HPC Research Publications

Physics and Astronomy ​​​

• Ball D, Sironi L, Ozel F. Electron and Proton Acceleration in Trans-Relativistic Magnetic Reconnection: Dependence on Plasma Beta and Magnetization. eprint arXiv:1803.05556
• Comisso L, Sironi L. Particle Acceleration in Relativistic Plasma Turbulence. eprint: arXiv:1809.01168
• Hendel D et al. SMHASH: Anatomy of the Orphan Stream using RR Lyrae stars. eprint; arXiv 1711.04663
• Guo X, Sironi L, Narayan R. Electron Heating in Low Mach Number Perpendicular shocks. II. Dependence on the Pre-Shock Conditions. eprint arXiv:1712.03239
• Guo X, Sironi L, Narayan R. Electron Heating in Low Mach Number Perpendicular shocks. I. Heating Mechanism. eprint arXiv:1710.07648
• Grcevich et al.,Potential New Local Group Dwarf Galaxies in the GALFA-HI Catalog,   ApJ.
• Lee, D.M., Johnston, K.V., Sen, B. & Jessop, W. "Deriving Milky Way Accretion Histories from Abundance Patterns," in preparation.
• Perez, K I, Bogdanov, S., Halpern J P, Gajjar, V. Green Bank Telescope Discovery of the Redback Binary Millisecond Pulsar PSR J0212+5321, 2023, The Astrophysical Journal.
• Plotnikov I and Sironi L. The synchrotron maser emission from relativistic shocks in Fast Radio Bursts: 1D PIC simulations of cold pair plasmas. eprint: arXiv:1901.01029
• Rowan ME, Sironi L, Narayan R. Electron and Proton Heating in Transrelativistic Guide Field Reconnection. eprint: arXiv:1901.05438
• Rowan ME, Sironi L, Narayan R. Electron and proton heating in trans-relativistic magnetic reconnection. eprint arXiv:1708.04627.
• P. Shih and T. C. Berkelbach*, “Anharmonic Lattice Dynamics from Vibrational Dynamical Mean-Field Theory”, arXiv:2109.00028, under review in Phys. Rev. Lett.
• I. Stone, R. L. Starr, N. Hoffmann†, X. Wang†, A. M. Evans, C. Nuckolls, T. H. Lambert, M. L. Steigerwald, T. C. Berkelbach*, X. Roy*, and L. Venkataraman*, “Electrified surfaces catalyze Ullmann coupling reactions”, under review in Angewandte Chemie
• Tavecchio F, Landoni M, Sironi L, Coppi P. Probing dissipation mechanisms in BL Lac jets through X-ray polarimetry. eprint arXiv: 1801.10060
• Lee, D.M., Johnston, K.V., Sen, B. & Jessop, W. "Deriving Milky Way Accretion Histories from Abundance Patterns."
• Abruzzo, M. W., Bryan, G. L., & Fielding, D. B. (2022), "A Simple Model for Mixing and Cooling in Cloud-Wind Interactions", The Astrophysical Journal, 925, 199.
• Y. Cho, S. J. Bintrim, and T. C. Berkelbach*, “A simplified GW/BSE approach for charged and neutral excitation energies of large molecules and nanostructures”, J. Chem. Theory Comput. in press (2022)
• Creel, R. C. et al. Postglacial relative sea level change in Norway. Quaternary Science Reviews 282, 107422 (2022).
• Nongnuch Artrith, José Antonio Garrido Torres, Alexander Urban, and Mark S. Hybertsen, Data-driven approach to parameterize SCAN + U for an accurate description of 3d transition metal oxide thermochemistry, Phys. Rev. Materials 6, 035003 – Published 23 March 2022, https://doi.org/10.1103/PhysRevMaterials.6.035003
• S. J. Bintrim, and T. C. Berkelbach*, “Full-frequency dynamical Bethe-Salpeter equation without frequency and a study of double excitations”, J. Chem. Phys. 156, 044114 (2022)
• J. M. Callahan, M. F. Lange, and T. C. Berkelbach*, “Dynamical correlation energy of metals in large basis sets from downfolding and composite approaches”, J. Chem. Phys. 154, 211105 (2021)
• Robert E. Colgan, Zsuzsa Márka, Jingkai Yan, Imre Bartos, John N. Wright, Szabolcs Márk. Detecting and Diagnosing Terrestrial Gravitational-Wave Mimics Through Feature Learning. arXiv preprint arXiv:2203.05086 – Published 9 March 2022
• Self-lensing flares from black hole binaries I: general-relativistic ray tracing of black hole binaries. J. Davelaar & Z. Haiman. Accepted to appear in Physical Review D, submitted January (2022) [arXiv:2112.05828]
• Self-lensing flares from black hole binaries II: observing black hole shadows via light-curve tomography. J. Davelaar & Z. Haiman. Accepted to appear in Physical Review Letters, submitted January (2022) [arXiv:2112.05829]
• Fielding, D. B., & Bryan, G. L. (2022), "The Structure of Multiphase Galactic Winds", The Astrophysical Journal, 924, 82.
• Grcevich et al.,Potential New Local Group Dwarf Galaxies in the GALFA-HI Catalog,   ApJ.
• S. M. Greene, R. J. Webber, J. E. T. Smith, J. Weare*, and T. C. Berkelbach*, “Full Configuration Interaction Excited-State Energies in Large Active Spaces from Randomized Subspace Iteration”, arXiv:2201.12164, under review in J. Chem. Theory Comput.
• A. Kusiak, B. Bolliet, A. Krolewski, and J. C. Hill. “Constraining the galaxy-halo connection of infrared-selected unWISE galaxies with galaxy clustering and galaxy-CMB lensing power spectra” (2022). Phys. Rev. D submitted, https://arxiv.org/abs/2203.12583
• Comparing weak lensing peak counts in baryonic correction models to hydrodynamical simulations. Max E. Lee, Tianhuan Lu, Zoltan Haiman, Jia Liu, Ken Osato. Submitted to Monthly Notices of the Royal Astronomical Society, January (2022)   [arXiv:2201.08320]
• Xiang Li,Xinhao Li,Lisa Monluc,Benjamin Chen,Mingxue Tang,Po-Hsiu Chien,Xuyong Feng,Ivan Hung,Zhehong Gan,Alexander Urban,Yan-Yan Hu, Stacking-Fault Enhanced Oxygen Redox in Li2MnO3, 2022,  https://doi.org/10.1002/aenm.202200427
• Simultaneously constraining cosmology and baryonic physics via deep learning from weak lensing. T. Lu, Z. Haiman & J. M. Zorrilla. Monthly Notices of the Royal Astronomical Society, Volume 511, Issue 1, pp.1518-1528 (2022)
• V. A. Neufeld, H.-Z. Ye, and T. C. Berkelbach*, “Ground-state properties of metallic solids from ab initio coupled-cluster theory”, arXiv:2204.01563. Published 4 April 2022
• Cosmological constraints from weak lensing peaks: Can halo models accurately predict peak counts? A. Sabyr, Z. Haiman, J. M. Zorrilla & T. Lu. Physical Review D, Volume 105, Issue 2, article id.023505 (2022)
•  A. Sabyr, J. C. Hill, and B. Bolliet. “Inverse-Compton Scattering of the Cosmic Infrared Background” (2022). Phys. Rev. D submitted, https://arxiv.org/abs/2202.02275
• Sridhar, N., Sironi, L., & Beloborodov, A. M. 2022. “Comptonization by Reconnection Plasmoids in Black Hole Coronae II: Electron-Ion Plasma.” arXiv:2203.02856
• Jingkai Yan, Mariam Avagyan, Robert E. Colgan, Doğa Veske, Imre Bartos, John Wright, Zsuzsa Márka, and Szabolcs Márka. Generalized approach to matched filtering using neural networks Phys. Rev. D 105, 043006 – Published 10 February 2022
• S. J. Bintrim and T. C. Berkelbach*, “Full-frequency GW without frequency”, J. Chem. Phys., 154, 041101 (2021)
• Y. Cho, S. M. Greene, and T. C. Berkelbach*, “Simulations of Trions and Biexcitons in Layered Hybrid Organic-Inorganic Lead Halide Perovskites”, Phys. Rev. Lett. 126, 216402 (2021)
• Tomer D. Yavetz, Xinyu Li, and Lam Hui, Construction of wave dark matter halos: Numerical algorithm and analytical constraints, Phys. Rev. D 105, 023512 – Published 10 January 2022. https://journals-aps-org.ezproxy.cul.columbia.edu/prd/abstract/10.1103/PhysRevD.105.023512
• J. H. Fetherolf and T. C. Berkelbach*, “Vibrational heat-bath configuration interaction”, J. Chem. Phys., 154, 074104 (2021)
• Kulkarni, M., Visbal, E., & Bryan, G. L. (2021), "The Critical Dark Matter Halo Mass for Population III Star Formation: Dependence on Lyman-Werner Radiation, Baryon-dark Matter Streaming Velocity, and Redshift", The Astrophysical Journal, 917, 40.
• B. T. G. Lau, G. Knizia*, and T. C. Berkelbach*, “Regional Embedding Enables High-Level Quantum Chemistry for Surface Science”, J. Phys. Chem. Lett. 12, 1104 (2021); Featured on the cover
• Garrido Torres, J.A., Gharakhanyan, V., Artrith, N. et al. Augmenting zero-Kelvin quantum mechanics with machine learning for the prediction of chemical reactions at high temperatures. Nat Commun 12, 7012 (2021). https://doi.org/10.1038/s41467-021-27154-2
•  N. M. Hoffmann^†, X. Wang^†, and T. C. Berkelbach*, “Linear free energy relationships in electrostatic catalysis”, arXiv:2111.14978, under review in J. Am. Chem. Soc.
• A. Kusiak, B. Bolliet, S. Ferraro, J. C. Hill, and A. Krolewski.  "Constraining the Baryon Abundance with the Kinematic Sunyaev-Zel'dovich Effect: Projected-Field Detection Using Planck, WMAP, and unWISE" (2021).  Phys. Rev. D, 104, 043518, https://arxiv.org/abs/2102.01068
• A. Sabyr, Z. Haiman, J. M. Zorrilla & T. Lu. Cosmological Constraints from Weak Lensing Peaks: Can Halo Models Accurately Predict Peak Counts? Submitted to Physical Review D, September (2021)
• Tonnesen, S., & Bryan, G. L. (2021), "It's Cloud's Illusions I Recall: Mixing Drives the Acceleration of Clouds from Ram Pressure Stripped Galaxies", The Astrophysical Journal, 911, 68.
• Wolcott-Green, J., Haiman, Z., & Bryan, G. L. (2021), "Suppression of H-cooling in protogalaxies aided by trapped Lyα cooling radiation", Monthly Notices of the Royal Astronomical Society, 500, 138.
• Sridhar, N., Sironi, L., & Beloborodov, A. M. 2021. “Comptonization by Reconnection Plasmoids in Black Hole Coronae I: Magnetically Dominated Pair Plasma” MNRAS 507, 5625-5640
• C. Xin & Z. Haiman. Ultra-short-period massive black hole binary candidates in LSST as LISA "verification binaries". Monthly Notices of the Royal Astronomical Society, Volume 506, Issue 2, pp.2408-2417 (2021)
• H.-Z. Ye and T. C. Berkelbach*, “Tight distance-dependent estimators for screening two-center and three-center short-range Coulomb integrals over Gaussian basis functions”, J. Chem. Phys. 155, 124106 (2021)
• H. Ye and T. C. Berkelbach*, “Fast periodic Gaussian density fitting by range separation”, J. Chem. Phys. 154, 131104 (2021)
• A. Derdzinski, D. D'Orazio, P. Duffell, Z. Haiman, A. MacFadyen.Evolution of gas disc-embedded intermediate mass ratio inspirals in the LISA band. Monthly Notices of the Royal Astronomical Society, Volume 501, Issue 3, pp. 3540-3557 (2021)
• B. X. Hu, D. J. D'Orazio, Z. Haiman, K. L. Smith, B. Snios, M. Charisi & R. Di Stefano Spikey. A Search for Lensing Flares from SMBH Binaries. Monthly Notices of the Royal Astronomical Society, vol. 495, pp. 4061-4070 (2020)
• M. F. Lange and T. C. Berkelbach*, “Active space approaches combining coupled-cluster and perturbation theory for ground states and excited states”, Mol. Phys. e1808726 (2020)
• Aaron Tran and Lorenzo Sironi 2020 ApJL 900 L36, https://doi.org/10.3847/2041-8213/abb19c
• J. Wolcott-Green, Z. Haiman & G. L. Bryan. Suppression of H2-cooling in protogalaxies aided by trapped Lyα cooling radiation. Monthly Notices of the Royal Astronomical Society, vol. 500, pp. 138-144 (2020)
• C. Xin, M. Charisi, Z. Haiman & D. Schiminovich. Correlation between Optical and UV Variability of Quasars. Monthly Notices of the Royal Astronomical Society, vol. 495, pp. 1403-1413 (2020). 
• C. Xin, M. Charisi, Z. Haiman, M. J. Graham, D. Stern, D. J D'Orazio & D. Schiminovich. Testing the relativistic Doppler boost hypothesis for the binary candidate quasar PG1302-102 with multi-band Swift data. Monthly Notices of the Royal Astronomical Society, vol. 496, pp. 1683-1696 (2020)
• J. M. Zorrilla, S. Waterval & Z. Haiman. Optimizing simulation parameters for weak lensing analyses involving non-Gaussian observables. The Astrophysical Journal, Volume 159, Issue 6, id.284 (2020)
• J. M. Zorrilla, M. Sharma, D. Hsu & Z. Haiman. Interpreting deep learning models for weak lensing. Physical Review D, Volume 102, Issue 12, article id.123506 (2020)
• J. M. Zorrilla & Z. Haiman. Probing gaseous galactic halos through the rotational kSZ effect
• Physical Review D, Volume 101, Issue 8, article id.083016 (2020).
• Robert E. Colgan, K. Rainer Corley, Yenson Lau, Imre Bartos, John N. Wright, Zsuzsa Márka, and Szabolcs Márka. Efficient gravitational-wave glitch identification from environmental data through machine learning. Phys. Rev. D 101, 102003 – Published 20 May 2020.
• Chakraborty, J. et al, “Hundreds of new periodic signals detected in the first year of TESS with the weirddetector”, 2020, MNRAS, 499, 4011.
