Research articles, presentations, and other scholarship

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  • MetaCompare: a computational pipeline for prioritizing environmental resistome risk 

    Oh, Min; Pruden, Amy; Chen, Chaoqi; Heath, Lenwood S.; Xia, Kang; Zhang, Liqing (2018-07)
    The spread of antibiotic resistance is a growing public health concern. While numerous studies have highlighted the importance of environmental sources and pathways of the spread of antibiotic resistance, a systematic means ...
  • Cyberbiosecurity Challenges of Pathogen Genome Databases 

    Vinatzer, Boris A.; Heath, Lenwood S.; Almohri, Hussain MJ J.; Stulberg, Michael J.; Lowe, Christopher; Li, Song (Frontiers, 2019-05-15)
    Pathogen detection, identification, and tracking is shifting from non-molecular methods, DNA fingerprinting methods, and single gene methods to methods relying on whole genomes. Viral Ebola and influenza genome data are ...
  • Polynomial-Sized Topological Approximations Using the Permutahedron 

    Choudhary, Aruni; Kerber, Michael; Raghvendra, Sharath (2019-01)
    Classical methods to model topological properties of point clouds, such as the Vietoris-Rips complex, suffer from the combinatorial explosion of complex sizes. We propose a novel technique to approximate a multi-scale ...
  • Reconstructing signaling pathways using regular language constrained paths 

    Wagner, Mitchell J.; Pratapa, Aditya; Murali, T. M. (2019-07-15)
    Motivation High-quality curation of the proteins and interactions in signaling pathways is slow and painstaking. As a result, many experimentally detected interactions are not annotated to any pathways. A natural question ...
  • Higher Education Student Body Diversification as Glocal Practice 

    Alvarado, Jose Gerardo (2012-07)
    Georg Simmel's assertion that strangeness organizes nearness and remoteness helps to understand how the social category of First Generation College Student (FGCS, first in the family to attend college) is used at a public ...
  • COSTA: Composite Trust-Based Asset-Task Assignment in Mobile Ad Hoc Networks 

    Cho, Jin-Hee; Al-Hamadi, Hamid; Chen, Ing-Ray (IEEE, 2019)
    In mobile ad hoc networks (MANETs), asset-task assignment problems have been explored with vastly different approaches. Considering the unique characteristics of MANET environments, such as no centralized trusted entity, ...
  • Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen 

