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Items: 1 to 50 of 53

1.

lncRNA-Induced Spread of Polycomb Controlled by Genome Architecture, RNA Abundance, and CpG Island DNA.

Schertzer MD, Braceros KCA, Starmer J, Cherney RE, Lee DM, Salazar G, Justice M, Bischoff SR, Cowley DO, Ariel P, Zylka MJ, Dowen JM, Magnuson T, Calabrese JM.

Mol Cell. 2019 Aug 8;75(3):523-537.e10. doi: 10.1016/j.molcel.2019.05.028. Epub 2019 Jun 27.

PMID:
31256989
2.

A 5' fragment of Xist can sequester RNA produced from adjacent genes on chromatin.

Lee DM, Trotman JB, Cherney RE, Inoue K, Schertzer MD, Bischoff SR, Cowley DO, Calabrese JM.

Nucleic Acids Res. 2019 Jul 26;47(13):7049-7062. doi: 10.1093/nar/gkz432.

3.

A piggyBac-based toolkit for inducible genome editing in mammalian cells.

Schertzer MD, Thulson E, Braceros KCA, Lee DM, Hinkle ER, Murphy RM, Kim SO, Vitucci ECM, Calabrese JM.

RNA. 2019 Aug;25(8):1047-1058. doi: 10.1261/rna.068932.118. Epub 2019 May 17.

PMID:
31101683
4.

Nonlinear sequence similarity between the Xist and Rsx long noncoding RNAs suggests shared functions of tandem repeat domains.

Sprague D, Waters SA, Kirk JM, Wang JR, Samollow PB, Waters PD, Calabrese JM.

RNA. 2019 Aug;25(8):1004-1019. doi: 10.1261/rna.069815.118. Epub 2019 May 16.

PMID:
31097619
5.

SWI/SNF remains localized to chromatin in the presence of SCHLAP1.

Raab JR, Smith KN, Spear CC, Manner CJ, Calabrese JM, Magnuson T.

Nat Genet. 2019 Jan;51(1):26-29. doi: 10.1038/s41588-018-0272-z. Epub 2018 Dec 3.

6.

Functional classification of long non-coding RNAs by k-mer content.

Kirk JM, Kim SO, Inoue K, Smola MJ, Lee DM, Schertzer MD, Wooten JS, Baker AR, Sprague D, Collins DW, Horning CR, Wang S, Chen Q, Weeks KM, Mucha PJ, Calabrese JM.

Nat Genet. 2018 Oct;50(10):1474-1482. doi: 10.1038/s41588-018-0207-8. Epub 2018 Sep 17.

7.

Male rutting calls synchronize reproduction in Serengeti wildebeest.

Calabrese JM, Moss Clay A, Estes RD, Thompson KV, Monfort SL.

Sci Rep. 2018 Jul 5;8(1):10202. doi: 10.1038/s41598-018-28307-y.

8.

Disentangling social interactions and environmental drivers in multi-individual wildlife tracking data.

Calabrese JM, Fleming CH, Fagan WF, Rimmler M, Kaczensky P, Bewick S, Leimgruber P, Mueller T.

Philos Trans R Soc Lond B Biol Sci. 2018 May 19;373(1746). pii: 20170007. doi: 10.1098/rstb.2017.0007.

9.

Correcting for missing and irregular data in home-range estimation.

Fleming CH, Sheldon D, Fagan WF, Leimgruber P, Mueller T, Nandintsetseg D, Noonan MJ, Olson KA, Setyawan E, Sianipar A, Calabrese JM.

Ecol Appl. 2018 Jun;28(4):1003-1010. doi: 10.1002/eap.1704. Epub 2018 Apr 26.

PMID:
29450936
10.

Moving in the Anthropocene: Global reductions in terrestrial mammalian movements.

