Publications - Amaral Lab

Aging is associated with a systemic length-associated transcriptome imbalance

Thomas Stoeger, Rogan A. Grant, Alexandra C. McQuattie-Pimentel, Kishore R. Anekalla, Sophia S. Liu, Heliodoro Tejedor-Navarro, Benjamin D. Singer, Hiam Abdala-Valencia, Michael Schwake, Marie-Pier Tetreault, Harris Perlman, William E. Balch, Navdeep S. Chandel, Karen M. Ridge, Jacob I. Sznajder, Richard I. Morimoto, Alexander V. Misharin, G. R. Scott Budinger & Luis A. Nunes Amaral

Nature Aging, https://doi.org/10.1 (2022)

Forecasting the evolution of fast-changing transportation networks using machine learning

Weihua Lei, Luiz G. A. Alves, Luís A. Nunes Amaral

Nature Communications , 4252 (2022)

Spreader events and the limitations of projected networks for capturing dynamics on multi-partite networks

Lee HA, Alves LGA, Amaral LAN

Physical Review E 103, 022320 (2021)

Meta-Research: COVID-19 research risks ignoring important host genes due to pre-established research patterns

Stoeger T, Amaral LAN

eLife 9, e61981 (2020)

Conformational stability of the bacterial adhesin, FimH, with an inactivating mutation

Liu J, Amaral LAN, Keten S

Proteins 89, 276-288 (2020)

How to build a more open justice system

Pah AR, Schwartz DL, Sanga S, Clopton ZD, DiCola P, Davis Mersey R, Alexander CS, Hammond KJ, Amaral LAN

Science 369, 134-136 (2020)

Long-term patterns of gender imbalance in an industry without ability or level of interest differences

Amaral LAN, Moreira JAG, Dunand ML, Tejedor Navarro H, Lee HA

PLOS One, 0229662 (2020)

Fly-QMA: Automated analysis of mosaic imaginal discs in Drosophila

Bernasek SM, Peláez N, Carthew RW, Bagheri N, Amaral LAN

PLOS Computational Biology, 1007406 (2020)

Centrality anomalies in complex networks as a result of model over-simplification

Alves LGA, Aleta A, Rodrigues FA, Moreno Y, Amaral LAN,

New Journal of Physics 23, 013043 (2020)

A universal information theoretic approach to the identification of stopwords

Gerlach M, Shi H, Amaral LAN

Nature Machine Intelligence 1, 606-612 (2019)

A quantitative approach for the analysis of clinician recognition of acute respiratory distress syndrome using electronic health record data

Bechel MA, Pah RA, Shi H, Mehrotra S, Persell SD, Weiner S, Wunderink RG, Amaral LAN, Weiss CH

PLOS One 14, e0222826 (2019)

Times cited: 1

Reply to: Four personality types may be neither robust nor exhaustive

Gerlach M, Revelle W. Amaral LAN

Nature Human Behaviour 3, 1047-1048 (2019)

Repressive gene regulation synchronizes development with cellular metabolism

Cassidy JJ, Bernasek SM, Bakker R, Giri R, Pelaez N, Eder B, Bobrowska A, Bagheri N, Amaral LAN, Carthew RW

Cell 178, 980-992 (2019)

A new evaluation framework for topic modeling algorithms based on synthetic corpora

Shi H, Gerlach M, Diersen I, Downey D, Amaral LAN

Proceedings of the 22nd International Conference on Artificial Intelligence and Statistics (AISTATS 2019) 89, 816-826 (2019)

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

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

Nature Human Behaviour 3, 568-575 (2019)

Reply to "Far away from the lamppost"

Stoeger T, Gerlach M, Morimoto RI, Amaral LAN

PLOS Biology 16, e3000075 (2018)

Large-scale investigation of the reasons why potentially important genes are ignored

Stoeger T, Gerlach M, Morimoto RI, Amaral LAN

PLOS Biology 16, e2006643 (2018)

