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Publications Acknowledging Odyssey

To acknowledge use of Odyssey in your publications please use the following text as a guideline: "The computations in this paper were run on the Odyssey cluster supported by the FAS Division of Science, Research Computing Group at Harvard University."

We are always very interested in hearing about research conducted with the help of our computing resources. If you do not find your publication listed below, we encourage you to send us details so that we can include them.

Total reported publications: 279

2017 (4 publications)

Baker, C., Martins, D.J., Pelaez, J.N., Billen, J., Pringle, A., Frederickson, M.E. and Pierce, N.E., 2017. Distinctive fungal communities in an obligate African ant plant mutualism. Proceedings of the Royal Society B, Biological Sciences.

Childs, L.M. and Buckee, C.O., 2015. Dissecting the determinants of malaria chronicity: why within-host models struggle to reproduce infection dynamics. Journal of The Royal Society Interface, 12(104), p.20141379.

Andam, C.P., Mitchell, P.K., Callendrello, A., Chang, Q., Corander, J., Chaguza, C., McGee, L., Beall, B.W. and Hanage, W.P., 2017. Genomic epidemiology of penicillin non-susceptible pneumococci with non-vaccine serotypes causing invasive disease in the USA. Journal of Clinical Microbiology, pp.JCM-02453.

Levin, B.J., Huang, Y.Y., Peck, S.C., Wei, Y., Martínez-del Campo, A., Marks, J.A., Franzosa, E.A., Huttenhower, C. and Balskus, E.P., 2017. A prominent glycyl radical enzyme in human gut microbiomes metabolizes trans-4-hydroxy-l-proline. Science 355:eaai8386.

2016 (62 publications)

Ishihara, K., Korolev, K.S. and Mitchison, T.J., 2016. Physical basis of large microtubule aster growth. eLife, 5, p.e19145.

Di, Q., Kloog, I., Koutrakis, P., Lyapustin, A., Wang, Y. and Schwartz, J., 2016. Assessing PM2. 5 exposures with high spatiotemporal resolution across the continental United States. Environmental science & technology, 50(9), pp.4712-4721.

Di, Q., Rowland, S., Koutrakis, P. and Schwartz, J., 2017. A hybrid model for spatially and temporally resolved ozone exposures in the continental United States. Journal of the Air & Waste Management Association, 67(1), pp.39-52.

Di, Q., Kloog, I., Koutrakis, P., Lyapustin, A., Wang, Y. and Schwartz, J., 2016. Assessing PM2. 5 exposures with high spatiotemporal resolution across the continental United States. Environmental science & technology, 50(9), pp.4712-4721.

Komiske, P.T., Metodiev, E.M. and Schwartz, M.D., 2016. Deep learning in color: towards automated quark/gluon jet discrimination. Journal of High Energy Physics 2017:110

Lemer, S., Gonzalez, V.L., Bieler, R. and Giribet, G., 2016. Cementing mussels to oysters in the pteriomorphian tree: a phylogenomic approach. Proc. R. Soc. B, 283, pp.20160857.

Choi, J., Dotter, A., Conroy, C., Cantiello, M., Paxton, B. and Johnson, B.D., 2016. Mesa Isochrones and Stellar Tracks (MIST). I. Solar-scaled Models. The Astrophysical Journal, 823, pp.102.

Ting, Yuan-Sen, Conroy, C. and Rix, Hans-Walter, 2016. Accelerated Fitting of Stellar Spectra. The Astrophysical Journal, 826, pp.83.

Gu, M., Conroy, C. and Behroozi, P., 2016. Hierarchical Galaxy Growth and Scatter in the Stellar Mass -- Halo Mass Relation. The Astrophysical Journal, 833, pp.2.

Rix, Hans-Walter, Ting, Yuan-Sen, Conroy, C. and Hogg, David W., 2016. Constructing Polynomial Spectral Models for Stars. The Astrophysical Journal Letters, 826, pp.L25.

Leja, J., Johnson, Benjamin D., Conroy, C., van Dokkum, P.G. and Byler, N., 2016. Deriving Physical Properties from Broadband Photometry with Prospector: Description of the Model and a Demonstration of its Accuracy Using 129 Galaxies in the Local Universe. arXiv preprint arXiv:1609.09073

Mistani, P.A., Sales, L.V., Pillepich, A., Sanchez-Janssen, R., Vogelsberger, M., Nelson, D., Rodriguez-Gomez, V. , Torrey, P. and Hernquist, L., 2016. On the assembly of dwarf galaxies in clusters and their efficient formation of globular clusters. Monthly Notices of the Royal Astronomical Society, 455, pp.2323--2336.

Blecha, L., Sijacki, D., Kelley, L.Z., Torrey, P., Vogelsberger, M., Nelson, D., Springel, V., Snyder, G. and Hernquist, L., 2016. Recoiling black holes: prospects for detection and implications of spin alignment. Monthly Notices of the Royal Astronomical Society, 456, pp.961--989.

Bray, A.D. , Pillepich, A., Sales, L. V., Zhu, E., Genel, S., Rodriguez-Gomez, V., Torrey, P. Nelson, D., Vogelsberger, M., Springel, V. and others, 2016. Modelling galactic conformity with the colour--halo age relation in the Illustris simulation. Monthly Notices of the Royal Astronomical Society, 455, pp.185--198.

Rodriguez-Gomez, V., Sales, L.V., Genel, S., Pillepich, A., Zjupa, J., Nelson, D., Griffen, B., Torrey, P., Snyder, G.F., Vogelsberger, M. and others, 2016. The role of mergers and halo spin in shaping galaxy morphology. arXiv preprint arXiv:1609.09498.

Rodriguez-Gomez, V., Pillepich, A., Sales, L.V., Genel, S., Vogelsberger, M., Zhu, Q., Wellons, S., Nelson, D., Torrey, P., Springel, V. and Ma, C.P., 2016. The stellar mass assembly of galaxies in the Illustris simulation: growth by mergers and the spatial distribution of accreted stars. Monthly Notices of the Royal Astronomical Society, 458(3), pp.2371-2390.

Kannan, R., Springel, V., Pakmor, R., Marinacci, F. and Vogelsberger, M., 2016. Accurately simulating anisotropic thermal conduction on a moving mesh. Monthly Notices of the Royal Astronomical Society, 458(1), pp.410-424.

McKinnon, R., Torrey, P. and Vogelsberger, M., 2016. Dust formation in Milky Way-like galaxies. Monthly Notices of the Royal Astronomical Society, 457(4), pp.3775-3800.

Mocz, P., Pakmor, R., Springel, V., Vogelsberger, M., Marinacci, F. and Hernquist, L., 2016. A moving mesh unstaggered constrained transport scheme for magnetohydrodynamics. Monthly Notices of the Royal Astronomical Society, 463(1), pp.477-488.

Nierenberg, A.M., Treu, T., Menci, N., Lu, Y., Torrey, P. and Vogelsberger, M., 2016. The missing satellite problem in 3D. Monthly Notices of the Royal Astronomical Society, 462(4), pp.4473-4481.
Vancouver

Taylor, C., Boylan-Kolchin, M., Torrey, P., Vogelsberger, M. and Hernquist, L., 2016. The mass profile of the Milky Way to the virial radius from the Illustris simulation. Monthly Notices of the Royal Astronomical Society, 461(4), pp.3483-3493.

Nelson, D., Genel, S., Pillepich, A., Vogelsberger, M., Springel, V. and Hernquist, L., 2016. Zooming in on accretion–I. The structure of halo gas. Monthly Notices of the Royal Astronomical Society, 460(3), pp.2881-2904.

Vogelsberger, M., Zavala, J., Cyr-Racine, F.Y., Pfrommer, C., Bringmann, T. and Sigurdson, K., 2016. ETHOS–an effective theory of structure formation: dark matter physics as a possible explanation of the small-scale CDM problems. Monthly Notices of the Royal Astronomical Society, 460(2), pp.1399-1416.

Popa, C., Naoz, S., Marinacci, F. and Vogelsberger, M., 2016. Gas-rich and gas-poor structures through the stream velocity effect. Monthly Notices of the Royal Astronomical Society, 460(2), pp.1625-1639.

Griffen, B.F., Ji, A.P., Dooley, G.A., Gómez, F.A., Vogelsberger, M., O’Shea, B.W. and Frebel, A., 2016. The Caterpillar Project: A Large Suite of Milky Way Sized Halos. The Astrophysical Journal, 818(1), p.10.

Kannan, R., Vogelsberger, M., Stinson, G.S., Hennawi, J.F., Marinacci, F., Springel, V. and Maccio, A.V., 2016. Galaxy formation with local photoionization feedback–II. Effect of X-ray emission from binaries and hot gas. Monthly Notices of the Royal Astronomical Society, 458(3), pp.2516-2529.

Torri, G. and Kuang, Z., 2016. A Lagrangian study of precipitation-driven downdrafts. Journal of the Atmospheric Sciences, 73(2), pp.839-854.