Tucker MA, Böhning-Gaese K, Fagan WF, Fryxell JM, Van Moorter B, Alberts SC, Ali AH, Allen AM, Attias N, Avgar T, Bartlam-Brooks H, Bayarbaatar B, Belant JL, Bertassoni A, Beyer D, Bidner L, van Beest FM, Blake S, Blaum N, Bracis C, Brown D, de Bruyn PJN, Cagnacci F, Calabrese JM, Camilo-Alves C, Chamaillé-Jammes S, Chiaradia A, Davidson SC, Dennis T, DeStefano S, Diefenbach D, Douglas-Hamilton I, Fennessy J, Fichtel C, Fiedler W, Fischer C, Fischhoff I, Fleming CH, Ford AT, Fritz SA, Gehr B, Goheen JR, Gurarie E, Hebblewhite M, Heurich M, Hewison AJM, Hof C, Hurme E, Isbell LA, Janssen R, Jeltsch F, Kaczensky P, Kane A, Kappeler PM, Kauffman M, Kays R, Kimuyu D, Koch F, Kranstauber B, LaPoint S, Leimgruber P, Linnell JDC, López-López P, Markham AC, Mattisson J, Medici EP, Mellone U, Merrill E, de Miranda Mourão G, Morato RG, Morellet N, Morrison TA, Díaz-Muñoz SL, Mysterud A, Nandintsetseg D, Nathan R, Niamir A, Odden J, O'Hara RB, Oliveira-Santos LGR, Olson KA, Patterson BD, Cunha de Paula R, Pedrotti L, Reineking B, Rimmler M, Rogers TL, Rolandsen CM, Rosenberry CS, Rubenstein DI, Safi K, Saïd S, Sapir N, Sawyer H, Schmidt NM, Selva N, Sergiel A, Shiilegdamba E, Silva JP, Singh N, Solberg EJ, Spiegel O, Strand O, Sundaresan S, Ullmann W, Voigt U, Wall J, Wattles D, Wikelski M, Wilmers CC, Wilson JW, Wittemyer G, Zięba F, Zwijacz-Kozica T, Mueller T.

Science. 2018 Jan 26;359(6374):466-469. doi: 10.1126/science.aam9712.

PMID:
29371471
11.

A framework for modelling range shifts and migrations: asking when, whither, whether and will it return.

Gurarie E, Cagnacci F, Peters W, Fleming CH, Calabrese JM, Mueller T, Fagan WF.

J Anim Ecol. 2017 Jul;86(4):943-959. doi: 10.1111/1365-2656.12674. Epub 2017 May 25.

PMID:
28369891
12.

Online games: a novel approach to explore how partial information influences human random searches.

Martínez-García R, Calabrese JM, López C.

Sci Rep. 2017 Jan 6;7:40029. doi: 10.1038/srep40029.

13.

Space Use and Movement of a Neotropical Top Predator: The Endangered Jaguar.

Morato RG, Stabach JA, Fleming CH, Calabrese JM, De Paula RC, Ferraz KM, Kantek DL, Miyazaki SS, Pereira TD, Araujo GR, Paviolo A, De Angelo C, Di Bitetti MS, Cruz P, Lima F, Cullen L, Sana DA, Ramalho EE, Carvalho MM, Soares FH, Zimbres B, Silva MX, Moraes MD, Vogliotti A, May JA Jr, Haberfeld M, Rampim L, Sartorello L, Ribeiro MC, Leimgruber P.

PLoS One. 2016 Dec 28;11(12):e0168176. doi: 10.1371/journal.pone.0168176. eCollection 2016.

14.

Epidemiology of La Crosse Virus Emergence, Appalachia Region, United States.

Bewick S, Agusto F, Calabrese JM, Muturi EJ, Fagan WF.

Emerg Infect Dis. 2016 Nov;22(11):1921-1929. doi: 10.3201/eid2211.160308.

15.

Oral Health and Interprofessional Collaborative Practice: Examples of the Team Approach to Geriatric Care.

Kaufman LB, Henshaw MM, Brown BP, Calabrese JM.

Dent Clin North Am. 2016 Oct;60(4):879-90. doi: 10.1016/j.cden.2016.05.007. Epub 2016 Aug 6. Review.

