Publications - Amaral Lab

Functional cartography of complex metabolic networks

Guimera R, Amaral LAN

Nature 433, 895-900 (2005)

Times cited: 1172

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

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

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

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

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

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

Module identification in bipartite and directed networks

Guimera R, Sales-Pardo M, Amaral LAN

Physical Review E 76, 036102 (2007)

Times cited: 155

Robust patterns in food web structure

Camacho J, Guimera R, Amaral LAN

Physical Review Letters 88, 228102 (2002)

Times cited: 154

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

Cartography of complex networks: modules and universal roles

Guimera R, Amaral LAN

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

Times cited: 133

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

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

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

On Universality in Human Correspondence Activity

Malmgren RD, Stouffer DB, Campanharo ASLO, Amaral LAN

Science 325, 1696-1700 (2009)

Times cited: 92

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

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

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

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

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

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

Analytical solution of a model for complex food webs

Camacho J, Guimera R, Amaral LAN

Physical Review E 65, 030901 (2002)

Times cited: 51

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

Quantifying the performance of individual players in a team activity

Duch J, Waitzman JS, Amaral LAN

PLoS ONE 5, e10937 (2010)

Times cited: 46

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

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

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

Moreira AA, Amaral LAN

Physical Review Letters 94, 218702 (2005)

Times cited: 38

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

Duality between time series and networks

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

PLoS ONE 6, e23378 (2011)

Times cited: 36

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 network-based method for target selection in metabolic networks

Guimera R, Sales-Pardo M, Amaral LAN

Bioinformatics 23, 1616-1622 (2007)

Times cited: 35

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

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

Asymmetrical singularities in real-world signals

Ohashi K, Amaral LAN, Natelson BH, Yamamoto Y

Physical Review E 68, 065204 (2003)

Times cited: 33

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

Heuristic segmentation of a nonstationary time series

Fukuda K, Stanley HE, Amaral LAN

Physical Review E 69, 021108 (2004)

Times cited: 30

Extremum statistics in scale-free network models

Moreira AA, Andrade JS, Amaral LAN

Physical Review Letters 89, 268703 (2002)

Times cited: 26

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

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

Fukuda K, Amaral LAN, Stanley HE

Europhysics Letters 62, 189-195 (2003)

Times cited: 24

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

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

The role of mentorship in protégé performance

Malmgren RD, Ottino JM, Amaral LAN

Nature 463, 622-626 (2010)

Times cited: 22

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

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

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

A truer measure of our ignorance

Amaral LAN

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

Times cited: 15

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

Lies, damned lies and statistics

Amaral LAN, Guimera R

Nature Physics 2, 75-76 (2006)

Times cited: 14

Poissonian bursts in e-mail correspondence

Anteneodo C, Malmgren RD, Chialvo DR

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

Times cited: 14

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

Rationality, irrationality and escalating behavior in lowest unique bid auctions

Radicchi F, Baronchelli A, Amaral LAN

PLoS ONE 7, e29910 (2012)

Times cited: 13

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

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

Sexual contacts and epidemic thresholds - Reply

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

Nature 423, 606-606 (2003)

Times cited: 8

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

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

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

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

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

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

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

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

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

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

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

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

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

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

The impact of individual biases on consensus formation

Sales-Pardo M, Diermeier D, Amaral LAN

PLOS ONE 8, e58989 (2013)

Times cited: 1

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

Novel collaborations within experienced teams lead to best research outcomes

Amaral LAN

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

Times cited: 1

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

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

Driving on cellular pathway 66

Amaral LAN

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

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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 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: 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)

Reply to "Far away from the lamppost"

Stoeger T, Gerlach M, Morimoto RI, Amaral LAN

PLOS Biology 16, e3000075 (2018)

A universal information theoretic approach to the identification of stopwords

Gerlach M, Shi H, Amaral LAN

Nature Machine Intelligence 1, 606-612 (2019)

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)

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)

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)

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)

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

Stoeger T, Amaral LAN

eLife 9, e61981 (2020)

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)

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

Liu J, Amaral LAN, Keten S

Proteins 89, 276-288 (2020)

The characteristics of early-stage research into human genes are substantially different from subsequent research

Stoeger T, Amaral LAN

PLOS Biology 20, e3001520 (2022)

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

Lei WH, Alves LGA, Amaral LAN

Nature Communications , 4252 (2022)