• Robert E. Colgan, K. Rainer Corley, Yenson Lau, Imre Bartos, John N. Wright, Zsuzsa Márka, and Szabolcs Márk.  Efficient gravitational-wave glitch identification from environmental data through machine learning Phys. Rev. D 101, 102003 – Published 20 May 2020
• Li, M., Li, Y., Bryan, G. L., Ostriker, E. C., & Quataert, E. (2020), "The Impact of Type Ia Supernovae in Quiescent Galaxies. II. Energetics and Turbulence", The Astrophysical Journal, 898, 23.
• Visbal, E., Bryan, G. L., & Haiman, Z. (2020), "Self-consistent Semianalytic Modeling of Feedback during Primordial Star Formation and Reionization", The Astrophysical Journal, 897, 95.
• DeFelippis, D., Genel, S., Bryan, G. L., Nelson, D., Pillepich, A., & Hernquist, L. (2020), "The Angular Momentum of the Circumgalactic Medium in the TNG100 Simulation", The Astrophysical Journal, 895, 17.
• Li, M., Li, Y., Bryan, G. L., Ostriker, E. C., & Quataert, E. (2020), "The Impact of Type Ia Supernovae in Quiescent Galaxies. I. Formation of the Multiphase Interstellar Medium", The Astrophysical Journal, 894, 44.
• Emerick, A., Bryan, G. L., & Mac Low, M.-M. (2020), "Simulating Metal Mixing of Both Common and Rare Enrichment Sources in a Low-mass Dwarf Galaxy", The Astrophysical Journal, 890, 155.
• T. Lu & Z. Haiman. The matter fluctuation amplitude inferred from the weak lensing power spectrum and correlation function in CFHTLenS data. Monthly Notices of the Royal Astronomical Society, vol. 490, pp. 5033-5042 (2019)
• D. Ribli, B. A. Pataki, J. M. Zorrilla, D. Hsu, Z. Haiman & I. Csabai. Weak lensing cosmology with convolutional neural networks on noisy data. Monthly Notices of the Royal Astronomical Society, vol. 490, pp. 1843-1860 (2019)
• M. Abruzzo & Z. Haiman. The Impact of Photometric Redshift Errors on Lensing Statistics in Ray-Tracing Simulations. Monthly Notices of the Royal Astronomical Society, vol. 486, pp. 2730-2753 (2019)
• J. Wolcott-Green & Z. Haiman. H2 self-shielding with non-LTE rovibrational populations: implications for cooling in protogalaxies. Monthly Notices of the Royal Astronomical Society, vol. 484, pp. 2467-2473 (2019)
• A. Derdzinski, D. D'Orazio, P. Duffell, Z. Haiman & A. MacFadyen. Probing gas disc physics with LISA: simulations of an intermediate mass ratio inspiral in an accretion disc. Monthly Notices of the Royal Astronomical Society, Volume 486, Issue 2, pp. 2754-2765 (2019)
• C. Fontecilla, Z. Haiman & J. Cuadra. Non-steady-state long-term evolution of supermassive black hole binaries surrounded by accretion discs. Monthly Notices of the Royal Astronomical Society, vol. 482, pp. 4383-4396 (2019)
• Li, Y., Bryan, G. L., & Quataert, E. (2019), "The Fate of Asymptotic Giant Branch Winds in Massive Galaxies and the Intracluster Medium", The Astrophysical Journal, 887, 41.
• Melso, N., Bryan, G. L., & Li, M. (2019), "Simulating Gas Inflow at the Disk-Halo Interface", The Astrophysical Journal, 872, 47.
• Visbal E, Haiman Z, Bryan GL. Self-consistent semi-analytic models of the first stars. 2018, Monthly Notices of the Royal Astronomical Society.
• Lam C, & Kipping D. Machine learns to predict the stability of circumbinary planets. 2018, MNRAS, In Press (arXiv e-prints:1801.03955)
• Jansen T, Kipping D. Kepler's Dark Worlds: a Low Albedo for an Ensemble of Neptunian and Terran Exoplanets. 2018, MNRAS, submitted (arXiv e-prints:1710.10213)
• Smith, B.D., Bryan, G. L., et al. 2017,  ``GRACKLE: a chemistry and cooling library for astrophysics", MNRAS, 466, 2217
• DeFelippis, D., Genel, S., Bryan, G., & Fall, S.M. 2017,  ``The Impact of Galactic Winds on the Angular Momentum of Disk Galaxies in the Illustris Simulation", ApJ, in press
• Li, M., Bryan, G.L., & Ostriker, J.P. 2017,  ``O VI Emission from the Supernovae-regulated Interstellar Medium: Simulation versus Observation", ApJ, 835, L10
• Li Y, Ruszkowski M, Bryan GL. AGN Heating in Simulated Cool-core Clusters. 2017, The Astrophysical Journal.
• Visbal E, Bryan GL, Haiman, Z. What is the maximum mass of a Population III galaxy? 2017,  Monthly Notices of the Royal Astronomical Society.
• Blancato K, Genel S, Bryan GL. Implications of Galaxy Buildup for Putative IMF Variations in Massive Galaxies. 2017, The Astrophysical Journal.
• Li M, Bryan GL, Ostriker JP. Quantifying Supernovae-driven Multiphase Galactic Outflows. 2017, The Astrophysical Journal.
• DeFelippis D, Genel S, Bryan GL, Fal SM. The Impact of Galactic Winds on the Angular Momentum of Disk Galaxies in the Illustris Simulation. 2017, The Astrophysical Journal.
• Li, M., Bryan, G.L., & Ostriker, J.P. 2016,  ``Quantifying Supernovae-Driven Multiphase Galactic Outflows", ApJ, in press
• Chen, J., Bryan, G.L., & Salem, M. 2016,  ``Cosmological simulations of dwarf galaxies with cosmic ray feedback", MNRAS, 460, 3335
• M. Charisi, I. Bartos, Z. Haiman, A. M. Price-Whelan, S. Marka submitted to Monthly Notices of the Royal Astronomical Society Letters, February (2015)
• A reduced orbital period for the supermassive black hole binary candidate in the quasar PG 1302-102? D. J. D'Orazio, Z. Haiman, P. Duffell, B. D. Farris, A. I. MacFadyen submitted to Monthly Notices of the Royal Astronomical Society Letters, February (2015)
• Cosmology Constraints from the Weak Lensing Peak Counts and the Power Spectrum in CFHTLenS J. Liu, A. Petri, Z. Haiman, L. Hui, J. M. Kratochvil & M. May Physical Review D, vol. 91, Issue 6, id. 063507 (2015)
• Voit, G.M., Donahue, M., Bryan, G.L., & McDonald, M. (2015), "Regulation of star formation in giant galaxies by precipitation, feedback and conduction", Nature, 519, 203
• Voit, G.M., Donahue, M., O'Shea, B.W., Bryan, G.L., Sun, M., & Werner, N. (2015), "Supernova Sweeping and Black-Hole Feedback in Elliptical Galaxies", Astrophys J Lett, in press
• Makoto Asai, Takuya Katashima, Takamasa Sakai, Mitsuhiro Shibayama (2015), "Supercoiling Transformation of Chemical Gels", Soft Matter, 10.1039/C5SM01550B
• The impact of spurious shear on cosmological parameter estimates from weak lensing observables A. Petri, M. May, Z. Haiman, J. M. Kratochvil Physical Review D, vol. 90, Issue 12, id. 123015 (2014)
• The Migration of Gap-opening Planets is Not Locked to Viscous Disk Evolution P. Duffell, Z. Haiman, A. I. MacFadyen, D. J. D'Orazio & B. D. Farris The Astronomical Journal Letters, vol. 792, issue 1, article id. L10, 4 pp. (2014)
• Lyman edges in supermassive black hole binaries A. Generozov & Z. Haiman, Monthly Notices of the Royal Astronomical Society, vol. 443, pp. L64-L68 (2014)
• The Impact of Magnification and Size Bias on Weak Lensing Power Spectrum and Peak Statistics J. Liu, Z. Haiman, L. Hui, J. M. Kratochvil & M. May Physical Review D, vol. 89, Issue 1, id. 023515 (2014)
• Catalog of Isolated Emission Episodes in Gamma-ray Bursts from Fermi, Swift and BATSE Charisi, Maria; Marka, Szabolcs; Bartos, Imre submitted to Monthly Notices of the Royal Astronomical Society Letters, September (2014)
• Inferring the Gravitational Potential of the Milky Way with a Few Precisely Measured Stars Price-Whelan, A. M. et al. 2014 ApJ 794 4
• Salem, M., Bryan, G.L., & Hummels, C. (2014), "Cosmological Simulations of Galaxy Formation with Cosmic Rays", Astrophys J Lett, 797, LL18
• Visbal, E., Haiman, Z., & Bryan, G.L. (2014), "Direct collapse black hole formation from synchronized pairs of atomic cooling haloes", Monthly Notices of the Royal Astronomical Society Letters, 445, 1056 
• Visbal, E., Haiman, Z., Terrazas, B., Bryan, G.L., & Barkana, R. (2014), "High-redshift star formation in a time-dependent Lyman-Werner background", Monthly Notices of the Royal Astronomical Society Letters, 445, 107
• Li, Yuan and Bryan, Greg L. (2014) "Modeling AGN Feedback in Cool-Core Clusters: The Formation of Cold Clumps", Astrophysical J., in press.
• Li, Yuan and Bryan, Greg L. (2014) "Modeling AGN Feedback in Cool-Core Clusters: The Balance between Heating and Cooling", Astrophysics J., in press.
• Salem, Munier and Bryan, Greg. L. (2014) "Cosmic ray driven outflows in global galaxy disc models", Monthly Notices of the Royal Astronomical Society, 437, 3314.
• Fernandez, R., Bryan, G.L., Haiman, Z. and Miao, Li (2014) "H_2 suppression with shocking inflows: testing a pathway for supermassive black hole formation", Monthly Notices of the Royal Astronomical Society, 439, 3798.
• Bryan, G.L. et al. (2014) "Enzo: An Adaptive Mesh Refinement Code for Astrophysics", Astrophysical J. Supplement, 211, 19.
• Passy, J.-C., & Bryan, G.L. (2014), "An Adaptive Particle-mesh Gravity Solver for ENZO", Astrophysical J, 215, 8
• Visbal, E., Haiman, Z., & Bryan, G.L. (2014), "A no-go theorem for direct collapse black holes without a strong ultraviolet background", Monthly Notices of the Royal Astronomical Society Letters, 442, L100
• Joshua Schroeder, Andrei Mesinger and Zoltan Haiman (2013). "Evidence of Gunn--Peterson damping wings in high-z quasar spectra.
• Corlies, Lauren; Johnston, Kathryn V.; Tumlinson, Jason; Bryan, Greg L., 2013, "Chemical Abundance Patterns and the Early Environment of Dwarf Galaxies", 2013, Astrophysical J., 773, 105.
• Lee, D.M., Johnston, K.V., Tumlinson, J.,  Sen, B, & Simon, J, (2013) "A Mass-Dependent-Yield Origin for Neutron-Capture Distributions in Ultra-Faint Dwarf Galaxies",  Astrophysical Journal, 774, 103
• Price-Whelan, Adrian and Johnston, Kathryn V. (2013) "Spitzer, Gaia and the Potential of the Milky Way", Astrophysical Journal Letters, 778, L12
• Hummels, C., Bryan, G., Smith, B., & Turk, M. (2013),  ``Constraints on Hydrodynamical Subgrid Models from Quasar Absorption Line Studies of the Simulated Circumgalactic Medium", Monthly Notices of the Royal Astronomical Society, 430, 1548.
• Simpson, C. M., Bryan, G. L., Johnston, K. V., Smith, B. D., Mac Low, M.-M., Sharma, S., & Tumlinson, J. (2013),  ``The effect of feedback and reionization on star formation in low-mass dwarf galaxy haloes", Monthly Notices of the Royal Astronomical Society, 432, 1989
• Grcevich, J. 2012, Neutral Hydrogen in Local Group Dwarf Galaxies, PhD thesis, Columbia University.
• Joung, M. R., Bryan, G. L., & Putman, M. E. (2012),  ``Gas Condensation in the Galactic Halo", Astrophysical J., 745, 148
• Li, Y., & Bryan, G. L. (2012),  ``Simulating the Cooling Flow of Cool-core Clusters", Astrophysical Journal, 747, 26
• Turk, M. J., Oishi, J. S., Abel, T., & Bryan, G. L. (2012),  ``Magnetic Fields in Population III Star Formation", Astrophysical Journal, 745, 154
• Hummels, C. B., & Bryan, G. L. (2012),  ``Adaptive Mesh Refinement Simulations of Galaxy Formation: Exploring Numerical and Physical Parameters", Astrophysical J., 749, 140
• Tonnesen, S., & Bryan, G. L. (2012)  ``Star formation in ram pressure stripped galactic tails", Monthly Notices of the Royal Astronomical Society, 422, 1609.
• Joung, M. R., Putman, M. E., Bryan, G. L., Fernandez, X., & Peek, J. E. G. (2012),  ``Gas Accretion is Dominated by Warm Ionized Gas in Milky Way Mass Galaxies at z ~ 0", Astrophysical J., 759, 137
• Yoon, J. H., Putman, M. E., Thom, C., Chen, H.-W., & Bryan, G. L. (2012),  ``Warm Gas in the Virgo Cluster. I. Distribution of Ly alpha Absorbers", Astrophysical Journal, 754, 84
• Hummels, C. (2012), "Comparing Simulations and Observations of Galaxy Evolution: Methods for Constraining the Nature of Stellar Feedback", Ph.D. Thesis, Columbia University
• Svedin, A. (2012), "Nonlinear Data Assimilation: towards a prediction of the solar cycle.", Ph.D. Thesis, Columbia University
• Teyssier, M., Johnston, Kathryn V., Kuhlen, M. (2012), "Identifying Local Group field galaxies that have interacted with the Milky Way", Monthly Notices of the Royal Astronomical Society, 436, 1808
• D'Orazio, D. J., Haiman, Z., MacFadyen, A. (2012), "Accretion into the Central Cavity of a Circumbinary Disk", Monthly Notices of the Royal Astronomical Society.