    Menden, Michael P.; Wang, Dennis; Mason, Mike J.; Szalai, Bence; Bulusu, Krishna C.; Guan, Yuanfang; Yu, Thomas; Kang, Jaewoo; Jeon, Minji; Wolfinger, Russ; Nguyen, Tin; Zaslavskiy, Mikhail; Jang, In Sock; Ghazoui, Zara; Ahsen, Mehmet Eren; Vogel, Robert; Neto, Elias Chaibub; Norman, Thea; Tang, Eric K. Y.; Garnett, Mathew J.; Di Veroli, Giovanni Y.; Fawell, Stephen; Stolovitzky, Gustavo; Guinney, Justin; Dry, Jonathan R.; Saez-Rodriguez, Julio; Abante, Jordi; Abecassis, Barbara Schmitz; Aben, Nanne; Aghamirzaie, Delasa; Aittokallio, Tero; Akhtari, Farida S.; Al-lazikani, Bissan; Alam, Tanvir; Allam, Amin; Allen, Chad; de Almeida, Mariana Pelicano; Altarawy, Doaa; Alves, Vinicius; Amadoz, Alicia; Anchang, Benedict; Antolin, Albert A.; Ash, Jeremy R.; Romeo Aznar, Victoria; Ba-alawi, Wail; Bagheri, Moeen; Bajic, Vladimir; Ball, Gordon; Ballester, Pedro J.; Baptista, Delora; Bare, Christopher; Bateson, Mathilde; Bender, Andreas; Bertrand, Denis; Wijayawardena, Bhagya; Boroevich, Keith A.; Bosdriesz, Evert; Bougouffa, Salim; Bounova, Gergana; Brouwer, Thomas; Bryant, Barbara; Calaza, Manuel; Calderone, Alberto; Calza, Stefano; Capuzzi, Stephen; Carbonell-Caballero, Jose; Carlin, Daniel; Carter, Hannah; Castagnoli, Luisa; Celebi, Remzi; Cesareni, Gianni; Chang, Hyeokyoon; Chen, Guocai; Chen, Haoran; Chen, Huiyuan; Cheng, Lijun; Chernomoretz, Ariel; Chicco, Davide; Cho, Kwang-Hyun; Cho, Sunghwan; Choi, Daeseon; Choi, Jaejoon; Choi, Kwanghun; Choi, Minsoo; De Cock, Martine; Coker, Elizabeth; Cortes-Ciriano, Isidro; Cserzo, Miklos; Cubuk, Cankut; Curtis, Christina; Van Daele, Dries; Dang, Cuong C.; Dijkstra, Tjeerd; Dopazo, Joaquin; Draghici, Sorin; Drosou, Anastasios; Dumontier, Michel; Ehrhart, Friederike; Eid, Fatma-Elzahraa; ElHefnawi, Mahmoud; Elmarakeby, Haitham; van Engelen, Bo; Engin, Hatice Billur; de Esch, Iwan; Evelo, Chris; Falcao, Andre O.; Farag, Sherif; Fernandez-Lozano, Carlos; Fisch, Kathleen; Flobak, Asmund; Fornari, Chiara; Foroushani, Amir B. K.; Fotso, Donatien Chedom; Fourches, Denis; Friend, Stephen; Frigessi, Arnoldo; Gao, Feng; Gao, Xiaoting; Gerold, Jeffrey M.; Gestraud, Pierre; Ghosh, Samik; Gillberg, Jussi; Godoy-Lorite, Antonia; Godynyuk, Lizzy; Godzik, Adam; Goldenberg, Anna; Gomez-Cabrero, David; Gonen, Mehmet; de Graaf, Chris; Gray, Harry; Grechkin, Maxim; Guimera, Roger; Guney, Emre; Haibe-Kains, Benjamin; Han, Younghyun; Hase, Takeshi; He, Di; He, Liye; Heath, Lenwood S.; Hellton, Kristoffer H.; Helmer-Citterich, Manuela; Hidalgo, Marta R.; Hidru, Daniel; Hill, Steven M.; Hochreiter, Sepp; Hong, Seungpyo; Hovig, Eivind; Hsueh, Ya-Chih; Hu, Zhiyuan; Huang, Justin K.; Huang, R. Stephanie; Hunyady, Laszlo; Hwang, Jinseub; Hwang, Tae Hyun; Hwang, Woochang; Hwang, Yongdeuk; Isayev, Olexandr; Walk, Oliver Bear Don't; Jack, John; Jahandideh, Samad; Ji, Jiadong; Jo, Yousang; Kamola, Piotr J.; Kanev, Georgi K.; Karacosta, Loukia; Karimi, Mostafa; Kaski, Samuel; Kazanov, Marat; Khamis, Abdullah M.; Khan, Suleiman Ali; Kiani, Narsis A.; Kim, Allen; Kim, Jinhan; Kim, Juntae; Kim, Kiseong; Kim, Kyung; Kim, Sunkyu; Kim, Yongsoo; Kim, Yunseong; Kirk, Paul D. W.; Kitano, Hiroaki; Klambauer, Gunter; Knowles, David; Ko, Melissa; Kohn-Luque, Alvaro; Kooistra, Albert