Jens Lichtenberg

Dipl. Wirtsch. Inf.[1]

 

Russ College of Engineering and Technology

School of Electrical Engineering and Computer Science

Center for Intelligent, Distributed and Dependable Systems

Ohio University, Athens OH, 45701-2979, U.S.A

 

 

Office: 321

Phone: +1 (740) 274-9495

Email: lichtenj@ohio.edu

URL:   http://oak.cats.ohiou.edu/~lichtenj/

 

 

Education

 

2005                       Doctor of Philosophy Candidate, Ohio University, USA

to present              Research: Genomic Signatures, Design Patterns, Proteomics

Dissertation Title: Signatura Genomica Regulata (SGR): Regulatory Genomic Signatures for Biological Processes, Functions and Components

Advisor: Dr. Lonnie Welch

 

2004                       Diploma in Business Informatics1, University of Technology Clausthal ,Germany

Thesis Title: Solution Identification and Ranking in Resource Allocation Diagnosis

Advisor: Dr. Jorge Marx-Gomez

 

2003                       Research Exchange, Autonomous University of Barcelona, Spain

                                Thesis Title: Multicast Based Client for Video-On-Demand Services

Advisor: Dr. Emilio Luque Fadon, Dr. Remo Suppi and Dr. Jorge Marx-Gomez

 

2002                       Pre-Diploma in Business Informatics[2], University of Technology Clausthal, Germany

 

1999                       Abitur in Mathematics, Physics, Politics and English, Gymnasium Warstade, Germany

 

 

Teaching Experience

 

2008                       Perl Programming for Bioinformatics, Primary Instructor, Ohio University

                                Preparation of course material, lecturing, grading, supervise in-class activity

 

2008                       Problem Solving with Bioinformatics Tools, Teaching Assistant, Ohio University

Grade assignments, present project solutions, supervise in-class activities, present bioinformatics tools

 

2008                       Bioinformatics Seminar, Secondary Instructor, Ohio University

                                Lead online and offline discussions, develop assignments and present solutions

 

2007                       Perl for Bioinformatics, Secondary Instructor, Ohio University

Teach courses, Grade assignments, Develop and present solutions and demonstrations

 

2007                       Problem Solving with Bioinformatics Tools, Teaching Assistant, Ohio University

Grade assignments, present project solutions, supervise in-class activities, present bioinformatics tools

 

2005                       Data Structures, Grading Assistant, Ohio University

                                Grade programming assignments and exams

 

2005                       Foundations of Electrical Engineering, Teaching Assistant, Ohio University

Teach numerous classes, design and grade homework assignments, develop and grade exams

 

2003                       Environmental Business Informatics, Teaching Assistant, University of Technology Clausthal

Grade homework assignments, create and supervise training lab

 

2002                       eCommerce, Teaching Assistant, University of Technology Clausthal

                                Grade homework assignments and supervise training lab

 

 

Professional Experience

 

2008-present        Visiting Faculty, Ohio University, Supervisor: Dr. Lonnie Welch, Dr. Sarah Wyatt

                                Lead Bioinformatics Consultant for the Genomics Facility

                                Project Manager: WordSeeker          (http://word-seeker.org)

                                Project Manager: MS-Seeker            (http://msseeker.org)

 

2007-2008            Manager and Leading Software Engineer, Ohio University, Supervisor: Dr. Lonnie Welch

                                Project Manager: WordSeeker          (http://seeker1.thruhere.net)

                                Project Manager: MS-Seeker            (http://msseeker.org)

 

2006 -2007           Software Engineer, Ohio University, Supervisor: Dr. Lonnie Welch

                                Project Manager: WordSeeker          (http://seeker1.thruhere.net)

                                Project Manager: MS-Seeker            (http://msseeker.org)

 

2005 - 2006          Research Associate, Ohio University, Supervisor: Dr. Lonnie Welch

 

2002 - 2003          Research/Teaching Assistant, University of Technology Clausthal, Supervisor: Dr. Jorge Marx-Gomez

 

 