Torri, G. and Kuang, Z., 2016. Rain evaporation and moist patches in tropical boundary layers. Geophysical Research Letters, 43(18), pp.9895-9902.

Tian, Y. and Kuang, Z., 2016. Dependence of entrainment in shallow cumulus convection on vertical velocity and distance to cloud edge. Geophysical Research Letters, 43(8), pp.4056-4065.

Singh, M.S., Kuang, Z. and Tian, Y., 2016. Eddy influences on the strength of the Hadley circulation: dynamic and thermodynamic perspectives. Journal of the Atmospheric Sciences, (2016).

Singh, M.S. and Kuang, Z., 2016. Exploring the role of eddy momentum fluxes in determining the characteristics of the equinoctial Hadley circulation: Fixed-SST simulations. Journal of the Atmospheric Sciences, 73(6), pp.2427-2444.

Nie, J., Kuang, Z., Jacob, D.J. and Guo, J., 2016. Representing effects of aqueous phase reactions in shallow cumuli in global models. Journal of Geophysical Research: Atmospheres, 121(10), pp.5769-5787.

Moore, M., Blossey, P.N., Muhlbauer, A. and Kuang, Z., 2016. Microphysical controls on the isotopic composition of wintertime orographic precipitation. Journal of Geophysical Research: Atmospheres, 121(12), pp.7235-7253.

Ma, D., Hassanzadeh, P. and Kuang, Z., 2016. Quantifying the eddy-jet feedback strength of the annular mode in an idealized GCM and the reanalysis data. Journal of the Atmospheric Sciences, (2016).

Hassanzadeh, P. and Kuang, Z., 2016. The Linear Response Function of an Idealized Atmosphere. Part II: Implications for the Practical Use of the Fluctuation–Dissipation Theorem and the Role of Operator’s Nonnormality. Journal of the Atmospheric Sciences, 73(9), pp.3441-3452.

Hassanzadeh, P. and Kuang, Z., 2016. The linear response function of an idealized atmosphere. Part I: Construction using Green’s functions and applications. Journal of the Atmospheric Sciences, 73(9), pp.3423-3439.

Ma, D., and Z. Kuang. "A mechanism‐denial study on the Madden‐Julian Oscillation with reduced interference from mean state changes." Geophysical Research Letters 43.6 (2016): 2989-2997.

Moore, M., Blossey, P.N., Muhlbauer, A. and Kuang, Z., 2016. Microphysical controls on the isotopic composition of wintertime orographic precipitation. Journal of Geophysical Research: Atmospheres, 121(12), pp.7235-7253.

Nie, J., Kuang, Z., Jacob, D.J. and Guo, J., 2016. Representing effects of aqueous phase reactions in shallow cumuli in global models. Journal of Geophysical Research: Atmospheres, 121(10), pp.5769-5787.

Singh, M.S. and Kuang, Z., 2016. Exploring the role of eddy momentum fluxes in determining the characteristics of the equinoctial Hadley circulation: Fixed-SST simulations. Journal of the Atmospheric Sciences, 73(6), pp.2427-2444.

Singh, M.S., Kuang, Z. and Tian, Y., 2016. Eddy influences on the strength of the Hadley circulation: dynamic and thermodynamic perspectives. Journal of the Atmospheric Sciences, (2016).

Torri, G. and Kuang, Z., 2016. Rain evaporation and moist patches in tropical boundary layers. Geophysical Research Letters, 43(18), pp.9895-9902.

Torri, G. and Kuang, Z., 2016. A Lagrangian study of precipitation-driven downdrafts. Journal of the Atmospheric Sciences, 73(2), pp.839-854.

Lopez, S.A., Pyzer-Knapp, E.O., Simm, G.N., Lutzow, T., Li, K., Seress, L.R., Hachmann, J. and Aspuru-Guzik, A., 2016. The Harvard organic photovoltaic dataset. Scientific Data, 3.

Gómez-Bombarelli, R., Aguilera-Iparraguirre, J., Hirzel, T.D., Duvenaud, D., Maclaurin, D., Blood-Forsythe, M.A., Chae, H.S., Einzinger, M., Ha, D.G., Wu, T. and Markopoulos, G., 2016. Design of efficient molecular organic light-emitting diodes by a high-throughput virtual screening and experimental approach. Nature Materials, 15(10), pp.1120-1127.

Lin, K., Gómez-Bombarelli, R., Beh, E.S., Tong, L., Chen, Q., Valle, A., Aspuru-Guzik, A., Aziz, M.J. and Gordon, R.G., 2016. A redox-flow battery with an alloxazine-based organic electrolyte. Nature Energy, 1, p.16102.

Häse, F., Valleau, S., Pyzer-Knapp, E. and Aspuru-Guzik, A., 2016. Machine learning exciton dynamics. Chemical Science.

Kreisbeck, C. and Aspuru-Guzik, A., 2016. Efficiency of energy funneling in the photosystem II supercomplex of higher plants. Chemical Science.

Blood-Forsythe, M.A., Markovich, T., DiStasio, R.A., Car, R. and Aspuru-Guzik, A., 2016. Analytical nuclear gradients for the range-separated many-body dispersion model of noncovalent interactions. Chemical Science, 7(3), pp.1712-1728.

Pyzer-Knapp, E.O., Simm, G.N. and Guzik, A.A., 2016. A Bayesian approach to calibrating high-throughput virtual screening results and application to organic photovoltaic materials. Materials Horizons, 3(3), pp.226-233.

Gelbwaser-Klimovsky, D., Saikin, S.K., Goldsmith, R.H. and Aspuru-Guzik, A., 2016. Optical Spectra of p-Doped PEDOT Nanoaggregates Provide Insight into the Material Disorder. ACS Energy Letters, 1(6), pp.1100-1105.

Wei, J.N., Duvenaud, D. and Aspuru-Guzik, A., 2016. Neural networks for the prediction of organic chemistry reactions. ACS Central Science, 2(10), pp.725-732.

Park, H.J., So, M.C., Gosztola, D., Wiederrecht, G.P., Emery, J.D., Martinson, A.B., Er, S., Wilmer, C.E., Vermeulen, N.A., Aspuru-Guzik, A. and Stoddart, J.F., 2016. Layer-by-Layer Assembled Films of Perylene Diimide-and Squaraine-Containing Metal–Organic Framework-like Materials: Solar Energy Capture and Directional Energy Transfer. ACS Applied Materials & Interfaces, 8(38), pp.24983-24988.

Fujita, T., Atahan-Evrenk, S., Sawaya, N.P. and Aspuru-Guzik, A., 2016. Coherent Dynamics of Mixed Frenkel and Charge-Transfer Excitons in Dinaphtho [2, 3-b: 2′ 3′-f] thieno [3, 2-b]-thiophene Thin Films: The Importance of Hole Delocalization. The journal of physical chemistry letters, 7(7), pp.1374-1380.

Alexander Mathis, Dan Rokni, Vikrant Kapoor, Matthias Bethge, Venkatesh N. Murthy (2016) Reading Out Olfactory Receptors: Feedforward Circuits Detect Odors in Mixtures without Demixing. Neuron first published September, 7, 2016.

Kaixiang Lin, Rafael Gómez-Bombarelli, Eugene S. Beh, Liuchuan Tong, Qing Chen, Alvaro Valle, Alán Aspuru-Guzik, Michael J. Aziz & Roy G. Gordon (2016) A redox-flow battery with an alloxazine-based organic electrolyte. Nature Energy first published July 18, 2016.

Paul Torrey, Sarah Wellons, Chung-Pei Ma, Philip F. Hopkins, and Mark Vogelsberger (2016) Forward and backward galaxy evolution in comoving number density space. Monthly Notices of the Royal Astronomical Society first published June 24, 2016.

Phoebe M. R. DeVries, Plamen G. Krastev, and Brendan J. Meade (2016) Geodetically constrained models of viscoelastic stress transferand earthquake triggering along the North Anatolian fault. Geochemistry, Geophysics, Geosystems/AGU first published June 20, 2016.

Fernández, R., Edgecombe, G.D. & Giribet, G. (2016) Exploring phylogenetic relationships within Myriapoda and the effects of matrix composition and occupancy on phylogenomic reconstruction. Systematic Biology, in press.

Jakob Wudarczyk, Dr. George Papamokos, Vasilis Margaritis, Dr. Dieter Schollmeyer, Dr. Felix Hinkel, Prof. Dr. Martin Baumgarten, Prof. Dr. George Floudas, Prof. Dr. Klaus Müllen, (2016). Hexasubstituted Benzenes with Ultrastrong Dipole Moments. Angewandte Chemie Int. first published February 2, 2016.

Bogiatzis, P., Ishii, M., and Davis, T. A., (2016). Toward using direct methods in seismic tomography: Computation of the full resolution matrix using high performance computing and sparse QR factorization. Geophys. J. Int. first published online February 8, 2016.