A robust data-driven approach identifies four personality types across four large data sets

Gerlach M, Farb B, Revelle W, Amaral LAN

Nature Human Behaviour 2, 735-742 (2018)

Within-gene Shine–Dalgarno sequences are not selected for function

Hockenberry AJ, Jewett MC, Amaral LAN, Wilke CO

Molecular Biology and Evolution 35, 2487-2498 (2018)

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

Liu SS, Hockenberry HJ, Jewett MC, Amaral LAN

Journal of the Royal Society Interface 15, 0170667 (2018)

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

Hockenberry AJ, Stern AJ, Amaral LAN, Jewett MC

Molecular Biology and Evolution 35, 582-592 (2017)

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

Physical Review E 96, 022417 (2017)

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 LAN

Open Biology 7, 160239 (2017)

Economic insecurity and the rise in gun violence at US schools

Pah AR, Hagan J, Jennings AL, Jain A, Albrecht K, Hockenberry AJ, Amaral LAN

Nature Human Behavior 1, 0040 (2017)

NullSeq: A tool for generating random coding sequences with desired amino acid and GC contents

Liu SS, Hockenberry AJ, Lancichinetti A, Jewett MC, Amaral LAN

PLOS Computational Biology 12, 1005184 (2016)

Differences in collaboration patterns across discipline, career stage, and gender

Zeng XHT, Duch J, Sales-Pardo M, Moreira JAG, Radicchi F, Ribeiro HV, Woodruff TK, Amaral LAN

PLOS Biology 14, 1002573 (2016)

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

Winter PB, Brielmann RB, Timkovich NP, Navarro HT, Teixeira-Castro A, Morimoto RI, Amaral LAN

Scientific Reports 6, 34859 (2016)

Depletion of Shine-Dalgarno sequences within bacterial coding regions Is expression dependent

Yang C, Hockenberry AJ, Jewett MC, Amaral LAN

G3 : Genes | Genomes | Genetics 6, 3467-3474 (2016)

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

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

eLife 4, e08924 (2015)

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 JAG, Zeng XHT, Amaral LAN

PLoS ONE 10, e0143108 (2015)

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

Massucci FA, Guimera R, Amaral LAN, Sales-Pardo M

Physical Review E 91, 062703 (2015)

Correlations between user voting data, budget, and box office for films in the Internet Movie Database

Wasserman M, Mukherjee S, Scott K, Zeng XHT, Radicchi F, Amaral LAN

Journal of the Association for Information Science and Technology 66(4), 858-868 (2015)

The currents beneath the "rising tide" of school choice: An analysis of student enrollment flows in the Chicago Public Schools

Sirer MI, Maroulis S, Guimerà R, Wilensky U, Amaral LAN

Journal of Policy Analysis and Management, 34, 358-377 (2015)

High-reproducibility and high-accuracy method for automated topic classification

Lancichinetti A, Sirer MI, Wang JX, Acuna D, Körding K, Amaral LAN

Physical Review X 5, 011007 (2015)

Social embeddedness in an online weight management programme is linked to greater weight loss

Poncela-Casasnovas J, Spring B, McClary D, Moller AC, Mukogo R, Pellegrini CA, Coons MJ, Davidson M, Mukherjee S, Amaral LAN

Journal of the Royal Society Interface 12, 20140686 (2015)

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

Wasserman M, Zeng XHT, Amaral LAN

Proc. Natl. Acad. Sci. U. S. A. 112(5), 1281-1286 (2015)

User Behavior and Change: File-sharers and Copyright Laws

Gavaldà-Miralles A, Otto JS, Bustamante FE, Amaral LAN, Duch J, Guimerà R

Proceedings of the 10th ACM CoNEXT 2014, 319-324 (2014)

Adoption of a high-impact innovation in a homogeneous population

Weiss CH, Poncela-Casasnovas J, Glaser JI, Pah AR, Persell SD, Baker DW, Wunderink RG, Amaral LAN

