Submissions from 2016
Draft Genome Sequence for a Urinary Isolate of Nosocomiicoccus ampullae, Evann Elizabeth Hilt, Travis Kyle Price, Katherine Diebel, Catherine Putonti, and Alan J. Wolfe
Genomes of Gardnerella Strains Reveal an Abundance of Prophages within the Bladder Microbiome, Kema Malki, Jason W. Shapiro, Travis Kyle Price, Evann Elizabeth Hilt, Krystal Thomas-White, Trina Sircar, Amy B. Rosenfeld, Michael J. Zilliox, Alan J. Wolfe, and Catherine Putonti
Seven Bacteriophages Isolated from the Female Urinary Microbiota, Kema Malki, Emily Sible, Alexandria Cooper, Andrea Garretto, Katherine Bruder, Siobhan C. Watkins, and Catherine Putonti
Genome Sequences and Annotation of Two Urinary Isolates of E.coli, Travis Kyle Price, Arya Mehtash, Laurynas Kalesinskas, Kema Malki, Evann Elizabeth Hilt, Catherine Putonti, and Alan J. Wolfe
Draft Genome for a Urinary Isolate of Lactobacillus crispatus, Travis Kyle Price, Majed Shaheen, Laurynas Kalesinskas, Kema Malki, Evann Elizabeth Hilt, Catherine Putonti, and Alan J. Wolfe
Freshwater Metaviromics and Bacteriophages: A Current Assessment of the State of the Art in Relation to Bioinformatic Challenges, Catherine Putonti, Katherine Bruder, Kema Malki, Alexandria Cooper, Emily Sible, Jason W. Shapiro, and Siobhan C. Watkins
Draft Genome Sequence for a Urinary Isolate of Nosocomiicoccus ampullae, Catherine Putonti, Evann E. Hilt, Travis K. Price, Katherine Diebel, and Alan J. Wolfe
A Polyglot Approach to Bioinformatics Data Integration: A Phylogenetic Analysis of HIV-1, Steven Reisman, Thomas Hatzopoulous, Konstantin Läufer, George K. Thiruvathukal, and Catherine Putonti
18S rDNA Dataset Profiling Microeukaryotic Populations Within Chicago Area Nearshore Waters, Daniel Searle, Emily Sible, Alexandria Cooper, and Catherine Putonti
Pharmacogenetic Discovery in CALGB (Alliance) 90401 and Mechanistic Validation of a VAC14 Polymorphism That Increases Risk of Docetaxel-Induced Neuropathy, Heather E. Wheeler
Variants in WFS1 and Other Mendelian Deafness Genes are Associated with Cisplatin-Associated Ototoxicity, Heather E. Wheeler, Eric R. Gamazon, Robert Frisina, Carlos Perez-Cervantes, Omar El Charif, Brandon Mapes, Sophie D. Fossa, Darren Feldman, Robert Hamilton, David J. Vaughn, Clair Beard, Chunkit Fung, Chiristian Kollmannsberger, Jeri Kim, Taisei Mushiroda, Michiaki Kubo, Shirin Ardeshir-Rouhani-Fard, Lawrence H. Einhorn, Nancy Cox, M. Eileen Dolan, and Lois Travis
Survey of the Heritability and Sparse Architecture of Gene Expression Traits across Human Tissues., Heather E. Wheeler, Kaanan P. Shah, Jonathon Brenner, Tzintzuni Garcia, Keston Aquino-Michaels, GTEx-Consortium, Nancy J. Cox, Dan L. Nicolae, and Hae Kyung Im
Clusters of Alpha Satellite on Human Chromosome 21 Are Dispersed Far onto the Short Arm and Lack Ancient Layers, William Ziccardi, Chongjian Zhao, Valery Shepelev, Lev Uralsky, Ivan Alexandrov, Tatyana Andreeva, Evgeny Rogaev, Christopher Bun, Emily Miller, Catherine Putonti, and Jeffrey Doering
Submissions from 2015
Finding Function in the Unknown, Kelly Boyd, Emma Highland, Amanda Misch, Amber Hu, Sushma Reddy, and Catherine Putonti