• Tonnesen, S., Bryan, G.L. & Chen, R. (2011) How To Light It Up: Simulating Ram-Pressure Stripped X-ray Bright Tails, Astrophysical J., 731, 98
• Wolcott-Green, J., Haiman, Z., Bryan, G.L. (2011), "Photodissociation of H2 in protogalaxies: modelling self-shielding in three-dimensional simulations", Mon. Not. Roy. Astro. Soc., 418, 838
• Yoon, J. H., Johnston, K.V. & Hogg, D.W., (2011) "Clumpy streams from clumpy halos: detecting Missing Satellites Using Thin Stellar Structures", Astrophysical Journal, 731, 58
• Passy, J.-C., De Marco, O. Fryer, Cc. L., Herwig, F., Diehl, S., Oishi, J. S., Mac Low, M.; Bryan, G. L.; Rockefeller, G. (2012), Astrophysical J., 744, 52
• Putman, M., Joung, M.R., Grcevich, J., Heitsch, F. 2010, in Galaxies and their Masks, eds. Block, D., Freeman, K.C., Puerari, I., Springer, p. 87  (ISBN 978-1-4419-7316-0).
• Pereira, M. and Bryan, G.L. (2010). Tidal Torquing of Galaxies in Cluster Environments, Astrophysical J., 721, 939.
• Shang, C., Bryan, G.L., Haiman, Z. (2010), Supermassive black hole formation by direct collapse: keeping protogalactic gas H2 free in dark matter haloes with virial temperatures Tvir > 104 K, Mon. Not. Royal Astro. Soc. 402, 1249
• Tonnesen, S., Bryan, G.L. (2010), The Tail of the Stripped Gas that Cooled: H I, Ha, and X-ray Observational Signatures of Ram Pressure Stripping, Astrophysical J., 709, 1203
• Putman, M.E., Joung, M.R., Grcevich, J., Heitsch, F. (2010), The Gaseous Halo Mask, to appear in the conference proceedings of "Galaxies and their Masks", held April 11, 2010
• Molnar, S.M., Chiu, I.-N., Umetsu, K., Chen, P., Hearn, N., Broadhurst, T., Bryan, G., Shang, C. (2010), Testing Strict Hydrostatic Equilibrium in Simulated Clusters of Galaxies: Implications for A1689, Astrophysical J. 724, L1

Biomedical Sciences 

• Carrillo-Reid L, Han S, Taralova E, Jebara T, Yuste R. Identification and Targeting of Cortical Ensembles. bioRxiv 226514; doi: https://doi.org/10.1101/226514
• Cassavim, M.I.A.*, Baker, Z.*, Hoge, C., Schierup, M.M., Schumer, M., and M. Przeworski, PRDM9 losses in vertebrates are coupled to those of paralogs ZCWPW1 and ZCWPW2. On BioRxiv. PNAS 119: e2114401119. *Contributed equally
• Grace W. Lindsay, Mattia Rigotti, Melissa R Warden, Earl K Miller and Stefano Fusi "Hebbian Learning in a Random Network Replicates Selectivity Properties of Prefrontal Cortical Neurons”
• de Manuel, M., Wu, F., and M. Przeworski. 2022 A paternal bias in mutation is widespread across amniotes and can arise independently of cell divisions. On BioRxiv.
• Guo, Q.; Boyce, C. M. Structured Bubbling in Layered Gas-Fluidized Beds Subject to Vibration: A CFD-DEM Study. AIChE J. 2022, e17709. https://doi.org/10.1002/aic.17709.
• Guo, Q.; Zhang, Y.; Vazquez, C.; Xi, K.; Boyce, C. M. Multi-Fluid Model Simulations of Gravitational Instabilities in Fluidized Binary Granular Materials. AIChE J. 2022.
• Jin, J, Schorpp K, Samaga D, Unger K, Hadian K*, Stockwell BR* (2022) ACS Chemical Biology. Mar 1. doi: 10.1021/acschembio.1c00953. PMID: 35230809
• Liu H, Forouhar F, Seibt T, Saneto R, Wigby K, Xia X, Shchepinov MS, Ramesh S, Conrad M, Stockwell BR* (2022) Characterization of a patient-derived variant of GPX4 and analysis of potential for precision therapy. Nature Chemical Biology. Jan;18(1):91-100. doi: 10.1038/s41589-021-00915-2. Epub 2021 Dec 20.
• Liu H, Iketani S, Zask A, Khanizeman N, Bednarova E, Forouhar F, Fowler B, Hong SJ, Mohri H, Nair MS, Huang Y, Tay NES, Lee S, Karan C, Resnick SJ, Quinn C, Li W, Shion H, Xia X, Daniels JD, Bartolo-Cruz M, Farina M, Rajbhandari P, Christopher C, Lauber MA, McDonald T, Stokes ME, Hurst B, Rovis T*, Chavez A*, Ho DD*, Stockwell BR* (2022) Development of optimized drug-like small molecule inhibitors of the SARS-CoV-2 3CL protease for treatment of COVID-19. Nature Communications, in press.
• Sundaresh, S. N., Finan, J. D., Elkin, B. S., Basilio, A. V., McKhann, G. M., & Morrison, B., 3rd. (2022). Region-Dependent Viscoelastic Properties of Human Brain Tissue Under Large Deformations. Ann Biomed Eng. doi:10.1007/s10439-022-02910-7
• Danil Tyulmankov, Guangyu Robert Yang, L.F. Abbott, "Meta-learning synaptic plasticity and memory addressing for continual familiarity detection" Neuron, Volume 110, Issue 3, 2022, Pages 544-557.e8, ISSN 0896-6273, https://doi.org/10.1016/j.neuron.2021.11.009. (https://www.sciencedirect.com/science/article/pii/S0896627321009478)
• Affo S, Nair A, Brundu F, Ravichandra A, Bhattacharjee S, Matsuda M, Chin L, Filliol A, Wen W, Song X, Decker A, Worley J, Caviglia JM, Yu L,Yin D, Saito Y, Savage T, Wells RG, Mack M, Zender L, Arpaia N, Remotti HE, Rabadan R, Sims P, Leblond AL, Weber A, Riener MO, Stockwell BR, Gaublomme J, Llovet JM, Michalopoulos GK, Seki E, Sia D, Chen X, Califano A, Schwabe RF. Promotion of cholangiocarcinoma growth by diverse cancer-associated fibroblast subpopulations. Cancer Cell. 2021 Jun.
• Affo S, Nair A, Brundu F, Ravichandra A, Bhattacharjee S, Matsuda M, Chin L, Filliol A, Wen W, Song X, Decker A, Worley J, Caviglia JM, Yu L,Yin D, Saito Y, Savage T, Wells RG, Mack M, Zender L, Arpaia N, Remotti HE, Rabadan R, Sims P, Leblond AL, Weber A, Riener MO, Stockwell BR, Gaublomme J, Llovet JM, Michalopoulos GK, Seki E, Sia D, Chen X, Califano A, Schwabe RF*. Promotion of cholangiocarcinoma growth by diverse cancer-associated fibroblast subpopulations. Cancer Cell. 2021, 39, 1-17, June 14, 2021. https://doi.org/10.1016/j.ccell.2021.03.012. PMCID: PMC8241235
• Agarwal, I. & M. Przeworski, 2021 Mutation saturation for fitness effects at human CpG sites. On BioRxiv. eLife 10:e71513.
• Biderman, N., Shohamy, D. Memory and decision making interact to shape the value of unchosen options. Nat Commun 12, 4648 (2021). https://doi.org/10.1038/s41467-021-24907-x
• C.S. Lee, M. Aly, C. Baldassano. "Anticipation of temporally structured events in the brain." eLife, 2021. DOI: 10.7554/eLife.64972
• Clark RD, Aardema ML., Andolfatto P, Barber PH, Hattori A, Hoey JA, Montes HR, Pinsky ML. 2021. Genomic signatures of spatially divergent selection at clownfish range margins. Proc. Royal Soc. B, 288: 20210407. https://tinyurl.com/3z2fazj7
• D. W. Laorenza, A. Kairalapova, S. L. Bayliss, T. Goldzak, S. M. Greene, L. R. Weiss, P. Deb, P. J. Mintun, K. A. Collins, D. D. Awschalom*, T. C. Berkelbach*, and D. E. Freedman*, “Tunable Cr4+ molecular color centers”, J. Am. Chem. Soc. 143, 21350 (2021); Featured on the cover
• Danil Tyulmankov, Guangyu Robert Yang, L.F. Abbott, "Meta-learning synaptic plasticity and memory addressing for continual familiarity detection" Neuron, Volume 110, Issue 3, 2022, Pages 544-557.e8, ISSN 0896-6273, https://doi.org/10.1016/j.neuron.2021.11.009. (https://www.sciencedirect.com/science/article/pii/S0896627321009478)
• Evan S. Schaffer, Neeli Mishra, Matthew R. Whiteway, Wenze Li, Michelle B. Vancura, Jason Freedman, Kripa B. Patel, Venkatakaushik Voleti, Liam Paninski, Elizabeth M.C. Hillman, L.F. Abbott, Richard Axel, Flygenvectors: The spatial and temporal structure of neural activity across the fly brain, 2021 doi: https://doi.org/10.1101/2021.09.25.461804
• Iketani S, Forouhar F, Liu H, Hong SJ, Lin FY, Nair MS, Zask A, Huang Y, Xing L, Stockwell BR, Chavez A, Ho DD. Lead compounds for the development of SARS-CoV-2 3CL protease inhibitors. Nat Comm. 2021 Apr.
• "Kang, Yul HR; Löffler, Anne; Jeurissen, Danique; Zylberberg, Ariel; Wolpert, Daniel M; Shadlen, Michael N; ",Multiple decisions about one object involve parallel sensory acquisition but time-multiplexed evidence incorporation,Elife,10,,e63721,2021
• Korgaonkar A, Han C., Lemire AL, Siwanowicz I, Bennouna D, Kopec R, Andolfatto P, Shigenobu S, Stern DL. 2021. A novel family of secreted insect proteins linked to plant gall development. Current Biology, in press. bioRXiv: https://tinyurl.com/5xf5h7n4. Current Biology, 31:1836–1849
• Liu H, Forouhar F, Seibt T, Saneto R, Wigby K, Xia X, Shchepinov MS, Ramesh S, Conrad M, Stockwell BR* (2022) Characterization of a patient-derived variant of GPX4 and analysis of potential for precision therapy. Nature Chemical Biology. Jan;18(1):91-100. doi: 10.1038/s41589-021-00915-2. Epub 2021 Dec 20.
• Logiaco, L.; Abbott, L. F.; Escola, G. S. A model of flexible motor sequencing through thalamic control of cortical dynamics. BioRxiv preprint, 2019; online June 1st 2021, Cell Reports.
• Mohammadi S, Yang L., Harpak A, Herrera-Alvarez S, Rodríguez-Ordoñez MP, Peng J, Zhang K, Storz JF, Dobler S, Crawford AJ, Andolfatto P. 2021. Concerted evolution reveals co-adapted amino acid substitutions in Na+K+-ATPase of frogs that prey on toxic toads. bioRXiv: https://tinyurl.com/2ru76fkk Current Biology 31:1–9.
• Probing molecular specificity with deep sequencing and biophysically interpretable machine learning, H. Tomas Rube, Chaitanya Rastogi, Siqian Feng, Judith F. Kribelbauer, Allyson Li, Basheer Becerra, Lucas A. N. Melo, Bach Viet Do, Xiaoting Li, Hammaad H. Adam, Neel H. Shah,Richard S. Mann, Harmen J. Bussemaker, 2021 doi: https://doi.org/10.1101/2021.06.30.450414
• R. Wiscons, Y. Cho, S. Y. Han, A. Dismukes, E. Meirzadeh, C. Nuckolls, T. C. Berkelbach, and X. Roy*, “Polytypism, Anisotropic Transport, and Weyl Nodes in the van der Waals Metal TaFeTe4”, J. Am. Chem. Soc. 143, 109 (2021)
• Ramin Khajeh, Francesco Fumarola, LF Abbott. Sparse balance: excitatory-inhibitory networks with small bias currents and broadly distributed synaptic weights. bioRxiv 2021
• Resnick SJ, Iketani S, Hong SJ, Zask A, Liu H, Kim S, Melore S, Lin FY, Nair MS, Huang Y, Lee S, Tay NES, Rovis T, Yang HW, Xing L, Stockwell BR, Ho DD, Chavez A. Inhibitors of coronavirus 3CL proteases protect cells from protease-mediated cytotoxicity. J Virol. 2021 Apr.
• Rodgers CC, Nogueira R, Pil BC, Greeman EA, Park JM, Hong YK, Fusi S, Bruno RM. Sensorimotor strategies and neuronal representations for shape discrimination. Neuron 109 (2021). Original preprint: bioRxiv (2020).
• SR Bittner, A Palmigiano, AT Piet, CA Duan, CD Brody, KD Miller, JP Cunningham. Interrogating theoretical models of neural computation with emergent property inference. bioRxiv, 837567102021
• Sundaresh, S. N., Finan, J. D., Elkin, B. S., Lee, C., Xiao, J., & Morrison, B. (2021). Viscoelastic characterization of porcine brain tissue mechanical properties under indentation loading. Brain Multiphysics, 2, 100041
• Xi, K.; Guo, Q.; Boyce, C. M. Comparison of CFD-DEM and TFM Simulations of Single Bubble Injection in 3D Gas-Fluidized Beds with MRI Results. Chem. Eng. Sci. 2021, 243, 116738. https://doi.org/10.1016/j.ces.2021.116738.
• Xi, K.; Kovar, T.; Fullmer, W. D.; Penn, A.; Musser, J.; Boyce, C. M. CFD-DEM Study of Bubble Properties in a Cylindrical Fluidized Bed of Geldart Group D Particles and Comparison with Prior MRI Data. Powder Technol. 2021, 389, 75–84. https://doi.org/10.1016/j.powtec.2021.04.075.
• Badgley MA, Kremer DM, Maurer HC, DelGiorno KE, Lee H-J, Purohit V, Sagalovskiy IR, Ma A, Kapilian J, Fir CEM, Decker AR, Sastra SA, Palermo CF, Andrade LR, Sajjakulnukit P, Zhang L, Tolstyka ZP, Hirschhorn T, Lamb C, Liu T, Gu W, Seeley ES, Stone E, Georgiou G, Manor U, Iuga A, Wahl GM, Stockwell BR, Lyssiotis CA, Olive KP. Cysteine depletion induces pancreatic tumor ferroptosis in mice. Science. 2020 Apr.
