Jarad Niemi

Publications

The list below is manually updated and therefore may not be as up to date as other lists:

* Indicates my advisee

Refereed Journal Articles

  1. Cole Dutter, Luis A. Damiano*, Jarad Niemi, Bradley A. Miller, Lisa A. Schulte, Matt Liebman, Matt Helmers, Rick Cruse, and Marshall D. McDaniel. (2023) Contour prairie strips affect adjacent soil but have only slight effects on crops. Field Crops Research 296. url doi
  2. Zachary P. Simpson, Jim Jordahl, Andrea Leptin, Fernando E. Miguez, Jarad Niemi, Lisa A. Schulte, Michael L. Thompson, Sebastian H. Villarino, and Marshall D. McDaniel (2023) No-tillage does not on average reduce soil carbon storage compared to conventional tillage. Geoderma 430. url doi
  3. Qinglong Tian, Colin Lewis-Beck*, Jarad Niemi, and William Meeker. (2023) Specifying prior distributions in reliability applications. Applied Stochastic Models in Business and Industry. url doi
  4. Matt Nowatzke, Luis Damiano*, Fernando Miguez, Gabe McNunn, Jarad Niemi, Lisa Schulte-Moore, Emily Heaton, Andy VanLoocke. (2022) Augmenting agroecosystem models with remote sensing data and machine learning changes overall estimates of nitrate-nitrogen leaching. Environmental Research Letters 17(11) 114010. url doi
  5. Estee Cramer, Yuxin Huang, Yijin Wang, Evan Ray, Matthew Cornell, Johannes Bracher, Andrea Brennen, Alvaro Castro Rivadeneira, Aaron Gerding, Katie H House, Dasuni Jayawardena, Abdul H Kanji, Ayush Khandelwal, Khoa Le, Vidhi Mody, Vrushti Mody, Jarad Niemi, Ariane Stark, Apurv Shah, Nutcha Wattanachit, Martha Zorn, and Nicholas Reich. (2022) The United States COVID-19 Forecast Hub Dataset. Scientific Data 9(462) url medRxiv pdf
  6. Estee Y Cramer, Evan L Ray, Velma K Lopez, Johannes Bracher, Andrea Brennen, Alvaro J Castro Rivadeneira, Aaron Gerding, Tilmann Gneiting, Katie H House, Yuxin Huang, Dasuni Jayawardena, Abdul H Kanji, Ayush Khandelwal, Khoa Le, Anja Muhlemann, Jarad Niemi, [256 other authors], Nicholas G Reich. (2022) “Evaluation of individual and ensemble probabilistic forecasts of COVID-19 mortality in the US” Proceedings of the National Academy of Sciences, 119(15), e2113561119. url doi pdf
  7. Matthew Stephenson, Lisa Schulte, Robert Klaver, and Jarad Niemi. (2021) “Miniature temperature data loggers increase precision and reduce bias when estimating the daily survival rate for bird nests.” Journal of Field Ornithology, 92(4): 492-505 url doi pdf
  8. Mark Tomer, Sarah Porter, David James, Jessica Van Horn, and Jarad Niemi. (2021) “Comparing riparian buffer design classification data among watersheds representing Iowa landscapes.” Agrosystems, Geosciences, and Environment. 4(2), e20159 url doi pdf
  9. Adam Martin-Schwarze*, Jarad Niemi, and Philip Dixon. (2021) “Joint modeling of distances and times in point-count surveys.” Journal of Agricultural, Biological, and Environmental Statistics. 26, 289-305 url doi pdf
  10. Ashley N. Dean, Jarad B. Niemi, John C. Tyndall, Erin W. Hodgson, and Matthew E. ONeal. (2021) “Developing a decision-making framework for insect pest management: a case study using soybean aphid (Hemiptera: Aphididae).” Pest Management Science. 77(2): 886-894 url doi pdf
  11. Nate Garton*, Jarad Niemi, and Alicia Carriquiry. (2020) “Knot selection in sparse Gaussian processes with a variational objective.” Statistical Analysis and Data Mining. 13(4): 324-336. url doi pdf
  12. Colin Lewis-Beck*, Victoria A. Walker, Jarad Niemi, Petrutza Caragea, and Brian K. Hornbuckle. (2020) “Extracting Agronomic Information from SMOS Vegetation Optical Depth in the US Corn Belt Using a Nonlinear Hierarchical Model.” Remote Sensing. 12(5): 827. url pdf
