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Large-scale analysis of micro-level citation patterns reveals nuanced selection criteria.

Poncela-Casasnovas J, Gerlach M, Aguirre N, Amaral LAN.

Nat Hum Behav. 2019 Jun;3(6):568-575. doi: 10.1038/s41562-019-0585-7. Epub 2019 Apr 15.


Single-Cell Transcriptomic Analysis of Human Lung Provides Insights into the Pathobiology of Pulmonary Fibrosis.

Reyfman PA, Walter JM, Joshi N, Anekalla KR, McQuattie-Pimentel AC, Chiu S, Fernandez R, Akbarpour M, Chen CI, Ren Z, Verma R, Abdala-Valencia H, Nam K, Chi M, Han S, Gonzalez-Gonzalez FJ, Soberanes S, Watanabe S, Williams KJN, Flozak AS, Nicholson TT, Morgan VK, Winter DR, Hinchcliff M, Hrusch CL, Guzy RD, Bonham CA, Sperling AI, Bag R, Hamanaka RB, Mutlu GM, Yeldandi AV, Marshall SA, Shilatifard A, Amaral LAN, Perlman H, Sznajder JI, Argento AC, Gillespie CT, Dematte J, Jain M, Singer BD, Ridge KM, Lam AP, Bharat A, Bhorade SM, Gottardi CJ, Budinger GRS, Misharin AV.

Am J Respir Crit Care Med. 2019 Jun 15;199(12):1517-1536. doi: 10.1164/rccm.201712-2410OC.


Reply to "Far away from the lamppost".

Stoeger T, Gerlach M, Morimoto RI, Amaral LAN.

PLoS Biol. 2018 Dec 11;16(12):e3000075. doi: 10.1371/journal.pbio.3000075. eCollection 2018 Dec.


Multidimensional Assessment of the Host Response in Mechanically Ventilated Patients with Suspected Pneumonia.

Walter JM, Ren Z, Yacoub T, Reyfman PA, Shah RD, Abdala-Valencia H, Nam K, Morgan VK, Anekalla KR, Joshi N, McQuattie-Pimentel AC, Chen CI, Chi M, Han S, Gonzalez-Gonzalez FJ, Soberanes S, Aillon RP, Watanabe S, Williams KJN, Lu Z, Paonessa J, Hountras P, Breganio M, Borkowski N, Donnelly HK, Allen JP, Amaral LA, Bharat A, Misharin AV, Bagheri N, Hauser AR, Budinger GRS, Wunderink RG.

Am J Respir Crit Care Med. 2019 May 15;199(10):1225-1237. doi: 10.1164/rccm.201804-0650OC.


Within-Gene Shine-Dalgarno Sequences Are Not Selected for Function.

Hockenberry AJ, Jewett MC, Amaral LAN, Wilke CO.

Mol Biol Evol. 2018 Oct 1;35(10):2487-2498. doi: 10.1093/molbev/msy150.


A novel framework for evaluating the performance of codon usage bias metrics.

Liu SS, Hockenberry AJ, Jewett MC, Amaral LAN.

J R Soc Interface. 2018 Jan;15(138). pii: 20170667. doi: 10.1098/rsif.2017.0667.


Diversity of translation initiation mechanisms across bacterial species is driven by environmental conditions and growth demands.

Hockenberry AJ, Stern AJ, Amaral LAN, Jewett MC.

Mol Biol Evol. 2017 Dec 6. doi: 10.1093/molbev/msx310. [Epub ahead of print]


Long-range correlations and fractal dynamics in C. elegans: Changes with aging and stress.

Alves LGA, Winter PB, Ferreira LN, Brielmann RM, Morimoto RI, Amaral LAN.

Phys Rev E. 2017 Aug;96(2-1):022417. doi: 10.1103/PhysRevE.96.022417. Epub 2017 Aug 29.


The Intersection of Aging Biology and the Pathobiology of Lung Diseases: A Joint NHLBI/NIA Workshop.

Budinger GRS, Kohanski RA, Gan W, Kobor MS, Amaral LA, Armanios M, Kelsey KT, Pardo A, Tuder R, Macian F, Chandel N, Vaughan D, Rojas M, Mora AL, Kovacs E, Duncan SR, Finkel T, Choi A, Eickelberg O, Chen D, Agusti A, Selman M, Balch WE, Busse P, Lin A, Morimoto R, Sznajder JI, Thannickal VJ.