• "Emergence of functional and structural properties of the head direction system by optimization of recurrent neural networks" Cueva CJ, Wang PY, Chin M, Wei X International Conference on Learning Representations (ICLR) 2020 https://arxiv.org/abs/1912.10189
• "Low‐dimensional dynamics for working memory and time encoding" Cueva CJ, Saez A, Marcos E, Genovesio A, Jazayeri M, Romo R, Salzman CD, Shadlen MN, Fusi S, Proceedings of the National Academy of Sciences (PNAS) 2020 https://www.pnas.org/content/117/37/23021.short
• Feng H, Schorpp K, Jin J, Yozwiak CE, Hoffstrom BG, Decker AM, Rajbhandari P, Stokes ME, Bender HG, Csuka JM, Upadhyayula PS, Canoll P, Uchida K, Soni RK, Hadian K, Stockwell BR. Transferrin Receptor Is a Specific Ferroptosis Marker. Cell Reports. 2020 Mar.
• Fuller Z, Mocellin VJL, Morris LA, Cantin N, Shepherd J, Sarre L., Peng J., Liao Y, Pickrell J, Andolfatto P, Matz M, Bay LK, Przeworski M. 2020. Population genetics of the coral Acropora millepora: Towards a genomic predictor of bleaching. Science 369:eaba4674. bioRXiv: 10.1101/867754v1
• Fuller, Z. L., Berg, J. J., Mostafavi, H., Sella, G., and M. Przeworski, 2019 Measuring intolerance to mutation in human genetics. On BioRxiv. Nature Genetics 51:772-776.
• Golan, Tal, Prashant C. Raju, and Nikolaus Kriegeskorte. "Controversial stimuli: Pitting neural networks against each other as models of human cognition." Proceedings of the National Academy of Sciences 117.47 (2020): 29330-29337.
• Harpak, A., Garud N., Rosenberg, N., Petrov, D., Pennings, P. and J. Munshi-South, 2020 Genetic adaptation in New York City rats. On BioRxiv. Genome Biology and Evolution evaa247, https://doi.org/10.1093/gbe/evaa247
• Iketani S, Forouhar F, Liu H, Hong SJ, Lin FY, Nair MS, Zask A, Huang Y, Xing L, Stockwell BR*, Chavez A*, Ho DD1*. Lead compounds for the development of SARS-CoV-2 3CL protease inhibitors. Nature Communications. 2021, 12:2016. https://www.nature.com/articles/s41467-021-22362-2bioRxiv. 2020 Aug 4: 2020.08.03.235291. doi: 10.1101/2020.08.03.235291. Preprint. PMID: 32793898
• Ingrosso A (2020) Optimal learning with excitatory and inhibitory synapses. PLOS Computational Biology 16(12): e1008536
• Jas M, Achakulvisut T, Idrizović A, Acuna D, Antalek M, Marques V, Odland T, Garg RP, Agrawal M, Umegaki Y, Foley P, Fernandes H, Harris D, Li B, Pieters O, Otterson S, De Toni G, Rodgers C, Dyer E, Hamalainen M, Kording K, Ramkumar P. Pyglmnet: Python implementation of elastic-net regularized generalized linear models. J Open Source Software 5:47 (2020).
• Judith F Kribelbauer, Ryan E Loker, Siqian Feng, Chaitanya Rastogi, Namiko Abe, H Tomas Rube, Harmen J Bussemaker, Richard S Mann. Context-Dependent Gene Regulation by Homeodomain Transcription Factor Complexes Revealed by Shape-Readout Deficient Proteins. Mol Cell. 2020 Apr 2;78(1):152-167.e11. doi: 10.1016/j.molcel.2020.01.027. Epub 2020 Feb 12.
• Andreas J. Keller, Mario Dipoppa, Morgane M. Roth, Matthew S. Caudill, Alessandro Ingrosso, Kenneth D. Miller, Massimo Scanziani, A Disinhibitory Circuit for Contextual Modulation in Primary Visual Cortex, Neuron, Volume 108, Issue 6, 2020. Neural trajectories in the supplementary motor area and motor cortex exhibit distinct geometries, compatible with different classes of computation.”
• Logiaco, L.; Escola G.S. Thalamocortical motor circuit insights for more robust hierarchical control of complex sequences. ArXiv preprint, 2020, submitted to NeurIPS.
• McIntosh, J. R., & Sajda, P. (2020). Decomposing Simon task BOLD activation using a drift-diffusion model framework. Scientific reports, 10(1), 1-11. https://doi.org/10.1038/s41598-020-60943-1
• McIntosh, J. R., Yao, J., Hong, L., Faller, J., & Sajda, P. (2020). Ballistocardiogram artifact reduction in simultaneous EEG-fMRI using deep learning. IEEE Transactions on Biomedical Engineering, 68(1), 78-89. https://doi.org/10.1109/TBME.2020.3004548
• KD Miller, A Palmigiano. Generalized paradoxical effects in excitatory/inhibitory networks. bioRxiv32020
• Odlum M, Cho H, Broadwell P, Davis N, Patrao M, Schauer D, Bales ME, Alcantara C, Yoon S (2020) Application of Topic Modeling to Tweets to Learn Insights on the African American Lived Experience of COVID-19. Stud Health Technol Inform. 272:24-7
• Pallares LF, Lea AJ, Han C., Filippova EV, Andolfatto P$, Ayroles JF$. 2020. Diet unmasks genetic variants that regulate lifespan in outbred Drosophila. #,$==contributed equally. bioRXiv: 2020.10.19.346312v2.
• A Palmigiano, F Fumarola, DP Mossing, N Kraynyukova, H Adesnik, KD Miller. Structure and variability of optogenetic responses identify the operating regime of cortex. bioRxiv32020
• Powell DL, Garcia M, Keegan M, Reilly P., Du K, Díaz-Loyo AP, Banerjee S, Blakkan D, Reich D, Andolfatto P, Rosenthal G, Schartl M, Schumer M. 2020. Natural hybridization reveals incompatible alleles that cause melanoma in swordtail fish. Science 368: 731-736. bioRXiv: 2019.12.12.874586v1
• Resnick SJ, Iketani S, Hong SJ, Zask A, Liu H, Kim S, Melore S, Nair MS, Huang Y, Tay NES, Rovis T, Yang HW, Stockwell BR*, Ho DD*, Chavez A*. A simplified cell-based assay to identify coronavirus 3CL protease inhibitors. bioRxiv. 2020 Aug 29:2020.08.29.272864. doi: 10.1101/2020.08.29.272864. Preprint. PMID: 32869020. Inhibitors of coronavirus 3CL proteases protect cells from protease-mediated cytotoxicity. J Virol. 2021 Apr 28;JVI.02374-20. doi: 10.1128/JVI.02374-20.
• Rodgers CC, Nogueira R, Pil BC, Greeman EA, Park JM, Hong YK, Fusi S, Bruno RM. Sensorimotor strategies and neuronal representations for shape discrimination. Neuron 109 (2021). Original preprint: bioRxiv (2020).
• Abigail A Russo, Ramin Khajeh, Sean R Bittner, Sean M Perkins, John P Cunningham, Laurence F Abbott, Mark M Churchland. Neuron 2020
• Stine, Gabriel M; Zylberberg, Ariel; Ditterich, Jochen; Shadlen, Michael N. Differentiating between integration and non-integration strategies in perceptual decision making,Elife,9,,e55365,2020
• Taverner A., Blaine .*, Andolfatto P. 2020. Epistasis and physico-chemical constraints contribute to spatial clustering of amino acid substitutions in protein evolution. bioRXiv https://tinyurl.com/yxp6dc97.
• Wu, F., Strand, A., Ober, C., Wall, J. D., Moorjani, P.+, and M. Przeworski+, 2020 A comparison of humans and baboons suggests germline mutations do not track cell divisions. On BioRxiv. PloS Biology 18:e3000838. +Co-supervised this project
• Ye LF, Reznik E, Korn JM, Lin F, Yang G, Malesky K, Gao H, Loo A, Pagliarini R, Mikkelsen T, Lo DC, deCarvalho AC*, Stockwell BR* (2020) Patient-derived glioblastoma cultures as a tool for small-molecule drug discovery. Oncotarget. Jan 28;11(4):443-451. doi: 10.18632/oncotarget.27457.
• Yoon S, Odlum M, Broadwell P, Davis N, Cho H, Deng N, Patrao M, Schauer D, Bales ME, Alcantara C. (2020) Application of Social Network Analysis of COVID-19 related Tweets mentioning Cannabis and Opioids to Gain Insights for Drug Abuse Research. Stud Health Technol Inform. 272:5-8
• Agarwal, I., and M. Przeworski, 2019 Signatures of replication, recombination and sex in the spectrum of rare variants on the human X chromosome and autosomes. On BioRxiv. PNAS 116: 17916-17924.
• Bakkour, Akram; Palombo, Daniela J; Zylberberg, Ariel; Kang, Yul HR; Reid, Allison; Verfaellie, Mieke; Shadlen, Michael N; Shohamy, Daphna. The hippocampus supports deliberation during value-based decisions,elife,8,,e46080,2019
• Bos PH, Lowry ER, Costa J, Thams, S, Garcia-Diaz A, Zask A, Wichterle H, Stockwell BR* (2019) Development of MAP4 kinase inhibitors as motor-neuron-protecting agents. Cell Chemical Biology. Dec 19;26(12):1703-1715.e37. doi: 10.1016/j.chembiol.2019.10.005. Epub 2019 Oct 31.
• Feng H, Zhang Y, Bos PH, Chambers JM, Dupont MM, Stockwell BR* (2019) K-RasG12D Has a Potential Allosteric Small Molecule Binding Site. Biochemistry. May 28;58(21):2542-2554. doi: 10.1021/acs.biochem.8b01300. Epub 2019 May 14.
• Fuller, Z. L., Berg, J. J., Mostafavi, H., Sella, G., and M. Przeworski, 2019 Measuring intolerance to mutation in human genetics. On BioRxiv. Nature Genetics 51:772-776.
• Gao, Z., Moorjani, P., Sasani, T. A., Pedersen, B. S., Quinlan, A. R., Jorde, L., Amster, G.*, and M. Przeworski,* 2019 Overlooked roles of DNA damage and maternal age in generating human germline mutations. On BioRxiv. PNAS 116:9491-9500. *Contributed equally
• Ingrosso A, Abbott LF (2019) Training dynamically balanced excitatory-inhibitory networks. PLOS ONE 14(8): e0220547
• Kraft VAN, Bezjian CT, Pfeiffer S, Ringelstetter L, Muller C, Zandkarimi F, Merl-Pham J, Bao X, Anastasov N, Kossl J, Brandner S, Daniels JD, Schmitt-Kopplin P, Hauck SM, Stockwell BR, Hadian K, Schick JA. GTP Cyclohydrolase 1/Tetrahydrobiopterin Counteract Ferroptosis through Lipid Remodeling. ACS Central Science. 2019 Dec.
• Liu Y, Ramos-Womack M, Han C., Reilly P., LaRue-Brackett K, Rogers W, Williams TM, Andolfatto P, Stern DL, Rebeiz M. 2019. Changes throughout a genetic network mask the contribution of Hox gene evolution. Current Biology, 29:2157-2166.e6. Read the accompanying dispatch by Prud’homme and Gompel.
• Liuqi G, Reilly PF., Lewis JL, Reed RD, Andolfatto P, Walters JR. 2019. Dichotomy of dosage compensation along the neo Z chromosome of the Monarch butterfly. Current Biology, 29:4071-7.
• Logiaco, L.; Abbott, L. F.; Escola, G. S. A model of flexible motor sequencing through thalamic control of cortical dynamics. BioRxiv preprint, 2019; online June 1st 2021, Cell Reports.
• Nogueira R., Rodgers CC., Fusi S, Bruno RM. Sensorimotor strategies and neuronal representations of whisker-based object recognition in mouse barrel cortex. Conference on Cognitive Computational Neuroscience, CCN (2019). https://www.sciencedirect.com/science/article/abs/pii/S0896627320308916
• Powell DL, Garcia M, Keegan M, Reilly P., Du K, Díaz-Loyo AP, Banerjee S, Blakkan D, Reich D, Andolfatto P, Rosenthal G, Schartl M, Schumer M. 2020. Natural hybridization reveals incompatible alleles that cause melanoma in swordtail fish. Science 368: 731-736. bioRXiv: 2019.12.12.874586v1
• Taverner AM., Yang L., Barile ZJ, Lin B, Peng J, Pinharanda A., Rao A., Roland BP, Talsma AD, Wei D, Petschenka G, Palladino MJ, Andolfatto P. 2019. Adaptive substitutions underlying cardiac glycoside insensitivity in insects exhibit epistasis in vivo. eLife, 8:e48224. bioRXiv: https://doi.org/10.1101/621185.
• van Arensbergen, J., Pagie, L., FitzPatrick, V.D. et al. High-throughput identification of human SNPs affecting regulatory element activity. Nat Genet 51, 1160–1169 (2019). https://doi.org/10.1038/s41588-019-0455-2
• Wu J, Minikes AM, Gao M, Bian H, Li Y, Stockwell BR, Chen ZN, Jiang X. Intercellular interaction dictates cancer cell ferroptosis via NF2-YAP signalling. Nature. 2019 Jul.
• Yang L., Ravikanthachari N, Mariño-Pérez R, Deshmukh R, Wu M, Rosenstein A*, Kunte K, Song H, Andolfatto P. 2019. Predictability in the evolution of Orthopteran cardenolide insensitivity.Philosophical Transactions of the Royal Society of London Series B, 374:20180246.
• Zhang Y, Tan H, Daniels JD, Zandkarimi F, Liu H, Brown LM, Uchida K, O'Connor OA, Stockwell BR. Imidazole Ketone Erastin Induces Ferroptosis and Slows Tumor Growth in a Mouse Lymphoma Model. Cell Chemical Biology. 2019 Feb.
• Agmon E, Solon J, Bassereau P, Stockwell BR* (2018) Modeling the effects of lipid peroxidation during ferroptosis on membrane properties. Scientific Reports. Mar 26;8(1):5155. doi: 10.1038/s41598-018-23408-0.
• "Emergence of grid‐like representations by training recurrent neural networks to perform spatial localization" Cueva CJ, Wei X.International Conference on Learning Representations (ICLR) 2018 https://arxiv.org/abs/1803.07770
• Hong YK, Lacefield CO, Rodgers CC, Bruno RM. Sensation, movement and learning in the absence of barrel cortex. Nature 561:7724 (2018).
