Recent Publications

Recent publications from our faculty and fellows during their time at WID are listed below. Please see each publication for additional information.

View Additional Publications:

2023A fully first-order method for stochastic bilevel optimizationJeongyeol Kwon, Dohyun Kwon, Stephen Wright, Robert NowakPreprint
2023Acss2 deletion reveals functional versatility via tissue-specific roles in transcriptional regulationNarayanan Puthillathu Vasudevan, Dharmendra K Soni, John R Moffett, Jishnu K S Krishnan, Abhilash P Appu, Sarani Ghoshal, Peethambaran Arun, John M Denu, Thomas P Flagg, Roopa Biswas, Aryan M Namboodiri Article
2023Algorithm selection for deep activelearning with imbalanced datasetsJifan Zhang, Shuai Shao, Saurabh Verma, Robert NowakPreprint
2023Augmented reality into live theatrical performanceD Lisowski, K Ponto, S Fan, C Probst, B SprecherArticle
2023Capital malleability and its implications for climate policy designThomas Rutherford, Christoh BöhringerProceeding
2023cMyBP-C ablation in human engineered cardiac tissue causes progressive Ca2+-handling abnormalitiesWillem J. De Lange, Emily T. Farrell, Jonathan J. Hernandez, Alana Stempien, Caroline R. Kreitzer, Derek R. Jacobs, Dominique L. Petty, Richard L. Moss, Wendy C. Crone, J. Carter RalpheArticle
2023College students and patient work: Health information management by emerging young adultsCatherine Arnott-Smith, Philip Romero MastersArticle
2023Cultivating well-being in engineering graduate students through mindfulness trainingWendy C. Crone, Pelin Kesebi, Beverly Hays, Shilagh A. Mirgain, Richard J. Davidson, Susan C. HagnessArticle
2023Cut your losses with squentropyLike Hui, Mikhail Belkin, Stephen WrightPreprint
2023Deep learning meets sparse regularization: A signal processing perspectiveRahul Parhi, Robert D. NowakPreprint
2023Depositing centromere repeats induces heritable intragenic heterochromatin establishment and spreading in ArabidopsisZhang-Wei Liu, Jie Liu, Fengquan Liu, Xuehua ZhongArticle
2023Development of runner reservoir and its effect on optical properties of small high-precision plastic injection molded partsDemitri Shotwell, Mong-Tung Lun, Jia-Hau Liu, Lih-Sheng TurngArticle
2023Differentially private optimization for smooth nonconvex ERMChangyu Gao, Stephen J. WrightPreprint
2023Efficiently learning relative similarity embeddings with crowdsourcingScott Sievert, Robert Nowak, Timothy RogersArticle
2023Expanded polytetrafluoroethylene/poly(3-hydroxybutyrate) (ePTFE/PHB) triboelectric nanogenerators and their potential applications as self-powered and sensing vascular graftsDongfang Wang, Chen Wang, Zhaojie Bi, Baokai Zhou, Lixia Wang, Qian Li, Lih-Sheng TurngArticle
2023Filtered iterative denoising for linear inverse problemsDanica Fliss, Willem Marais, Robert D. NowakPreprint
2023Guanidinium-rich lipopeptide-based nanoparticle enables efficient gene editing in skeletalmusclesMin Zhu, Xiuxiu Wang, Ruosen Xie, Yuyuan Wang, Xianghui Xu, Jacobus Burger, Shaoqin GongArticle
2023Identifying microbial drivers in biological phenotypes with a Bayesian Network Regression modelSamuel Ozminkowski, Claudia Solís-LemusPreprint
2023Label-free in vitro assays predict the potency of anti-disialoganglioside chimeric antigen receptor T-cell productsMeghan Logun, Maxwell B. Colonna, Katherine P. Mueller, Divya Ventarapragada, Riley Rodier, Chaitanya Tondepu, Nicole J. Piscopo, Amritava Das, Stacie Chvatal, Heather B. Hayes, Christian M. Capitini, Daniel J. Brat, Theresa Kotanchek, Arthur S. Edison, Krishanu Saha, Lohitash KarumbaiahArticle