J.; Kuenemann, Melaine A.; Kuiper, Martin; Kurz, Christoph; Kwon, Mijin; van Laarhoven, Twan; Laegreid, Astrid; Lederer, Simone; Lee, Heewon; Lee, Jeon; Lee, Yun Woo; Leppaho, Eemeli; Lewis, Richard; Li, Jing; Li, Lang; Liley, James; Lim, Weng Khong; Lin, Chieh; Liu, Yiyi; Lopez, Yosvany; Low, Joshua; Lysenko, Artem; Machado, Daniel; Madhukar, Neel; De Maeyer, Dries; Malpartida, Ana Belen; Mamitsuka, Hiroshi; Marabita, Francesco; Marchal, Kathleen; Marttinen, Pekka; Mason, Daniel; Mazaheri, Alireza; Mehmood, Arfa; Mehreen, Ali; Michaut, Magali; Miller, Ryan A.; Mitsopoulos, Costas; Modos, Dezso; Van Moerbeke, Marijke; Moo, Keagan; Motsinger-Reif, Alison; Movva, Rajiv; Muraru, Sebastian; Muratov, Eugene; Mushthofa, Mushthofa; Nagarajan, Niranjan; Nakken, Sigve; Nath, Aritro; Neuvial, Pierre; Newton, Richard; Ning, Zheng; De Niz, Carlos; Oliva, Baldo; Olsen, Catharina; Palmeri, Antonio; Panesar, Bhawan; Papadopoulos, Stavros; Park, Jaesub; Park, Seonyeong; Park, Sungjoon; Pawitan, Yudi; Peluso, Daniele; Pendyala, Sriram; Peng, Jian; Perfetto, Livia; Pirro, Stefano; Plevritis, Sylvia; Politi, Regina; Poon, Hoifung; Porta, Eduard; Prellner, Isak; Preuer, Kristina; Angel Pujana, Miguel; Ramnarine, Ricardo; Reid, John E.; Reyal, Fabien; Richardson, Sylvia; Ricketts, Camir; Rieswijk, Linda; Rocha, Miguel; Rodriguez-Gonzalvez, Carmen; Roell, Kyle; Rotroff, Daniel; de Ruiter, Julian R.; Rukawa, Ploy; Sadacca, Benjamin; Safikhani, Zhaleh; Safitri, Fita; Sales-Pardo, Marta; Sauer, Sebastian; Schlichting, Moritz; Seoane, Jose A.; Serra, Jordi; Shang, Ming-Mei; Sharma, Alok; Sharma, Hari; Shen, Yang; Shiga, Motoki; Shin, Moonshik; Shkedy, Ziv; Shopsowitz, Kevin; Sinai, Sam; Skola, Dylan; Smirnov, Petr; Soerensen, Izel Fourie; Soerensen, Peter; Song, Je-Hoon; Song, Sang Ok; Soufan, Othman; Spitzmueller, Andreas; Steipe, Boris; Suphavilai, Chayaporn; Tamayo, Sergio Pulido; Tamborero, David; Tang, Jing; Tanoli, Zia-ur-Rehman; Tarres-Deulofeu, Marc; Tegner, Jesper; Thommesen, Liv; Tonekaboni, Seyed Ali Madani; Tran, Hong; De Troyer, Ewoud; Truong, Amy; Tsunoda, Tatsuhiko; Turu, Gabor; Tzeng, Guang-Yo; Verbeke, Lieven; Videla, Santiago; Vis, Daniel; Voronkov, Andrey; Votis, Konstantinos; Wang, Ashley; Wang, Hong-Qiang Horace; Wang, Po-Wei; Wang, Sheng; Wang, Wei; Wang, Xiaochen; Wang, Xin; Wennerberg, Krister; Wernisch, Lorenz; Wessels, Lodewyk; van Westen, Gerard J. P.; Westerman, Bart A.; White, Simon Richard; Willighagen, Egon; Wurdinger, Tom; Xie, Lei; Xie, Shuilian; Xu, Hua; Yadav, Bhagwan; Yau, Christopher; Yeerna, Huwate; Yin, Jia Wei; Yu, Michael; Yu, MinHwan; Yun, So Jeong; Zakharov, Alexey; Zamichos, Alexandros; Zanin, Massimiliano; Zeng, Li; Zenil, Hector; Zhang, Frederick; Zhang, Pengyue; Zhang, Wei; Zhao, Hongyu; Zhao, Lan; Zheng, Wenjin; Zoufir, Azedine; Zucknick, Manuela (Springer Nature, 2019-06-17)
    The effectiveness of most cancer targeted therapies is short-lived. Tumors often develop resistance that might be overcome with drug combinations. However, the number of possible combinations is vast, necessitating data-driven ...
  • Crossing the Borders: Re-Use of Smart Learning Objects in Advanced Content Access Systems 