• Lye TH, Vincent KP, McCulloch AD, Hendon CP. Tissue-Specific Optical Mapping Models of Swine Atria Informed by Optical Coherence Tomography. Biophysical Journal. Volume 114, Issue 6, 27 March 2018, Pages 1477-1489
• Rastogi C, Rube HT, Kribelbauer JF, Crocker J, Loker RE, Martini GD, Laptenko O, Freed-Pastor WA, Prives C, Stern DL, Mann RS, Bussemaker HJ. Accurate and sensitive quantification of protein-DNA binding affinity. Proc Natl Acad Sci U S A. 2018 Apr 2. pii: 201714376. doi: 10.1073/pnas.1714376115. [Epub ahead of print]
• Rube HT, Rastogi C, Kribelbauer JF, Bussemaker HJ. A unified approach for quantifying and interpreting DNA shape readout by transcription factors. Molecular systems biology. 2018; 14(2):e7902.
• Schumer M., Xu C, Powell DL, Durvasula A, Skov L, Holland C, Blazier JC, Sankararaman S, Andolfatto P, Rosenthal GG, Przeworski M. 2018. Natural selection interacts with recombination to shape the evolution of hybrid genomes. Science, 360:656-660. https://www.ncbi.nlm.nih.gov/pubmed/29674434.
• Shimada K, Reznik E, Stokes ME, Krishnamoorthy L, Bos PH, Song Y, Quartararo CE, Pagano NC, Carpizo DR, deCarvalho AC, Lo DC, Stockwell BR* (2018) Copper-Binding Small Molecule Induces Oxidative Stress and Cell-Cycle Arrest in Glioblastoma-Patient-Derived Cells. Cell Chemical Biology. May 17;25(5):585-594.e7. doi: 10.1016/j.chembiol.2018.02.010. Epub 2018 Mar 22.
• Yang L., Ravikanthachari N, Mariño-Pérez R, Deshmukh R, Wu M, Rosenstein A*, Kunte K, Song H, Andolfatto P. 2019. Predictability in the evolution of Orthopteran cardenolide insensitivity.Philosophical Transactions of the Royal Society of London Series B, 374:20180246.
• Zhang L, Martini GD, Rube HT, Kribelbauer JF, Rastogi C, FitzPatrick VD, Houtman JC, Bussemaker HJ, Pufall MA. SelexGLM differentiates androgen and glucocorticoid receptor DNA-binding preference over an extended binding site. Genome research. 2018; 28(1):111-121.
• Zhang Y, Larraufie MH, Musavi L, Akkiraju H, Brown LM, Stockwell BR. Design of small molecules that compete with nucleotide binding to an engineered oncogenic KRAS allele. Biochemistry2018 Jan
• Zhou X, Li G, Kaplan A, Gaschler MM, Zhang X, Hou Z, Mali J, Zott R, Cremers S, Stockwell BR, Duan W. Small molecule modulator of protein disulfide isomerase attenuates mutant huntingtin toxicity and inhibits endoplasmic reticulum stress in a mouse model of Huntington's disease. Hum Mol Genet. 2018 Feb.
• Zylberberg, Ariel; Wolpert, Daniel M; Shadlen, Michael N; ",Counterfactual reasoning underlies the learning of priors in decision making,Neuron,99,5,1083-1097. e6,2018
• Agmon E, Stockwell BR. Lipid homeostasis and regulated cell death. Curr Opin Chem Biol. 2017 Jun;39:83-89
• Batty, E. et al (2017). Multilayer Network Models of Primate Retinal Ganglion Cells. ICLR.
• Buesing et al (2017). A Statistical Model of Shared Variability in the Songbird Auditory System. bioRxiv.
• J. van Arensbergen, V.D. FitzPatrick, M. de Haas, L. Pagie, J, Sluimer, H.J. Bussemaker*, and B. van Steensel* Genome-wide mapping of autonomous promoter activity in human cells. Nat. Biotechnol. 35(2):145-153 (2017)
• Kagan VE*, Mao G, Qu F, Angeli JP, Doll S, St. Croix C, Dar H, Liu B, Tyurin V, Ritov V, Kapralov O, Amoscato A, Jiang J, Anthonymuthu T, Mohammadyani D, Yang Q, Proneth B, Klein-Seetharaman J, Watkins S, Bahar I, Greenberger J, Mallampalli R, Stockwell BR, Tyurina Y, Conrad M, Bayır H (2017) Oxidized Arachidonic and Adrenic Phosphatidylethanolamines Navigate Cells to Ferroptosis. Nature Chemical Biology, Jan;13(1):81-90. doi: 10.1038/nchembio.2238.
• Kribelbauer JF, Laptenko O, Chen S, Martini GD, Freed-Pastor WA, Prives C, Mann RS, Bussemaker HJ. Quantitative Analysis of the DNA Methylation Sensitivity of Transcription Factor Complexes. Cell reports. 2017; 19(11):2383-2395. NIHMSID: NIHMS881434
• Kishore V. Kuchibhotla, Jonathan V. Gill, Grace W. Lindsay, Rachel E. Field, Tom A. Hindmarsh Sten, Kenneth D. Miller, Eleni S. Papadoyannis and Robert C. Froemke "Parallel processing by cortical inhibition enables flexible behavior”. 2017
• Rastogi C, Rube HT, Kribelbauer JF, Crocker J, Loker RE, Martini GD, Laptenko O, Freed-Pastor WA, Prives C, Stern DL, Mann RS, Bussemaker HJ. Accurate and sensitive quantification of protein-DNA binding affinity. Proc Natl Acad Sci U S A. 2018 Apr 2. pii: 201714376. doi: 10.1073/pnas.1714376115. [Epub ahead of print]
• Welsch ME, Kaplan A, Chambers JM, Stokes ME, Bos PH, Zask A, Zhang Y, Sanchez-Martin M, Badgley MA, Huang CS, Tran TH, Akkiraju H, Brown LM, Nandakumar R, Cremers S, Yang WS, Tong L, Olive KP, Ferrando A, Stockwell BR* (2017) Multivalent Small-Molecule Pan-RAS Inhibitors. Cell, Feb 23;168(5):878-889.e29. doi: 10.1016/j.cell.2017.02.006
• Brian DePasquale, Christopher J. Cueva, Raoul-Martin Memmesheimer, L.F. Abbott, G. Sean Escola (2016) "FULL-FORCE Learning in Continuous Variable Networks"
• Gabitto M., Pakman A., Bikoff J., Abbott L., Jessell T. & Paninski, L. (2016). Bayesian sparse regression analysis reveals the extent of spinal V1 interneuron diversity. Cell.
• Gao, Y., Archer, E., Paninski, L. & Cunningham, J. (2016). Latent linear-dynamical neural population models through nonlinear embedding. NIPS; Arxiv 1605.08454.
• Gerhard DS, Clemons PA, Shamji AF, Hon C, Wagner BK, Schreiber SL, Krasnitz A, Sordella R, Sander C, Lowe SW, Powers S, Smith K, Aburi M, Iavarone A, Lasorella A, Silva J, Stockwell BR, Califano A, Boehm JS, Vazquez F, Weir BA, Hahn WC, Khuri FR, Moreno CS, Johns M, Fu H, Nikolova O, Mendez E, Gadi VK, Margolin AA, Grandori C, Kemp CJ, Warren EH, Riddell SR, McIntosh MW, Gevaert O, Kuo CJ, Ji HP, Dhruv H, Finlay D, Kiefer J, Kim S, Vuori K, Berens ME, Hangauer M, Boettcher M, Weissman JS, Bivona TG, Bandyopadhyay S, McManus MT, McCormick F, Aksoy O, Simonds EF, Zheng T, Chen J, An Z, Balmain A, Weiss WA, Chen K, Liang H, Scott KL, Mills GB, Posner BA, MacMillan J, Minna J, White M, Roth MG, Jagu S, Mazerik J. (2016) Transforming Big Data into cancer-relevant insight: An initial, multi-tier approach to assess reproducibility and relevance. Molecular Cancer Research, DOI: 10.1158/1541-7786.MCR-16-0090 Published July 2016.
• Iketani S, Forouhar F, Liu H, Hong SJ, Lin FY, Nair MS, Zask A, Huang Y, Xing L, Stockwell BR*, Chavez A*, Ho DD1*. Lead compounds for the development of SARS-CoV-2 3CL protease inhibitors. Nature Communications. 2021, 12:2016. https://www.nature.com/articles/s41467-021-22362-2 bioRxiv. 2020 Aug 4: 2020.08.03.235291. doi: 10.1101/2020.08.03.235291. Preprint. PMID: 32793898
• Shimada K, Hayano M, Pagano NC, Stockwell BR* (2016) Cell-Line Selectivity Improves the Predictive Power of Pharmacogenomic Analyses and Helps Identify NADPH as Biomarker for Ferroptosis Sensitivity. Cell Chemical Biology Feb 18;23(2):225-35. PMID: 26853626, PMCID: PMC4792701, DOI: 10.1016/j.chembiol.2015.11.016
• Shimada K, Skouta R, Kaplan A, Yang WS, Hayano M, Dixon SJ, Brown LM, Valenzuela CA, Wolpaw AJ, Stockwell BR* (2016) Global survey of cell death mechanisms reveals metabolic regulation of ferroptosis. Nature Chemical Biology, Jul; 12(7): 497-503. PMID: 27159577, PMCID: PMC4920070, DOI: 10.1038/nchembio.2079
• Sumbul, U., Roossien, D., Chen, F., Barry, N., Boyden, E., Cai, D., Cunningham, J. & Paninski, L. (2016). Automated scalable segmentation of neurons from multispectral images. NIPS; Arxiv 1611.00388.
• Kaplan A, Gaschler MG, Dunn DE, Colligan R, Brown LM, Palmer AG, Lo DC, Stockwell, BR. Small molecule-induced oxidation of protein disulfide isomerase is neuroprotective. Proc Natl Acad Sci USA 2015 Mar [pdf]
• Larraufie MH, Yang WS, Jiang E, Thomas AG, Slusher BS, Stockwell BR. Incorporation of metabolically stable ketones into a small molecule probe to increase potency and water solubility.Bioorg Med Chem Let. 2015 Nov; 25(21):4787-92
• Shimada K, Hayano M, Pagano NC, Stockwell BR* (2016) Cell-Line Selectivity Improves the Predictive Power of Pharmacogenomic Analyses and Helps Identify NADPH as Biomarker for Ferroptosis Sensitivity. Cell Chemical Biology Feb 18;23(2):225-35. PMID: 26853626, PMCID: PMC4792701, DOI: 10.1016/j.chembiol.2015.11.016
• Soudry, D., Keshri, S., Stinson, P., Oh, M.-W., Iyengar, G. & Paninski, L. (2015). Efficient ``shotgun" inference of neural connectivity from highly sub-sampled activity data. PLoS Comp. Bio.
• Buesing, L., Machado, T., Cunningham, J. & Paninski, L. (2014). Clustered factor analysis of multineuronal spike data. NIPS.
• Julien O, Kampmann M, Bassik MC, Zorn JA, Venditto VJ, Shimbo K, Agard NJ, Shimada K, Rheingold AL, Stockwell BR, Weissman JS, Wells JA. Unraveling the mechanism of cell death induced by chemical fibrils. Nat Chem Biol. 2014 Sep 28; 10(11): 969-76
• Skouta R, Dixon SJ, Wang J, Dunn DE, Orman M, Shimada K, Rosenberg P, Lo D, Weinberg J, Linkermann A, Stockwell BR. Ferrostatins inhibit oxidative lipid damage and cell death in diverse disease models. J Am Chem Soc 2014 Mar 4; 136(12):4551-6
• Pakman, A., Huggins, J., Smith, C. & Paninski, L. (2013). Fast penalized state-space methods for inferring dendritic synaptic connectivity. J. Comput. Neurosci.
• Ramirez, A. & Paninski, L. (2012), "Fast generalized linear model estimation via expected log-likelihoods." J. Comput. Neurosci.
• Sadeghi et al. (2012), "Monte Carlo methods for localization of cones given multielectrode retinal ganglion cell recordings," Network: Computation in Neural Systems.
• Saul, D. et al. 2012, The GALFA-HI Compact Cloud Catalog, ApJ, 758, 44.
• Smith, C. & Paninski, L. (2012). "Computing loss of efficiency in optimal Bayesian decoders given noisy or incomplete spike trains." Network: Computation in Neural Systems.
• Vidne et al. (2012), "The impact of common noise on the activity of a large network of retinal ganglion cells," J. Comput. Neuro.
• Agne, M., Huang, C.-H., Hu, I., Wang, H., Zheng, T., and Lo, S.-H. (2011) GAW17-Identifying Influential Regions in Extremely Rare Variants via Fixed Bin Approach. BMC Proceedings for Genetic Analysis Workshop 17 (Boston, MA).
• Calabrese, A., Schumacher, J., Schneider, D., Paninski, L. & Woolley, S. (2011). A penalized GLM approach for estimating spectrotemporal receptive fields from responses to natural sounds. PLoS One.
• D. Pfau, N. Bartlett, and F. Wood. Probabilistic Deterministic Infinite Automata, In Advances in Neural Information Processing Systems, 2011.
• Fan, R., Huang, C.-H., Lo, S.-H., Zheng, T., and Ionita-Laza, I. (2011) On Identifying Rare Disease Variants in the GAW17 Simulated Data: A Comparison of Several Statistical Approaches. BMC Proceedings for Genetic Analysis Workshop 17 (Boston, MA).
• Huggins, J. & Paninski, L. (2011). Optimal experimental design for sampling voltage on dendritic trees. J. Computational Neurosci.
• Liu, Y., Huang, C.-H., Hu, I., Lo, S.-H., and Zheng, T. (2011) Association Screening for Genes with Multiple Potentially Rare Variants: an Inverse-Probability Weighted Clustering Approach. BMC Proceedings for Genetic Analysis Workshop 17 (Boston, MA).
• Mishchenko, Y. & Paninski, L. (2011). Efficient methods for sampling spike trains in networks of coupled neurons. Annals of Applied Statistics.
• Ramirez, A., Ahmadian, Y., Schumacher, J., Schneider, D., Woolley, S. & Paninski, L. (2011). Incorporating naturalistic correlation structure improves spectrogram reconstruction from neuronal activity in the songbird auditory midbrain. J. Neurosci.