HAsh-MaP-ERadicator: Filtering Non-Target Sequences from Next Generation Sequencing Reads, Jonathon Brenner and Catherine Putonti
The Genetic Architecture of Fluctuating aSymmetry of Mandible Size and Shape in a Population of Mice: Another Look, James M. Cheverud, Larry J. Leamy, Christian Peter Klingenberg, Emma Sherratt, and Jason B. Wolf
Identification of eQTLs for Hepatic Xbp1s and Socs3 Gene Expression in Mice Fed a High-Fat, High Caloric Diet, James M. Cheverud, Sarina Pasricha, Jane Kenney-Hunt, Kristy Anderson, Naderah Jafari, Rabea A. Hall, Frank Lammert, and Richard M. Green
A Gene-Based Association Method for Mapping Traits Using Reference Transcriptome Data, Eric R. Gamazon, Heather Wheeler, Kaanan P. Shah, Sahar V. Mozaffari, Keston Aquino-Michaels, Robert J. Carroll, Anne E. Eyler, Joshua C. Denny, GTEx Consortium, Dan L. Nicolae, Nancy J. Cox, and Hae Kyung Im
Hands-on Python Tutorial, Andrew N. Harrington
Survey of Microbial Populations within Lake Michigan Nearshore Waters at Two Chicago Public Beaches, Kema Malki, Katherine Bruder, and Catherine Putonti
Bacteriophages isolated from Lake Michigan demonstrate broad host-range across several bacterial phyla, Kema Malki, Alex Kula, Katherine Bruder, Emily Sible, Thomas Hatzopoulos, Stephanie Steidel, Siobhan C. Watkins, and Catherine Putonti
A Polyglot Approach to Bioinformatics Data Integration: a Phylogenetic Analysis of HIV-1, Steven Reisman, Thomas Hatzopoulos, Konstantin Laufer, George K. Thiruvathukal, and Catherine Putonti
Software Metrics and Dashboard, Shilpika Shilpika, George K. Thiruvathukal, Saulo Aguiar, Konstantin Läufer, and Nicholas J. Hayward
Assessment of Microbial Populations within Chicago Area Nearshore Waters and Interfaces with River Systems, Emily Sible, Alexandria Cooper, Kema Malki, Katherine Bruder, Thomas Hatzopoulos, Siobhan C. Watkins, and Catherine Putonti
Survey of Viral Populations within Lake Michigan Nearshore Waters at Four Chicago Area Beaches, Emily Sible, Alexandria Cooper, Kema Malki, Katherine Bruder, Siobhan C. Watkins, Yuriy Fofanov, and Catherine Putonti
Assessment of a Metaviromic Dataset Generated from Nearshore Lake Michigan, Siobhan C. Watkins, Neil Kuehnle, C Anthony Ruggeri, Kema Malki, Katherine Bruder, Jinan Elayyan, Kristina Damisch, Naushin Vahora, Paul O'Malley, Brianne Ruggles-Sage, Zachary Romer, and Catherine Putonti
Vesicle Biomechanics in a Time-Varying Magnetic Field, Hui Ye and Austen Curcuru
Submissions from 2014
A Novel Dual Allosteric Activation Mechanism of Escherichia coli ADP-Glucose Pyrophosphorylase: The Role of Pyruvate, Matías D. Asención Diez, Mabel C. Aleanzi, Alberto A. Iglesias, and Miguel Ballicora
Single Page Apps for Humanists: A Case Study Using the Perseus Richmond Times Corpus, Trevor Borg and George K. Thiruvathukal
ECS Evaluation Survey Instruments, Ronald I. Greenberg and Steven McGee
Parkinson Disease-Associated Mutation R1441H in LRRK2 Prolongs the “Active State” of its GTPase Domain, Jingling Liao, Chun-Xiang Wu, Christopher Burlak, Sheng Zhang, and Dali Liu
The Effect of Dietary Fat Intake on Hepatic Gene Expression in LG/J and SM/J Mice, Charlyn G. Partridge, Gloria L. Fawcett, Bing Wang, Clay F. Semenkovich, and James M. Cheverud