  13. M.D. Tomer, J.D. Van Horn, S.A. Porter, D.E. James, and J. Niemi. (2020) ``Comparing agricultural conservation planning framework (ACPF) practice placements for runoff mitigation and controlled drainage among 32 watersheds representing Iowa landscapes.’’ Journal of Soil and Water Conservation. 75(4): 460-271. url doi pdf
  14. E. A. Hines, M. R. Romoser, Z. E. Kiefer, A. F. Keating, L. H. Baumgard, J. Niemi, N. K. Gabler, J. F. Patience, G. Haberl, N. H. Williams, B. J. Kerr, K. J. Touchette, and J. W. Ross. (2019) ``The impact of dietary supplementation of arginine during gestation in a commercial swine herd: II. Offspring performance’’ Journal of Animal Science, 97(9), 3626-3635. url doi pdf
  15. E. A. Hines, M. R. Romoser, Z. E. Kiefer, A. F. Keating, L. H. Baumgard, J. Niemi, N. K. Gabler, J. F. Patience, G. Haberl, N. H. Williams, B. J. Kerr, K. J. Touchette, and J. W. Ross. (2019) ``The impact of dietary supplementation of arginine during gestation in a commerical herd: I. Gilt.’’ (2019) Journal of Animal Science. 97(9), 3617-3625. url doi pdf
  16. Ignacio Alvarez* and Jarad Niemi. (2019) ``Fully Bayesian analysis of allele-specific RNA-seq data.’’ Mathematical Biosciences and Engineering. 16(6), 7751-7770. url pdf
  17. Nathaniel Garton* and Jarad Niemi. (2019) ``Multivariate temporal modeling of crime with dynamic linear models.’’ PLOS ONE. 14(7), e0218375. url pdf
  18. Will Landau*, Jarad Niemi, and Dan Nettleton. (2019) ``Fully Bayesian analysis of RNA-seq counts for the detection of gene expression heterosis.’’ Journal of the American Statistical Association, 114(526), 610-621. url pdf
  19. Craig J. McGowan, Matthew Biggerstaff, Michael Johansson, Karyn M. Apfeldorf, Michal Ben-Nun, Logan Brooks, Matteo Convertino, Madhav Erraguntla, David C. Farrow, John Freeze, Saurav Ghosh, Sangwon Hyun, Sasikiran Kandula, Joceline Lega, Yang Liu, Nicholas Michaud*, Haruka Morita, Jarad Niemi, Naren Ramakrishnan, Evan L. Ray, Nicholas G. Reich, Pete Riley, Jeffrey Shaman, Ryan Tibshirani, Alessandro Vespignani, Qian Zhang, Carrie Reed & The Influenza Forecasting Working Group (2019) ``Collaborative efforts to forecast seasonal influenza in the United States, 2015–2016.’’ Scientific Reports, 9, 683, url
  20. Lisa A. Schulte, Jarad Niemi, Matthew J. Helmers, Matt Liebman, J. Gordon Arbuckle, David E. James, Randall K. Kolka, Matthew E. O’Neal, Mark D. Tomer, John C. Tyndall, Heidi Asbjornsen, Pauline Drobney, Jeri Neal, Gary Van Ryswyk, and Chris Witte (2017) ``Prairie strips improve biodiversity and the delivery of multiple ecosystem services from corn–soybean croplands.’’ Proceedings of the National Academy of Sciences, 114(42), 11247-11252. url pdf
  21. Adam Martin-Schwarze*, Jarad Niemi, and Philip Dixon (2017) ``Assessing the impacts of time to detection distribution assumptions on detection probability estimation.’’ Journal of Agricultural, Biological, and Environmental Statistics. 22, 465-480 url pdf
  22. Matt Simpson*, Vivek Roy, and Jarad Niemi (2017) ``Interweaving Markov chain Monte Carlo strategies for efficient estimation of dynamic linear models.’’ Journal of Computational and Graphical Statistics, 26(1), 152-159 url pdf
  23. Lisa Schulte, Anna MacDonald, Jarad Niemi, and Matthew Helmers. (2016) ``Prairie strips as a mechanism to promote land sharing by birds in industrial agricultural landscapes.’’ Agriculture, Ecosystems and Environment 220: 55-63
  24. David M. Brenner, Jack Dekker, Jarad Niemi, and Lisa Pfiffner. (2016) ``Medical Oxygen Concentrators for Releasing Seed Dormancy.’’ Crop Science 55:2291-2293 pdf url