2023Multi-trait analysis of gene-by-environment interactions in large-scale genetic studiesLan Luo, Devan V Mehrotra, Judong Shen, Zheng-Zheng TangArticle
2023Operator inference for non-intrusive model reduction with quadratic manifoldsRudy Geelen, Stephen Wright, Karen WillcoxArticle
2023Plant-specific histone deacetylases associate with ARGONAUTE4 to promote heterochromatin stabilization and plant heat toleranceFangfang Yang, Yingnan Sun, Xiaoxuan Du, Zhaohui Chu, Xuehua Zhong, Xiangsong ChenArticle
2023Red and blue states: dichotomized maps mislead and reduce perceived voting influenceRémy A. Furrer, Karen Schloss, Gary Lupyan, Paula M. Niedenthal, Adrienne WoodArticle
2023SPEED: Experimental design for policy evaluation in linear heteroscedastic banditsSubhojyoti Mukherjee, Qiaomin Xie, Josiah Hanna, Robert NowakPreprint
2023Targeted PERK inhibition with biomimetic nanoclusters confers preventative and interventional benefits to elastase-induced abdominal aortic aneurysmsNisakorn Yodsanit, Takuro Shirasu, Yitao Huang, Li Yin, Zain Husain Islam, Alexander Christopher Gregg, Alessandra Marie Riccio, Runze Tang, Eric William Kent, Yuyuan Wang, Ruosen Xie, Yi Zhao, Mingzhou Ye, Jingcheng Zhu, Yi Huang, Nicholas Hoyt, Mengxue Zhang, John A. Hossack, Morgan Salmon, K. Craig Kent, Lian-Wang Guo, Shaoqin Gong, Bowen Wang Article
2023The effect of the pediatric upper respiratory tract fungal microbiome on the risk of childhood asthmaC. Rosas-Salazar, B. Strickland, M.H. Shilts, H.H. Boone, K.N. Turi, S.S. Rajagopala, S. Ma, T. Gebretsadik, Q. Hong, Z. Tang, L.J. Anderson, R.S. Peebles, T.V. Hartert, S.R. DasProceeding
2023Transfer learning of machine learning models for multi-objective process optimization of a transferred mold to ensure efficient and robust injection molding of high surface quality partsJinsu Gim, Huaguang Yang, Lih-Sheng TurngArticle
2023Visualizing grassmannians via poincare embeddingsHuanran Li, Daniel Pimentel-AlarcónProceeding
2022A better way to decay: Proximal gradient training algorithms for neural netsLiu Yang, Jifan Zhang, Joseph Shenouda, Dimitris Papailiopoulos, Kangwook Lee, Robert D. NowakPreprint
2022A graphical model for fusing diverse microbiome dataMehmet Aktukmak, Haonon Zhu, Marc Chevrette, Julia Nepper, Shruthi Magesh, Jo Handelsman, Alfred HeroPreprint
2022A perturbation bound on the subspace estimator from canonical projectionsKaran Srivastava, Daniel Pimentel-AlarcónPreprint
2022A review of current advancements in high surface quality injection molding: Measurement, influencing factors, prediction, and controlJinsu Gim, Lih-Sheng TurngArticle
2022ACEs in spaces: Autocatalytic chemical ecosystems in spatial settingsAlex M. Plum, David A. BaumPreprint
2022Achieving STEM diversity: Fix the classroomsJo Handelsman, Sarah Elgin, Mica Estrada Shan Hays, Tracy Johnson, Sarah Miller, Vida Mingo, Christopher Shaffer, Jason WilliamsArticle
2022Active learning with neural networks: Insights from nonparametric statisticsYinglun Zhu, Robert NowakPreprint
2022AJEDI in science: leveraging instructor communities to create antiracist curriculaSarah Miller, Jennifer E. Kerr, Jo HandelsmanArticle
2022All-in-one virus-free manufacturing process of allogeneic chimeric antigen receptor (CAR) T cells using CRISPR/CAS9SCG Lima, D Cappabianca, MH Forsberg, C Capitini, DT Covas, K Saha, LEB SouzaArticle
