Recent Publications

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

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YearTitleAuthor(s)Type
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
2022Potential impacts and challenges of border carbon adjustmentsC. Böhringer, C. Fischer, K.E. Rosendahl, T.F. Rutherford, T.F.Article
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
2021k-median: exact recovery in the extended stochastic ball modelAlberto Del Pia, Mingchen MaArticle
2021A biomimetic basement membrane consisted of hybrid aligned nanofibers and microfibers with immobilized collagen IV and laminin for rapid endothelializationChenglong Yu, Guoping Guan, Stefanie Glas, Lu Wang, Zhutong Li, Lih-Sheng TurngArticle
2021A comparative mixed methods study on health information seeking among US-born/US-dwelling, Korean-born/US-dwelling, and Korean-born/Korean-dwelling mothersHanseul Stephanie Lee, Catherine Arnott-SmithArticle
2021A dual-responsive antibiotic-loaded nanoparticle specifically binds pathogens and overcomes antimicrobial-resistant infectionsMingzhou Ye, Yi Zhao, Yuyuan Wang, Miao Zhao, Nisakorn Yodsanit, Ruosen Xie, David Andes, Shaoqin GongArticle
2021A phylogeny-based test of mediation effect in microbiomeQilin Hong, Guanhua Chen, Zheng-Zheng TangPreprint
2021A review of thermoplastic polymer foams for functional applicationsGaojian Wu, Pengcheng Xie, Huaguang Yang, Kaifang Dang, Yuxuan Xu, Mohini Sain, Lih-Sheng Turng, Weimin Yang Article
2021A roadmap to robust science for high-throughput applications: The developers' perspectiveM. Taufer, E. Deelman, R. Ferreira da Silva, T. Estrada, M. Hall, M. LivnyProceeding
2021Acetyl-CoA flux from the cytosol to the ER regulates engagement and quality of the secretory pathwayIA Dieterich, Y Cui, MM Braun, AJ Lawton, NH Robinson, JL Peotter, Q Yu, JC Casler, BS Glick, A Audhya, JM Denu, L Li, L PuglielliArticle
2021An adventitial painting modality of local drug delivery to abate intimal hyperplasiaTakuro Shirasu, Nisakorn Yodsanit, Xiujie Xie, Yi Zhao, Yuyuan Wang, Ruosen Xie, Yitao Huang, Bowen Wang, Go Urabe, Shaoqin Gong, Lian-Wang Guo, K. Craig KentArticle
2021An Approximation algorithm for indefinite mixed integer quadratic programmingAlberto Del PiaPreprint
2021Application of quantum machine learning using the quantum kernel algorithm on high energy physics analysis at the LHCSau Lan Wu, Shaojun Sun, Wen Guan, Chen Zhou, Jay Chan, Chi Lung Cheng, Tuan Pham, Yan Qian, Alex Zeng Wang, Rui Zhang, Miron Livny, Jennifer Glick, Panagiotis Kl. Barkoutsos, Stefan Woerner, Ivano Tavernelli, Federico Carminati, Alberto Di Meglio, Andy C. Y. Li, Joseph Lykken, Panagiotis Spentzouris, Samuel Yen-Chi Chen, Shinjae Yoo, Tzu-Chieh WeiPreprint
2021BAF155 methylation drives metastasis by hijacking super-enhancers and subverting anti-tumor immunityEui-Jun Kim, Peng Liu, Shengjie Zhang, Kristine Donahue, Yidan Wang, Jennifer L Schehr, Serena K Wolfe, Amber Dickerson, Li Lu, Lixin Rui, Xuehua Zhong, Kari B Wisinski, Min Yu, Aussie Suzuki, Joshua M Lang, Irene M Ong, Wei XuArticle
2021BedsideNotes: Sharing physicians' notes with parents during hospitalizationBenjamin M. Zellmer, Carrie L. Nacht, Ryan J. Coller, Peter L.T. Hoonakker, Catherine Arnott-Smith, Daniel J. Sklansky, Shannon M. Dean, Windy Smith, Carley M. Sprackling, Brad D. Ehlenfeld, Michelle M. KellyArticle