PMID:
27671959
16.

SHAPE reveals transcript-wide interactions, complex structural domains, and protein interactions across the Xist lncRNA in living cells.

Smola MJ, Christy TW, Inoue K, Nicholson CO, Friedersdorf M, Keene JD, Lee DM, Calabrese JM, Weeks KM.

Proc Natl Acad Sci U S A. 2016 Sep 13;113(37):10322-7. doi: 10.1073/pnas.1600008113. Epub 2016 Aug 30.

17.

Uncovering periodic patterns of space use in animal tracking data with periodograms, including a new algorithm for the Lomb-Scargle periodogram and improved randomization tests.

Péron G, Fleming CH, de Paula RC, Calabrese JM.

Mov Ecol. 2016 Aug 1;4:19. doi: 10.1186/s40462-016-0084-7. eCollection 2016.

18.

Estimating where and how animals travel: an optimal framework for path reconstruction from autocorrelated tracking data.

Fleming CH, Fagan WF, Mueller T, Olson KA, Leimgruber P, Calabrese JM.

Ecology. 2016 Mar;97(3):576-82.

PMID:
27197385
19.

Detection of RNA-Protein Interactions in Living Cells with SHAPE.

Smola MJ, Calabrese JM, Weeks KM.

Biochemistry. 2015 Nov 24;54(46):6867-75. doi: 10.1021/acs.biochem.5b00977. Epub 2015 Nov 11.

20.

Rigorous home range estimation with movement data: a new autocorrelated kernel density estimator.

Fleming CH, Fagan WF, Mueller T, Olson KA, Leimgruber P, Calabrese JM.

Ecology. 2015 May;96(5):1182-8.

PMID:
26236833
21.

Maximum-entropy description of animal movement.

Fleming CH, Subaşı Y, Calabrese JM.

Phys Rev E Stat Nonlin Soft Matter Phys. 2015 Mar;91(3):032107. Epub 2015 Mar 4.

PMID:
25871054
22.

How far to go? Determinants of migration distance in land mammals.

Teitelbaum CS, Fagan WF, Fleming CH, Dressler G, Calabrese JM, Leimgruber P, Mueller T.

Ecol Lett. 2015 Jun;18(6):545-52. doi: 10.1111/ele.12435. Epub 2015 Apr 12.

PMID:
25865946
23.

Systematic discovery of Xist RNA binding proteins.

Chu C, Zhang QC, da Rocha ST, Flynn RA, Bharadwaj M, Calabrese JM, Magnuson T, Heard E, Chang HY.

Cell. 2015 Apr 9;161(2):404-16. doi: 10.1016/j.cell.2015.03.025. Epub 2015 Apr 2.

24.

A survey of imprinted gene expression in mouse trophoblast stem cells.

Calabrese JM, Starmer J, Schertzer MD, Yee D, Magnuson T.

G3 (Bethesda). 2015 Feb 23;5(5):751-9. doi: 10.1534/g3.114.016238.

25.

Minimal mechanisms for vegetation patterns in semiarid regions.

Martínez-García R, Calabrese JM, Hernández-García E, López C.

Philos Trans A Math Phys Eng Sci. 2014 Oct 28;372(2027). pii: 20140068. doi: 10.1098/rsta.2014.0068.

26.

Small RNA expression from the human macrosatellite DXZ4.

Pohlers M, Calabrese JM, Magnuson T.

G3 (Bethesda). 2014 Aug 21;4(10):1981-9. doi: 10.1534/g3.114.012260.

27.

From fine-scale foraging to home ranges: a semivariance approach to identifying movement modes across spatiotemporal scales.

Fleming CH, Calabrese JM, Mueller T, Olson KA, Leimgruber P, Fagan WF.

Am Nat. 2014 May;183(5):E154-67. doi: 10.1086/675504. Epub 2014 Mar 17.

PMID:
24739204
28.

