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This page will list citations for research that was aided by the Ginsburg HPC cluster.


Question:

How do I acknowledge the resources I have used on Ginsburg, Terremoto and Habanero in publications?


Answer:

Published research emerging out of computations run on the Ginsburg, Terremoto, Habanero and/or Yeti machines must recognize the grants that have made this service possible. 


We ask that all related publications include the following acknowledgement text: 


"We acknowledge computing resources from Columbia University's Shared Research Computing Facility project, which is supported by NIH Research Facility Improvement Grant 1G20RR030893-01, and associated funds from the New York State Empire State Development, Division of Science Technology and Innovation (NYSTAR) Contract C090171, both awarded April 15, 2010."

Please send citations to hpc-support@columbia.edu.

For more info please visit:

https://research.columbia.edu/content/srcpac/habaneropublications

To add publications to this listing, please email srcpac@columbia.edu.

Updated March 2019.

Physics and Astronomy (17)

Tavecchio F, Landoni M, Sironi L, Coppi P. Probing dissipation mechanisms in BL Lac jets through X-ray polarimetry. eprint arXiv: 1801.10060

Rowan ME, Sironi L, Narayan R. Electron and proton heating in trans-relativistic magnetic reconnection. eprint arXiv:1708.04627.

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

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

Visbal E, Haiman Z, Bryan GL. Self-consistent semi-analytic models of the first stars. 2018, Monthly Notices of the Royal Astronomical Society.

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.

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)

Hendel D et al. SMHASH: Anatomy of the Orphan Stream using RR Lyrae stars. eprint; arXiv 1711.04663

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

Comisso L, Sironi L. Particle Acceleration in Relativistic Plasma Turbulence. eprint: arXiv:1809.01168

 

Biomedical Sciences (9)

Wesch 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. Multivalent Small-Molecule Pan-RAS Inhibitors Cell 2017 Feb [pubmedpdf]

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.

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.

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

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]

Wesch 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. Multivalent Small-Molecule Pan-RAS Inhibitors Cell 2017 Feb [pubmedpdf]

Agmon E, Solon J, Bassereau P, Stockwell BR. Modeling the effects of lipid peroxidation during ferroptosis on membrane properties. Scientific Reports. 2018 Mar [pubmedpdf]

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

Agmon E, Stockwell BR. Lipid homeostasis and regulated cell death. Curr Opin Chem Biol. 2017 Jun;39:83-89

 

Statistics, Computer Science, and Engineering (34)

Ma Y, Zheng T. Stabilized Sparse Online Learning for Sparse Data. Journal of Machine Learning Research. [Abstract]

Zhou W, Veitch V, Austern M, Adams RP, Orbanz P. Compressibility and Generalization in Large-Scale Deep Learning. Eprint = 1804.05862.

Yousuf K. Variable screening for high dimensional time series. 2018, Electronic Journal of Statistics 12, 667-702.

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

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

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, Blei D. Dynamic Embeddings for Language Evolution, In Proceedings of WWW, 2018

Rudolph M, Ruiz F, Athey S, Blei D. Structured Embedding Models for Grouped Data, In Proceedings of NIPS, 2017

Rudolph M , Ruiz F, Mandt S, Blei D. Exponential Family Embeddings, In Proceedings of NIPS, 2016

Rudolph M , Ruiz F, Blei D. Word2Net: Deep Representations of Language, Submitted to ICML, 2018

Krstovski K, Blei DM. "Equation Embeddings", Submitted to ICML , 2018

Krstovski K, Blei DM. "ArXivLab: A Platform for Developing and Evaluating Exploratory Tools for the Scientific Literature", Submitted to SIGIR, 2018

Liu L, Blei DM. "Zero-Inflated Exponential Family Embeddings." NIPS 2017

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.

Abernathey R, Haller G. Transport by lagrangian vortices in the eastern pacific. 2018, Journal of Physical Oceanography, 48(3), 667-685.

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.

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.

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).

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).

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, 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

Rudolph M, Blei DM. "Dynamic Embeddings for Language Evolution." In proceedings of WWW, 2018

Rudolph M, Ruiz FJR,  Athey S, Blei DM. "Structured Embedding Models for Grouped Data." Advances in Neural Information Processing Systems, 2017

Rudolph M, Ruiz FJR, Mandt S, Blei DM. "Exponential Family Embeddings." Advances in Neural Information Processing Systems, 2016

Rudolph M, Ruiz FJR, Blei DM. "Word2Net: Deep Representations of Language." Under review in International Conference on Machine Learning, 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." Under review in SIGIR, 2018

Liu L, Blei DM. "Zero-Inflated Exponential Family Embeddings." International Conference on Machine Learning, 2017

Liu L, Ruiz FJR, Athey S, Blei DM. "Context Selection for Embedding Models." Advances in Neural Information Processing Systems, 2017.

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 ] ]

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 ] ]

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.

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.

 

Environmental Sciences (3)

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.
 
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.
  
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
 

Social Sciences (1)

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 (Forthcoming).


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