J Gerontol A Biol Sci Med Sci. 2017 Oct 12;72(11):1492-1500. doi: 10.1093/gerona/glx090. Review.


Leveraging genome-wide datasets to quantify the functional role of the anti-Shine-Dalgarno sequence in regulating translation efficiency.

Hockenberry AJ, Pah AR, Jewett MC, Amaral LA.

Open Biol. 2017 Jan;7(1). pii: 160239. doi: 10.1098/rsob.160239.


NullSeq: A Tool for Generating Random Coding Sequences with Desired Amino Acid and GC Contents.

Liu SS, Hockenberry AJ, Lancichinetti A, Jewett MC, Amaral LA.

PLoS Comput Biol. 2016 Nov 11;12(11):e1005184. doi: 10.1371/journal.pcbi.1005184. eCollection 2016 Nov.


Differences in Collaboration Patterns across Discipline, Career Stage, and Gender.

Zeng XH, Duch J, Sales-Pardo M, Moreira JA, Radicchi F, Ribeiro HV, Woodruff TK, Amaral LA.

PLoS Biol. 2016 Nov 4;14(11):e1002573. doi: 10.1371/journal.pbio.1002573. eCollection 2016 Nov.


A network approach to discerning the identities of C. elegans in a free moving population.

Winter PB, Brielmann RM, Timkovich NP, Navarro HT, Teixeira-Castro A, Morimoto RI, Amaral LA.

Sci Rep. 2016 Oct 11;6:34859. doi: 10.1038/srep34859.


Depletion of Shine-Dalgarno Sequences Within Bacterial Coding Regions Is Expression Dependent.

Yang C, Hockenberry AJ, Jewett MC, Amaral LAN.

G3 (Bethesda). 2016 Nov 8;6(11):3467-3474. doi: 10.1534/g3.116.032227.


Antimicrobial Resistance and Virulence Factors of Escherichia coli in Cheese Made from Unpasteurized Milk in Three Cities in Brazil.

Ribeiro LF, Barbosa MM, Pinto Fde R, Maluta RP, Oliveira MC, de Souza V, de Medeiros MI, Borges LA, do Amaral LA, Fairbrother JM.

Foodborne Pathog Dis. 2016 Sep;13(9):469-76. doi: 10.1089/fpd.2015.2106. Epub 2016 Jun 3.


Detection of pathogenic Escherichia coli and microbiological quality of chilled shrimp sold in street markets.

Barbosa LJ, Ribeiro LF, Lavezzo LF, Barbosa MM, Rossi GA, do Amaral LA.

Lett Appl Microbiol. 2016 May;62(5):372-8. doi: 10.1111/lam.12562. Epub 2016 Mar 30.


Shiga toxigenic and enteropathogenic Escherichia coli in water and fish from pay-to-fish ponds.

Ribeiro LF, Barbosa MM, de Rezende Pinto F, Guariz CS, Maluta RP, Rossi JR, Rossi GA, Lemos MV, do Amaral LA.

Lett Appl Microbiol. 2016 Mar;62(3):216-20. doi: 10.1111/lam.12536.


Dynamics and heterogeneity of a fate determinant during transition towards cell differentiation.

Peláez N, Gavalda-Miralles A, Wang B, Navarro HT, Gudjonson H, Rebay I, Dinner AR, Katsaggelos AK, Amaral LA, Carthew RW.

Elife. 2015 Nov 19;4. pii: e08924. doi: 10.7554/eLife.08924.


The Distribution of the Asymptotic Number of Citations to Sets of Publications by a Researcher or from an Academic Department Are Consistent with a Discrete Lognormal Model.

Moreira JA, Zeng XH, Amaral LA.

PLoS One. 2015 Nov 16;10(11):e0143108. doi: 10.1371/journal.pone.0143108. eCollection 2015.


Prevention of lower-limb lesions and reduction of morbidity in diabetic patients.

do Amaral Júnior AH, do Amaral LA, Bastos MG, do Nascimento LC, Alves MJ, de Andrade MA.

Rev Bras Ortop. 2014 Jul 4;49(5):482-7. doi: 10.1016/j.rboe.2014.06.001. eCollection 2014 Sep-Oct.