Reis, S A, Ghosh, B, Hendricks, J A, Szantai-Kis, D M, Tork, L, Ross, K N, Lamb, J, Read-Button, W, Zheng, B, Wang, H, Salthouse, C, Haggarty, S J, and Mazitschek, R. (2016) Light-controlled modulation of gene expression by chemical optoepigenetic probes. Nature Chemical Biology Published online 14 March 2016.

2015 (59 publications)

Ade, P. A. R., Aikin, R. W., Amiri, M., Barkats, D., Benton, S. J., Bischoff, C. A., ... & Richter, S. (2015). Antenna-coupled TES bolometers used in BICEP2, Keck array, and SPIDER. arXiv preprint arXiv:1502.00619. URL

Ade, P. A. R., Ahmed, Z., Aikin, R. W., Alexander, K. D., Barkats, D., Benton, S. J., ... & Sudiwala, R. V. (2015). BICEP2/Keck Array V: Measurements of B-mode Polarization at Degree Angular Scales and 150 GHz by the Keck Array.arXiv preprint arXiv:1502.00643. URL

Arnold, N. P., & Tziperman, E. (2015). Reductions in mid‐latitude upwelling‐favorable winds implied by weaker large‐scale Pliocene SST gradients.Paleoceanography. URL

Ade, P. A. R., Aikin, R. W., Barkats, D., Benton, S. J., Bischoff, C. A., Bock, J. J., ... & BICEP2 Collaboration. (2015). BICEP2 III: Instrumental Systematics.arXiv preprint arXiv:1502.00608. URL

Aspuru‐Guzik, A., Adams, R., Baldo, M., Aguilera‐Iparraguirre, J., & Gómez‐Bombarelli, R. (2015, June). 34.4: Invited Paper: Combinatorial Design of OLED‐Emitting Materials. In SID Symposium Digest of Technical Papers (Vol. 46, No. 1, pp. 505-506). URL

BICEP, T., Collaborations, K. A., Ade, P. A. R., Aikin, R. W., Barkats, D., Benton, S. J., ... & Vieregg, A. G. (2015). BICEP2/Keck Array IV: Optical Characterization and Performance of the BICEP2 and Keck Array Experiments.arXiv preprint arXiv:1502.00596. URL

Blecha, L., Sijacki, D., Kelley, L. Z., Torrey, P., Vogelsberger, M., Nelson, D., ... & Hernquist, L. (2015). Recoiling black holes: prospects for detection and implications of spin alignment. arXiv preprint arXiv:1508.01524.

Bray, A. D., Pillepich, A., Sales, L. V., Zhu, E., Genel, S., Rodriguez-Gomez, V., ... & Hernquist, L. (2015). Modeling Galactic Conformity with the Color-Halo Age Relation in the Illustris Simulation. arXiv preprint arXiv:1508.05393. URL

Chéron, N., Jasty, N., & Shakhnovich, E. I. (2015). OpenGrowth: an automated and rational algorithm for finding new protein ligands. Journal of medicinal chemistry. URL

Chéron, N., Yu, C., Kolawole, A. O., Shakhnovich, E. I., & Wobus, C. E. (2015). Repurposing of rutin for the inhibition of norovirus replication.Archives of virology, 160(9), 2353-2358. URL

Chotibut, T., & Nelson, D. R. (2015). Evolutionary dynamics with fluctuating population sizes and strong mutualism. Physical Review E, 92(2), 022718. URL

Corbett-Detig, R. B., Hartl, D. L., & Sackton, T. B. (2015). Natural selection constrains neutral diversity across a wide range of species. PLoS Biol doi:10.1371/journal.pbio.1002112

Cvijović, I., Good, B. H., Jerison, E. R., & Desai, M. M. (2015). Fate of a mutation in a fluctuating environment. Proceedings of the National Academy of Sciences, 201505406. URL

Fang, S., Defo, R. K., Shirodkar, S. N., Lieu, S., Tritsaris, G. A., & Kaxiras, E. (2015). Ab initio tight-binding Hamiltonian for transition metal dichalcogenides. Physical Review B, 92(20), 205108. URL

Farhadifar, R., Baer, C. F., Valfort, A. C., Andersen, E. C., Müller-Reichert, T., Delattre, M., & Needleman, D. J. (2015). Scaling, selection, and evolutionary dynamics of the mitotic spindle. Current Biology25(6), 732-740. URL

Feng, Y., Di-Matteo, T., Croft, R. A., Bird, S., Battaglia, N., & Wilkins, S. (2015). The BlueTides Simulation: First Galaxies and Reionization. arXiv preprint arXiv:1504.06619. URL

Fernández, R., Giribet, G. 2015. Unnoticed in the tropics: phylogenomic resolution of the poorly-known arachnid order Ricinulei (Arachnida). Royal Society Open Science, 2:150065

French, R. G., Dawson, R. I., & Showalter, M. R. (2015). Resonances, Chaos, and Short-term Interactions Among the Inner Uranian Satellites. The Astronomical Journal149(4), 142. URL

Genel, S., Fall, S. M., Hernquist, L., Vogelsberger, M., Snyder, G. F., Rodriguez-Gomez, V., ... & Springel, V. (2015). Galactic Angular Momentum in the Illustris Simulation: Feedback and the Hubble Sequence. arXiv preprint arXiv:1503.01117. URL

Giesa, T., Perry, C. C., & Buehler, M. J. (2015). Secondary Structure Transition and Critical Stress for a Model of Spider Silk Assembly.Biomacromolecules. URL

Green, G. M., Schlafly, E. F., Finkbeiner, D. P., Jurić, M., Rix, H. W., Burgett, W., ... & Waters, C. (2014). Measuring Distances and Reddenings for a Billion Stars: Toward a 3D Dust Map from Pan-STARRS 1. The Astrophysical Journal,783(2), 114. URL

González, V. L., Andrade, S. C., Bieler, R., Collins, T. M., Dunn, C. W., Mikkelsen, P. M., ... & Giribet, G. (2015). A phylogenetic backbone for Bivalvia: an RNA-seq approach. Proceedings of the Royal Society B: Biological Sciences282(1801), 20142332. URL

Häse, F., Valleau, S., Pyzer-Knapp, E., & Aspuru-Guzik, A. (2015). Machine Learning Exciton Dynamics. arXiv preprint arXiv:1511.07883.

Holmes, Avram J., et al. "Brain Genomics Superstruct Project initial data release with structural, functional, and behavioral measures." (Nature) Scientific data 2 (2015).

Huang, D., Song, C. L., Webb, T. A., Fang, S., Chang, C. Z., Moodera, J. S., ... & Hoffman, J. E. (2015). Revealing the Empty-State Electronic Structure of Single-Unit-Cell FeSe/SrTiO $ _ {3} $. arXiv preprint arXiv:1503.04792. URL

Hung, C. L., Hayward, C. C., Smith, H. A., Ashby, M. L., Lanz, L., Martínez-Galarza, J. R., ... & Zezas, A. (2015). Merger Signatures in the Dynamics of Star-forming Gas. arXiv preprint arXiv:1511.08481.

Julio D Perez, Nimrod D Rubinstein, Daniel E Fernandez, Stephen W Santoro, Leigh A Needleman, Olivia Ho-Shing, John J Choi, Mariela Zirlinger, Shau-Kwaun Chen, Jun S Liu, Catherine Dulac. (2015). Quantitative and functional interrogation of parent-of-origin allelic expression biases in the brain. eLife 2015;10.7554/eLife.07860. URL

Kim, S. I., & Farrell, B. D. (2015). Phylogeny of world stag beetles (Coleoptera: Lucanidae) reveals a Gondwanan origin of Darwin’s stag beetle. Molecular phylogenetics and evolution86, 35-48. URL

Koo, B. J., Huynh, M., Halbach, R. L., Stubbe, J., & Nocera, D. G. (2015). Modulation of Phenol Oxidation in Cofacial Dyads. Journal of the American Chemical Society. URL

Kreisbeck, C., & Aspuru-Guzik, A. (2015). Efficiency of energy funneling in the photosystem II supercomplex of higher plants. arXiv preprint arXiv:1502.02657. URL

Kumar, S., Gezari, S., Heinis, S., Chornock, R., Berger, E., Rest, A., ... & Wainscoat, R. J. (2015). Selection of Burst-like Transients and Stochastic Variables Using Multi-Band Image Differencing in the Pan-STARRS1 Medium-Deep Survey. arXiv preprint arXiv:1501.01314. URL

Kwan, E. E., & Liu, R. Y. (2015). Enhancing NMR Prediction for Organic Compounds Using Molecular Dynamics. Journal of Chemical Theory and Computation. doi:10.1021/acs.jctc.5b00856. URL

Laumer, C. E., Hejnol, A., & Giribet, G. (2015). Nuclear genomic signals of the ‘microturbellarian’roots of platyhelminth evolutionary innovation. eLife4, e05503. URL