Physical Review X 4, 041008 (2014)

Times cited: 2

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 LAN, Duch J, Guimerà R

Proc. Natl. Acad. Sci. U. S. A. 111, 15322-15327 (2014)

Quantifying position-dependent codon usage bias

Hockenberry AJ, Sirer MI, Amaral LAN, Jewett MC

Molecular Biology and Evolution 31(7), 1880-1893 (2014)

Times cited: 2

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

Melo HPM, Franks A, Moreira AA, Diermeier D Andrade Jr JS, Amaral LAN

PLOS ONE 8, e78401 (2013)

Envisioning sophisticated electronic health records through the lens of health care reform

Weiss CH, Amaral LAN

Am. J. of Respirat. and Crit. Care Med. 188, 636-638 (2013)

Times cited: 1

The impact of individual biases on consensus formation

Sales-Pardo M, Diermeier D, Amaral LAN

PLOS ONE 8, e58989 (2013)

Times cited: 1

Use of a global metabolic network to predict organismal metabolic networks

Pah AR, Guimera R, Mustoe AM, Amaral LAN

Scientific Reports 3, 1695 (2013)

Times cited: 1

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

Wang JX, Bartolotti J, Amaral LAN, Booth JR

PLOS ONE 8, e59204 (2013)

Times cited: 4

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 LAN

PLOS ONE 8, e54165 (2013)

Times cited: 4

The possible role of resource requirements and academic career-choice risk on gender differences in publication rate and impact

Duch J, Zeng XHT, Sales-Pardo M, Radicchi F, Otis S, Woodruff TK, Amaral LAN

PLOS ONE 7, e51332 (2012)

Times cited: 20

Phenomenological model for predicting the catabolic potential of an arbitrary nutrient

Seaver SMD, Sales-Pardo M, Guimerà R, Amaral LAN

PLOS Computational Biology 8, e1002762 (2012)

Times cited: 1

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

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

PLoS Computational Biology 8, e1002338 (2012)

Times cited: 9

Rationality, irrationality and escalating behavior in lowest unique bid auctions

Radicchi F, Baronchelli A, Amaral LAN

PLoS ONE 7, e29910 (2012)

Times cited: 13

Duality between time series and networks

Campanharo ASLO, Sirer MI, Malmgren RD, Ramos FM, Amaral LAN

PLoS ONE 6, e23378 (2011)

Times cited: 36

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 LAN, Kwasny M, Watts CM, Persell SD, Baker DW, Sznajder JI, Wunderink RG

American Journal of Respiratory and Critical Care Medicine 184, 680-686 (2011)

Times cited: 58

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

Stouffer DB, Rezende EL, Amaral LAN

Journal of Animal Ecology 80, 632-639 (2011)

Times cited: 21

Origin of compartmentalization in food webs

Guimera R, Stouffer DB, Sales-Pardo M, Leicht EA, Newman MEJ, Amaral LAN

Ecology 91, 2941-2951 (2010)

Times cited: 43

Complex systems view of educational policy research

Maroulis S, Guimera R, Petry H, Stringer MJ, Gomez LM, Amaral LAN, Wilensky U

Science 330, 38-39 (2010)

Times cited: 25

Physically grounded approach for estimating gene expression from microarray data

McMullen PD, Morimoto RI, Amaral, LAN

Proc. Natl. Acad. Sci. U. S. A. 107, 13690-13695 (2010)

Times cited: 6

Quantifying the performance of individual players in a team activity

Duch J, Waitzman JS, Amaral LAN

PLoS ONE 5, e10937 (2010)

Times cited: 46

The role of mentorship in protégé performance

Malmgren RD, Ottino JM, Amaral LAN

Nature 463, 622-626 (2010)

Times cited: 22

Poissonian bursts in e-mail correspondence

Anteneodo C, Malmgren RD, Chialvo DR

European Physical Journal B 75, 389-394 (2010)