Aging is associated with a systemic length-associated transcriptome imbalance

Stoeger T, Grant RA, McQuattie-Pimentel AC, Anekalla KR, Liu SS, Tejedor-Navarro H, Singer BD, Abdala-Valencia H, Schwake M, Tetreault M-P, Perlman H, Balch WE, Chandel NE, Ridge KM, Sznajder JI, Morimoto RI, Misharin AV, Budinger GRS, Amaral LAN

Nature Aging 2, 1191-1206 (2022)

Ratiometric sensing of Pnt and Yan transcription factor levels confers ultrasensitivity to photoreceptor fate transitions in Drosophila

Bernasek SM, Hur SSJ, Peláez-Restrepo N, Boisclair Lachance JF, Bakker R, Tejedor Navarro H, Sanchez-Luege N, Amaral LAN, Bagheri N, Rebay I, Carthew RW

Development 150, dev.201467 (2023)

A new approach for extracting information from protein dynamics

Liu J, Amaral LAN, Keten S

Proteins: Structure, Function, and Bioinformatics 91, 183-195 (2023)

The first step is recognizing there is a problem: a methodology for adjusting for variability in disease severity when estimating clinician performance

Bechel MA, Pah RA, Persell SD, Weiss CH, Amaral LAN

BMC Medical Research Methodology 22, 69 (2022)

A cautionary tale from the machine scientist

Amaral LAN

Nature Machine Intelligence 4, 416-417 (2022)

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 LAN, 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.

Journals of Gerontology Series A: Biomedical Sciences and Medical Sciences 72, 1492-1500 (2017)

Moving the science of quality improvement in critical care medicine forward

Weiss CH, Amaral LAN

Am. J. of Respirat. and Crit. Care Med. 182, 1461-1462 (2010)

Opinion: Measuring Impact

Amaral LAN

The Scientist, 37921 (2014)

Quantifying the impact of uninformative features on the performance of supervised classification and dimensionality reduction algorithms

Lei W, Zanchettin C, Ho ZE, Amaral LAN

APL Machine Learning 1, 046118 (2023)

Energy metabolism modulates the regulatory impact of activators on gene expression

Qiao S, Bernasek S, Gallagher KD, O'Connell J, Yamada S, Bagheri N, Amaral LAN, Carthew RW

Development 151, dev201986 (2024)

Artificial intelligence needs a scientific method-driven reset

Amaral, LAN

Nature Physics 20, 523-524 (2024)

The Promise of AI in an Open Justice System

Pah AR, Schwartz DL, Sanga S, Alexander CS, Hammond K, Amaral LAN, SCALES OKN Consortium

AI Magazine 43, 69-74 (2022)

Computational experiments with cellular-automata generated images reveal intrinsic limitations of convolutional neural networks on pattern recognition tasks

Lei W, Zanchettin C, Santos FAO, Amaral LAN

APL Machine Learning 2, 036102 (2024)

Ethical considerations in utilizing artificial intelligence for analyzing the NHGRI’s History of Genomics and Human Genome Project archives

Hosseini M, Hong S, Holmes K, Wetterstrand K, Donohue C, Amaral LAN, Stoeger T

Journal of eScience Librarianship 13, e811 (2024)

On the improvement of handwritten text line recognition with octave convolutional recurrent neural networks

Castro D, Zanchettin C, Amaral LAN

International Journal on Document Analysis and Recognition, (2024)

Validation of a tool for estimating clinician recognition of ARDS using data from the international LUNG SAFE study

Bechel MA, Madotto F, Pah AR, Bellani G, Laffey JG, Pham T, Amaral LAN, Weiss CH

PLOS Digital Health 2, e0000325 (2023)

Robust extraction of pneumonia-associated clinical states from electronic health records

Xu F, Morales FL, Amaral LAN

Proc. Natl. Acad. Sci. U. S. A. 121 (45), e2417688121 (2024)

Adversarial training and attribution methods enable evaluation of robustness and interpretability of deep learning models for image classification

Santos FAO, Zanchettin C, Lei W, Amaral LAN

Physical Review E 110, 054310 (2024)

The SCALES project: Making federal court records free

Schwartz DL, Albrecht KM, Pah AR, Cotropia CA, Sanders AK, Sanga S, Alexander CS, Amaral LAN, Clopton ZD, Tucker AM, Gaylord TW, Daniel SG, Dahlberg N

Northwestern University Law Review 119, 23-64 (2024)

Lab Publications