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Submissions from 2016

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Freshwater Metaviromics and Bacteriophages: A Current Assessment of the State of the Art in Relation to Bioinformatic Challenges, Katherine Bruder, Kema Malki, Alexandria Cooper, Emily Sible, Jason W. Shapiro, Siobhan C. Watkins, and Catherine Putonti

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PhagePhisher: a Pipeline for the Discovery of Covert Viral Sequences in Complex Genomic Datasets, Thomas Hatzopoulos, Siobhan C. Watkins, and Catherine Putonti

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Draft Genome Sequence for a Urinary Isolate of Nosocomiicoccus Ampullae, Evann Elizabeth Hilt, Travis Kyle Price, Katherine Diebel, Catherine Putonti, and Alan J. Wolfe

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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

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Seven Bacteriophages Isolated from the Female Urinary Microbiota, Kema Malki, Emily Sible, Alexandria Cooper, Andrea Garretto, Katherine Bruder, Siobhan C. Watkins, and Catherine Putonti

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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

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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

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18S rDNA Dataset Profiling Microeukaryotic Populations Within Chicago Area Nearshore Waters, Daniel Searle, Emily Sible, Alexandria Cooper, and Catherine Putonti

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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

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Finding Function in the Unknown, Kelly Boyd, Emma Highland, Amanda Misch, Amber Hu, Sushma Reddy, and Catherine Putonti

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HAsh-MaP-ERadicator: Filtering Non-Target Sequences from Next Generation Sequencing Reads, Jonathon Brenner and Catherine Putonti

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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

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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

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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

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Hands-on Python Tutorial, Andrew N. Harrington

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Survey of Microbial Populations within Lake Michigan Nearshore Waters at Two Chicago Public Beaches, Kema Malki, Katherine Bruder, and Catherine Putonti

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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

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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

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Software Metrics and Dashboard, Shilpika Shilpika, George K. Thiruvathukal, Saulo Aguiar, Konstantin Läufer, and Nicholas J. Hayward

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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

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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

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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

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Vesicle Biomechanics in a Time-Varying Magnetic Field, Hui Ye and Austen Curcuru

Submissions from 2014

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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

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Single Page Apps for Humanists: A Case Study Using the Perseus Richmond Times Corpus, Trevor Borg and George K. Thiruvathukal

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ECS Evaluation Survey Instruments, Ronald I. Greenberg and Steven McGee

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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

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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

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Characterizing the Evolutionary Path(s) to Early Homo, Lauren Schroeder, Charles C. Roseman, James M. Cheverud, and Rebecca R. Ackermann

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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

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Statistical Analysis of Aerosol Species, Trace Gases, and Meteorology in Chicago, Katrina Binaku, Timothy O'Brien, Martina Schmeling, and Tinamarie Fosco

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Software Engineering Need Not Be Difficult, Jeffrey C. Carver and George K. Thiruvathukal

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Building Capable, Energy-Efficient, Flexible Visualization and Sensing Clusters from Commodity Tablets, Thomas Delgado Dias, Xian Yan, Konstantin Läufer, and George K. Thiruvathukal

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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

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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

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The Ancestral Activation Promiscuity of ADP-glucose Pyrophosphorylases from Oxygenic Photosynthetic Organisms, Misty L. Kuhn, Carlos M. Figueroa, Alberto A. Iglesias, and Miguel Ballicora

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Using Scala Strategically Across the Undergraduate Curriculum, Mark Lewis, Konstantin Läufer, and George K. Thiruvathukal

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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

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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

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Comparative phyloclimatic analysis and evolution of ecological niches in the scimitar babblers (Aves: Timaliidae: Pomatorhinus), Arpad S. Nyari and Sushma Reddy

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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

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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

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A Polyglot Approach to Bioinformatics Data Integration: Phylogenetic Analysis of HIV-1, Steven Reisman, Catherine Putonti, George K. Thiruvathukal, and Konstantin Läufer

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Network Technologies Used to Aggregate Environmental Data, Paul Stasiuk, Konstantin Läufer, and George K. Thiruvathukal

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The Education Issue, George K. Thiruvathukal

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Gendered Jobs and the New Gender Gap, George K. Thiruvathukal and Jon Ross

Submissions from 2012

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MiIP: The Monomer Identification and Isolation Program, Christopher Bun, William Ziccardi, Jeffrey Doering, and Catherine Putonti

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Rotating Magnets Produce a Prompt Analgesia Effect in Rats, Zhong Chen, Hui Ye, Haiyun Xu, Shukang An, Anmin Jin, Chusong Zhou, and Shaoan Yang

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My Materials Supporting the Exploring Computer Science Curriculum, Ronald I. Greenberg

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Introduction to Computer Science in C#, Andrew N. Harrington and George K. Thiruvathukal

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CBDB: The codon bias database, Adam Hilterbrand, Joseph Saelens, and Catherine Putonti

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Simplifying Domain Modeling and Memory Management in User-Mode Filesystems with the NOFS Framework, Joseph P. Kaylor, Konstantin Läufer, and George K. Thiruvathukal

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Collaboration and Health Care Diagnostics: an Agent Based Model Simulation, Sebastian Linde and George K. Thiruvathukal

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Innovation Mashups: Academic Rigor Meets Social Networking Buzz, Dejan S. Milojicic, Martin Arlitt, Dorée Duncan Seligmann, George K. Thiruvathukal, and Christian Timmerer