• Mischchencko, Y., Vogelstein, J. & Paninski, L. (2009). A Bayesian approach for inferring neuronal connectivity from calcium fluorescent imaging data. Annals of Applied Statistics.

Statistics, Computer Science, and Engineering 

• Robert E. Colgan, Jingkai Yan, Zsuzsa Márka, Imre Bartos, Szabolcs Márka, John N. Wright Architectural Optimization and Feature Learning for High-Dimensional Time Series Datasets. arXiv preprint arXiv:2202.13486
• Davis D, Diaz M, Wang K. Clustering a Mixture of Gaussians with Unknown Covariance. arXiv preprint arXiv:2110.01602.
• Davis, R.A. and Yau, C-Y. Likelihood Inference for Discriminating Between Long-Memory and Change-point Models. J. Time Series Analysis.
• Davis, R.A., and Song, L. Noncausal Vector AR Processes with Application to Financial Time Series.
• Hoffman, M.D. and Gelman, A. The No-U-Turn Sampler: Adaptively Setting Path Lengths in Hamiltonian Monte Carlo. Journal of Machine Learning Research
• Ma Y, Zheng T. Stabilized Sparse Online Learning for Sparse Data. Journal of Machine Learning Research. [Abstract]
• S. M. Greene, R. J. Webber, T. C. Berkelbach*, and J. Weare*, “Approximating matrix eigenvalues by subspace iteration with repeated random sparsification”, arXiv:2103.12109, under review in SIAM J. Sci. Comput.
• Zhou W, Veitch V, Austern M, Adams RP, Orbanz P. Compressibility and Generalization in Large-Scale Deep Learning. Eprint = 1804.05862.
• Duan, Y. and Wang, K., 2022. Adaptive and Robust Multi-task Learning. arXiv preprint arXiv:2202.05250.
• La Spina, Andrea, and Jacob Fish. "A superconvergent hybridizable discontinuous Galerkin method for weakly compressible magnetohydrodynamics." Computer Methods in Applied Mechanics and Engineering 388 (2022): 114278.
• Singal, Raghav, Omar Besbes, Antoine Desir, Vineet Goyal, and Garud Iyengar. "Shapley meets uniform: An axiomatic framework for attribution in online advertising." Management Science (2022)
• H. Su, D. Xu, S.-W. Cheng, B. Li, S. Liu, K. Watanabe, T. Taniguchi, T. C. Berkelbach, J. Hone, and M. Delor*, “Dark-exciton driven energy funneling into dielectric inhomogeneities in two-dimensional semiconductors”, Nano Lett. Article ASAP (2022)
• H.-Z. Ye and T. C. Berkelbach*, “Correlation-consistent Gaussian basis sets for solids made simple”, J. Chem. Theory Comput. 18, 1595 (2022)
• “Identifying the Popularity and Persuasiveness of Right- and Left-Leaning Group Videos on Social Media” Lin Ai, Anika Kathuria, Subhadarshi Panda, Arushi Sahai, Yuwen Yu, Sarah Ita Levitan, Julia Hirschberg. IEEE Big Data Deviance Workshop 2021. » PDF
• Lin Ai, Run Chen, Ziwei Gong, Julia Guo, Shayan Hooshmand, Zixiaofan Yang, Julia Hirschberg. “Exploring New Methods for Identifying False Information and the Intent Behind It on Social Media: COVID-19 Tweets”. Sixth International Workshop on Social Sensing (SocialSens 2021), ICWSM, Atlanta.
• Ardeshir, Navid and Sanford, Clayton and Hsu, Daniel J, Support vector machines and linear regression coincide with very high-dimensional features, 2021, https://proceedings.neurips.cc/paper/2021/file/26d4b4313a7e5828856bc0791fca39a2-Paper.pdf
• B. Bahmani, W.C. Sun, A kd-tree accelerated hybrid data-driven/model-based approach for poroelasticity problems with multi-fidelity multi-physics data, Computer Methods in Applied Mechanics and Engineering, doi:10.1016/j.cma.2021.113868, 2021. [Video] [PDF]
• Siddhartha Dalal, Zihe Wang, Siddhanth Sabharwal., 2021. Identifying Ransomware Actors in the Bitcoin Network arXiv:2108.13807
• Davis, D., Diaz, M. and Wang, K., 2021. Clustering a mixture of gaussians with unknown covariance. arXiv preprint arXiv:2110.01602.
• A. Fuchs, Y. Heider", K. Wang, W.C. Sun, M. Kaliske, DNN2: A hyper-parameter reinforcement learning game for self-design neural network elasto-plastic constitutive laws, Computer and Structures, 249:106505, doi:10.1016/j.compstruc.2021.106505, 2021.
• Guo, Q.; Padash, A.; Boyce, C. M. A Two Fluid Modeling Study of Bubble Collapse Due to Bubble Interaction in a Fluidized Bed. Chem. Eng. Sci. 2021, 232, 116377.
• Guo, Q.; Zhang, Y.; Padash, A.; Xi, K.; Kovar, T. M.; Boyce, C. M. Dynamically Structured Bubbling in Vibrated Gas-Fluidized Granular Materials. Proc. Natl. Acad. Sci. 2021, 118 (35).
• Y. Heider", H.S. Suh, W.C. Sun, An offline multi-scale unsaturated poromechanics model enabled by self-designed/self-improved neural network, International Journal for Numerical and Analytical Methods in Geomechanics, doi:10.1002/nag.3196, 2021.
• “Automatic Detection and Prediction of Psychiatric Hospitalizations From Social Media Posts” Zhengping Jiang, Jonathan Zomick, Sarah Ita Levitan, Mark Serper, Julia Hirschberg. Workshop on Computational Linguistics and Clinical Psychology (CLPsych) 2021, NAACL 2021. » PDF
• R. Ma", W.C. Sun, C. R. Picu, Atomistic-model informed pressure-sensitive crystal plasticity for crystalline HMX, International Journal of Solid and Structures, 232:111170, doi:10.1016/j.ijsolstr.2021.111170, 2021.
• H. Suh, W.C. Sun, Asynchronous phase field fracture model for porous media with thermally non-equilibrated constituents, Computer Methods in Applied Mechanics and Engineering, accepted, 2021. [Preprint]
• H.S. Suh, W.C. Sun, An immersed phase field model for microporomechanics of fracture-induced leakage, Physics of Fluids (Editor's pick), doi:10/1063/5.0035602, 2021. [long Video][short video][preprint]
• X. Sun, B. Bahmani, N. Vlassis, W.C. Sun, Y. Xu, Data-driven discovery of interpretable causal relations for deep learning material laws with uncertainty propagation, Granular Matter, accepted, 2021. [arxiv]
• Tang, C., Uriarte, M., Jin, H., C Morton, D., & Zheng, T. (2021). Large‐scale, image‐based tree species mapping in a tropical forest using artificial perceptual learning. Methods in Ecology and Evolution, 12(4), 608-618.
• Tang, C., Yuan, G., & Zheng, T. (2021). Weakly Supervised Learning Creates a Fusion of Modeling Cultures. Observational Studies 7(1), 203-211. doi:10.1353/obs.2021.0011.
• A Generative Modeling Approach to Calibrated Predictions: A Use Case on Menstrual Cycle Length Prediction, Inigo Urteaga, Kathy Li, Amanda Shea, Virginia J. Vitzthum, Chris H. Wiggins, Noemie Elhadad Proceedings of the 6th Machine Learning for Healthcare Conference, PMLR 149:535-566, 2021. https://proceedings.mlr.press/v149/urteaga21a.html
• van Geen, C., & Gerraty, R. T. (2021). Hierarchical Bayesian Models of Reinforcement Learning: Introduction and comparison to alternative methods. Journal of Mathematical Psychology, 105, 102602.
• N. Vlassis, W.C. Sun, Sobolev training of thermodynamic-informed neural network for interpretable elasto-plasticity models with level set hardening, Computer Methods in Applied Mechanics and Engineering, doi:10.1016/j.cma.2021.113695, 2021. [Video][preprint]
• Owen G Ward, Zhen Huang, Andrew Davison, Tian Zheng. Next waves in veridical network embedding. Statistical Analysis and Data Mining: The ASA Data Science Journal. 2021.
• M. Xiao, W.C. Sun, C. Liu", DP-MPM: Domain partitioning material point method for evolving multi-body thermal-mechanical contacts and fragmentation, Computer Methods in Applied Mechanics and Engineering, 385:114063, doi:10.1016/j.cma.2021.114063, 2021. [Video]
• Xi, K.; Guo, Q.; Boyce, C. M. Comparison of CFD-DEM and TFM Simulations of Single Bubble Injection in 3D Gas-Fluidized Beds with MRI Results. Chem. Eng. Sci. 2021, 243, 116738.
• Xi, K.; Guo, Q.; Boyce, C. M. Comparison of Two-Fluid Model Simulations of Freely Bubbling Three-Dimensional Gas-Fluidized Beds with Magnetic Resonance Imaging Results. Ind. Eng. Chem. Res. 2021, 60 (19), 7429–7442.
• Xi, K.; Kovar, T.; Fullmer, W. D.; Penn, A.; Musser, J.; Boyce, C. M. CFD-DEM Study of Bubble Properties in a Cylindrical Fluidized Bed of Geldart Group D Particles and Comparison with Prior MRI Data. Powder Technol. 2021, 389, 75–84.
• Kevin Xia, Kai-Zhan Lee, Yoshua Bengio, Elias Bareinboim. The Causal-Neural Connection: Expressiveness, Learnability, and Inference. 2021. arXiv:2107.00793.
• T. Xue, W.C. Sun, S. Adriaenssens, Y. Wei, C. Liu", a new finite element level set re-initialization based on the shifted boundary method, Journal of Computational Physics, doi:10.1016/j.jcp.2021.110360, 2021.
• “CHoRaL: Collecting Humor Reaction Labels from Millions of Social Media Users” Zixiaofan Yang, Shayan Hooshmand, Julia Hirschberg.EMNLP 2021 (Best Short Paper Award), Punta Cana, Dominican Republic. » PDF » PDF Poster
• “What Makes People Laugh? Multimodal Humor Detection and Analysis in Videos” Zixiaofan Yang, Lin Ai, Julia Hirschberg. Asilomar Conference on Signals, Systems, and Computers 2021. » PDF
• E.C. Bryant, W.C. Sun, Phase field modeling of frictional slip with slip weakening/strengthening under non-isothermal conditions, Computer Methods in Applied Mechanics and Engineering, accepted, 2020.
• N. de Marchi*, W.C. Sun, V. Salomoni, Shear wave splitting and polarization in anisotropic fluid-infiltrating porous media: a numerical study, Materials, doi:10.3390/ma13214988, 2020. [preprint]
• Y. Heider", K. Wang, W.C. Sun, SO(3)-invariance of graph-based deep neural network for anisotropic elastoplastic materials, Computer Methods in Applied Mechanics and Engineering, 363:112875, doi:10.1016/j.cma.2020.112875, 2020. [PDF]
• “Detection of Mental Health Conditions from Reddit via Deep Contextualized Representations” Zhengping Jiang, Sarah Ita Levitan, Jonathan Zomick, Julia Hirschberg. the 11th International Workshop on Health Text Mining and Information Analysis, November 2020. » PDF
• K. Wang, W.C. Sun, Q. Du, A non-cooperative meta-modeling game for automated third-party training, validating, and falsifying constitutive laws with adversarial attacks, Computer Methods in Applied Mechanics and Engineering, doi:10.1016/j.cma.2020.113514, 2020. [arxiv][Video]
• C. Liu", W.C. Sun, ILS-MPM: an unbiased implicit level-set-based material point method for frictional particulate contact mechanics of deformable particles, Computer Methods in Applied Mechanics and Engineering, accepted, doi:10.1016/j.cma.2020.113168, 2020. [PDF]
• R. Ma", W.C. Sun, Computational thermomechanics for crystalline rock. Part II: chemo-damage-plasticity and healing in strongly anisotropic polycrystals, Computer Methods in Applied Mechanics and Engineering, doi:10.1016/j.cma.2020.113184, 2020. [PDF]
• R. Ma", W.C. Sun, FFT-based solver for higher-order and multi-phase-field fracture models applied to strongly anisotropic brittle materials and poly-crystals, Computer Methods in Applied Mechanics and Engineering, 362:112781, doi:10.1016/j.cma.2019.112781, 2020.
• R. Ma", W.C. Sun, Phase field modeling of coupled crystal plasticity and deformation twinning in polycrystals with monolithic and splitting solvers, International Journal for Numerical Method in Engineering, doi:10.1002/nme.6577, 2020. [PDF]
• Padash, A.; Boyce, C. M. Collapse of a Bubble Injected Side-by-Side with Another Bubble into an Incipiently Fluidized Bed: A CFD-DEM Study. Phys. Rev. Fluids 2020, 5 (3), 034304.
• Penn, A.; Padash, A.; Lehnert, M.; Pruessmann, K. P.; Müller, C. R.; Boyce, C. M. Asynchronous Bubble Pinch-off Pattern Arising in Fluidized Beds Due to Jet Interaction: A Magnetic Resonance Imaging and Computational Modeling Study. Phys. Rev. Fluids 2020, 5 (9), 094303.
• Arthur Prat-Carrabin, Michael Woodford. "Efficient coding of numbers explains decision bias and noise." bioRxiv 2020.02.18.942938; doi: https://doi.org/10.1101/2020.02.18.942938
• H.S. Suh, D. O'Conner, W.C. Sun, A phase field model for cohesive fracture in micropolar continua, Computer Methods in Applied Mechanics and Engineering, doi:10.1016/j.cma.2020.113181, 2020. [Video]
• H.S. Suh, W.C. Sun, An open source FEniCS implementation of a phase field fracture model for micropolar continua, International Journal of Multiscale Computational Engineering, doi:10.1615/IntJMultCompEng.2020033422, 2019. [open source code]
• N. Vlassis, R. Ma", W.C. Sun, Geometric deep learning for computational mechanics Part I: Anisotropic Hyperelasticity, Computer Methods in Applied Mechanics and Engineering, doi:10.1016/j.cma.2020.113299, 2020. [PDF]
• X. Zhong*, W.C. Sun, Y. Dai, A reduced-dimensional explicit discrete element solver for simulating granular mixing problems, Granular Matter, accepted, 2020.