Characterizing the Evolutionary Path(s) to Early Homo, Lauren Schroeder, Charles C. Roseman, James M. Cheverud, and Rebecca R. Ackermann
Unveiling the Impact of Human Influence on Species Distributions in Vietnam: A Case Study Using Babblers (Aves: Timaliidae), Laurel R. Yohe, Johnathan Flanders, Hoang Minh Duc, Long Vu, and Sushma Reddy
Submissions from 2013
Statistical Analysis of Aerosol Species, Trace Gases, and Meteorology in Chicago, Katrina Binaku, Timothy O'Brien, Martina Schmeling, and Tinamarie Fosco
Software Engineering Need Not Be Difficult, Jeffrey C. Carver and George K. Thiruvathukal
Building Capable, Energy-Efficient, Flexible Visualization and Sensing Clusters from Commodity Tablets, Thomas Delgado Dias, Xian Yan, Konstantin Läufer, and George K. Thiruvathukal
Unraveling the Activation Mechanism of the Potato Tuber ADP-Glucose Pyrophosphorylase, Carlos M. Figueroa, Misty L. Kuhn, Christine A. Falaschetti, Ligin Solamen, Kenneth W. Olsen, Miguel Ballicora, and Alberto A. Iglesias
Spring11: PDC in CS1/2 and a mobile/cloud intermediate mobile/cloud intermediate software design course, Joseph P. Kaylor, Konstantin Läufer, Chandra N. Sekharan, and George K. Thiruvathukal
The Ancestral Activation Promiscuity of ADP-glucose Pyrophosphorylases from Oxygenic Photosynthetic Organisms, Misty L. Kuhn, Carlos M. Figueroa, Alberto A. Iglesias, and Miguel Ballicora
Using Scala Strategically Across the Undergraduate Curriculum, Mark Lewis, Konstantin Läufer, and George K. Thiruvathukal
Investigating the Electrostatic Role of a Critical Arginine for the Catalysis of E. Coli ADP-Glucose Pyrophosphorylase, Angela Mahaffey, Saleh Aiyash, Miguel Ballicora, and Ligin Solamen
Identification of a Histidine Metal Ligand in the argE-Encoded N-Acetyl-L-Ornithine Deacetylase from Escherichia coli, Wade C. McGregor, Danuta M. Gillner, Sabina I. Swierczek, Dali Liu, and Richard C. Holz
Comparative phyloclimatic analysis and evolution of ecological niches in the scimitar babblers (Aves: Timaliidae: Pomatorhinus), Arpad S. Nyari and Sushma Reddy
Genomic Correlates of Relationship QTL Involved in Fore- Versus Hind Limb Divergence in Mice, Mihaela Palicev, Gunter P. Wagner, James P. Noonan, Benedikt Hallgrimsson, and James M. Cheverud
Where does Neisseria acquire foreign DNA from: an examination of the source of genomic and pathogenic islands and the evolution of the Neisseria genus, Catherine Putonti, Bogdan Nowicki, Michael Shaffer, Yuriy Fofanov, and Stella Nowicki
A Polyglot Approach to Bioinformatics Data Integration: Phylogenetic Analysis of HIV-1, Steven Reisman, Catherine Putonti, George K. Thiruvathukal, and Konstantin Läufer
Network Technologies Used to Aggregate Environmental Data, Paul Stasiuk, Konstantin Läufer, and George K. Thiruvathukal
The Education Issue, George K. Thiruvathukal
Gendered Jobs and the New Gender Gap, George K. Thiruvathukal and Jon Ross
Submissions from 2012
MiIP: The Monomer Identification and Isolation Program, Christopher Bun, William Ziccardi, Jeffrey Doering, and Catherine Putonti