Optimal search in interacting populations: Gaussian jumps versus Lévy flights.

Martínez-García R, Calabrese JM, López C.

Phys Rev E Stat Nonlin Soft Matter Phys. 2014 Mar;89(3):032718. Epub 2014 Mar 26.

PMID:
24730885
29.

Conserving the world's finest grassland amidst ambitious national development.

Batsaikhan N, Buuveibaatar B, Chimed B, Enkhtuya O, Galbrakh D, Ganbaatar O, Lkhagvasuren B, Nandintsetseg D, Berger J, Calabrese JM, Edwards AE, Fagan WF, Fuller TK, Heiner M, Ito TY, Kaczensky P, Leimgruber P, Lushchekina A, Milner-Gulland EJ, Mueller T, Murray MG, Olson KA, Reading R, Schaller GB, Stubbe A, Stubbe M, Walzer C, Von Wehrden H, Whitten T.

Conserv Biol. 2014 Dec;28(6):1736-9. doi: 10.1111/cobi.12297. Epub 2014 Apr 8. No abstract available.

PMID:
24712745
30.

Evidence for local regulatory control of escape from imprinted X chromosome inactivation.

Mugford JW, Starmer J, Williams RL Jr, Calabrese JM, Mieczkowski P, Yee D, Magnuson T.

Genetics. 2014 Jun;197(2):715-23. doi: 10.1534/genetics.114.162800. Epub 2014 Mar 19.

31.

fourSig: a method for determining chromosomal interactions in 4C-Seq data.

Williams RL Jr, Starmer J, Mugford JW, Calabrese JM, Mieczkowski P, Yee D, Magnuson T.

Nucleic Acids Res. 2014 Apr;42(8):e68. doi: 10.1093/nar/gku156. Epub 2014 Feb 20.

32.

Topoisomerases facilitate transcription of long genes linked to autism.

King IF, Yandava CN, Mabb AM, Hsiao JS, Huang HS, Pearson BL, Calabrese JM, Starmer J, Parker JS, Magnuson T, Chamberlain SJ, Philpot BD, Zylka MJ.

Nature. 2013 Sep 5;501(7465):58-62. doi: 10.1038/nature12504. Epub 2013 Aug 28.

33.

Optimizing the search for resources by sharing information: Mongolian gazelles as a case study.

Martínez-García R, Calabrese JM, Mueller T, Olson KA, López C.

Phys Rev Lett. 2013 Jun 14;110(24):248106. Epub 2013 Jun 14.

PMID:
25165967
34.

Spatial patterns in mesic savannas: the local facilitation limit and the role of demographic stochasticity.

Martínez-García R, Calabrese JM, López C.

J Theor Biol. 2013 Sep 21;333:156-65. doi: 10.1016/j.jtbi.2013.05.024. Epub 2013 Jun 7.

PMID:
23747988
35.

Differentiation-driven nucleolar association of the mouse imprinted Kcnq1 locus.

Fedoriw AM, Calabrese JM, Mu W, Yee D, Magnuson T.

G3 (Bethesda). 2012 Dec;2(12):1521-8. doi: 10.1534/g3.112.004226. Epub 2012 Dec 1.

36.

Site-specific silencing of regulatory elements as a mechanism of X inactivation.

Calabrese JM, Sun W, Song L, Mugford JW, Williams L, Yee D, Starmer J, Mieczkowski P, Crawford GE, Magnuson T.

Cell. 2012 Nov 21;151(5):951-63. doi: 10.1016/j.cell.2012.10.037.

37.

The mouse DXZ4 homolog retains Ctcf binding and proximity to Pls3 despite substantial organizational differences compared to the primate macrosatellite.

Horakova AH, Calabrese JM, McLaughlin CR, Tremblay DC, Magnuson T, Chadwick BP.

Genome Biol. 2012 Aug 20;13(8):R70. doi: 10.1186/gb-2012-13-8-r70.

38.

Partitioning the aggregation of parasites on hosts into intrinsic and extrinsic components via an extended Poisson-gamma mixture model.