Scaling and optimal synergy: Two principles determining microbial growth in complex media.

Massucci FA, Guimerà R, Amaral LA, Sales-Pardo M.

Phys Rev E Stat Nonlin Soft Matter Phys. 2015 Jun;91(6):062703. Epub 2015 Jun 8.


Cross-evaluation of metrics to estimate the significance of creative works.

Wasserman M, Zeng XH, Amaral LA.

Proc Natl Acad Sci U S A. 2015 Feb 3;112(5):1281-6. doi: 10.1073/pnas.1412198112. Epub 2015 Jan 20.


Impact of heterogeneity and socioeconomic factors on individual behavior in decentralized sharing ecosystems.

Gavaldà-Miralles A, Choffnes DR, Otto JS, Sánchez MA, Bustamante FE, Amaral LA, Duch J, Guimerà R.

Proc Natl Acad Sci U S A. 2014 Oct 28;111(43):15322-7. doi: 10.1073/pnas.1309389111. Epub 2014 Oct 6.


Quantifying position-dependent codon usage bias.

Hockenberry AJ, Sirer MI, Amaral LA, Jewett MC.

Mol Biol Evol. 2014 Jul;31(7):1880-93. doi: 10.1093/molbev/msu126. Epub 2014 Apr 7.


A solution to the challenge of optimization on ''golf-course''-like fitness landscapes.

Melo HP, Franks A, Moreira AA, Diermeier D, Andrade JS Jr, Amaral LA.

PLoS One. 2013 Nov 5;8(11):e78401. doi: 10.1371/journal.pone.0078401. eCollection 2013.


The impact of individual biases on consensus formation.

Sales-Pardo M, Diermeier D, Amaral LA.

PLoS One. 2013 May 28;8(5):e58989. doi: 10.1371/journal.pone.0058989. Print 2013.


Use of a global metabolic network to curate organismal metabolic networks.

Pah AR, Guimerà R, Mustoe AM, Amaral LA.

Sci Rep. 2013;3:1695. doi: 10.1038/srep01695.


Changes in task-related functional connectivity across multiple spatial scales are related to reading performance.

Wang JX, Bartolotti J, Amaral LA, Booth JR.

PLoS One. 2013;8(3):e59204. doi: 10.1371/journal.pone.0059204. Epub 2013 Mar 27.


Protegemed2: an extended platform based on RFID to identify EME and improve the detection of microshocks.

Rebonatto MT, Spalding LE, Hessel FP, Amaral LA.

Med Biol Eng Comput. 2013 Jun;51(6):719-27. doi: 10.1007/s11517-013-1041-x. Epub 2013 Feb 19.


Move-by-move dynamics of the advantage in chess matches reveals population-level learning of the game.

Ribeiro HV, Mendes RS, Lenzi EK, del Castillo-Mussot M, Amaral LA.

PLoS One. 2013;8(1):e54165. doi: 10.1371/journal.pone.0054165. Epub 2013 Jan 30.


Phenomenological model for predicting the catabolic potential of an arbitrary nutrient.

Seaver SM, Sales-Pardo M, Guimerà R, Amaral LA.

PLoS Comput Biol. 2012;8(11):e1002762. doi: 10.1371/journal.pcbi.1002762. Epub 2012 Nov 1.


Influence of chlorine added to drinking water during the preslaughter feed withdrawal on microbiology and morphology of the broiler gastrointestinal tract.

Barreiro FR, Baraldi-Artoni SM, Pinto FR, Barbosa MM, Barbosa JC, Amaral LA.

Poult Sci. 2012 Nov;91(11):2778-84. doi: 10.3382/ps.2012-02455.


Macro-level modeling of the response of C. elegans reproduction to chronic heat stress.

McMullen PD, Aprison EZ, Winter PB, Amaral LA, Morimoto RI, Ruvinsky I.

PLoS Comput Biol. 2012 Jan;8(1):e1002338. doi: 10.1371/journal.pcbi.1002338. Epub 2012 Jan 26.


Rationality, irrationality and escalating behavior in lowest unique bid auctions.

Radicchi F, Baronchelli A, Amaral LA.

PLoS One. 2012;7(1):e29910. doi: 10.1371/journal.pone.0029910. Epub 2012 Jan 18.