2021Benchmarking quantitative performance in label-free proteomicsJames A. Dowell, Logan J. Wright, Eric A. Armsrong, John M. DenuArticle
2021Biological role and mechanism of chromatin readers in plantsRay Scheid, Jiani Chen, Xuehua ZhongArticle
2021Biomimetic, ROS-detonable nanoclusters - A multimodal nanoplatform for anti-restenotic therapyYi Zhao, Takuro Shirasu, Nisakorn Yodsanit, Eric Kent, Mingzhou Ye, Yuyuan Wang, Ruosen Xie, Alexander C. Gregg, Yitao Huang, K. Craig Kent, Lian-Wang Guo, Shaoqin Gong, Bowen WangArticle
2021Classification of animal sounds in a hyperdiverse rainforest using Convolutional Neural NetworksYuren Sun, Tatiana Midori Maeda, Claudia Solís-Lemus, Daniel Pimentel-Alarcón, Zuzana BurivalovaPreprint
2021Climate policies after Paris: Pledge, trade, and recycle. Insights from the 36th Energy Modeling Forum study (EMF36)Christoph Böhringer, Sonja Peterson, Thomas F. Rutherford, Jan Schneider, Malte WinklerProceeding
2021Complexity of projected Newton methods for bound-constrained optimizationYue Xie, Stephen J. WrightPreprint
2021Context matters: A theory of semantic discriminability for receptual encoding systemsKushin Mukherjee, Brian Yin, Brianne E. Sherman, Laurent Lessard, Karen B. SchlossPreprint
2021Controlling CRISPR with small molecule regulation for somatic cell genome editingNamita Khajanchi, Krishanu SahaArticle
2021CRISPR base editing as a potential therapeutic approach for Kir7.1 channelopathyMeha Kabra, Pawan K Shahi, Allison Spillane, Yuyuan Wang, Divya Sinha, Gregory A Newby, Sivani Saxena, Krishanu Saha, Mariya Moosajee, David Gamm, David R Liu, Shaoqin Gong, Bikash R PattnaikArticle
2021Current state of magnetic levitation and its applications in polymers: A reviewJun Xie, Peng Zhao, Chengqian Zhang, Jianzhong Fu, Lih-Sheng TurngPreprint
2021DNA methyltransferanse CHROMOMETHYLASE3 prevents ONSEN transposon silencing under heat stressXuehua Zhong, Kosuke Nozawa, Jiani Chen, Jianjun Jiang, Sarah M. Leichter, Masataka Yamada, Takamasa Suzuki, Fengquan Liu, Hidetaka ItoArticle
2021DOT1L inhibition enhances pluripotency beyond acquisition of epithelial identity and without immediate suppression of the somatic transcriptomeCoral K.Wille, Rupa SridharanArticle
2021Economic and environmental impacts of a proposed 'Carbon adder' on New York's energy marketGökçe Akin-Olçum, Christoph Böhringer, Thomas Rutherford, Andrew SchreiberArticle
2021Eggshell membrane and expanded polytetrafluoroethylene piezoelectric-enhanced triboelectric bio-nanogenerators for energy harvestingShujie Yan, Zhi Zhang, Xingxing Shi, Yiyang Xu, Yuan Li, Xiaofeng Wang, Qian Li, Lih-Sheng TurngArticle
2021Endoplasmic reticulum acetyltransferases Atase1 and Atase2 differentially regulate reticulophagy, macroautophagy and cellular acetyl-CoA metabolismMichael J. Rigby, Alexis J. Lawton, Gulpreet Kaur, Varuna C. Banduseela, William E. Kamm, Aparna Lakkaraju, John M. Denu, Luigi PuglielliArticle
2021Erratum for: Multiplex CRISPR-Cas9 editing of DNA methyltransferases in rice uncovers a class of non-CG methylation specific for GC-rich regionsDaoheng Hu, Yiming Yu, Chun Wang, Yanping Long, Yue Liu, Li Feng, Dongdong Lu, Bo Liu, Jinbu Jia, Rui Xia, Jiamu Du, Xuehua Zhong, Lei Gong, Kejian Wang, Jixian ZhaiOther