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Computational and Experimental Analyses of Retrotransposon-Associated Minisatellite DNAs in the Soybean Genome, Lauren S. Mogil, Kamil Slowikowski, and Howard M. Laten

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An Object-Oriented Framework for Userland Filesystem Development, George K. Thiruvathukal, Joseph P. Kaylor, and Konstantin Läufer

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Filesystems: Addressing the Last-mile “problem” in Services-Oriented/Cloud Computing, George K. Thiruvathukal, Joseph P. Kaylor, and Konstantin Läufer

Submissions from 2011

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Initial experience in moving key academic department functions to social networking sites, David Dennis, George K. Thiruvathukal, and Konstantin Läufer

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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

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The Object of Platform Studies: Relational Materialities and the Social Platform (the case of the Nintendo Wii), Steven E. Jones and George K. Thiruvathukal

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RestFS: Resources and Services are Filesystems, Too, Joseph P. Kaylor, Konstantin Läufer, and George K. Thiruvathukal

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RestFS: The Filesystem as a Connector Abstraction for Flexible Resource and Service Composition, Joseph P. Kaylor, Konstantin Läufer, and George K. Thiruvathukal

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REST on Routers? Preliminary Lessons for Language Designers, Framework Architects, and App Developers, Joseph P. Kaylor, Konstantin Läufer, and George K. Thiruvathukal

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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

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Mapping Short Sequencing Reads to Distant Relatives, Vinicio Reynoso and Catherine Putonti

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An Exceptionally Useful Exploration, George K. Thiruvathukal

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Beyond CiSE and Back to the Future, George K. Thiruvathukal

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Novel Architectures and Accelerators, George K. Thiruvathukal

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Moving Academic Department Functions to Social Networks and Clouds: Initial Experiences, George K. Thiruvathukal, Konstantin Läufer, and David Dennis

Submissions from 2010

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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

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Mechanisms Responsible for a ΦX174 Mutant's Ability To Infect Escherichia coli by Phosphorylation, Jennifer Cox and Catherine Putonti

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Adaptive evolution and inherent tolerance to extreme thermal environments, Jennifer Cox, Alyxandria Schubert, Michael Travisano, and Catherine Putonti

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csPCR: A computational tool for the simulation of the Polymerase Chain Reaction, Sandhya Dasu, April Williams, Yuriy Fofanov, and Catherine Putonti

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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

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Online Layered File System (OLFS): A layered and versioned filesystem and performance analysis, Joseph P. Kaylor, Konstantin Läufer, and George K. Thiruvathukal

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Evolution of the Sequence Composition of Flaviviruses, Alyxandria M. Schubert and Catherine Putonti

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Your Local Cloud-Enabled Library, George K. Thiruvathukal

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Virtualization for Computational Scientists, George K. Thiruvathukal, Konrad Hinsen, Joseph P. Kaylor, and Konstantin Läufer

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E-Carrel: An Environment for Collaborative Textual Scholarship, George K. Thiruvathukal, Steven E. Jones, and Peter Shillingsburg

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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

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Essential Tools: Version Control Systems, Konrad Hinsen, Konstantin Läufer, and George K. Thiruvathukal

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The Promises of Typed, Pure, and Lazy Functional Programming: Part II, Konstantin Läufer and George K. Thiruvathukal

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Putting a Slug to Work, Konstantin Läufer, George K. Thiruvathukal, Ryohei Nishimura, and Carlos Ramirez Martinez-Eiroa

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Computational Thinking...and Doing, George K. Thiruvathukal

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Introducing Computing Now, George K. Thiruvathukal

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Web 2.0 Publishing and Happy 1.0, Computing Now!, George K. Thiruvathukal

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Comparison of the Compositional Proclivities of the Complete Genomes of Plasmodium Falciparum and Human, April Williams, Yuriy Fofanov, and Catherine Putonti

Submissions from 2008

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Taming XML: Objects first, then markup, Matt Bone, Peter Nabicht, Konstantin Läufer, and George K. Thiruvathukal

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At Issue, Bill Feireisen and George K. Thiruvathukal

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Combining SOA and BPM Technologies for Cross-System Process Automation, Sebastian Herr, John Shafaee, Konstantin Läufer, George K. Thiruvathukal, and Guido Wirtz

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A Virtual Computing Laboratory, Joseph P. Kaylor and George K. Thiruvathukal

Submissions from 2007

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A Model-Driven Approach to Job/Task Composition in Cluster Computing, Yogesh Kanitkar, Konstantin Läufer, Neeraj Mehta, and George K. Thiruvathukal

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The Eyes Absent Family of Phosphotyrosine Phosphatases: Properties and Roles in Developmental Regulation of Transcription, Jennifer Mierisch and Illaria Rebay

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Project Hosting: Expanding the Scientific Programmer's Toolbox, George K. Thiruvathukal

Submissions from 2006

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Scalable Approaches for Supporting MPI-IO Atomicity, Peter Aarestad, George K. Thiruvathukal, Avery Ching, and Alok Choudhary

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The Hydra Filesystem: A Distrbuted Storage Famework, Benjamin Gonzalez and George K. Thiruvathukal

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Home Networking, George K. Thiruvathukal

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Electronic Editing of Anglo-Saxon Texts, George K. Thiruvathukal and Allen J. Frantzen

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Unit Testing Considered Useful, George K. Thiruvathukal, Konstantin Läufer, and Benjamin Gonzalez

Submissions from 2005

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Guest Editor's Introduction: Cluster Computing, George K. Thiruvathukal