• Jiaxuan Zhang, Sarah Ita Levitan, Julia Hirschberg. “Multimodal Deception Detection using Automatically Extracted Acoustic, Visual, and Lexical Features”. Interspeech, October 2020.
• E.C. Bryant, W.C. Sun, A micromorphic-regularized anisotropic Cam-clay-type model for capturing size-dependent anisotropy, Computer Methods in Applied Mechanics and Engineering, 354:56-95, doi:10.1016/j.cma.2019.05.003, 2019. [PDF]
• Y. Heider", W.C. Sun, Phase field modeling of capillary-induced fracture in unsaturated porous media: drying-induced vs. hydraulic-driven cracking, Computer Methods in Applied Mechanics and Engineering, doi:10.1016/j.cma.2019.112647, 2019. [PDF]
• K. Wang, W.C. Sun, An updated Lagrangian LBM-DEM-FEM coupling model for dual-permeability porous media with embedded discontinuities, Computer Methods in Applied Mechanics and Engineering, 344:276-305, doi:10.1016/j.cma.2018.09.034, 2019. [PDF][Bibtex]
• K. Wang, W.C. Sun, Meta-modeling game for deriving theory-consistent, micro-structure-based traction-separation laws via deep reinforcement learning, Computer Methods in Applied Mechanics and Engineering, 346:216-241, doi:10.1016/j.cma.2018.11.026, 2019. [PDF][Bibtex][Data]
• K. Wang, W.C. Sun, Q. Du, A cooperative game for automated learning of elasto-plasticity knowledge graphs and models with AI-guided experimentation, Computational Mechanics, special issue for Data-Driven Modeling and Simulations: Theory, Methods and Applications, 64(2):67–499, doi:,10.1007/s00466-019-01723-1, 2019. [PDF]
• C. Liu", W.C. Sun, Shift domain material point method for solids in the finite deformation range, special thematic issue for Meshfree and Particle Methods for Modeling Extreme Loadings, Computational Particle Mechanics, doi: 10.1007/s40571-019-00239-y, 2019. [PDF]
• C.-H. Liu, Y. Tao, D. Hsu, Q. Du and S. J. L. Billinge. Using a machine learning approach to determine the space group of a structure from the atomic pair distribution function. Acta Cryst. (2019). A75, 633-643
• McLaren, C. P.; Kovar, T. M.; Penn, A.; Müller, C. R.; Boyce, C. M. Gravitational Instabilities in Binary Granular Materials. Proc. Natl. Acad. Sci. 2019, 201820820.
• A. Qinami, E.C. Bryant, W.C. Sun, M. Kaliske, Circumventing mesh bias by r- and h-adaptive techniques for variational eigen-fracture, International Journal of Fracture, doi:10.1007/s10704-019-00349-x, 2019.
• S. Na, E.C. Bryant, W.C. Sun, A configurational force for adaptive re-meshing of gradient-enhanced poromechanics problems with history-dependent variables, Computer Methods in Applied Mechanics and Engineering, doi:10.1016/j.cma.2019.112572, 2019. [PDF]
• Victor Soto, Julia Hirschberg. "Improving Code-Switched Language Modeling Performance Using Cognate Features” Interspeech, September 2019, Graz, Austria.
• Zixiaofan Yang and Julia Hirschberg. “Linguistically-Informed Training of Acoustic Word Embeddings for Low-Resource Languages”. Interspeech, September 2019, Graz, Austria.
• Zixiaofan Yang, Bingyan Hu, and Julia Hirschberg. “Predicting Humor by Learning from Time-Aligned Comments”. Interspeech, September 2019, Graz, Austria.
• Zixiaofan Yang, Lin Ai, and Julia Hirschberg. “Multimodal Indicators of Humor in Videos". IEEE Conference on Multimedia Information Processing and Retrieval, March 2019. San Jose, CA.
• Abernathey R, Haller G. Transport by lagrangian vortices in the eastern pacific. 2018, Journal of Physical Oceanography, 48(3), 667-685.
• Timothy Chan and Raghav Singal. A Bayesian regression approach to handicapping tennis players based on a rating system. Submitted. 2018.
• Martin B. Haugh and Raghav Singal. How to play strategically in fantasy sports (and win). MIT Sloan Sports Analytics Conference. 2018.
• J. Choo", W.C. Sun, Coupled phase-field and plasticity modeling of geological materials: From brittle fracture to ductile flow, Computer Methods in Applied Mechanics and Engineering, 330:1-32, doi:10.1016/j.cma.2017.10.009, 2018. [PDF][Bibtex [ poromechanics. weebly. com/uploads/2/2/9/7/22975762/s0045782517306783. bib ] ]
• J. Choo", W.C. Sun, Cracking and damage from crystallization in pores: Coupled chemo-poro-mechanics and phase-field modeling, Computer Methods in Applied Mechanics and Engineering, 335:347-379, doi:10.1016/j.cma.2018.01.044, 2018. [PDF][Bibtex [ poromechanics. weebly. com/uploads/2/2/9/7/22975762/s0045782518300513. bib ] ]
• Yousuf K. Variable screening for high dimensional time series. 2018, Electronic Journal of Statistics 12, 667-702.
• K. Wang, W.C. Sun, A multiscale multi-permeability poroplasticity model linked by recursive homogenizations and deep learning , Computer Methods in Applied Mechanics and Engineering, 334(1):337-380, doi:10.1016/j.cma.2018.01.036, 2018. [PDF][Bibtex [ poromechanics. weebly. com/uploads/2/2/9/7/22975762/s0045782518300380. bib ] ]
• Krstovski K, Blei DM, "ArXivLab: A Platform for Developing and Evaluating Exploratory Tools for the Scientific Literature." Under review in SIGIR, 2018
• Krstovski K, Blei DM, "Equation Embeddings." Under review in International Conference on Machine Learning, 2018
• Krstovski K, Blei DM. "ArXivLab: A Platform for Developing and Evaluating Exploratory Tools for the Scientific Literature", Submitted to SIGIR, 2018
• Krstovski K, Blei DM. "Equation Embeddings", Submitted to ICML , 2018
• Kumar Jain P, Mandli K, Hoteit I, Knio O, Dawson C. Dynamically adaptive data-driven simulation of extreme hydrological flows. Ocean Modelling 122, 85–103 (2018).
• Rudolph M , Ruiz F, Blei D. Word2Net: Deep Representations of Language, Submitted to ICML, 2018
• Rudolph M, Blei D. Dynamic Embeddings for Language Evolution, In Proceedings of WWW, 2018
• Rudolph M, Blei DM. "Dynamic Embeddings for Language Evolution." In proceedings of WWW, 2018
• Rudolph M, Ruiz FJR, Blei DM. "Word2Net: Deep Representations of Language." Under review in International Conference on Machine Learning, 2018
• Ruiz FJR, Titsias MK, Dieng AB, Blei DM. "Augment and Reduce: Stochastic Inference for Large Categorical Distributions." International Conference on Machine Learning, 2018. Arxiv link: https://arxiv.org/abs/1802.04220
• Ruiz FJR, Titsias MK, Dieng AB, Blei DM. Augment and Reduce: Stochastic Inference for Large Categorical Distributions. Under review in International Conference on Machine Learning. Stockholm (Sweden), July 2018. Arxiv link: https://arxiv.org/abs/1802.04220
• S. Na, W.C. Sun, Computational thermomechanics of crystalline rock. Part I: a combined multi-phase-field/crystal plasticity approach for single crystal simulations, Computer Methods in Applied Mechanics and Engineering, doi:10.1016/j.cma.2017.12.022, 2018.
• Tamsitt V, Abernathey RP, Mazloff MR, Wang J, Talley LD. Transformation of deep water masses along Lagrangian upwelling pathways in the Southern Ocean. 2018, Journal of Geophysical Research: Oceans.
• Tesdal JE, Abernathey RP, Goes JI, Gordon AL, Haine TW. Salinity trends within the upper layers of the subpolar North Atlantic. 2018, Journal of Climate, 31(7), 2675-2698.
• ​W.C. Sun, T-F. Wong, Prediction of hydraulic and electrical transport properties of sandstone with multiscale lattice Boltzmann/finite element simulation on microtomographic images, International Journal of Rock Mechanics and Mining Sciences, 106, 269-277, doi:10. 1016/ j. ijrmms. 2018. 04. 020, 2018.
• Busecke J, Abernathey RP, Gordon AL. Lateral eddy mixing in the subtropical salinity maxima of the global ocean. 2017, Journal of Physical Oceanography, 47(4), 737-754.
• Cheng, Y., C. Sayde, Q. Li, J. Basara, J. Selker, E. Tanner, and P. Gentine (2017), Failure of Taylor's hypothesis in the atmospheric surface layer and its correction for eddy-covariance measurements, Geophys. Res. Lett., 44, doi:10.1002/2017GL073499.
• Giraldi, L., Le Maître, O.P., Mandli, K.T. et al. Bayesian inference of earthquake parameters from buoy data using a polynomial chaos-based surrogate. 1–17 (2017).
• Liu L, Blei DM. "Zero-Inflated Exponential Family Embeddings." International Conference on Machine Learning, 2017
• Liu L, Blei DM. "Zero-Inflated Exponential Family Embeddings." NIPS 2017
• Liu L, Ruiz FJR, Athey S, Blei DM. "Context Selection for Embedding Models." Advances in Neural Information Processing Systems, 2017.
• Liu L, Ruiz FJR, Athey S, Blei DM. Context Selection for Embedding Models. Advances in Neural Information Processing Systems. Long Beach (CA, USA), December 2017.
• Rudolph M, Ruiz F, Athey S, Blei D. Structured Embedding Models for Grouped Data, In Proceedings of NIPS, 2017
• Rudolph M, Ruiz FJR, Athey S, Blei DM. "Structured Embedding Models for Grouped Data." Advances in Neural Information Processing Systems, 2017
• Ruiz FJR, Athey S, Blei DM. "SHOPPER: A Probabilistic Model of Consumer Choice with Substitutes and Complements." Under review in Annals of Applied Statistics. 2017. Arxiv link: http://arxiv.org/abs/1711.03560
• Ruiz FJR, AtheyS , Blei DM. SHOPPER: A Probabilistic Model of Consumer Choice with Substitutes and Complements. Under review in Annals of Applied Statistics. 2017. Arxiv link: http://arxiv.org/abs/1711.03560
• Sraj I, Mandli KT, Knio OM, Dawson CN, Hoteit I. Quantifying uncertainties in fault slip distribution during the Tōhoku tsunami using polynomial chaos. Ocean Dynamics (2017).
• Mandli, K. T. et al. Clawpack: building an open source ecosystem for solving hyperbolic PDEs. PeerJ Comput. Sci. 2, e68 (2016).
• McCormick, T., Madigan, D., Raftery, A.E., and Burd, R.S. Dynamic Logistic Regression and Dynamic Model Averaging for Binary Classification. Biometrics.
• Rudolph M , Ruiz F, Mandt S, Blei D. Exponential Family Embeddings, In Proceedings of NIPS, 2016
• Rudolph M, Ruiz FJR, Mandt S, Blei DM. "Exponential Family Embeddings." Advances in Neural Information Processing Systems, 2016
• Boyi Xie, Rebecca J. Passonneau. Graph Structured Semantic Representation and Learning for Financial News. In Proceedings of the 28th International Conference of the Florida Artificial Intelligence Research Society (FLAIRS-28). Hollywood, Florida, USA. May 18-20, 2015 (to appear).
• He, R., and Zheng, T. (2015) GLMLE: Graph-limit Enabled Fast Computation for Fitting Exponential Random Graph Models to Large Social Networks. Social Network Analysis and Mining 5.
• K. W. Knehr, Nicholas W. Brady, Christianna N. Lininger, Christina A. Cama, David C. Bock, Amy C. Marschilok, Kenneth J. Takeuchi, Esther S. Takeuchi, and Alan C. West, “Mesoscale transport in magnetite electrodes for lithium-ion batteries,” ECS Transactions, 67, 7-19 (2015). doi:10.1149/06901.0007ecst
• K. W. Knehr, Nicholas W. Brady, Christina A. Cama, David C. Bock, Zhou Lin, Christianna N. Lininger, Amy C. Marschilok, Kenneth J. Takeuchi, Esther S. Takeuchi, and Alan C. West, “Modeling mesoscale transport of lithium-magnetite electrodes using insight from discharge and voltage recovery experiments,” Journal of the Electrochemical Society, 162, A2817-A2826 (2015). DOI:10.1149/2.0961514jes
• Tan, L.S.L., Chan, A.H., and Zheng, T. (2015) Latent quality models for document networks. Submitted to Annals of Applied Statistics.
• Davis, R.A., and Song, L. (2012). Unit Roots in Moving Averages Beyond First Order. Annals of Statistics
• Hoffman, M.D. (2012). Poisson-Uniform Nonnegative Matrix Factorization. Proceedings of the IEEE Conference on Audio, Speech, and Signal Processing (ICASSP).
• N. Bartlett and F. Wood (2011). Deplump for Streaming Data. Data Compression Conference.
• N. Bartlett, D. Pfau, and F. Wood. Forgetting counts: Constant Memory inference for a Dependent hierarchical Pitman-Yor Process. In Proceedings of the 17th International Conference on Machine Learning, 2010.
• Chen, M., Davis, R.A., and Song, L. (2010). Inference for Regression Models with Errors From a Non-invertible MA(1) Process. (To appear in Journal of Forecasting.)
• Yu-Sung Su, Andrew Gelman, Jennifer Hill, and Masanao Yajima, (2010). Multiple imputation with diagnostics in R: Opening windows into the black box. Journal of Statistical Software.
• Davis, R.A. and Yau, C-Y (2009). Comments on Pairwise Likelihood in Time Series Models.

Social Sciences 

• Adonis Antoniades, "Liquidity Risk and the Credit Crunch of 2007-2009."
• Pierre-André Chiappori, Bernard Salanié and Yoram Weiss, "Partner Choice and the Marital College Premium", under revision.
• Pierre-André Chiappori, Bernard Salanié, François Salanié, and Amit Gandhi, "From Aggregate Betting Data to Individual Risk Preferences," Econometrica (under review).
• Davis, R.A., and Song, L. Noncausal Vector AR Processes with Application to Financial Time Series
• G. Laroque and B. Salanié, 'Identifying the Response of Fertility to Financial Incentives", forthcoming at J. Applied Econometrics.
• Alfred Galichon and Bernard Salanié, "Cupid's Invisible Hand", Review of Economic Studies.