2021Evaluating the gas-laden ability of polymer melt under atmospheric conditions using a modified torque rheometerXing-Yu Mei, Ying-Guo Zhou, Hong-Long Sun, Bin-Bin Dong, Chun-Tai Liu, Li-Sheng TurngArticle
2021Evidence for distinct facial signals of reward, affiliation, and dominance from both perception and production tasksJared D. Martin, Adrienne Wood, William T. L. Cox, Scott Sievert, Robert Nowak, Eva Gilboa-Schechtman, Fangyun Zhao, Zachary Witkower, Andrew T. Langbehn, Paula M. Niedenthal Article
2021Expanded polytetrafluoroethylene/silk fibroin/salicin vascular graft fabrication for improved endothelialization and anticoagulationShujie Yan, Yuan Lie Yong, Chao Jiang, Yiyang Xu, Dongfang Wang, Xiang Zhang, Qian Li, Lih-Sheng TurngArticle
2021Factors influencing willingness to share health misinformation videos on the internet: Web-based surveyAlla Keselman, Catherine Arnott-Smith, Gondy Leroy, David R KaufmanArticle
2021Fasting drives the metabolic, molecular and geroprotective effects of a calorie-restricted diet in miceHeidi H. Pak, Spencer A. Haws, Cara L. Green, Mikaela Koller, Mitchell T. Lavarias, Nicole E. Richardson, Shany E. Yang, Sabrina N. Dumas, Michelle Sonsalla, Lindsey Bray, Michelle Johnson, Stephen Barnes, Victor Darley-Usmar, Jianhua Zhang, Chi-Liang Eric Yen, John M. Denu, Dudley W. LammingArticle
2021From metagenomes to molecules: innovations in functinoal metagenomics unlock hidden chemistry in the human microbiomeMarc G. Chevrette, Jo HandelsmanArticle
2021Gender can influence student experiences in MD-PhD trainingAnna S. Heffron, Katarina M. Braun, Cora Allen-Savietta, Amarette Filut, Chelsea Hanewall, Anna Huttenlocher, Jo Handelsman, Molly CarnesArticle
2021GNPS Dashboard: collaborative exploration of mass spectrometry data in the web browserDaniel Petras, Vanessa V. Phelan, Deepa Acharya, Andrew E. Allen, Allegra T. Aron, Nuno Bandeira, Benjamin P. Bowen, Deirdre Belle-Oudry, Simon Boecker, Dale A. Cummings Jr., Jessica M. Deutsch, Eoin Fahy, Neha Garg, Rachel Gregor, Jo Handelsman, Mirtha Navarro-Hoyos, Alan K. Jarmusch, Scott A. Jarmusch, Katherine Louie, Katherine N. Maloney, Michael T. Marty, Michael M. Meijler, Itzhak Mizrahi, Rachel L. Neve, Trent R. Northen, Carlos Molina-Santiago, Morgan Panitchpakdi, Benjamin Pullman, Aaron W. Puri, Robin Schmid, Shankar Subramaniam, Monica Thukral, Felipe Vasquez-Castro, Pieter C. Dorrestein & Mingxun Wang Other
2021Heteroscedasticity-aware residuals-basedcontextual stochastic optimizationRohit Kannan, Güzin Bayraksan, James R. LuedtkePreprint
2021High-rank matrix completion by integer programmingJeff Linderoth, Akhilesh Soni, Jim Luedtke, Daniel Pimentel-AlarcónPreprint
2021Hybrid liquid-metal heat dissipation structure enabled by phase transition for flexible electronicsHaicheng Li, Huilong Zhang, Seunghwan Min, Tao Zhou, Shaoqin Gong, Xue Feng, Zhenqiang MaPreprint
2021Hydrogen peroxide-responsive platelet membrane-coated nanoparticles for thrombus therapyYi Zhao, Ruosen Xie, Nisakorn Yodsanit, Mingzhou Ye, Yuyuan Wang, Bowen Wang, Lian-Wang Guo, K Craig Kent, Shaoqin GongArticle