Rotating Magnets Produce a Prompt Analgesia Effect in Rats, Zhong Chen, Hui Ye, Haiyun Xu, Shukang An, Anmin Jin, Chusong Zhou, and Shaoan Yang
My Materials Supporting the Exploring Computer Science Curriculum, Ronald I. Greenberg
Introduction to Computer Science in C#, Andrew N. Harrington and George K. Thiruvathukal
CBDB: The Codon Bias Database, Adam Hilterbrand, Joseph Saelens, and Catherine Putonti
Simplifying Domain Modeling and Memory Management in User-Mode Filesystems with the NOFS Framework, Joseph P. Kaylor, Konstantin Läufer, and George K. Thiruvathukal
Evolution of Interactomes, Monica Micek
Innovation Mashups: Academic Rigor Meets Social Networking Buzz, Dejan S. Milojicic, Martin Arlitt, Dorée Duncan Seligmann, George K. Thiruvathukal, and Christian Timmerer
Computational and Experimental Analyses of Retrotransposon-Associated Minisatellite DNAs in the Soybean Genome, Lauren S. Mogil, Kamil Slowikowski, and Howard M. Laten
An Object-Oriented Framework for Userland Filesystem Development, George K. Thiruvathukal, Joseph P. Kaylor, and Konstantin Läufer
Filesystems: Addressing the Last-mile “problem” in Services-Oriented/Cloud Computing, George K. Thiruvathukal, Joseph P. Kaylor, and Konstantin Läufer
Submissions from 2011
Initial Experience in Moving Key Academic Department Functions to Social Networking Sites, David Dennis, George K. Thiruvathukal, and Konstantin Läufer
PCR Detection of Nearly Any Dengue Virus Strain Using a Highly Sensitive Primer ‘Cocktail’, Charul Gijavanekal, Maria Anez-Lingerfelt, Chen Feng, Catherine Putonti, George E. Fox, Aniko Sabo, Yuriy Fofanov, and Richard C. Wilson
The Object of Platform Studies: Relational Materialities and the Social Platform (the case of the Nintendo Wii), Steven E. Jones and George K. Thiruvathukal
RestFS: Resources and Services are Filesystems, Too, Joseph P. Kaylor, Konstantin Läufer, and George K. Thiruvathukal
RestFS: The Filesystem as a Connector Abstraction for Flexible Resource and Service Composition, Joseph P. Kaylor, Konstantin Läufer, and George K. Thiruvathukal
REST on Routers? Preliminary Lessons for Language Designers, Framework Architects, and App Developers, Joseph P. Kaylor, Konstantin Läufer, and George K. Thiruvathukal
PDC Modules for Every Level: A Comprehensive Model for Incorporating PDC Topics into the Existing Undergraduate Curriculum, Konstantin Läufer, Chandra N. Sekharan, and George K. Thiruvathukal
Mapping Short Sequencing Reads to Distant Relatives, Vinicio Reynoso and Catherine Putonti
An Exceptionally Useful Exploration, George K. Thiruvathukal
Beyond CiSE and Back to the Future, George K. Thiruvathukal
Novel Architectures and Accelerators, George K. Thiruvathukal
Submissions from 2010
Improved Detection of Bartonella DNA in Mammalian Hosts and Arthropod Vectors by Real-Time PCR Using the NADH Dehydrogenase Gamma Subunit (nuoG), James M. Colborn, Michael Y. Kosoy, Vladimir L. Motin, Maxim V. Telepnev, Gustavo Valbuena, Khin S. Myint, Yuri Fofanov, Catherine Putonti, Chen Feng, and Leonard Peruski
Mechanisms Responsible for a ΦX174 Mutant's Ability To Infect Escherichia coli by Phosphorylation, Jennifer Cox and Catherine Putonti