Times cited: 14

Statistical validation of a global model for the distribution of the ultimate number of citations accrued by papers published in a scientific journal

Stringer MJ, Sales-Pardo M, Amaral LAN

Journal of the American Society for Information Science and Technology 61, 1377-1385 (2010)

Times cited: 31

Strange bedfellows: Community identification in BitTorrent

Choffnes D Duch J, Malmgren RD, Guimera R, Bustamante F, Amaral LAN

Proceedings of the 9th ACM IPTPS International Conference on Peer-to-Peer Systems, 13 (2010)

Missing and spurious interactions and the reconstruction of complex networks

Guimera R, Sales-Pardo M

Proc. Natl. Acad. Sci. U. S. A. 106, 22073-22078 (2009)

Times cited: 129

Comparison of methods for the detection of node group membership in bipartite networks

Sawardecker EN, Amundsen CA, Sales-Pardo M, Amaral LAN

European Physical Journal B 72, 671-677 (2009)

Times cited: 6

On Universality in Human Correspondence Activity

Malmgren RD, Stouffer DB, Campanharo ASLO, Amaral LAN

Science 325, 1696-1700 (2009)

Times cited: 92

Characterizing individual communication patterns

Malmgren RD, Hofman JM, Amaral LAN, Watts DJ

Proceedings of the 15th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, 607-616 (2009)

Times cited: 22

Levels of complexity in scale-invariant neural signals

Ivanov PC, Ma QDY, Bartsch RP, Hausdorff JM, Amaral LAN, Schulte-Frohlinde V, Stanley HE, Yoneyama M

Physical Review E 79, 041920 (2009)

Times cited: 34

Detection of node group membership in networks with group overlap

Sawardecker EN, Sales-Pardo M, Amaral LAN

European Physical Journal B 67, 277-284 (2009)

Times cited: 25

Micro-bias and macro-performance

Seaver SMD, Moreira AA, Sales-Pardo M, Malmgren RD, Diermeier D, Amaral LAN

European Physical Journal B 67, 369-375 (2009)

Times cited: 3

Price dynamics in political prediction markets

Majumder SR, Diermeier D, Rietz TA, Amaral LAN

Proc. Natl. Acad. Sci. U. S. A. 106, 679-684 (2009)

Times cited: 8

Ecological Engineering and Sustainabitity: A New Opportunity for Chemical Engineering

Stouffer DB, Ng CA, Amaral LAN

AICHE Journal 54, 3040-3047 (2008)

Times cited: 5

A Poissonian explanation for heavy tails in e-mail communication

Malmgren RD, Stouffer DB, Motter AE, Amaral LAN

Proc. Natl. Acad. Sci. U. S. A. 105, 18153-18158 (2008)

Times cited: 156

Chemical amplification in an invaded food web: Seasonality and ontogeny in a high-biomass, low-diversity ecosystem

Ng CA, Berg MB, Jude DJ, Janssen J, Charlebois PM, Amaral LAN, Gray KA

Environmental Toxicology and Chemistry 27, 2186-2195 (2008)

Times cited: 14

Cascading failure and robustness in metabolic networks

Smart AG, Amaral LAN, Ottino JM

Proc. Natl. Acad. Sci. U. S. A. 105, 13223-13228 (2008)

Times cited: 35

A truer measure of our ignorance

Amaral LAN

Proc. Natl. Acad. Sci. U. S. A. 105, 6795-6796 (2008)

Times cited: 15

Effectiveness of journal ranking schemes as a tool for locating information

Stringer MJ, Sales-Pardo M, Amaral LAN

PLoS ONE 3(2), e1683 (2008)

Times cited: 58

From Clean Dishes to Clean Hands Novel Perspectives in the Fight Against Infections

Kho, A, Sales-Pardo, M, Wilson, J

IEEE Eng. Med. Biol. Mag. 27, 26-28 (2008)

Times cited: 1

Evolution of protein families: Is it possible to distinguish between domains of life?