2021Improving polylactide toughness by plasticizing with low molecular weight polylactide-poly(butylene succinate) copolymerYottha Srithep1, Onpreeya Veang-in, Dutchanee Pholharn, Lih-Sheng Turng, John MorrisArticle
2021Industrial, large-scale model predictive control with structured neural networksPratyush Kuman, James B. Rawlings, Stephen J. WrightArticle
2021Injectable hydrogel capable of in situ covalent crosslinking for permanent embolizationRuosen Xie, Yu-Chung Chen, Yi Zhao, Nisakorn Yodsanit, Yuyuan Wang, Naoaki Yamamoto, Dai Yamanouchi, Shaoqin GongArticle
2021Integer programming approaches to subspace clustering with missing dataAkhilesh Soni, Jeff Linderoth, Jim Luedtke, Daniel Pimentel-AlarcónProceeding
2021Integrating biomaterials and genome editing approaches to advance biomedical scienceAmr A. Abdeen, Brian D. Cosgrove, Charles A. Gersbach, Krishanu SahaArticle
2021Integrating United States biomanufacturing across vaccines and therapeuticsKrishanu Saha, Krishnendu RoyArticle
2021Investigating coloration as an emotion expressive cue for social robotsKaren B. Schloss, Christopher ThornstensonArticle
2021Kinetics and potency of T cell and CAR-T cell mediated cytolysis of glioma stem cellsHeather Brant Hayes, Meghan T. Logun, Stacie A. Chvatal, Katie Mueller, Nicole Piscopo, Amritava Das, Krishanu Saha, Daniel C. Millard, Lohitash KarumbaiahProceeding
2021Label-free imaging to track reprogramming of human somatic cellsK Molugu, GA Battistini, TM Heaster, J Rouw, EC Guzman, MC Skala, K SahaPreprint
2021Label-free metabolic imaging of tumor-induced T cell exhaustionDan L. Pham, Katherine Mueller, Krishanu Saha, Melissa C. SkalaProceeding
2021Machine learning approach to measurement of criticism: The core dimension of ecpressed emotionArezoo Movaghar, David Page, Krishanu Saha, Moira Rynn, Jan GreenbergArticle
2021Mapping a low-dimensional space of color-concept associationsKaren B. Schloss, Kushin Mukherjee, Timothy T. Rogers, Laurent Lessard, Michael GleicherArticle
2021Metabolism in the Midwest: research from the Midwest Aging Consortium at the 49th Annual Meeting of the American Aging AssociationMichaela E. Murphy, Akilavalli Narasimhan, Alexis Adrian, Ankur Kumar, Cara L. Green, Carolina Soto-Christina Camell, Christopher S. Morrow, Chung-Yang Yeh, Claire E. Richardson, Cristal M. Hill, Darcie L. Moore, Dudley W. Lamming, Eric R. McGregor, Heather A. Simmons, Heidi H. Pak, Hua Bai, John M. Denu, Josef Clark, Judith Simcox, Kishore Chittimalli, Korbyn Dahlquist, Kyoo-a Lee, Mariah Calubag, Mark Bouska, Matthew J. Yousefzadeh, Michelle Sonsalla, Reji Babygirija, Rong Yuan, Tadataka Tsuji, Timothy Rhoads, Vinal Menon, Yagna PR. Jarajapu, Yun ZhuProceeding
2021Microbe-diet interactions influence the effects of fiber on host metabolismSofia M. Murga-Garrido, Qilin Hong, Tzu-Wen L. Cross, Evan R. Hutchison, Jessica Han, Sydney P. Thomas, Eugenio I. Vivas, John Denu, Danilo G. Ceschin, Zheng-Zheng Tang, Federico E. ReyPreprint
2021Micropattern platform promotes extracellular matrix remodeling by human PSC-derived cardiac fibroblasts and enhances contractility of co-cultured cardiomyocytesB.N. Napiwocki, A. Stempien, D. Lang, R.A. Kruepke, G. Kim, J. Zhang, L.L. Eckhardt, A.V. Glukhov, T.J. Kamp, W.C. CroneArticle
2021More of what: Does the dark-is-more bias for colormap data visualizations operate on numeric or conceptual magnitude?Karen B. Schloss, Melissa A. Schoenlein, Alexis V. SotoArticle
