular Autopsy Consortium of Houston (MATCH).

Genome Res. 2016 Sep;26(9):1165-9. doi: 10.1101/gr.192401.115. Epub 2016 Jul 13. No abstract available.


Discovery of an expanded set of avian leukosis subgroup E proviruses in chickens using Vermillion, a novel sequence capture and analysis pipeline [corrected].

Rutherford K, Meehan CJ, Langille MG, Tyack SG, McKay JC, McLean NL, Benkel K, Beiko RG, Benkel B.

Poult Sci. 2016 Oct 1;95(10):2250-8. doi: 10.3382/ps/pew194. Epub 2016 Jun 27. Erratum in: Poult Sci. 2016 Oct 19;:.


Uncovering the pathways underlying whole body regeneration in a chordate model, Botrylloides leachi using de novo transcriptome analysis.

Zondag LE, Rutherford K, Gemmell NJ, Wilson MJ.

BMC Genomics. 2016 Feb 16;17:114. doi: 10.1186/s12864-016-2435-6.


INTEGRATED CARE. New, cutting-edge social networking, the old way.

Rutherford K.

Health Serv J. 2015 Dec 2;125(6470):19-21. No abstract available.


Psycho-social resilience, vulnerability and suicide prevention: impact evaluation of a mentoring approach to modify suicide risk for remote Indigenous Australian students at boarding school.

McCalman J, Bainbridge R, Russo S, Rutherford K, Tsey K, Wenitong M, Shakeshaft A, Doran C, Jacups S.

BMC Public Health. 2016 Feb 1;16:98. doi: 10.1186/s12889-016-2762-1.


Early experiences matter: a review of the effects of prenatal environment on offspring characteristics in poultry.

Dixon LM, Sparks NH, Rutherford KM.

Poult Sci. 2016 Mar;95(3):489-99. doi: 10.3382/ps/pev343. Epub 2015 Nov 27. Review.


Large-scale transcriptome sequencing reveals novel expression patterns for key sex-related genes in a sex-changing fish.

Liu H, Lamm MS, Rutherford K, Black MA, Godwin JR, Gemmell NJ.

Biol Sex Differ. 2015 Nov 25;6:26. doi: 10.1186/s13293-015-0044-8. eCollection 2015.


Review: Assessment of completeness of reporting in intervention studies using livestock: an example from pain mitigation interventions in neonatal piglets.

O'Connor A, Anthony R, Bergamasco L, Coetzee JF, Dzikamunhenga RS, Johnson AK, Karriker LA, Marchant-Forde JN, Martineau GP, Millman ST, Pajor EA, Rutherford K, Sprague M, Sutherland MA, von Borell E, Webb SR.

Animal. 2016 Apr;10(4):660-70. doi: 10.1017/S1751731115002323. Epub 2015 Nov 11. Review.


Why are most EU pigs tail docked? Economic and ethical analysis of four pig housing and management scenarios in the light of EU legislation and animal welfare outcomes.

D'Eath RB, Niemi JK, Vosough Ahmadi B, Rutherford KM, Ison SH, Turner SP, Anker HT, Jensen T, Busch ME, Jensen KK, Lawrence AB, Sandøe P.

Animal. 2016 Apr;10(4):687-99. doi: 10.1017/S1751731115002098. Epub 2015 Nov 2.


Geographic Variations in Prescription Opioid Dispensations and Deaths Among Women and Men in British Columbia, Canada.

Gladstone EJ, Smolina K, Weymann D, Rutherford K, Morgan SG.

Med Care. 2015 Nov;53(11):954-9. doi: 10.1097/MLR.0000000000000431.


Pain management in the neonatal piglet during routine management procedures. Part 2: grading the quality of evidence and the strength of recommendations.

O'Connor A, Anthony R, Bergamasco L, Coetzee J, Gould S, Johnson AK, Karriker LA, Marchant-Forde JN, Martineau GS, McKean J, Millman ST, Niekamp S, Pajor EA, Rutherford K, Sprague M, Sutherland M, von Borell E, Dzikamunhenga RS.

Anim Health Res Rev. 2014 Jun;15(1):39-62. doi: 10.1017/S1466252314000073. Review.


Molecular evolution of Dmrt1 accompanies change of sex-determining mechanisms in reptilia.

Janes DE, Organ CL, Stiglec R, O'Meally D, Sarre SD, Georges A, Graves JA, Valenzuela N, Literman RA, Rutherford K, Gemmell N, Iverson JB, Tamplin JW, Edwards SV, Ezaz T.

Biol Lett. 2014 Dec;10(12):20140809. doi: 10.1098/rsbl.2014.0809.


Attitudes of farmers and veterinarians towards pain and the use of pain relief in pigs.

Ison SH, Rutherford KM.

Vet J. 2014 Dec;202(3):622-7. doi: 10.1016/j.tvjl.2014.10.003. Epub 2014 Oct 8.


PomBase 2015: updates to the fission yeast database.

McDowall MD, Harris MA, Lock A, Rutherford K, Staines DM, Bähler J, Kersey PJ, Oliver SG, Wood V.

Nucleic Acids Res. 2015 Jan;43(Database issue):D656-61. doi: 10.1093/nar/gku1040. Epub 2014 Oct 31.


Endogenous avian leukosis viral loci in the Red Jungle Fowl genome assembly.

Benkel B, Rutherford K.

Poult Sci. 2014 Dec;93(12):2988-90. doi: 10.3382/ps.2014-04309. Epub 2014 Oct 11.


Biplanar superficial musculoaponeurotic system imbrication rhytidectomy.

Rousso DE, Rutherford KD.

Facial Plast Surg. 2014 Aug;30(4):380-93. doi: 10.1055/s-0034-1383556. Epub 2014 Jul 30.


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