• Roger Gordon and Wojciech Kopczuk, "The Choice of Personal Income Tax Base"
• M. Henry, Y. Kitamura, B. Salanié, "Partial identification of finite mixtures in econometric models", forthcoming at Quantitative Economics.
• Ho, K. and Pakes, A. "Hospital Choices, Hospital Prices and Financial Incentives to Physicians."
• Wojciech Kopczuk and David Munroe, "Mansion tax: The Effect of Transfer Taxes on Residential Real Estate Market", in preparation.
• Wojciech Kopczuk, "The Polish busines 'flat' tax and its effect on reported incomes: a Pareto improving tax reform?", in preparation.
• Dennis Kristensen and Bernard Salanié, "Higher-order improvements for approximate estimators"
• Salanie, Bernard. Cupid’s Invisible Hand: Social Surplus and Identification in Matching Models (with Alfred Galichon), forthcoming in the Review of Economic Studies
• Emilia Simeonova, Costas Meghir, and Marten Palme, "Marriage, Bereavement and Mortality: The Role of Health Care Utilization," forthcoming at the Journal of Health Economics.
• Emilia Simeonovam, Randall Akee, William Copeland, Adrian Angold, and Jane E. Costello, "Young Adult Obesity and Household Income: Effects of Unconditional Cash Transfers," IZA Discussion Paper 5135 and forthcoming at the American Economic Journal – Applied Economics.
• Simpson, Shawn E. A Positive Event Dependence Model for Self-Controlled Case Series with Applications in Postmarketing Surveillance. Biometrics.
• Broadwell P, Davis N, Yoon S. Using Artificial Intelligence to Develop a Lexicon-Based African American Tweet Detection Algorithm to Inform Culturally Sensitive Twitter-Based Social Support Interventions for African American Dementia Caregivers. InInformatics and Technology in Clinical Care and Public Health 2022 (pp. 1-4). IOS Press.
• Yoon S, Alcantara C, Davis N, Broadwell P, Lee H, Bristol A, Tipiani D, Nho JY, Mittelman M. Applying Social Network Analysis to Compare Dementia Caregiving Networks on Twitter in Hispanic and Black Communities. InInformatics and Technology in Clinical Care and Public Health 2022 (pp. 232-235). IOS Press.
• Yoon S, Broadwell P, Alcantara C, Davis N, Lee H, Bristol A, Tipiani D, Nho JY, Mittelman M. Analyzing Topics and Sentiments from Twitter to Gain Insights to Refine Interventions for Family Caregivers of Persons with Alzheimer’s Disease and Related Dementias (ADRD) During COVID-19 Pandemic. InInformatics and Technology in Clinical Care and Public Health 2022 (pp. 170-173). IOS Press.
• DiGiovanni, A. M., Vannucci, A., Ohannessian, C. M., & Bolger, N. (2021). Modeling heterogeneity in the simultaneous emotional costs and social benefits of co-rumination. Emotion, 21(7), 1470–1482. https://doi.org/10.1037/emo0001028
• Milligan, W., Fuller, Z.L., Agarwal, I., Eisen, M.B., Przeworski, M., and G. Sella, 2021 Impact of essential workers in the context of social distancing for epidemic control. Main text: PDF. Supplement: as PDF or Jupyter Notebook. On MedRxiv. PLoS One 16: e0255680.
• Xu, W. (2021). The contingency of neighbourhood diversity: Variation of social context using mobile phone application data. Urban Studies, 00420980211019637.\
• Salanie, Bernard. From Aggregate Betting Data to Individual Risk Preferences (with Pierre-André Chiappori, François Salanié, and Amit Gandhi), Econometrica (2019), 86, 1-37.
• DiPrete TA, Burik C, Koellinger P. Genetic Instrumental Variable (GIV) regression: Explaining socioeconomic and health outcomes in non-experimental data.” Proceedings of the National Academy of Sciences. 2018.
• Salanie, Bernard. Fast, “Robust”, and Approximately Correct: Estimating Mixed Demand Systems (with Frank Wolak), Center for Economic Policy Research DP 13236 (2018)
• Sisco, M.R., & Weber, E.U. (2017). Evaluating computational methods and inferential procedures for automatically detecting emotions in text. In preparation.
• Sisco, M.R., Bosetti, V. & Weber, E.U. (2017). When do weather events generate attention to climate change? Climatic Change, 143 (1-2), 227-241. doi:10.1007/s10584-017-1984-2
• Cornwell, Christopher, David Mustard, and Jessica Van Parys. 2013. “Noncognitive Skills and the Gender Disparities in Test Scores and Teacher Assessments: Evidence from Primary School.” The Journal of Human Resources, 48(1), 238-266.
• Fang, Y., Feng, Y. and Yuan, M., (2013), Regularized principal components of heritability, Computational Statistics, to appear
• Johnston G., Smith, D., Fidock, F., "Malaria’s Missing Number: Calculating the Human Component of R0 by a Within-Host Mechanistic Model of Plasmodium falciparum Infection and Transmission," PLoS Computational Biology, 9(4) 2013.
• Jessie Handbury (2013), "Essays on Prices and Product Variety Across Cities," PhD Thesis, Columbia University.
• Legewie, Joscha 2013. "School Context, Peers and the Educational Achievement of Girls and Boys". Dissertation, Columbia University.
• Legewie, Joscha. 2013. “Terrorist Events and Attitudes towards Immigrants: A Natural Experiment.” American Journal of Sociology (forthcoming).
• Pop-Eleches, Cristian and Miguel Urquiola. 2013. "Going to a Better School: Effects and Behavioral Responses."American Economic Review, 103(4): 1289-1324.
• Van Parys, Jessica. 2013. “What Makes an Efficient Physician? Evidence from Florida Emergency Room Visits.” Columbia University Department of Economics Discussion Paper No. 1213-14.
• Yu, Y. and Feng, Y., (2013), APPLE: Approximate Path for Penalized Likelihood Estimators, Statistics and Computing, to appear
• Yu, Y. and Feng, Y., (2013), Modified Cross-Validation for LASSO Penalized High-Dimensional Linear Models, Journal of Computational and Graphical Statistics
• Costas Meghir, Marten Palme, and Emilia Simeonovam (2012), "Education, Health and Mortality: Evidence from a Social Experiment," NBER Working Paper 17932.
• Daniel Carvell, Janet Currie and W. Bentley MacLeod. "Accidental Death and the Rule of Joint and Several Liability". RAND Journal of Economics volume 43 issue 1, Spring 2012, pp. 51-77.
• Donald R. Davis and Jonathan I. Dingel, "A Spatial Knowledge Economy", NBER Working Paper 18188, June 2012, http://www.nber.org/papers/w18188
• Kate Ho, Justin Ho and Julie Mortimer (2012), “The Use of Full-line Forcing Contracts in the Video Rental Industry,” American Economic Review 2012, 102(2): 686-719. Also available as NBER Working Paper 14588.
• Kate Ho, Justin Ho and Julie Mortimer (2012),“Analyzing the Welfare Impacts of Full-line Forcing Contracts”. Journal of Industrial Economics 2012, 60(3): 468-498. Also available as NBER Working Paper 16318).
• Nakamura, E., J. Steinsson, and D. Sergeyev (2012): "Growth-Rate and Uncertainty Shocks in Consumption: Cross-Country Evidence," NBER Working Paper No. 18128.
• Ottonello P. (2012) "Optimal Exchange Rate Policy Under Collateral Constraint and Wage Rigidity", mimeo, Columbia University.
• Kate Ho and Joy Ishii (2011), “Location and Competition in Retail Banking,” International Journal of Industrial Organization 2011, 29(5): 537-546. (Winner: Paul Geroski Award for best paper of the year, IJIO)
• Emilia Simeonovam (2011), "Out of Sight, Out of Mind? The Impact of Natural Disasters on Pregnancy Outcomes," CESifo Economic Studies.
• Emilia Simeonovam, Douglas Almond, and Janet Currie (2011), "Public vs. Private Provision of Charity Care? Evidence from Hill-Burton Hospitals in Florida," Journal of Health Economics, (also NBER Working Paper 15798).
• Kate Ho, Leemore Dafny and Mauricio Varela (2010), “An Individual Healthplan Exchange: Which Employees Would Benefit and Why?,” American Economic Review, May 2010 (Papers and Proceedings), 100: 485-489.
• Kate Ho (2009), “Insurer-Provider Networks in the Medical Care Market,” American Economic Review 2009, 99(1): 393-430. Also available as NBER Working Paper 11822_._ (Winner: Arrow Award for best paper of the year, International Health Economics Association.)
• Emilia Simeonovam (2009), "Race, Quality of Care and Patient Outcomes: What Can We Learn from the Veterans Health Administration?" , Atlantic Economic Journal.

Environmental Sciences

• Anber U, Gentine P, Wang S, Sobel AH, Fog and rain in the Amazon. Proceedings of the National Academy of Sciences. 11473-11477, doi: 10.1073/pnas.1505077112
• Daleu CL., Woolnough S, Plant R, Sessions S, Herman M, Sobel A, Wang S, Kim D, Cheng A, Bellon G, Peyrill P, Siebesma P, Ferry F, van Ulft B, 2015: Intercomparison of methods of coupling between convection and large-scale circulation. 2. Comparison over nonuniform surface conditions. Journal of Advances in Modeling Earth Systems. 8, 387-405, doi:10.1002/2015MS000570.
• Delaria, Erin; Place, Bryan; Turner, Alexander; Zhu, Qindan; Jin, Xiaomeng; Cohen, Ronald, Development of a solar induced fluorescence-canopy conductance model and its application to stomatal reactive nitrogen deposition, under review at ACS Earth and Space Chemistry.
• Amonkar, Yash, David J. Farnham, and Upmanu Lall. "A k-nearest neighbor space-time simulator with applications to large-scale wind and solar power modeling." Patterns 3.3 (2022): 100454.
• Roger C.Creel,JacquelineAustermann,Nicole S.KhanbWilliam J.D'Andrea,NicholasBalascio,BlakeDyer,EricaAshe,WilliamMenke, Postglacial relative sea level change in Norway, https://doi.org/10.1016/j.quascirev.2022.107422
• Jacqueline Austermann, Mark J Hoggard, Konstantin Latychev, Fred D Richards, Jerry X Mitrovica, The effect of lateral variations in Earth structure on Last Interglacial sea level Geophysical Journal International, Volume 227, Issue 3, December 2021, Pages 1938–1960, https://doi.org/10.1093/gji/ggab289
• Blatter, D., Ray, A., & Key, K. (2021). Two-dimensional Bayesian inversion of magnetotelluric data using trans-dimensional Gaussian processes. Geophysical Journal International, 226(1), 548–563. https://doi.org/10.1093/gji/ggab110
• Chesley, C., Naif, S., Key, K., & Bassett, D. (2021). Fluid-rich subducting topography generates anomalous forearc porosity. Nature, 595(7866), 255–260. https://doi.org/10.1038/s41586-021-03619-8
• Sea-level trends across The Bahamas constrain peak last interglacial ice melt. Blake Dyer, Jacqueline Austermann, William J. D’Andrea, Roger C. Creel, Michael R. Sandstrom, Miranda Cashman, Alessio Rovere, Maureen E. Raymo, 2021, 118 (33) e2026839118, https://doi.org/10.1073/pnas.2026839118
• Giacomini, B. and Giometto, M. G.: On the suitability of second-order accurate finite-volume solvers for the simulation of atmospheric boundary layer flow, Geosci. Model Dev., 14, 1409–1426, https://doi.org/10.5194/gmd-14-1409-2021, 2021.
• Mark Hoggard,Jacqueline Austermann,Cody Randel,Simon Stephenson, Observational Estimates of Dynamic Topography Through Space and Time, 2021 https://doi.org/10.1002/9781119528609.ch15
• Mostafa Momen,Marc B. Parlange,Marco G. Giometto. Scrambling and Reorientation of Classical Atmospheric Boundary Layer Turbulence in Hurricane Winds, https://doi.org/10.1029/2020GL091695, 2021
• Steckler, M.S., B. Oryan, C.A. Wilson, C. Grall, S.L. Nooner, D.R. Mondal, S.H. Akhter, S. DeWolf and S.L. Goodbred (2021) Synthesis of the Distribution of Subsidence of the Lower Ganges-Brahmaputra Delta, Bangladesh, submitted to Earth-Science Reviews, August 20, 2021.
• Jin, Xiaomeng (2020), Observing the distributions and chemistry of major air pollutants (O3 and PM2.5) from space: trends, uncertainties, and health implications, Columbia University, https://doi.org/10.7916/d8-cxn5-h474
• Oryan, B., & Buck, W. R. (2020). Larger tsunamis from megathrust earthquakes where slab dip is reduced. Nature Geoscience, 1-6.
• Oryan, Bar, and W. Roger Buck. "Larger tsunamis from megathrust earthquakes where slab dip is reduced." Nature Geoscience 13.4 (2020): 319-324.
• Blatter, D., Key, K., Ray, A., Gustafson, C., & Evans, R. (2019). Bayesian joint inversion of controlled source electromagnetic and magnetotelluric data to image freshwater aquifer offshore New Jersey. Geophysical Journal International, 218(3), 1822–1837. https://doi.org/10.1093/gji/ggz253
• Chesley, C., Key, K., Constable, S., Behrens, J., & MacGregor, L. (2019). Crustal Cracks and Frozen Flow in Oceanic Lithosphere Inferred From Electrical Anisotropy. Geochemistry, Geophysics, Geosystems, 20(12), 5979–5999. https://doi.org/10.1029/2019gc008628
• Gustafson, C., Key, K., & Evans, R. L. (2019). Aquifer systems extending far offshore on the U.S. Atlantic margin. Scientific Reports, 9(1), 1–10. https://doi.org/10.1038/s41598-019-44611-7
• Anber U, Wang S, Sobel AH, 2017: Coupling with Ocean Mixed Layer leads to Intraseasonal variability in tropical deep convection - evidence from Cloud-resolving Simulations. Journal of Advances in Modeling Earth Systems. 9, 616-626, doi:10.1002/2016MS000803.
• Sun, L and Goldberg, ME. (2016) Cortical Mechanisms for Spatial Accuracy. Ann. Rev. Vis. Sci. , 2016 Oct 14;2:61-84. doi: 10.1146/annurev-vision-082114-035407. Epub 2016 Aug 19.