Lavrentovich, M. O. (2015). Critical Fitness Collapse in Three-Dimensional Spatial Population Genetics. arXiv preprint arXiv:1504.00748. URL

Lemon, C. M., Halbach, R. L., Huynh, M., & Nocera, D. G. (2015). Photophysical Properties of β-Substituted Free-Base Corroles. Inorganic chemistry54(6), 2713-2725. URL

Malone, J. H. (2015). Balancing copy number in ribosomal DNA. Proceedings of the National Academy of Sciences112(9), 2635-2636. URL

Menegas, W., Bergan, J. F.,Ogawa, S. K., Isogai, Y., Venkataraju, K. U., Osten, P., Uchida, N., Mitsuko Watabe-Uchida, M. (2015). Dopamine neurons projecting to the posterior striatum form an anatomically distinct subclass. eLife 2015;10.7554/eLife.10032 URL

Moreno, J., Torrey, P., Ellison, S. L., Patton, D. R., Bluck, A. F., Bansal, G., & Hernquist, L. (2015). Mapping galaxy encounters in numerical simulations: The spatial extent of induced star formation. arXiv preprint arXiv:1501.03573. URL

Novitsky, V., Moyo, S., Lei, Q., DeGruttola, V., & Essex, M. (2015). Importance of Viral Sequence Length and Number of Variable and Informative Sites in Analysis of HIV Clustering. AIDS research and human retroviruses, 31(5), 531-542. URL

Parker, A. H. (2015). The intrinsic Neptune Trojan orbit distribution: Implications for the primordial disk and planet migration. Icarus247, 112-125. URL

Perez, J. D., Rubinstein, N. D., Fernandez, D. E., Santoro, S. W., Needleman, L. A., Ho-Shing, O., ... & Dulac, C. (2015). Quantitative and functional interrogation of parent-of-origin allelic expression biases in the brain. eLife, 4, e07860. URL

Prescott, J., Setiawan, V. W., Wentzensen, N., Schumacher, F., Yu, H., Delahanty, R., ... & Friedenreich, C. (2015). Body Mass Index Genetic Risk Score and Endometrial Cancer Risk. PloS one, 10(11). URL

Pyzer‐Knapp, E. O., Li, K., & Aspuru‐Guzik, A. (2015). Learning from the Harvard Clean Energy Project: The Use of Neural Networks to Accelerate Materials Discovery. Advanced Functional Materials, 25(41), 6495-6502. URL

Pyzer-Knapp, E. O., Simm, G. N., & Aspuru-Guzik, A. (2015). A Bayesian Approach to Calibrating High-Throughput Virtual Screening Results and Application to Organic Photovoltaic Materials. arXiv preprint arXiv:1510.00388.

Sales, L. V., Vogelsberger, M., Genel, S., Torrey, P., Nelson, D., Rodriguez-Gomez, V., ... & Hernquist, L. (2015). The colours of satellite galaxies in the Illustris simulation. Monthly Notices of the Royal Astronomical Society: Letters, 447(1), L6-L10. URL

Sanders, J. N., Andrade, X., & Aspuru-Guzik, A. (2015). Compressed Sensing for the Fast Computation of Matrices: Application to Molecular Vibrations. ACS Central Science. URL

Sawaya, N. P., Huh, J., Fujita, T., Saikin, S. K., & Aspuru-Guzik, A. (2015). Fast Delocalization Leads To Robust Long-Range Excitonic Transfer in a Large Quantum Chlorosome Model. Nano letters15(3), 1722-1729. URL

Shapiro, L. R., Scully, E. D., Roberts, D., Straub, T. J., Geib, S. M., Park, J., ... & Zhaxybayeva, O. (2015). Draft genome sequence of Erwinia tracheiphila, an economically important bacterial pathogen of cucurbits. Genome announcements, 3(3), e00482-15. URL

Shapiro, Lori R., et al. “Horizontal gene acquisitions, mobile element proliferation, and genome decay in the host-restricted plant pathogen Erwinia tracheiphila." Genome Biology and Evolution (accepted)

Sharma, P., Fernández, R., González Santillán, E., Monod, L. 2015. Phylogenomic resolution of scorpions reveals multilevel discordance with morphological phylogenetic signal. Proceedings of the Royal Society B: Biological Sciences 282: 20142953.

Shechner, D. M., Hacisuleyman, E., Younger, S. T., & Rinn, J. L. (2015). Multiplexable, locus-specific targeting of long RNAs with CRISPR-Display.Nature methods. URL

SINGH, M. S., & KUANG, Z. (2015). Revisiting the role of eddies in determining the strength of the equinoctial Hadley circulation.

Snoek, J., Rippel, O., Swersky, K., Kiros, R., Satish, N., Sundaram, N., ... & Adams, R. P. (2015). Scalable Bayesian Optimization Using Deep Neural Networks. arXiv preprint arXiv:1502.05700. URL

Thompson, T. B., Plesch, A., Shaw, J. H., & Meade, B. J. (2015). Rapid slip‐deficit rates at the eastern margin of the Tibetan Plateau prior to the 2008 Mw 7.9 Wenchuan earthquake. Geophysical Research Letters42(6), 1677-1684. URL

Wallace EWJ, Kear-Scott JL, Pilipenko EV, Schwartz MH, Laskowski PR, Rojek AE, Katanski CD, Riback JA, Dion MF, Franks AM, Airoldi EM, Pan T, Budnik BA, and Drummond DA. (2015) Reversible, specific, active aggregates of endogenous proteins assemble upon heat stress. Cell 162(6). URL

Wordsworth, R. D., Kerber, L., Pierrehumbert, R. T., Forget, F., & Head, J. W. (2015). Comparison of “warm and wet” and “cold and icy” scenarios for early Mars in a 3‐D climate model. Journal of Geophysical Research: Planets, 120(6), 1201-1219. URL

Yang, S., Santillana, M., & Kou, S. C. (2015). ARGO: a model for accurate estimation of influenza epidemics using Google search data. arXiv preprint arXiv:1505.00864.

Zhou, Q., Xia, X., Luo, Z., Liang, H. and Eugene Shakhnovich, E. 2015. Searching the Sequence Space for Potent Aptamers Using SELEX in Silico. J. Chem. Theory Comput., Article ASAP DOI: 10.1021/acs.jctc.5b00707

Zimmerman, K., Levitis, D., Addicott, E., & Pringle, A. (2015). Selection of Pairings Reaching Evenly Across the Data (SPREAD): A simple algorithm to design maximally informative fully crossed mating experiments. Heredity 2015/09/30/online URL

2014 (47 publications)

Ade, P. A. R., Aikin, R. W., Barkats, D., Benton, S. J., Bischoff, C. A., Bock, J. J., ... & Bicep2 Collaboration. (2014). Detection of B-mode polarization at degree angular scales by BICEP2. Physical Review Letters112(24), 241101. URL

Ade, P. A. R., Aikin, R. W., Amiri, M., Barkats, D., Benton, S. J., Bischoff, C. A., ... & Wong, C. L. (2014). BICEP2. II. Experiment and three-year Data Set. The Astrophysical Journal792(1), 62. URL

Akeju, O., Davis-Dusenbery, B. N., Cassel, S. H., Ichida, J. K., & Eggan, K. (2014). Ketamine exposure in early development impairs specification of the primary germ cell layers. Neurotoxicology and teratology43, 59-68. URL

Boyle, J. H., Kaliszewska, Z. A., Espeland, M., Suderman, T. R., Fleming, J., Heath, A., & Pierce, N. E. (2015). Phylogeny of the Aphnaeinae: myrmecophilous African butterflies with carnivorous and herbivorous life histories. Systematic Entomology40(1), 169-182. URL

Carter, A. C., Davis-Dusenbery, B. N., Koszka, K., Ichida, J. K., & Eggan, K. (2014). Nanog-independent reprogramming to iPSCs with canonical factors.Stem cell reports2(2), 119-126. URL

Chornock, R., Berger, E., Gezari, S., Zauderer, B. A., Rest, A., Chomiuk, L., ... & Wainscoat, R. (2014). The Ultraviolet-bright, Slowly Declining Transient PS1-11af as a Partial Tidal Disruption Event. The Astrophysical Journal780(1), 44. URL

Cubuk, E. D., & Kaxiras, E. (2014). Theory of structural transformation in lithiated amorphous silicon. Nano letters14(7), 4065-4070. URL

Drout, M. R., Chornock, R., Soderberg, A. M., Sanders, N. E., McKinnon, R., Rest, A., ... & Waters, C. (2014). Rapidly Evolving and Luminous Transients from Pan-STARRS1. The Astrophysical Journal794(1), 23. URL

Dasmeh, P., Serohijos, A. W., Kepp, K. P., & Shakhnovich, E. I. (2014). The influence of selection for protein stability on dN/dS estimations. Genome biology and evolution6(10), 2956-2967. URL

Fernández, R., Hormiga, G., Giribet, G. 2014. Phylogenomic analysis of spiders reveals non-monophyly of orb-weavers. Current Biology 24, 1772-1777

Fernández, R., Vahtera, V., Laumer, C.E., Libro, S., Kaluziak, S., Sharma, P.P., Pérez-Porro, A., Edgecombe, G.D., Giribet, G., 2014. Evaluating topological conflict in centipede phylogeny using transcriptomic data sets. Molecular Biology and Evolution, 31(6): 1500-1513.