Duality between time series and networks.

Campanharo AS, Sirer MI, Malmgren RD, Ramos FM, Amaral LA.

PLoS One. 2011;6(8):e23378. doi: 10.1371/journal.pone.0023378. Epub 2011 Aug 11.


Prompting physicians to address a daily checklist and process of care and clinical outcomes: a single-site study.

Weiss CH, Moazed F, McEvoy CA, Singer BD, Szleifer I, Amaral LA, Kwasny M, Watts CM, Persell SD, Baker DW, Sznajder JI, Wunderink RG.

Am J Respir Crit Care Med. 2011 Sep 15;184(6):680-6. doi: 10.1164/rccm.201101-0037OC. Epub 2011 May 26.


The role of body mass in diet contiguity and food-web structure.

Stouffer DB, Rezende EL, Amaral LA.

J Anim Ecol. 2011 May;80(3):632-9. doi: 10.1111/j.1365-2656.2011.01812.x. Epub 2011 Mar 14.


Moving the science of quality improvement in critical care medicine forward.

Weiss CH, Amaral LA.

Am J Respir Crit Care Med. 2010 Dec 15;182(12):1461-2. doi: 10.1164/rccm.201009-1483ED. No abstract available.


Origin of compartmentalization in food webs.

Guimerà R, Stouffer DB, Sales-Pardo M, Leicht EA, Newman ME, Amaral LA.

Ecology. 2010 Oct;91(10):2941-51.


Education. Complex systems view of educational policy research.

Maroulis S, Guimerà R, Petry H, Stringer MJ, Gomez LM, Amaral LA, Wilensky U.

Science. 2010 Oct 1;330(6000):38-9. doi: 10.1126/science.1195153. No abstract available.


Physically grounded approach for estimating gene expression from microarray data.

McMullen PD, Morimoto RI, Amaral LA.

Proc Natl Acad Sci U S A. 2010 Aug 3;107(31):13690-5. doi: 10.1073/pnas.1000938107. Epub 2010 Jul 19.


Quantifying the performance of individual players in a team activity.

Duch J, Waitzman JS, Amaral LA.

PLoS One. 2010 Jun 16;5(6):e10937. doi: 10.1371/journal.pone.0010937.


Escherichia coli phylogenetic group determination and its application in the identification of the major animal source of fecal contamination.

Carlos C, Pires MM, Stoppe NC, Hachich EM, Sato MI, Gomes TA, Amaral LA, Ottoboni LM.

BMC Microbiol. 2010 Jun 1;10:161. doi: 10.1186/1471-2180-10-161.


Microcystin-LR in Brazilian aquaculture production systems.

Barros LS, de Souza FC, Tavares LH, Amaral LA.

Water Environ Res. 2010 Mar;82(3):240-8.


An outbreak of orthopoxvirus-associated disease in horses in southern Brazil.

Brum MC, Anjos BL, Nogueira CE, Amaral LA, Weiblen R, Flores EF.

J Vet Diagn Invest. 2010 Jan;22(1):143-7.


On universality in human correspondence activity.

Malmgren RD, Stouffer DB, Campanharo AS, Amaral LA.

Science. 2009 Sep 25;325(5948):1696-700. doi: 10.1126/science.1174562.


Micro-bias and macro-performance.

Seaver SM, Moreira AA, Sales-Pardo M, Malmgren RD, Diermeier D, Amaral LA.

Eur Phys J B. 2009 Feb 1;67(3):369-375.


Price dynamics in political prediction markets.

Majumder SR, Diermeier D, Rietz TA, Amaral LA.

Proc Natl Acad Sci U S A. 2009 Jan 20;106(3):679-84. doi: 10.1073/pnas.0805037106.


A Poissonian explanation for heavy tails in e-mail communication.

Malmgren RD, Stouffer DB, Motter AE, Amaral LA.

Proc Natl Acad Sci U S A. 2008 Nov 25;105(47):18153-8. doi: 10.1073/pnas.0800332105. Epub 2008 Nov 18.


Cascading failure and robustness in metabolic networks.

Smart AG, Amaral LA, Ottino JM.

Proc Natl Acad Sci U S A. 2008 Sep 9;105(36):13223-8. doi: 10.1073/pnas.0803571105. Epub 2008 Sep 2.

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