Calabrese JM, Brunner JL, Ostfeld RS.

PLoS One. 2011;6(12):e29215. doi: 10.1371/journal.pone.0029215. Epub 2011 Dec 22.

39.

Statistical inference for stochastic simulation models--theory and application.

Hartig F, Calabrese JM, Reineking B, Wiegand T, Huth A.

Ecol Lett. 2011 Aug;14(8):816-27. doi: 10.1111/j.1461-0248.2011.01640.x. Epub 2011 Jun 17. Review.

PMID:
21679289
40.

A latent pro-survival function for the mir-290-295 cluster in mouse embryonic stem cells.

Zheng GX, Ravi A, Calabrese JM, Medeiros LA, Kirak O, Dennis LM, Jaenisch R, Burge CB, Sharp PA.

PLoS Genet. 2011 May;7(5):e1002054. doi: 10.1371/journal.pgen.1002054. Epub 2011 May 5.

41.

Dynamical phase coexistence: a simple solution to the "savanna problem".

Vazquez F, López C, Calabrese JM, Muñoz MA.

J Theor Biol. 2010 May 21;264(2):360-6. doi: 10.1016/j.jtbi.2010.02.011. Epub 2010 Feb 11.

PMID:
20153337
42.

The independent and interactive effects of tree-tree establishment competition and fire on savanna structure and dynamics.

Calabrese JM, Vazquez F, López C, San Miguel M, Grimm V.

Am Nat. 2010 Mar;175(3):E44-65. doi: 10.1086/650368.

PMID:
20100108
43.

Reproductive asynchrony in spatial population models: how mating behavior can modulate allee effects arising from isolation in both space and time.

Fagan WF, Cosner C, Larsen EA, Calabrese JM.

Am Nat. 2010 Mar;175(3):362-73. doi: 10.1086/650373.

PMID:
20100104
44.

A comprehensive geriatric dental model in a long-term care facility.

Calabrese JM.

J Mass Dent Soc. 2008 Fall;57(3):28-30. No abstract available.

PMID:
19146113
45.

Divergent transcription from active promoters.

Seila AC, Calabrese JM, Levine SS, Yeo GW, Rahl PB, Flynn RA, Young RA, Sharp PA.

Science. 2008 Dec 19;322(5909):1849-51. doi: 10.1126/science.1162253. Epub 2008 Dec 4.

46.

Connecting microRNA genes to the core transcriptional regulatory circuitry of embryonic stem cells.

Marson A, Levine SS, Cole MF, Frampton GM, Brambrink T, Johnstone S, Guenther MG, Johnston WK, Wernig M, Newman J, Calabrese JM, Dennis LM, Volkert TL, Gupta S, Love J, Hannett N, Sharp PA, Bartel DP, Jaenisch R, Young RA.

Cell. 2008 Aug 8;134(3):521-33. doi: 10.1016/j.cell.2008.07.020.

47.

Reproductive asynchrony in natural butterfly populations and its consequences for female matelessness.

Calabrese JM, Ries L, Matter SF, Debinski DM, Auckland JN, Roland J, Fagan WF.

J Anim Ecol. 2008 Jul;77(4):746-56. doi: 10.1111/j.1365-2656.2008.01385.x. Epub 2008 May 9.

PMID:
18479341
48.

RNA sequence analysis defines Dicer's role in mouse embryonic stem cells.

Calabrese JM, Seila AC, Yeo GW, Sharp PA.

Proc Natl Acad Sci U S A. 2007 Nov 13;104(46):18097-102. Epub 2007 Nov 7. Erratum in: Proc Natl Acad Sci U S A. 2007 Dec 26;104(52):21021.

49.
50.

Quantitative analysis of Argonaute protein reveals microRNA-dependent localization to stress granules.

Leung AK, Calabrese JM, Sharp PA.

Proc Natl Acad Sci U S A. 2006 Nov 28;103(48):18125-30. Epub 2006 Nov 20.

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