2022An LCO-responsive homolog of NODULE INCEPTION positively regulates lateral root formation in Populus sp. Thomas B Irving, Sanhita Chakraborty, Lucas Gontijo Silva Maia, Sara Knaack, Daniel Conde, Henry W Schmidt, Paolo M Triozzi, Carl H Simmons, Sushmita Roy, Matias Kirst, Jean-Michel AnéArticle
2022An SDP relaxation for the sparse integer least square problemAlberto Del Pia, Dekun ZhouPreprint
2022Application of quantum machine learning to HEP analysis at LHC using quantum computer simulators and quantum computer hardwareS. L. Wu, J. Chan, A. Cheng, W. Guan, S. J. Sun, R. Zhang, C. Zhou, M. Livny, A. D. Meglio, A. C. Y. Li, J. Lykken, P. Spentzouris, S. Y.-C. Chen, S. Yoo, T.-C. Wei, P. Lougovski, S. Padhi, S. Severini, and D. WalkerProceeding
2022Authentic Undergraduate Research in Machine Learning with The Informatics Skunkworks: A Strategy for Scalable Apprenticeship Applied to Materials Informatics ResearchBenjamin Afflerbach, Wendy Crone, Dane Morgan, Anne Gillian-Daniel, Nafsaniath FathemaProceeding
2022BioKlustering: a web app for semi-supervised learning of maximally imbalanced genomic dataSamuel Ozminkowski, Yuke Wu, Liule Yang, Zhiwen Xu, Luke Selberg, Chunrong Huang, Claudia Solís-LemusPreprint
2022Chernoff Sampling for Active Testing and Extension to Active RegressionSubhojyoti Mukherjee, Ardhendu Tripathy, Robert NowakPreprint
2022Classification of animal sounds in a hyperdiverse rainforest using convolutional neural networks with data augmentationYuren Sun, Tatiana Midori Maeda, Claudia Solís-Lemus, Daniel Pimentel-Alarcón, Zuzana BuřivalováArticle
2022Classifying incomplete data with a mixture of subspace expertsBen A. Kizaric, Daniel L. Pimentel-AlarcónProceeding
2022Cognitive and cultural factors that affect general vaccination and COVID-19 vaccination attitudesAlla Keselman, Catherine Arnott-Smith, Amanda J. Wilson,Gondy Leroy , David R. KaufmanArticle
2022Color category boundaries predict generalization of color-concept associationsMelissa A. Schoenlein; Karen B. SchlossProceeding
2022Color-concept associations reveal an abstract conceptual spaceKushin Mukherjee, Karen Schloss, Laurent Lessard, Michael Gleicher, Timothy RogersProceeding
2022Colour-concept association formation for novel conceptsMelissa A. Schoenlein, Karen B. SchlossArticle
2022Combating online health misinformation: A professional's guide to helping the publicA Keselman, C Arnott-Smith, AJ WilsonBook
2022Cyclic block coordinate descent with variance reduction for composite nonconvex optimizationXufeng Cai, Chaobing Song, Stephen J. Wright, Jelena DiakonikolasPreprint
2022Detectability of varied hybridization scenarios using genome-scale hybrid detection methodsMarianne Bjorner, Erin K. Molloy, Colin N. Dewey, Claudia Solís-LemusPreprint
2022Discovery and mechanism of small molecule inhibitors selective for the chromatin-binding domains of oncogenic UHRF1Wallace H. Liu, Robert E. Miner III, Brittany N. Albaugh, Gene E. Ananiev, Scott A. Wildman, and John M. DenuArticle
2022Effect of static mixer on fiber orientation of injection molded fiber-reinforced compositesDemitri Shotwell, Allen Jonathan Román, Huaguang Yang, Chung-Yin Lin, Stefanie Glas, Edward Chen, Tim A. Osswald, Lih-Sheng TurngArticle
2022Effective mechanical properties of injection-molded short fiber reinforced PEEK composites using periodic homogenizationJian Zhao, Chengjie Guo, Xiubin Zuo, Allen Jonathan Román, Yinghao Nie, Dong-Xiao Su, Lih-Sheng Turng, Tim A. Osswald, Gengdong Cheng, Weidong Chen Article