    Manzoor, Hamza; Akhuseyinoglu, Kamil; Wonderly, Jackson; Brusilovsky, Peter; Shaffer, Clifford A. (MDPI, 2019-07-19)
    Researchers in many disciplines are developing novel interactive smart learning objects like exercises and visualizations. Meanwhile, Learning Management Systems (LMS) and eTextbook systems are also becoming more sophisticated ...
  • A stochastic model of size control in the budding yeast cell cycle 

    Ahmadian, Mansooreh; Tyson, John J.; Cao, Yang (2019-06-20)
    Abstract Background Cell size is a key characteristic that significantly affects many aspects of cellular physiology. There are specific control mechanisms during cell cycle ...
  • Analysis and remedy of negativity problem in hybrid stochastic simulation algorithm and its application 

    Chen, Minghan; Cao, Yang (2019-06-20)
    Abstract Background The hybrid stochastic simulation algorithm, proposed by Haseltine and Rawlings (HR), is a combination of differential equations for traditional deterministic ...
  • NanoARG: a web service for detecting and contextualizing antimicrobial resistance genes from nanopore-derived metagenomes 

    Arango-Argoty, Gustavo; Dai, Dongjuan; Pruden, Amy; Vikesland, Peter J.; Heath, Lenwood S.; Zhang, Liqing (2019-06-07)
    Background Direct and indirect selection pressures imposed by antibiotics and co-selective agents and horizontal gene transfer are fundamental drivers of the evolution and spread of antibiotic resistance. ...
  • A dual boundary classifier for predicting acute hypotensive episodes in critical care 

    Bhattacharya, Sakyajit; Huddar, Vijay; Rajan, Vaibhav; Reddy, Chandan K. (PLOS, 2018-02-23)
    An Acute Hypotensive Episode (AHE) is the sudden onset of a sustained period of low blood pressure and is one among the most critical conditions in Intensive Care Units (ICU). Without timely medical care, it can lead to ...
  • Comparing time series transcriptome data between plants using a network module finding algorithm 

    Lee, Jiyoung; Heath, Lenwood S.; Grene, Ruth; Li, Song (2019-06-01)
    Abstract Background Comparative transcriptome analysis is the comparison of expression patterns between homologous genes in different species. Since most molecular mechanistic ...
  • Surrogate-Based Robust Design for a Non-Smooth Radiation Source Detection Problem 

    Ştefănescu, Răzvan; Hite, Jason; Cook, Jared; Smith, Ralph C.; Mattingly, John (MDPI, 2019-05-28)
    In this paper, we develop and numerically illustrate a robust sensor network design to optimally detect a radiation source in an urban environment. This problem exhibits several challenges: penalty functionals are non-smooth ...
  • A Transcriptome Post-Scaffolding Method for Assembling High Quality Contigs 

    Liu, Mingming; Adelman, Zach N.; Myles, Kevin M.; Zhang, Liqing (Hindawi Publishing Corp, 2014-05-28)
    With the rapid development of high throughput sequencing technologies, new transcriptomes can be sequenced for little cost with high coverage. Sequence assembly approaches have been modified to meet the requirements for ...
  • Trust Management of Smart Service Communities 

    Al-Hamadi, Hamid; Chen, Ing-Ray; Cho, Jin-Hee (IEEE, 2019)
    In this paper, the notion of a smart service community is proposed to address the grand challenge of a huge number of the Internet-of-Things (IoT) devices providing similar services in a smart city environment (e.g., ...
  • Parallel Evolution of Genome Streamlining and Cellular Bioenergetics across the Marine Radiation of a Bacterial Phylum 

    Getz, Eric W.; Tithi, Saima Sultana; Zhang, Liqing; Aylward, Frank O. (American Society for Microbiology, 2018-09)
    Diverse bacterial and archaeal lineages drive biogeochemical cycles in the global ocean, but the evolutionary processes that have shaped their genomic properties and physiological capabilities remain obscure. Here we track ...
  • Mining and visualization of microarray and metabolomic data reveal extensive cell wall remodeling during winter hardening in Sitka spruce (Picea sitchensis) 

    Grene, Ruth; Klumas, Curtis; Suren, Haktan; Yang, Kuan; Collakova, Eva; Myers, Elijah; Heath, Lenwood S.; Holliday, Jason A. (Frontiers, 2012)
    Microarray gene expression profiling is a powerful technique to understand complex developmental processes, but making biologically meaningful inferences from such studies has always been challenging. We previously reported ...
  • H++: a server for estimating pK(a)s and adding missing hydrogens to macromolecules 

    Gordon, John C.; Myers, Jonathan B.; Folta, Timothy; Shoja, Valia; Heath, Lenwood S.; Onufriev, Akexet (2005-07-01)
    The structure and function of macromolecules depend critically on the ionization (protonation) states of their acidic and basic groups. A number of existing practical methods predict protonation equilibrium pK constants ...
  • VMD: a community annotation database for oomycetes and microbial genomes 

    Tripathy, Sucheta; Pandey, Varun N.; Fang, Bing; Salas, Fidel; Tyler, Brett M. (2006-01-01)
    The VBI Microbial Database (VMD) is a database system designed to host a range of microbial genome sequences. At present, the database contains genome sequence and annotation data of two plant pathogens Phytophthora sojae ...

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