Frenkel, E. M., Good, B. H., & Desai, M. M. (2014). The fates of mutant lineages and the distribution of fitness effects of beneficial mutations in laboratory budding yeast populations. Genetics196(4), 1217-1226. URL

Gibbons, J. G., Branco, A. T., Yu, S., & Lemos, B. (2014). Ribosomal DNA copy number is coupled with gene expression variation and mitochondrial abundance in humans. Nature communications5. URL

Guo, X., Sironi, L., & Narayan, R. (2014). Non-thermal Electron Acceleration in Low Mach Number Collisionless Shocks. I. Particle Energy Spectra and Acceleration Mechanism. The Astrophysical Journal794(2), 153. URL

Hayward, C. C., Lanz, L., Ashby, M. L., Fazio, G., Hernquist, L., Martínez-Galarza, J. R., ... & Zezas, A. (2014). The total infrared luminosity may significantly overestimate the star formation rate of quenching and recently quenched galaxies. Monthly Notices of the Royal Astronomical Society445(2), 1598-1604. URL

Hyland, E. M., Wallace, E. W., & Murray, A. W. (2014). A Model for the Evolution of Biological Specificity: a Cross-Reacting DNA-Binding Protein Causes Plasmid Incompatibility. Journal of bacteriology196(16), 3002-3011. URL

Johnson, A. S., Yuen-Zhou, J., Aspuru-Guzik, A., & Krich, J. J. (2014). Practical witness for electronic coherences. The Journal of chemical physics141(24), 244109. URL

Karkare, K. S., Ade, P. A. R., Ahmed, Z., Aikin, R. W., Alexander, K. D., Amiri, M., ... & Schwarz, R. (2014, August). Keck Array and BICEP3: spectral characterization of 5000+ detectors. In SPIE Astronomical Telescopes+ Instrumentation (pp. 91533B-91533B). International Society for Optics and Photonics. URL

Kim, K. H., Ramadhar, T. R., Beemelmanns, C., Cao, S., Poulsen, M., Currie, C. R., & Clardy, J. (2014). Natalamycin A, an ansamycin from a termite-associated Streptomyces sp. Chemical Science5(11), 4333-4338. URL

Kolesov, G., Vinichenko, D., Tritsaris, G. A., Friend, C. M., & Kaxiras, E. (2015). Anatomy of the Photo-chemical Reaction: Excited State Dynamics Reveals CH Acidity Mechanism of Methoxy Photo-oxidation on Titania. The Journal of Physical Chemistry Letters. URL

Lanz, L., Hayward, C. C., Zezas, A., Smith, H. A., Ashby, M. L., Brassington, N., ... & Hernquist, L. (2014). Simulated Galaxy Interactions as Probes of Merger Spectral Energy Distributions. The Astrophysical Journal785(1), 39. URL

Laumer, C. E., & Giribet, G. (2014). Inclusive taxon sampling suggests a single, stepwise origin of ectolecithality in Platyhelminthes. Biological Journal of the Linnean Society111(3), 570-588. URL

Lemer, S., Kawauchi, GY, Andrade, CS, Boyle, MJ, Giribet, G. 2014. Re-evaluating the phylogeny of Sipuncula through transcriptomics. Molecular Phylogenetics and Evolution, 83: 174-183

Lemer, S., Buge, B., Bemis, A., Giribet, G. 2014. First molecular phylogeny of the circumtropical bivalve family Pinnidae (Mollusca, Bivalvia): evidence for high levels of cryptic species diversity. Molecular Phylogenetics and Evolution, 75: 11-23

Ma, D., Boos, W., & Kuang, Z. (2014). Effects of orography and surface heat fluxes on the south Asian summer monsoon. Journal of Climate27(17), 6647-6659. URL

Martínez-Galarza, J. R., Smith, H. A., Lanz, L., Hayward, C. C., Zezas, A., Rosenthal, L., ... & Groves, B. (2014). Variations of the ISM Conditions Across the Main Sequence of Star-Forming Galaxies: Observations and Simulations.arXiv preprint arXiv:1412.2760. URL

Miller, A., Bornn, L., Adams, R., & Goldsberry, K. (2014). Factorized point process intensities: A spatial analysis of professional basketball. arXiv preprint arXiv:1401.0942. URL

Mckenna, D. D., Farrell, B. D., Caterino, M. S., Farnum, C. W., Hawks, D. C., Maddison, D. R., ... & Thayer, M. K. (2015). Phylogeny and evolution of Staphyliniformia and Scarabaeiformia: forest litter as a stepping stone for diversification of nonphytophagous beetles. Systematic Entomology,40(1), 35-60. URL

Moore, M., Kuang, Z., & Blossey, P. N. (2014). A moisture budget perspective of the amount effect. Geophysical Research Letters41(4), 1329-1335. URL

Moreno, J. (2014). Rings of star formation: Imprints of a close galaxy encounter.arXiv preprint arXiv:1412.4443. URL

Muñoz, D. J., Kratter, K., Vogelsberger, M., Hernquist, L., & Springel, V. (2015). Stellar orbit evolution in close circumstellar disc encounters. Monthly Notices of the Royal Astronomical Society446(2), 2010-2029. URL

Parr, C. S., Wilson, M. N., Leary, M. P., Schulz, K. S., Lans, M. K., Walley, M. L., ... & Corrigan Jr, M. R. J. (2014). The encyclopedia of life v2: providing global access to knowledge about life on Earth. Biodiversity data journal, (2). URL

Punk, M., Chowdhury, D., & Sachdev, S. (2014). Topological excitations and the dynamic structure factor of spin liquids on the kagome lattice. Nature Physics10(4), 289-293. URL

Riesgo, A., Novo, M., Sharma, P. P., Peterson, M., Maldonado, M., & Giribet, G. (2014). Inferring the ancestral sexuality and reproductive condition in sponges (Porifera). Zoologica Scripta43(1), 101-117. URL

Sackton, T. B., Corbett‐Detig, R. B., Nagaraju, J., Vaishna, L., Arunkumar, K. P., & Hartl, D. L. (2014). POSITIVE SELECTION DRIVES FASTER‐Z EVOLUTION IN SILKMOTHS. Evolution68(8), 2331-2342. URL

Sanders, J. N., Andrade, X., & Aspuru-Guzik, A. (2014). A sparse-sampling approach for the fast computation of matrices: application to molecular vibrations. arXiv preprint arXiv:1410.4848. URL

Sanders, N., Betancourt, M., & Soderberg, A. (2014). Unsupervised Transient Light Curve Analysis Via Hierarchical Bayesian Inference. arXiv preprint arXiv:1404.3619. URL

Steiner, J. F., McClintock, J. E., Orosz, J. A., Remillard, R. A., Bailyn, C. D., Kolehmainen, M., & Straub, O. (2014). The Low-Spin Black Hole in LMC X-3.The Astrophysical Journal Letters793(2), L29. URL

Subramaniam, A. R., Zid, B. M., & O’Shea, E. K. (2014). An Integrated Approach Reveals Regulatory Controls on Bacterial Translation Elongation.Cell159(5), 1200-1211. URL

Suchow, J. W. (2014). Measuring, monitoring, and maintaining memories in a partially observable mind. URL

Schlafly, E. F., Green, G., Finkbeiner, D. P., Jurić, M., Rix, H. W., Martin, N. F., ... & Waters, C. (2014). A Map of Dust Reddening to 4.5 kpc from Pan-STARRS1. The Astrophysical Journal789(1), 15. URL

Tan, S. M., Kirchner, R., Jin, J., Hofmann, O., McReynolds, L., Hide, W., & Lieberman, J. (2014). Sequencing of captive target transcripts identifies the network of regulated genes and functions of primate-specific miR-522. Cell reports8(4), 1225-1239. URL

Villaescusa-Navarro, F., Viel, M., Alonso, D., Datta, K. K., Bull, P., & Santos, M. G. (2014). Cross-correlating 21cm intensity maps with Lyman Break Galaxies in the post-reionization era. arXiv preprint arXiv:1410.7393. URL

Vogelsberger, M., Genel, S., Springel, V., Torrey, P., Sijacki, D., Xu, D., ... & Hernquist, L. (2014). Properties of galaxies reproduced by a hydrodynamic simulation. Nature509(7499), 177-182. URL

Wallace, E. W., Airoldi, E. M., & Drummond, D. A. (2013). Estimating selection on synonymous codon usage from noisy experimental data. Molecular biology and evolution, mst051. URL

Wordsworth, R. (2014). Atmospheric heat redistribution and collapse on tidally locked rocky planets. arXiv preprint arXiv:1412.5575.