2021Multiphoton autofluorescence imaging of immune cells in cancerMelissa C. Skala, Tiffany M. Heaster, Kelsey Tweed, Alexa Heaton, Dan Pham, Katherine Mueller, Dave Beebe, Paul Sondel, Krishanu SahaProceeding
2021Multi-stable bacterial communities exhibit extreme sensitivity to initial conditionsErik S Wrignt, Raveena Gupta, Kalin H VetsigianArticle
2021Nearest Neighbor Search Under UncertaintyBlake Mason, Ardhendu Tripathy, Robert NowakPreprint
2021Needles in haystacks: reevaluating old paradigms for the discovery of bacterial secondary metabolitesMarc G. Chevrette, Jo HandelsmanArticle
2021New valid inequalities and formulation for the static chance-constrained lot-sizing problemZeyang Zhang, Chuanhou Gao, James LuedtkePreprint
2021Non-viral nanocarriers for CRISPR-based genome editing tool deliveryYuyuan Wang, Shaoqin GongOther
2021On generating Lagrangian cuts for two-stage stochastic integer programsRui Chen, James LuedtkePreprint
2021On the complexity of separation from the knapsack polytopeAlberto Del Pia, Jeff Linderoth, Haoran ZhuPreprint
2021On the hole, interpretations of Venn diagrams are influenced by perceptual organizationKaren B. Schloss, Anna Bartel, Kevin Lande, Joris RoosArticle
2021Overparameterization of deep ResNet: zero loss and mean-field analysisZhiyan Ding, Shi Chen, Qin Li, Stephen J. WrightPreprint
2021Pareto optimal model selection in linear banditsYinglun Zhu, Robert NowakPreprint
2021Patterns of virus growth across the diversity of lifeTianyi Jin, John YinArticle
2021Quality control and evaluation of plant epigenomics dataRobert J. Schmitz, Alexandre P. Marand, Xuan Zhang, Rebecca A. Mosher, Franziska Turck, Xuemei Chen, Michael J. Axtell, Xuehua Zhong, Siobhan M. Brady, Molly Megraw, Blake C. MeyersArticle
2021Randomized algorithms for scientific computing (RASC)Aydın Buluç, Tamara G. Kolda, Stefan M. Wild, Mihai Anitescu, Anthony DeGennaro, John Jakeman, Chandrika Kamath, Ramakrishnan (Ramki) Kannan, Miles, E. Lopes, Per-Gunnar Martinsson, Kary Myers, Jelani Nelson, Juan M. Restrepo, C. Seshadhri, Draguna Vrabie, Brendt Wohlberg, Stephen J. Wright, Chao Yang, Peter ZwartProceeding
2021Red state, blue state: The polarizing influence of color in political mapsRémy A. Furrer, Karen Schloss, Gary Lupyan, Paula M. Niedenthal, Adrienne WoodPreprint
2021S- to X-band stretchable inductors and filters for gigahertz soft and epidermal electronicsYu Lan, Huilong Zhang, Seunghwan Min, Donghyeok Kim, Shaoqin Gong, Linda Katehi, Yuehang Xu, Zhenqiang MaArticle
2021Science education as a barrier against "Fake Health News""Alla Keselman, Catherine Arnott-Smith, Gondy Leroy, David R. KaufmanArticle
2021Short-chain fatty acids activate acetyltransferase p300Sydney P. Thomas, John M. DenuPreprint
2021Simple odd β-cycle inequalities for binary polynomial optimizationAlberto Del Pia, Matthias WalterPreprint
2021Single cell technologies to dissect heterogenous immune cell therapy productsKatherine Mueller, Krishanu SahaArticle
2021Social motility of biofilm-like microcolonies in a gliding bacteriumChao Li, Amanda Hurley, Wei Hu, Jay W. Warrick, Gabriel L. Lozano, Jose M. Ayuso, Wenxiao Pan, Jo Handelsman, David J. BeebeArticle