2022Evolutionary genome mining for the discovery and engineering of natural product biosynthesisMarc G Chevrette, Nelly Selem-Mojica, César Aguilar, Kristin Labby, Edder D Bustos-Diaz, Jo Handelsman, Francisco Barona-GómezArticle
2022Exclusive breast-feeding, the early-life microbiome and immune response, and common childhood respiratory illnessesChristian Rosas-Salazar, Meghan H. Shilts, Zheng-Zheng Tang, Qilin Hong, Kedir N.Turi, Brittney M.Snyder, Derek A.Wiggins, Christian E. Lynch, Tebeb Gebretsadik, R. Stokes Peebles Jr., Larry J. Anderson, Suman R. Das, Tina V. HartertArticle
2022Flexible lumped microwave passive components and filters on cellulose nanofibril substratesShuoyang Qiu, Huilong Zhang, Qiangu Yan, Linda Katehi, Shaoqin Gong, Zhiyong Cai, Zhenqiang MaArticle
2022Fusion subspace clustering for incomplete dataUsman Mahmood, Daniel Pimentel-AlarcónPreprint
2022Geometry of the minimum volume confidence setsHeguang Lin, Mengze Li, Daniel Pimentel-Alarcón, Matthew L. MalloyPreprint
2022Hierarchical OptimizationKristin P. Bennett, Michael C. Ferris, Jong-Shi Pang, Mikhail V. Solodov, Stephen J. WrightArticle
2022High dimensional stochastic linear contextual bandit with missing covariatesByoungwook Jang, Julia Nepper, Marc Chevrette, Jo Handelsman, Alfred O. Hero IIIPreprint
2022Histone acid extraction and high throughput mass spectrometry to profile histone modifications in Arabidopsis thalianaRay Scheid, James A. Dowell, Dean Sanders, Jianjun Jiang, John M. Denu, Xuehua ZhongArticle
2022Impacts of climate changes on land allocation and land values: An application of the thimble REAP modelLingxiao Wang, Thomas RutherfordProceeding
2022Implementing systems thinking and data science in the training of the regenerative medicine workforceAnne L. Plant, Nicole Piscopo, Krishanu Saha, Claudia Zylberberg, Krishnendu Roy, Katherine Tsokas, Samantha N. Schumm, Sarah H. BeachyArticle
2022In situ autofluorescence lifetime assay of a photoreceptor stimulus response in mouse retina and human retinal organoidsKayvan Samimi, Bikash R. Pattnaik, Elizabeth E. Capowski, Krishanu Saha, David M. Gamm, and Melissa C. SkalaArticle
2022Increased expression of SLC25A1/CIC causes an autistic-like phenotype with altered neuron morphologyMichael J Rigby, Nicola Salvatore Orefice, Alexis J Lawton, Min Ma, Samantha L Shapiro, Sue Y Yi, Inca A Dieterich, Alyssa Frelka, Hannah N Miles, Robert A Pearce, John Paul J Yu, Lingjun Li, John M Denu, Luigi PuglielliArticle
2022Learning preference distributions from distance measurementsGokcan Tatli, Rob Nowak, Ramya Korlakai VinayakProceeding
2022Mechanistic basis for maintenance of CHG DNA methylation in plantsJian Fang, Jianjun Jiang, Sarah M. Leichter, Jie Liu, Mahamaya Biswal, Nelli Khudaverdyan, Xuehua Zhong, Jikui SongArticle
2022Metabolomic analysis of carbohydrate and amino acid changes induced by hypoxia in naked mole-rat brain and liverHang Cheng, Yiming (Amy) Qin, Rashpal Dhillon, James Dowell, John M. Denu, Matthew E. PamenterArticle
2022Microbiome composition modulates secondary metabolism in a multispecies bacterial communityMarc G. Chevrette, Chris S. Thomas, Amanda Hurley, Natalia Rosario-Meléndez, Kris Sankaran, Yixing Tu, Austin Hall, Shruthi Magesh, Jo HandelsmanProceeding
2022MiNAA: Microbiome network alignment algorithmReed Nelson, Rosa Aghdam, Claudia Solís-LemusPreprint