Zimmerman, K., Levitis, D., Addicott, E., & Pringle, A. (2014). Maximizing the mean nearest neighbor distance of a trait to choose among potential crosses and design a fully crossed mating experiment. bioRxiv, 009720. URL

 

2013 (29 publications)

Blasi, T., Borunda, M. F., Räsänen, E., & Heller, E. J. (2013). Optimal local control of coherent dynamics in custom-made nanostructures. Physical Review B87(24), 241303. URL

Chornock, R., Berger, E., Rest, A., Milisavljevic, D., Lunnan, R., Foley, R. J., ... & Price, P. A. (2013). PS1-10afx at z= 1.388: Pan-STARRS1 Discovery of a New Type of Superluminous Supernova. The Astrophysical Journal767(2), 162. URL

Cobey, S., & Lipsitch, M. (2013). Pathogen diversity and hidden regimes of apparent competition. The American naturalist181(1), 12. URL

Dalla Torre, E. G., Otterbach, J., Demler, E., Vuletic, V., & Lukin, M. D. (2013). Dissipative preparation of spin squeezed atomic ensembles in a steady state.Physical review letters110(12), 120402. URL

David, L. A., Maurice, C. F., Carmody, R. N., Gootenberg, D. B., Button, J. E., Wolfe, B. E., ... & Turnbaugh, P. J. (2014). Diet rapidly and reproducibly alters the human gut microbiome. Nature505(7484), 559-563. URL

Dawson, R. I., Johnson, J. A., Morton, T. D., Crepp, J. R., Fabrycky, D. C., Murray-Clay, R. A., & Howard, A. W. (2012). The photoeccentric effect and proto-hot Jupiters. II. KOI-1474.01, a candidate eccentric planet perturbed by an unseen companion. The Astrophysical Journal761(2), 163. URL

Grabowski, W. W. (2003). MJO-like coherent structures: Sensitivity simulations using the cloud-resolving convection parameterization (CRCP). Journal of the Atmospheric Sciences60(6), 847-864. URL

Gudjonson, H., Kats, M. A., Liu, K., Nie, Z., Kumacheva, E., & Capasso, F. (2014). Accounting for inhomogeneous broadening in nano-optics by electromagnetic modeling based on Monte Carlo methods. Proceedings of the National Academy of Sciences111(6), E639-E644. URL

Hachmann, J., Olivares-Amaya, R., Jinich, A., Appleton, A. L., Blood-Forsythe, M. A., Seress, L. R., ... & Aspuru-Guzik, A. (2014). Lead candidates for high-performance organic photovoltaics from high-throughput quantum chemistry–the Harvard Clean Energy Project. Energy & Environmental Science7(2), 698-704. URL

Hayward, C. C., Narayanan, D., Kereš, D., Jonsson, P., Hopkins, P. F., Cox, T. J., & Hernquist, L. (2013). Submillimetre galaxies in a hierarchical universe: number counts, redshift distribution and implications for the IMF. Monthly Notices of the Royal Astronomical Society428(3), 2529-2547. URL

Herman, M. J., & Kuang, Z. (2013). Linear response functions of two convective parameterization schemes. Journal of Advances in Modeling Earth Systems, 5(3), 510-541. doi:10.1002/jame.20037.

Ingram, T., & Mahler, D. L. (2013). SURFACE: detecting convergent evolution from comparative data by fitting Ornstein‐Uhlenbeck models with stepwise Akaike Information Criterion. Methods in Ecology and Evolution4(5), 416-425. URL

Kawauchi, G. Y., & Giribet, G. (2014). Sipunculus nudus Linnaeus, 1766 (Sipuncula): cosmopolitan or a group of pseudo‐cryptic species? An integrated molecular and morphological approach. Marine Ecology35(4), 478-491. URL

Keenan, T. F., Davidson, E. A., Munger, J. W., & Richardson, A. D. (2013). Rate my data: quantifying the value of ecological data for the development of models of the terrestrial carbon cycle. Ecological Applications23(1), 273-286. URL

Knap, M., Kantian, A., Giamarchi, T., Bloch, I., Lukin, M. D., & Demler, E. (2013). Probing real-space and time-resolved correlation functions with many-body Ramsey interferometry. Physical review letters111(14), 147205. URL

Lunnan, R., Chornock, R., Berger, E., Milisavljevic, D., Drout, M., Sanders, N. E., ... & Price, P. A. (2013). PS1-10bzj: A fast, hydrogen-poor superluminous supernova in a metal-poor host galaxy. The Astrophysical Journal771(2), 97. URL

Nicolaisen, L. E., & Desai, M. M. (2013). Distortions in genealogies due to purifying selection and recombination. Genetics195(1), 221-230. URL

Mansuripur, T. S., & Mansuripur, M. (2014). Fresnel reflection from a cavity with net roundtrip gain. Applied Physics Letters104(12), 121106. URL

Sanders, N. E., Soderberg, A. M., Foley, R. J., Chornock, R., Milisavljevic, D., Margutti, R., ... & Price, P. A. (2013). PS1-12sk is a Peculiar Supernova From a He-rich Progenitor System in a Brightest Cluster Galaxy Environment. The Astrophysical Journal769(1), 39. URL

Snyder, G. F., Hayward, C. C., Sajina, A., Jonsson, P., Cox, T. J., Hernquist, L., ... & Yan, L. (2013). Modeling Mid-infrared Diagnostics of Obscured Quasars and Starbursts. The Astrophysical Journal768(2), 168. URL

Snyder, G. F. (2013). Modeling spatially and spectrally resolved observations to diagnose the formation of elliptical galaxies. URL

Suzuki, N., Maroof, A. M., Merkle, F. T., Koszka, K., Intoh, A., Armstrong, I., ... & Eggan, K. (2013). The mouse C9ORF72 ortholog is enriched in neurons known to degenerate in ALS and FTD. Nature neuroscience16(12), 1725-1727. URL

Tingley, M. P., & Huybers, P. (2013). Recent temperature extremes at high northern latitudes unprecedented in the past 600 years. Nature496(7444), 201-205. URL

Tritsaris, G. A., Kaxiras, E., Meng, S., & Wang, E. (2013). Adsorption and diffusion of lithium on layered silicon for Li-ion storage. Nano letters13(5), 2258-2263. URL

Tritsaris, G. A., Malone, B. D., & Kaxiras, E. (2013). Optoelectronic properties of single-layer, double-layer, and bulk tin sulfide: A theoretical study. Journal of Applied Physics113(23), 233507. URL

Tritsaris, G. A., Kaxiras, E., Meng, S., & Wang, E. (2013). Adsorption and diffusion of lithium on layered silicon for Li-ion storage. Nano letters13(5), 2258-2263. URL

Vahtera, V., Edgecombe, G. D., & Giribet, G. (2013). Phylogenetics of scolopendromorph centipedes: can denser taxon sampling improve an artificial classification?. Invertebrate Systematics27(5), 578-602. URL

Vikas, S. (2013). Quasars, Carbon, and supernovae: Exploring the distribution of elements in an expanding universe (Doctoral dissertation, University of Pittsburgh). URL

Zhao, S. D., Parmigiani, G., Huttenhower, C., & Waldron, L. (2014). Más-o-menos: a simple sign averaging method for discrimination in genomic data analysis. Bioinformatics30(21), 3062-3069. URL

 

2012 (31 publications)

Agarwal, N. (2014). An empirical model of the medical match (No. w20767). National Bureau of Economic Research. URL

Andrade, X., Sanders, J. N., & Aspuru-Guzik, A. (2012). Application of compressed sensing to the simulation of atomic systems. Proceedings of the National Academy of Sciences109(35), 13928-13933. URL

Clements, M. D., Bart, H. L., & Hurley, D. L. (2012). A different perspective on the phylogenetic relationships of the Moxostomatini (Cypriniformes: Catostomidae) based on cytochrome-b and Growth Hormone intron sequences.Molecular phylogenetics and evolution63(1), 159-167. URL

Derr, J., Manapat, M. L., Rajamani, S., Leu, K., Xulvi-Brunet, R., Joseph, I., ... & Chen, I. A. (2012). Prebiotically plausible mechanisms increase compositional diversity of nucleic acid sequences. Nucleic acids research40(10), 4711-4722. URL

Edgecombe, G. D., Vahtera, V., Stock, S. R., Kallonen, A., Xiao, X., Rack, A., & Giribet, G. (2012). A scolopocryptopid centipede (Chilopoda: Scolopendromorpha) from Mexican amber: synchrotron microtomography and phylogenetic placement using a combined morphological and molecular data set. Zoological Journal of the Linnean Society166(4), 768-786. URL