  25. Jarad Niemi, Eric Mittman*, Will Landau*, and Dan Nettleton (2015) ``Empirical Bayes analysis of RNA-seq data for detection of gene expression heterosis.’’ Journal of Agricultural, Biological, and Environmental Statistcs, 20(4): 614-628 url
  26. Robert B. Gramacy, Jarad Niemi, Robin Weiss. (2014) ``Massively parallel approximate Gaussian process regression.’’ SIAM/ASA Journal on Uncertainty Quantification 2(1) 564-584. arXiv url pdf DOI
  27. Daniel Sheinson*, Jarad Niemi, and Wendy Meiring. (2014) ``Comparison of the performance of particle filter algorithms applied to tracking of a disease epidemic.’’ Journal of Mathematical Biosciences, 255, 21-32 url pdf DOI
  28. Jonathan Dess, Jennifer L. Momsen, Jarad Niemi, Lisa Montplaisir. (2014) ``Student interpretations of phylogenetic trees in an introductory biology course.’’ CBE - Life Sciences Education url
  29. Jo Eidsvik, Benjamin A. Shaby, Brian J. Reich, Matthew Wheeler*, and Jarad Niemi. (2013) ``Estimation and prediction in spatial models with block composite likelihoods.’’ Journal of Computational and Graphical Statistics, 23:2, 295-315. pdf DOI url
  30. Bernie J Daigle Jr, Min K Roh, Linda R Petzold and Jarad Niemi. (2012) ``Accelerated maximum likelihood parameter estimation for stochastic biochemical systems.’’ BMC Bioinformatics 13:68.
  31. David Banks, Gauri Datta, Alan Karr, James Lynch, Jarad Niemi, and Francisco Vera. (2012) ``Bayesian CAR models for syndromic surveillance on multiple data streams: theory and practice.’’ Information Fusion: 13(2): 105–116.
  32. Mike Ludkovski and Jarad B. Niemi. (2010) ``Optimal dynamic policies for influenza management.’’ Statistical Communications in Infectious Diseases: 2(1): 5.
  33. Jarad B. Niemi and Mike West. (2010), ``Adaptive mixture modelling Metropolis methods for Bayesian analysis of non-linear state-space models.’’ Journal of Computational and Graphical Statistics. 19(2): 260–280.
  34. Quanli Wang, Jarad Niemi, Cheemeng Tan, Lingchong You, and Mike West. (2010), ``Image segmentation and dynamic lineage analysis in single-cell fluorescent microscopy.’’ Cytometry: Part A 77A(1): 101–110
  35. Jarad Niemi, Brad Carlin, and Jon Alexander. (2008), ``Contrarian strategies for NCAA tournament pools: a cure for March madness?’’ Chance 21(1): 39–46
  36. Michael J. Simmons, Jarad B. Niemi, Don-Felix Ryzek, Cecile Lamour, Joseph W. Goodman, Wojtek Kraszkiewicz, and Ryan Wolff. (2007), ``Cytotype regulation by telomeric P elements in Drosophila melanogaster: Interactions with P elements from M’ strains.’’ Genetics 176(4): 1957–1966
  37. Cheemeng Tan, Hao Song, Jarad Niemi, and Lingchong You. (2007), ``A synthetic biology challenge: making cells compute.’’ Molecular BioSystems 3: 343–353
  38. Kevin J. Haley, Jeremy R. Stuart, John D. Raymond, Jarad B. Niemi, and Michael J. Simmons. (2005), ``Mutations in the Su(var)2-5 gene impair cytotype-mediated regulation of P element activity in Drosophila melanogaster through a Maternal Effect.’’ Genetics 171: 583–595.
  39. Jarad B. Niemi, John D. Raymond, Ryan Patrek, and Michael J. Simmons. (2004), ``Establishment and maintenance of the P cytotype associated with telomeric P elements in Drosophila melanogaster.’’ Genetics 166: 255–264.
  40. Michael J. Simmons, John D. Raymond, Jarad B. Niemi, Jeremy R. Stuart, and Peter J. Merriman. (2004), ``The P cytotype in Drosophila melanogaster: A maternally transmitted regulatory state of the germ line associated with telomeric P elements.’’ Genetics 166: 243–254.
  41. Michael J. Simmons, Kevin J. Haley, Craig D. Grimes, John D. Raymond, and Jarad B. Niemi. (2002), ``A hobo transgene that encodes the P element transposase in Drosophila melanogaster: Autoregulation and cytotype control of transposase activity.’’ Genetics 161: 195–204.