2022Minimum-length trace reconstruction via integer programmingH. Li, D. Pimentel-AlarcónProceeding
2022Modular derivation of diverse, regionally discrete human posterior CNS neurons enables discovery of transcriptomic patternsNisha R. Iyer, Junha Shin, Stephanie Cuskey, Yucheng Tian, Noah R. Nicol, Tessa E. Doersch, Frank Seipel, Sunnie Grace McCalla, Sushmita Roy, Randolph S. AshtonArticle
2022Multifunctional nanoparticle potentiates the in situ vaccination effect of radiation therapy and enhances response to immune checkpoint blockadeYing Zhang, Raghava N. Sriramaneni, Paul A. Clark, Justin C. Jagodinsky, Mingzhou Ye, Wonjong Jin, Yuyuan Wang, Amber Bates, Caroline P. Kerr, Trang Le, Raad Allawi, Xiuxiu Wang, Ruosen Xie, Thomas C. Havighurst, Ishan Chakravarty, Alexander L. Rakhmilevich, Kathleen A. O'Leary, Linda A. Schuler, Paul M. Sondel, Kyungmann Kim, Shaoqin Gong, Zachary S. MorrisArticle
2022NAD(H)-loaded nanoparticles for efficient sepsis therapy via modulating immune and vascular homeostasisMingzhou Ye, Yi Zhao, Yuyuan Wang, Ruosen Xie, Yao Tong, John-Demian Sauer, Shaoqin GongArticle
2022New classes of facets for complementarity knapsack problemsAlberto Del Pia, Jeff Linderoth, Haoran ZhuPreprint
2022New valid inequalities and formulations for the static joint Chance-constrained Lot-sizing problemZeyang Zhang, Chuanhou Gao, James LuedtkeArticle
2022Oct4:Sox2 binding is essential for establishing but not maintaining active and silent states of dynamically regulated genes in pluripotent cellsJerry Hung-Hao Lo, Miguel Edwards, Justin Langerman, Rupa Sridharan, Kathrin Plath, Stephen T. SmaleArticle
2022On continuous-domain inverse problems with sparse superpositions of decaying sinusoids as solutionsRahul Parhi, Robert D. NowakProceeding
2022One for all: Simultaneous metric and preference learning over multiple usersGregory Canal, Blake Mason, Ramya Korlakai Vinayak, Robert NowakPreprint
2022Operator inference for non-intrusive model reduction with nonlinear manifoldsRudy Geelen, Stephen Wright, Karen WilcoxPreprint
2022Opportunities for utilizing consumer grade 3D capture tools for insurance documentationKevin Ponto, Ross TredinnickArticle
2022Parent perspectives on sharing pediatric hospitalization clinical notesMichelle M. Kelly, MD, PhD, Peter L.T. Hoonakker, PhD, Carrie L. Nacht, MPH, Catherine Arnott-Smith, PhD, Shannon M. Dean, MD, MMM, Daniel J. Sklansky, MD, Windy Smith, MSN, RN, CPN, Carley M. Sprackling, Benjamin M. Zellmer, MD, Ryan J. Coller, MD, MPHArticle
2022Pelletizing ultra-high molecular weight polyethylene (UHMWPE) powders with a novel tapered die and addition of high density polyethylene (HDPE): Processing, morphology, and propertiesHuaguang Yang, Galip Yilmaz, Jing Jiang, Jun Xie, Thomas Langstraat, Raymond Chu, Martin van Es, Priya Garg, Lih-Sheng TurngArticle
2022pH-Responsive polymer nanoparticles for efficient delivery of Cas9 ribonucleoprotein with or without donor DNARuosen Xie, Xiuxiu Wang, Yuyuan Wang, Mingzhou Ye, Yi Zhao, Brian S. Yandell, Shaoqin GongArticle
2022Physical shish-kebab modification vs. chemical surface coating on expanded polytetrafluoroethylene vascular grafts for enhanced endothelial cell adhesionDongfang Wang, Xueke Yu, Yiyang Xu, Xiaofeng Wang, Haonan Wang, YangZhang, Qian Li, Lih-Sheng TurngArticle
2022Potential impacts and challenges of border carbon adjustmentsC. Böhringer, C. Fischer, K.E. Rosendahl, T.F. Rutherford, T.F.Article