Fung, J., Perry, R. W., Dimiduk, T. G., & Manoharan, V. N. (2012). Imaging multiple colloidal particles by fitting electromagnetic scattering solutions to digital holograms. Journal of Quantitative Spectroscopy and Radiative Transfer,113(18), 2482-2489. URL

Giribet, G., Sharma, P. P., Benavides, L. R., Boyer, S. L., Clouse, R. M., De Bivort, B. L., ... & Schwendinger, P. J. (2012). Evolutionary and biogeographical history of an ancient and global group of arachnids (Arachnida: Opiliones: Cyphophthalmi) with a new taxonomic arrangement. Biological Journal of the Linnean Society105(1), 92-130. URL

Hayward, C. C., Jonsson, P., Kereš, D., Magnelli, B., Hernquist, L., & Cox, T. J. (2012). How to distinguish starbursts and quiescently star-forming galaxies: the ‘bimodal’submillimetre galaxy population as a case study. Monthly Notices of the Royal Astronomical Society424(2), 951-970. URL

Kawauchi, G. Y., Sharma, P. P., & Giribet, G. (2012). Sipunculan phylogeny based on six genes, with a new classification and the descriptions of two new families. Zoologica Scripta41(2), 186-210. URL

Kaz, D. M., McGorty, R., Mani, M., Brenner, M. P., & Manoharan, V. N. (2012). Physical ageing of the contact line on colloidal particles at liquid interfaces.Nature materials11(2), 138-142. URL

Kim, D. W., Protopapas, P., Trichas, M., Rowan-Robinson, M., Khardon, R., Alcock, C., & Byun, Y. I. (2012). A Refined QSO Selection Method Using Diagnostics Tests: 663 QSO Candidates in the Large Magellanic Cloud. The Astrophysical Journal747(2), 107. URL

Liu, J., Orosz, J., & Bregman, J. N. (2012). Dynamical mass constraints on the ultraluminous X-ray source NGC 1313 X-2. The Astrophysical Journal745(1), 89. URL

Padmanabhan, N., Xu, X., Eisenstein, D. J., Scalzo, R., Cuesta, A. J., Mehta, K. T., & Kazin, E. (2012). A 2 per cent distance to z= 0.35 by reconstructing baryon acoustic oscillations–I. Methods and application to the Sloan Digital Sky Survey. Monthly Notices of the Royal Astronomical Society427(3), 2132-2145. URL

Pichara, K., Protopapas, P., Kim, D. W., Marquette, J. B., & Tisserand, P. (2012). An improved quasar detection method in EROS-2 and MACHO LMC data sets. Monthly Notices of the Royal Astronomical Society427(2), 1284-1297. URL

Räsänen, E., Blasi, T., Borunda, M. F., & Heller, E. J. (2012). Optical control of entangled states in semiconductor quantum wells. Physical Review B86(20), 205308. URL

Rotz, D. (2012). Do Outside Options Matter Inside Marriage? Evidence from State Welfare Reforms. Evidence from State Welfare Reforms (June 20, 2012). URL

Sanders, J. N., Saikin, S. K., Mostame, S., Andrade, X., Widom, J. R., Marcus, A. H., & Aspuru-Guzik, A. (2012). Compressed sensing for multidimensional spectroscopy experiments. The Journal of Physical Chemistry Letters3(18), 2697-2702. URL

Sharma, P. P., Schwager, E. E., Extavour, C. G., & Giribet, G. (2012). Hox gene expression in the harvestman Phalangium opilio reveals divergent patterning of the chelicerate opisthosoma. Evolution & development14(5), 450-463. URL

Sharma, P. P., González, V. L., Kawauchi, G. Y., Andrade, S. C., Guzmán, A., Collins, T. M., ... & Giribet, G. (2012). Phylogenetic analysis of four nuclear protein-encoding genes largely corroborates the traditional classification of Bivalvia (Mollusca). Molecular Phylogenetics and Evolution65(1), 64-74. URL

Sharma, P. P. (2012). New Australasian Zalmoxidae (Opiliones: Laniatores) and a new case of male polymorphism in Opiliones. Zootaxa3236, 1-35. URL

Sijacki, D., Vogelsberger, M., Kereš, D., Springel, V., & Hernquist, L. (2012). Moving mesh cosmology: the hydrodynamics of galaxy formation. Monthly Notices of the Royal Astronomical Society424(4), 2999-3027. URL

Steiner, J. F., McClintock, J. E., & Reid, M. J. (2012). The Distance, Inclination, and Spin of the Black Hole Microquasar H1743-322. The Astrophysical Journal Letters745(1), L7. URL

Tritsaris, G. A., Zhao, K., Okeke, O. U., & Kaxiras, E. (2012). Diffusion of lithium in bulk amorphous silicon: a theoretical study. The Journal of Physical Chemistry C116(42), 22212-22216. URL

Tritsaris, G. A., Mathioudakis, C., Kelires, P. C., & Kaxiras, E. (2012). Optical and elastic properties of diamond-like carbon with metallic inclusions: A theoretical study. Journal of Applied Physics112(10), 103503. URL

Vahtera, V., Edgecombe, G. D., & Giribet, G. (2012). Evolution of blindness in scolopendromorph centipedes (Chilopoda: Scolopendromorpha): insight from an expanded sampling of molecular data. Cladistics28(1), 4-20. URL

Wang, Y., Khardon, R., & Protopapas, P. (2012). Nonparametric bayesian estimation of periodic light curves. The Astrophysical Journal756(1), 67. URL

Wang, A., Kaz, D. M., McGorty, R., & Manoharan, V. N. (2013, February). Relaxation dynamics of colloidal particles at liquid interfaces. In 4th International Symposium on Slow Dynamics in Complex Systems: Keep Going Tohoku (Vol. 1518, No. 1, pp. 336-343). AIP Publishing. URL

Watson, M. A., Rappoport, D., Lee, E. M., Olivares-Amaya, R., & Aspuru-Guzik, A. (2012). Electronic structure calculations in arbitrary electrostatic environments. The Journal of chemical physics136(2), 024101. URL

Youdin, A. N., Kratter, K. M., & Kenyon, S. J. (2012). Circumbinary Chaos: Using Pluto's Newest Moon to Constrain the Masses of Nix and Hydra. The Astrophysical Journal755(1), 17. URL

Zhao, K., Tritsaris, G. A., Pharr, M., Wang, W. L., Okeke, O., Suo, Z., ... & Kaxiras, E. (2012). Reactive flow in silicon electrodes assisted by the insertion of lithium. Nano letters12(8), 4397-4403. URL

 

2011 (23 publications)

Aktipis, S. W., & Giribet, G. (2011). Testing relationships among the vetigastropod taxa: a molecular approach. Journal of Molluscan Studies, eyr023. URL

Andrade, S. C., Norenburg, J. L., & Solferini, V. N. (2011). Worms without borders: genetic diversity patterns in four Brazilian Ototyphlonemertes species (Nemertea, Hoplonemertea). Marine biology158(9), 2109-2124. URL

Berezovsky, J., Borunda, M. F., Heller, E. J., & Westervelt, R. M. (2010). Imaging coherent transport in graphene (part I): mapping universal conductance fluctuations. Nanotechnology21(27), 274013. URL

Berg, E., Levin, M., & Altman, E. (2011). Quantized Pumping and Topology of the Phase Diagram for a System of Interacting Bosons. Physical review letters,106(11), 110405. URL

Casse, B. D. F., Lu, W. T., Huang, Y. J., & Sridhar, S. (2011). Robust method to determine the resolution of a superlens by analyzing the near-field image of a two-slit object. arXiv preprint arXiv:1105.0182. URL

Dawson, R. I., Murray-Clay, R. A., & Fabrycky, D. C. (2011). On the Misalignment of the Directly Imaged Planet β Pictoris b with the System's Warped Inner Disk. The Astrophysical Journal Letters743(1), L17. URL

Goldman, J., & Gabrielse, G. (2010). Optimized planar Penning traps for quantum-information studies. Physical Review A81(5), 052335. URL

Fields, A. P., & Cohen, A. E. (2011). Electrokinetic trapping at the one nanometer limit. Proceedings of the National Academy of Sciences108(22), 8937-8942. URL

Gou, L., McClintock, J. E., Reid, M. J., Orosz, J. A., Steiner, J. F., Narayan, R., ... & Davis, S. W. (2011). The extreme spin of the black hole in Cygnus X-1.The Astrophysical Journal742(2), 85. URL

Hachmann, J., Olivares-Amaya, R., Atahan-Evrenk, S., Amador-Bedolla, C., Sánchez-Carrera, R. S., Gold-Parker, A., ... & Aspuru-Guzik, A. (2011). The Harvard clean energy project: large-scale computational screening and design of organic photovoltaics on the world community grid. The Journal of Physical Chemistry Letters2(17), 2241-2251. URL