Book Chapters

  1. Jarad B. Niemi and Gerald J. Niemi. ``Linear regression, model averaging, and Bayesian techniques for predicting chemical activities from structure.’’ Ebook chapter on Advances in Mathematical Chemistry: With applications to chemoinformatics, bioinformatics, drug discovery, and predictive toxicology , Editors: Subhash C. Basak, Guillermo Restrepo and Jose Luis Villaveces, Bentham Publishers (accepted)

Refereed Conference Proceeding

  1. Michael Ludkovski and Jarad Niemi (2011) ``Optimal disease outbreak decisions using stochastic simulation.’’ Proceedings of the 2011 Winter Simulation Conference, eds. S. Jain, R. R. Creasey, J. Himmelspack, K. P. White, and M. Fu.
  2. Jarad Niemi, Meredith Smith, and David Banks. (2008),``Test power for drug abuse surveillance.’’ in Biosurveillance and Biosecurity, Proceedings of BioSecure 2008, Lecture Notes in Computer Science, eds. Daniel Zeng, Hsinchun Chen, Henry Rolka, and William B. Lober. pp. 131–142

Refereed Abstracts

  1. Ignacio Alvarez, Jarad Niemi, and Matt Simpson. (2014) ``Bayesian inference for a covariance matrix.’’ for the Conference on Applied Statistics in Agriculture
  2. Jarad Niemi. (2013) ``A Tool for Interactive Disease Outbreak Visualization, Detection, and Forecasting’’ Online Journal of Public Health Informatics
  3. Jarad Niemi and Michael Ludkovski. (2013) ``Tau-leaped particle learning.’’ Online Journal of Public Health Informatics 5:1 url
  4. Jarad Niemi and Michael Ludkovski. (2011) ``Optimal sequential management decisions for measles outbreaks.’’ Emerging Health Threats Journal 4 url
  5. Jarad Niemi. (2011) ``An exploratory analysis of the 2010 measles outbreak in Zimbabwe.’’ Emerging Health Threats Journal 4 url
  6. Jarad B. Niemi, Michael D. Porter, and Brian J. Reich. (2008), ``Mixture likelihood ratio scan statistic for disease outbreak detection.’’ Advances in Disease Surveillance 5:49

Book reviews

  1. Jarad B. Niemi. (2010) Dynamic Linear Models with R. The American Statistician 64:3, pg 268 url

Other publications

  1. Jarad Niemi and Andrew Gelman. (2011) ``Statistical graphics: making information clear – and beautiful.’’ Significance 8, 135–137
  2. Jarad B. Niemi. (2010) ``Evaluating individual player contributions to team offense and defense: a model based approach.’’ JSM Proceedings, Section on Statistics in Sports. Vancouver, BC, Canada: American Statistical Association. 4914–4923. pdf
  3. Jarad B. Niemi and Matthew Wheeler*. ``Efficient Bayesian inference in stochastic chemical kinetic models using graphical processing units.’’ arXiv
  4. Tim W. Dake, Jarad B. Niemi, Don L. Hughes, Jeff J. Kester, Don B. Compton, Jon J. Calderas, Rich G. Schafermeyer, Kevin P. Christmas. ``Compositions having enhanced aqueous solubility and methods of their preparation.’’ PCT/US2002/014505 filed