2021Sparse multi-term disjunctive cuts for the epigraph of a function of binary variablesRui Chen, James LuedtkePreprint
2021Sparsity of integral points on moduli spaces of varietiesJordan S. Ellenberg, Brian Lawrence, Akshay VenkateshArticle
2021The incidence of CO2 emissions pricing under alternative international market responses a computable general equilibrium analysis for GermanyChristoph Böhringer, Thomas F. Rutherford, Jan SchneiderPreprint
2021The mathematical foundations of epistemic network analysisDale Bowman, Zachari Swiecki, Zhiqiang Cai, Yeyu Wang, Brendan Eagan, Jeff Linderoth, David Williamson ShafferProceeding
2021The NIH somatic cell genome editing programKrishanu Saha, Erik J. Sontheimer, et alArticle
2021The UW virtual brain project: An immersive approach to teaching functional neuroanatomyKaren B. Schloss, Melissa A. Schoenlein, Ross Tredinnick, Simon Smith, Nathaniel Miller, Chris Racey, Christian Castro, Bas RokersArticle
2021Tiny Earth: A big idea for STEM education and antibiotic discoveryAmanda Hurley, Marc G. Chevrette, Deepa D. Acharya, Gabriel L. Lozano, Manuel Garavito, Jen Heinritz, Luis Balderrama, Mara Beebe, Martel L. DenHartog, Kamiyah Corinaldi, Renee Engels, Alyssa Gutierrez, Orli Jona, Josephine H. I. Putnam, Brody Rhodes, Tiffany Tsang, Simon Hernandez, Carol Bascom-Slack, Jessamina E. Blum, Paul A. Price, Debra Davis, Joanna Klein, Joshua Pultorak, Nora L. Sullivan, Nigel J. Mouncey, Pieter C. Dorrestein, Sarah Miller, Nichole A. Broderick, Jo HandelsmanArticle
2021Toward molecular cooperation by de novo peptidesIzabela K. Sibilska-Kaminski, John YinArticle
2021Toward understanding everyday lives of older adults: A methodological explorationJung-hye Shin, Youhung Her-Xiong, Ross Tredinnick, Kevin PontoArticle
2021Ultrasound-activable piezoelectric membranes for accelerating wound healingXingxing Shiab, Yingxin Chen, Yi Zhaoad, Mingzhou Ye, Shuidong Zhang, Shaoqin GongArticle
2021Ultrathin micromolded 3D scaffolds for high-density photoreceptor layer reconstructionIn-Kyu Lee, Allison L. Ludwig, M. Joseph Phillips, Juhwan Lee, Ruosen Xie, Benjamin S. Sajdak, Lindsey D. Jager, Shaoqin Gong, David M. Gamm, Zhenqiang MaArticle
2021Upper respiratory tract bacterial-immune interactions during respiratory syncytial virus infection in infancyChristian Rosas-Salazar, Zheng-Zheng Tang, Meghan H. Shilts, Kedir N. Turi, Qilin Hong, Derek A. Wiggins, Christian E. Lynch, Tebeb Gebretsadik, James D. Chappell, R. Stokes Peebles, Jr, Larry J. Anderson, Suman R. Das, Tina V. HartertArticle
2021UVR8 interacts with de novo DNA methyltransferase and suppresses DNA methylation in arabidopsisJianjun Jiang, Jie Liu, Dean Sanders, Shuiming Qian, Wendan Ren, Jikui Song, Fengquan Liu, Xuehua ZhongArticle
2021Variance reduction via primal-dual accelerated dual averaging for nonsmooth convex finite-sumsChaobing Song, Stephen J. Wright, Jelena DiakonikolasPreprint
2021Viscosity characterization and flow simulation and visualization of polytetrafluoroethylene paste extrusion using a green and biofriendly lubricantGeorge A. Schmidt II, Yu-Jyun Lin, Yiyang Xu, Dongfang Wang, Galip Yilmaz, Lih-Sheng TurngArticle
2021What kinds of functions do deep neural networks learn? Insights from variational spline theoryRahul Parhi, Robert D. NowakArticle