Hartman, K., Johnson, J. L., Bertoni, M. I., Recht, D., Aziz, M. J., Scarpulla, M. A., & Buonassisi, T. (2011). SnS thin-films by RF sputtering at room temperature. Thin Solid Films519(21), 7421-7424. URL

Hayward, C. C., Kereš, D., Jonsson, P., Narayanan, D., Cox, T. J., & Hernquist, L. (2011). What Does a Submillimeter Galaxy Selection Actually Select? The Dependence of Submillimeter Flux Density on Star Formation Rate and Dust Mass. The Astrophysical Journal743(2), 159. URL

Kajiharal, H., Yamasaki, H., & Andrade, S. C. (2011). Carinoma hamanako sp. nov.(Nemertea: Palaeonemertea), the First Representative of the Genus from the Northwest Pacific. Species Diversity16, 149-165. URL

Kim, D. W., Protopapas, P., Byun, Y. I., Alcock, C., Khardon, R., & Trichas, M. (2011). Quasi-stellar object selection algorithm using time variability and machine learning: Selection of 1620 quasi-stellar object candidates from MACHO Large Magellanic Cloud database. The Astrophysical Journal735(2), 68. URL

Krich, J. J., & Aspuru-Guzik, A. (2011). Scaling and localization lengths of a topologically disordered system. Physical review letters106(15), 156405. URL

Ma, D., & Kuang, Z. (2011). Modulation of radiative heating by the Madden‐Julian Oscillation and convectively coupled Kelvin waves as observed by CloudSat. Geophysical Research Letters38(21). URL

Narayanan, D., Cox, T. J., Hayward, C. C., & Hernquist, L. (2011). The Kennicutt–Schmidt star formation relation at z∼ 2. Monthly Notices of the Royal Astronomical Society412(1), 287-294. URL

Olivares-Amaya, R., Stopa, M., Andrade, X., Watson, M. A., & Aspuru-Guzik, A. (2011). Anion stabilization in electrostatic environments. The Journal of Physical Chemistry Letters2(7), 682-688. URL

Rotz, D. (2011). Why have divorce rates fallen? The role of women’s age at marriage. The Role of Women’s Age at Marriage (December 20, 2011). URL

Sharma, P. P., Vahtera, V., Kawauchi, G. Y., & Giribet, G. (2011). Running WILD: the case for exploring mixed parameter sets in sensitivity analysis.Cladistics27(5), 538-549. URL

Sinkinson, M. (2014). Pricing and entry incentives with exclusive contracts: Evidence from smartphones. Available at SSRN 2391745. URL

Smith, S. A., Wilson, N. G., Goetz, F. E., Feehery, C., Andrade, S. C., Rouse, G. W., ... & Dunn, C. W. (2011). Resolving the evolutionary relationships of molluscs with phylogenomic tools. Nature480(7377), 364-367. URL

Snyder, G. F., Cox, T. J., Hayward, C. C., Hernquist, L., & Jonsson, P. (2011). K+ A Galaxies as the Aftermath of Gas-rich Mergers: Simulating the Evolution of Galaxies as Seen by Spectroscopic Surveys. The Astrophysical Journal,741(2), 77. URL

 

2010 (21 publications)

Aktipis, S. W., Boehm, E., & Giribet, G. (2011). Another step towards understanding the slit‐limpets (Fissurellidae, Fissurelloidea, Vetigastropoda, Gastropoda): a combined five‐gene molecular phylogeny. Zoologica Scripta,40(3), 238-259. URL

Bush, S. J., Cox, T. J., Hayward, C. C., Thilker, D., Hernquist, L., & Besla, G. (2010). Spiral-Induced Star Formation in the Outer Disks of Galaxies. The Astrophysical Journal713(2), 780. URL

Foley, R. J., Narayan, G., Challis, P. J., Filippenko, A. V., Kirshner, R. P., Silverman, J. M., & Steele, T. N. (2010). SN? 2006bt: A Perplexing, Troublesome, and Possibly Misleading Type Ia Supernova. The Astrophysical Journal708(2), 1748. URL

Kim, D. W., Protopapas, P., Alcock, C., Byun, Y. I., Kyeong, J., Lee, B. C., ... & Zhang, Z. W. (2010). The Taiwan-American Occultation Survey Project Stellar Variability. I. Detection of Low-Amplitude δ Scuti Stars. The Astronomical Journal139(2), 757. URL

Leinhardt, Z. M., Marcus, R. A., & Stewart, S. T. (2010). The formation of the collisional family around the dwarf planet Haumea. The Astrophysical Journal,714(2), 1789. URL

Marcus, R. A., Sasselov, D., Hernquist, L., & Stewart, S. T. (2010). Minimum radii of super-Earths: constraints from giant impacts. The Astrophysical Journal Letters712(1), L73. URL

Marcus, R. A., Sasselov, D., Stewart, S. T., & Hernquist, L. (2010). Water/icy super-Earths: giant impacts and maximum water content. The Astrophysical Journal Letters719(1), L45. URL

McEachern, F. M., Ćuk, M., & Stewart, S. T. (2010). Dynamical evolution of the Hungaria asteroids. Icarus210(2), 644-654. URL

Murienne, J., Edgecombe, G. D., & Giribet, G. (2010). Including secondary structure, fossils and molecular dating in the centipede tree of life. Molecular Phylogenetics and Evolution57(1), 301-313. URL

Murienne, J., Karaman, I., & Giribet, G. (2010). Explosive evolution of an ancient group of Cyphophthalmi (Arachnida: Opiliones) in the Balkan Peninsula.Journal of Biogeography37(1), 90-102. URL

Nadell, C. D., Foster, K. R., & Xavier, J. B. (2010). Emergence of spatial structure in cell groups and the evolution of cooperation. PLoS computational biology6(3), e1000716. URL

Narayanan, D., Hayward, C. C., Cox, T. J., Hernquist, L., Jonsson, P., Younger, J. D., & Groves, B. (2010). The formation of high-redshift submillimetre galaxies. Monthly Notices of the Royal Astronomical Society401(3), 1613-1619. URL

Narayanan, D., Dey, A., Hayward, C. C., Cox, T. J., Bussmann, R. S., Brodwin, M., ... & Hernquist, L. (2010). A physical model for z∼ 2 dust-obscured galaxies.Monthly Notices of the Royal Astronomical Society407(3), 1701-1720. URL

Narayanan, D., Hayward, C. C., Cox, T. J., Hernquist, L., Jonsson, P., Younger, J. D., & Groves, B. (2010). The formation of high-redshift submillimetre galaxies. Monthly Notices of the Royal Astronomical Society401(3), 1613-1619. URL

Narayanan, D., Cox, T. J., Hayward, C. C., Younger, J. D., & Hernquist, L. (2009). The star-forming molecular gas in high-redshift Submillimetre Galaxies.Monthly Notices of the Royal Astronomical Society400(4), 1919-1935. URL

Rogers, R. L., Bedford, T., Lyons, A. M., & Hartl, D. L. (2010). Adaptive impact of the chimeric gene Quetzalcoatl in Drosophila melanogaster. Proceedings of the National Academy of Sciences107(24), 10943-10948. URL

Romps, D. M., & Kuang, Z. (2010). Nature versus nurture in shallow convection.Journal of the Atmospheric Sciences67(5), 1655-1666. URL

Tingley, M. P., & Huybers, P. (2010). A Bayesian algorithm for reconstructing climate anomalies in space and time. Part I: Development and applications to paleoclimate reconstruction problems. Journal of Climate23(10), 2759-2781. URL

Tingley, M. P., & Huybers, P. (2010). A Bayesian algorithm for reconstructing climate anomalies in space and time. Part II: Comparison with the regularized expectation-maximization algorithm. Journal of Climate23(10), 2782-2800. URL

Tchekhovskoy, A., Narayan, R., & McKinney, J. C. (2011). Efficient generation of jets from magnetically arrested accretion on a rapidly spinning black hole.Monthly Notices of the Royal Astronomical Society: Letters418(1), L79-L83. URL

Xu, X., Narayanan, D., & Walker, C. (2010). Molecular Disk Properties in Early-type Galaxies. The Astrophysical Journal Letters721(2), L112. URL

 

2009 (3 publications)

Blocker, A. W., Protopapas, P., & Alcock, C. R. (2009). A Bayesian approach to the analysis of time symmetry in light curves: reconsidering Scorpius X-1 occultations. The Astrophysical Journal701(2), 1742. URL

Likovich, E. M., Russell, K. J., Narayanamurti, V., Lu, H., & Gossard, A. C. (2009). Direct injection tunnel spectroscopy of a pn junction. Applied Physics Letters95(2), 022106_1-022106_3. URL

Younger, J. D., Hayward, C. C., Narayanan, D., Cox, T. J., Hernquist, L., & Jonsson, P. (2009). The merger-driven evolution of warm infrared luminous galaxies. Monthly Notices of the Royal Astronomical Society: Letters396(1), L66-L70. URL

Last updated: April 20, 2017 at 14:55 pm