Sales-Pardo M, Chan AOB, Amaral LAN, Guimera R

Gene 402, 81-93 (2007)

Times cited: 2

Extracting the hierarchical organization of complex systems

Sales-Pardo M, Guimera R, Moreira AA, Amaral LAN

Proc. Natl. Acad. Sci. U. S. A. 104, 15224-15229 (2007)

Times cited: 221

Module identification in bipartite and directed networks

Guimera R, Sales-Pardo M, Amaral LAN

Physical Review E 76, 036102 (2007)

Times cited: 155

Evidence for the existence of a robust pattern of prey selection in food webs

Stouffer DB, Camacho J, Jiang W, Amaral LAN

Proc. R. Soc. B-Biol. Sci. 274, 1931-1940 (2007)

Times cited: 68

Complex systems - A new paradigm for the integrative study of management, physical, and technological systems

Amaral LAN, Uzzi B

Management Science 53, 1033-1035 (2007)

Times cited: 46

A network-based method for target selection in metabolic networks

Guimera R, Sales-Pardo M, Amaral LAN

Bioinformatics 23, 1616-1622 (2007)

Times cited: 35

Quantitative analysis of the local structure of food webs

Camacho J, Stouffer DB, Amaral LAN

Journal of Theoretical Biology 246, 260-268 (2007)

Times cited: 22

Driving on cellular pathway 66

Amaral LAN

AIP Conf. Proc. 922, 641-646 (2007)

Complex fluctuations and robustness in stylized signalling networks

Diaz-Guilera A, Moreira AA, Guzman L, Amaral LAN

Journal of Statistical Mechanics - Theory and Experiment, P01013 (2007)

Times cited: 1

Classes of complex networks defined by role-to-role connectivity profiles

Guimera R, Sales-Pardo M, Amaral LAN

Nature Physics 3, 63-69 (2007)

Times cited: 150

A robust measure of food web intervality

Stouffer DB, Camacho J, Amaral LAN

Proc. Natl. Acad. Sci. U. S. A. 103, 19015-19020 (2006)

Times cited: 68

Lies, damned lies and statistics

Amaral LAN, Guimera R

Nature Physics 2, 75-76 (2006)

Times cited: 14

Novel collaborations within experienced teams lead to best research outcomes

Amaral LAN

Annals of Vascular Surgery 19, 753-754 (2005)

Times cited: 1

Scaling phenomena in the growth dynamics of scientific output

Matia K, Amaral LAN, Luwel M, Moed HF, Stanley HE

Journal of the American Society for Information Science and Technology 56, 893-902 (2005)

Times cited: 19

Canalizing Kauffman networks: Nonergodicity and its effect on their critical behavior

Moreira AA, Amaral LAN

Physical Review Letters 94, 218702 (2005)

Times cited: 38

The worldwide air transportation network: Anomalous centrality, community structure, and cities' global roles

Guimera R, Mossa S, Turtschi A, Amaral LAN

Proc. Natl. Acad. Sci. U. S. A. 102, 7794-7799 (2005)

Times cited: 574

Mesoscopic modeling for nucleic acid chain dynamics

Sales-Pardo M, Guimera R, Moreira AA, Widom J, Amaral LAN

Physical Review E 71, 051902 (2005)

Times cited: 103

Quantitative patterns in the structure of model and empirical food webs

Stouffer DB, Camacho J, Guimera R, Ng CA, Amaral LAN

Ecology 86, 1301-1311 (2005)

Times cited: 99

Team assembly mechanisms determine collaboration network structure and team performance

Guimera R, Uzzi B, Spiro J, Amaral LAN

Science 308, 697-702 (2005)

Times cited: 316

Functional cartography of complex metabolic networks

Guimera R, Amaral LAN

Nature 433, 895-900 (2005)