Adaptive Evolution and Inherent Tolerance to Extreme Thermal Environments, Jennifer Cox, Alyxandria Schubert, Michael Travisano, and Catherine Putonti
csPCR: A Computational Tool for the Simulation of the Polymerase Chain Reaction, Sandhya Dasu, April Williams, Yuriy Fofanov, and Catherine Putonti
Naked Object File System (NOFS): A Framework to Expose an Object-Oriented Domain Model as a File System, Joseph P. Kaylor, Konstantin Läufer, and George K. Thiruvathukal
Online Layered File System (OLFS): A Layered and Versioned Filesystem and Performance Analysis, Joseph P. Kaylor, Konstantin Läufer, and George K. Thiruvathukal
Evolution of the Sequence Composition of Flaviviruses, Alyxandria M. Schubert and Catherine Putonti
Your Local Cloud-Enabled Library, George K. Thiruvathukal
Virtualization for Computational Scientists, George K. Thiruvathukal, Konrad Hinsen, Joseph P. Kaylor, and Konstantin Läufer
E-Carrel: An Environment for Collaborative Textual Scholarship, George K. Thiruvathukal, Steven E. Jones, and Peter Shillingsburg
A New Species of Boubou (Malaconotidae: Laniarius) from the Albertine Rift, Gary Voelker, Robert K. Outlaw, Sushma Reddy, Michael Tobler, John M. Bates, Shannon J. Hackett, Charles Kahindo, Ben D. Marks, Julian C. Kerbis Peterhans, and Thomas P. Gnoske
Submissions from 2009
Essential Tools: Version Control Systems, Konrad Hinsen, Konstantin Läufer, and George K. Thiruvathukal
Scientific Programming: The Promises of Typed, Pure, and Lazy Functional Programming: Part II, Konstantin Läufer and George K. Thiruvathukal
Putting a Slug to Work, Konstantin Läufer, George K. Thiruvathukal, Ryohei Nishimura, and Carlos Ramirez Martinez-Eiroa
Computational Thinking...and Doing, George K. Thiruvathukal
Introducing Computing Now, George K. Thiruvathukal
Web 2.0 Publishing and Happy 1.0, Computing Now!, George K. Thiruvathukal
Comparison of the Compositional Proclivities of the Complete Genomes of Plasmodium Falciparum and Human, April Williams, Yuriy Fofanov, and Catherine Putonti
Submissions from 2008
Taming XML: Objects first, then markup, Matt Bone, Peter Nabicht, Konstantin Läufer, and George K. Thiruvathukal
At Issue, Bill Feireisen and George K. Thiruvathukal
Combining SOA and BPM Technologies for Cross-System Process Automation, Sebastian Herr, John Shafaee, Konstantin Läufer, George K. Thiruvathukal, and Guido Wirtz
A Virtual Computing Laboratory, Joseph P. Kaylor and George K. Thiruvathukal
Submissions from 2007
A Model-Driven Approach to Job/Task Composition in Cluster Computing, Yogesh Kanitkar, Konstantin Läufer, Neeraj Mehta, and George K. Thiruvathukal
The Eyes Absent Family of Phosphotyrosine Phosphatases: Properties and Roles in Developmental Regulation of Transcription, Jennifer Mierisch and Illaria Rebay
Project Hosting: Expanding the Scientific Programmer's Toolbox, George K. Thiruvathukal
Submissions from 2006
Scalable Approaches for Supporting MPI-IO Atomicity, Peter Aarestad, George K. Thiruvathukal, Avery Ching, and Alok Choudhary
The Hydra Filesystem: A Distrbuted Storage Famework, Benjamin Gonzalez and George K. Thiruvathukal
Home Networking, George K. Thiruvathukal