2022Rank-one Boolean tensor factorization and the multilinear polytope?Albeto Del Pia, Aida KhajaviradPreprint
2022Relaxations and cutting planes for linear programs with complementarity constraintsAlberto Del Pia, Jeff Linderoth, Haoran ZhuPreprint
2022Renewable electricity capacity planning with uncertainty at multiple scales Michael C. Ferris, Andy PhilipottPreprint
2022Single-nuclei transcriptome analysis of the shoot apex vascular system differentiation in Populus Daniel Conde, Paolo M. Triozzi, Wendell J. Pereira, Henry W. Schmidt, Kelly M. Balmant, Sara A. Knaack, Arturo Redondo-López, Sushmita Roy, Christopher Dervinis, Matias KirstArticle
2022SLC13A5/NaCT overexpression causes disrupted white matter integrity and an autistic-like phenotype Michael J. Rigby, Nicola Salvatore Orefice, Alexis J. Lawton, Min Ma, Samantha L. Shapiro, Sue Y. Yi, Inca A. Dieterich, Alyssa Frelka, Hannah N. Miles, Robert A. Pearce, John Paul J. Yu, Lingjun Li, John M. Denu, Luigi PuglielliPreprint
2022Sparse Gaussian chain graphs with the spike-and-slab LASSO: Algorithms and asymptoticsYunyi Shen, Claudia Solís-Lemus, Sameer K. DeshpandePreprint
2022Special Issue: Global solution of integer, stochastic and nonconvex optimization problemsSS Dey, JR Luedtke, NV SahinidisArticle
2022Squares vs. Maps: effects of configuration on the dark-is-more bias?Clementine Zimnicki, Karen B. SchlossProceeding
2022Stochastic dynamic lot-sizing with supplier-driven substitution and service level constraintsNarges Sereshti, Merve Bodur, James R. LuedtkePreprint
2022Structure and mechanism of plant DNA methyltransferasesSM Leichter, J Du, X ZhongArticle
2022The autism-associated gene SYNGAP1 regulates human cortical neurogenesisGiorgia Quadrato, Marcella Birtele, Ashley Del Dosso, Tiantian Xu, Tuan Nguyen, Brent Wilkinson, Jean-Paul Urenda, Gavin Knight, Roger Moore, Ritin Sharma, Patrick Pirrotte, Randolph Ashton, Eric Huang, Marcelo CobaPreprint
2022The hierarchical organization of autocatalytic reaction networks and its relevance to the origin of lifeZhen Peng, Jeff Linderoth, David A. BaumArticle
2022The multilinear polytope of beta-acyclic hypergraphs has polynomial extension complexityAlberto Del Pia, Aida KhajaviradPreprint
2022Thermal, rheological, and mechanical characterization of compression and injection molded ultra-high molecular weight polyethylene, high density polyethylene, and their blendsHuaguang Yang, Galip Yilmaz, Jing Jiang, Thomas Langstraat, Raymond Chu, Martin van Es, Priya Garg, Lih-Sheng TurngArticle
2022THOR's Hammer: the antibiotic koreenceine drives gene expression in a model microbial communityAmanda Hurley, Marc G. Chevrette, Natalia Rosario-Meléndez, Jo HandelsmanArticle
2022Ultrafast learning of 4-node hybridization cycles in phylogenetic networks using algebraic invariantsZhaoxing Wu, Claudia Solís-LemusOther
2022Unifying effects of direct and relational associations for visual communicationMelissa A. Schoenlein, Johnny Campos, Kevin J. Lande, Laurent Lessard, Karen B. SchlossPreprint
2022Virus-Free CRISPR CAR T cells induce solid tumor regressionLauren E. Sarko, Katherine P. Mueller, Nicole J. Piscopo, Matthew H. Forsberg, Louise A. Saraspe, Amritava Das, Brittany Russell, Madeline Smerchansky, Lei Shi, Adeela Ali, Cicera R. Lazzarotto, Shengdar Q. Tsai, Christian M. Capitini, Krishanu SahaProceeding
2022Virus-like particles: Measures and biological functionsTara Bhat, Amy Cao, John YinArticle