Times cited: 1172

Cartography of complex networks: modules and universal roles

Guimera R, Amaral LAN

Journal of Statistical Mechanics - Theory and Experiment, P02001 (2005)

Times cited: 133

Emergence of complex dynamics in a simple model of signaling networks

Amaral LAN, Diaz-Guilera A, Moreira AA, Goldberger AL, Lipsitz LA

Proc. Natl. Acad. Sci. U. S. A. 101, 15551-15555 (2004)

Times cited: 66

Efficient system-wide coordination in noisy environments

Moreira AA, Mathur A, Diermeier D, Amaral LAN

Proc. Natl. Acad. Sci. U. S. A. 101, 12085-12090 (2004)

Times cited: 38

Modularity from fluctuations in random graphs and complex networks

Guimera R, Sales-Pardo M, Amaral LAN

Physical Review E 70, 025101 (2004)

Times cited: 330

Power law temporal auto-correlations in day-long records of human physical activity and their alteration with disease

Amaral LAN, Soares DJB, da Silva LR, Lucena LS, Saito M, Kumano H, Aoyagi N, Yamamoto Y

Europhysics Letters 66, 448-454 (2004)

Times cited: 7

Complex networks - Augmenting the framework for the study of complex systems

Amaral LAN, Ottino JM

European Physical Journal B 38, 147-162 (2004)

Times cited: 205

Modeling the world-wide airport network

Guimera R, Amaral LAN

European Physical Journal B 38, 381-385 (2004)

Times cited: 200

Heuristic segmentation of a nonstationary time series

Fukuda K, Stanley HE, Amaral LAN

Physical Review E 69, 021108 (2004)

Times cited: 30

Complex systems and networks: challenges and opportunities for chemical and biological engineers

Amaral LAN, Ottino JM

Chemical Engineering and Science 59, 1653-1666 (2004)

Times cited: 33

Decreased fractal correlation in diurnal physical activity in chronic fatigue syndrome

Ohashi K, Bleijenberg G, van der Werf S, Prins J, Amaral LAN, Natelson BH, Yamamoto Y

Methods of Information in Medicine 43, 26-29 (2004)

Times cited: 13

Asymmetrical singularities in real-world signals

Ohashi K, Amaral LAN, Natelson BH, Yamamoto Y

Physical Review E 68, 065204 (2003)

Times cited: 33

Sexual contacts and epidemic thresholds - Reply

Liljeros F, Edling CR, Stanley HE, Aberg Y, Amaral LAN

Nature 423, 606-606 (2003)

Times cited: 8

Fukuda K, Amaral LAN, Stanley HE

Europhysics Letters 62, 189-195 (2003)

Times cited: 24

Sexual networks: implications for the transmission of sexually transmitted infections

Liljeros F, Edling CR, Amaral LAN

Microbes and Infections 5, 189-196 (2003)

Times cited: 133

Dynamics of temporal correlation in daily Internet traffic

Fukuda K, Amaral LAN, Stanley HE

IEEE 2003 Global Communications Conference (GlobeComm 2003), 4069-4073 (2003)

Times cited: 4

Extremum statistics in scale-free network models

Moreira AA, Andrade JS, Amaral LAN

Physical Review Letters 89, 268703 (2002)

Times cited: 26

Robust patterns in food web structure

Camacho J, Guimera R, Amaral LAN

Physical Review Letters 88, 228102 (2002)

Times cited: 154

Truncation of power law behavior in "scale-free" network models due to information filtering

Mossa S, Barthelemy M, Stanley HE, Amaral LAN

Physical Review Letters 88, 138701 (2002)

Times cited: 88

Analytical solution of a model for complex food webs

Camacho J, Guimera R, Amaral LAN

Physical Review E 65, 030901 (2002)

Times cited: 51

A model for the growth dynamics of economic organizations

Amaral, LAN, Gopikrishnan, P, Plerou, V, Stanley, HE

Physica A 299, 127-136 (2001)

Times cited: 41

Lab Publications