Awards and Honors

 

2008                       Ph.D. Candidacy, Ohio University

 

2006                       Stocker Fellowship, Ohio University

 

2005                       Stocker Fellowship, Ohio University

 

2003                       Travel Grant to Spain, European Community Action Scheme for the Mobility of University Students

 

Journal Publications

 

H-factor: 2 (March 2009)

 

2009

 

Lichtenberg J., Yilmaz A., Welch J.D., Kurz K., Liang X., Drews F., Ecker K., Lee S.S., Grotewold E., Welch L.R., The Word Landscape of the Non-Coding Segments of the Arabidopsis thaliana Genome, BMC Genomics, 2009, under review

 

Drews F., Lichtenberg J., Welch L., Scalable Parallel Word Search in Multicore/Multiprocessor Systems, Journal of Supercomputing, 2009, in press

 

Lichtenberg J., Jacox E., Welch J.D., Kurz K., Liang X., Yang M.Q., Drews F., Ecker K., Lee S.S., Elnitski L.E., Welch L.R., Word-based Characterization of Promoters involved in the Human DNA-repair Pathways, BMC Genomics, 2009, in press

[Citations: 1 (March 2009)]

 

2008

 

Ecker K., Lichtenberg J., Welch L., The SiteSeeker Motif Discovery Tool, In Silico Biology, 2008, 9 (2), pp. 11-22

 

Lichtenberg J., Welch L., A Pattern for Protein Identification, International Journal of Computational Sciences, Special Issue on Bioinformatics and Computational Biology, 2008, 2(4)

 

2007

 

Lichtenberg J., Marx Gomez J., Intrusion Detection Management System for eCommerce Security, Journal of Information Privacy and Security, 2007, 3(4), pp. 19-31

 

List E., Berryman D., Palmer A., Gosney E., Okada S., Kelder B., Lichtenberg J., Welch L., Kopchick J., Application of bioinformatics and scalable computing to perform proteomic analysis of stomach tissue from diabetic mice, Scalable Computing: Practice and Experience, Special Issue on Bioinformatics, 2007, 8(2), pp. 173-183

[Citations: 2 (November 2008)]

 

Conference Publications

 

2009

 

Lichtenberg J., Alam M., Bitterman T., Drews F., Ecker K., Elnitski L., Evans S., Grotewold E., Gu D., Jacox E., Kurz K., Lee S.S., Liang X., Majmudar P.M., Morris P., Nelson C., Stockinger E., Welch J.D., Wyatt S., Yilmaz A., Welch L.R., Construction of Regulatory Encyclopedias of Genomes: Strategies and Case Studies, Ohio Collaborative Conference, 2009, Cleveland, Ohio (USA)

 

2008

 

Drews F., Petri E., Lichtenberg J., Welch L., Scalable Parallel Word Search in Multi-Core/Multiprocessor Systems, Biocomp, 2008, Las Vegas (USA)

 

Lichtenberg J., Jacox E., Yang M.Q., Elnitski L., Welch L., Word-based Characterization of the Bidirectional Promoters from the Human DNA-repair Pathways, Biocomp, 2008, Las Vegas (USA)

[Citations: 3 (March 2009)]

 

Lichtenberg J., Morris P., Ecker K., Welch L., Discovery of Regulatory Elements in Oomycete Orthologs, Biocomp, 2008, Las Vegas (USA)

[Citations: 3 (March 2009)]

 

Morris P., Lichtenberg J., Welch L., In Silico Identification of Regulatory Elements in Oomycete genomes using WordSeeker, Oomycete Molecular Genetics Workshop, 2008, Birnam, Scotland (UK)

[Citations: 1 (March 2009)]

 

2006

 

Lichtenberg J., Marx-Gomez J., Development of an eElection Application for University Purposes In XII CLAIO: Operations Research - Applications in Business Informatics and Soft Computing, eds. J. Marx Gomez and Baldoquin de la Pena, Shaker, Aachen, Germany 2006, pp. 167-186.

 

Ecker K., Drews F., Lichtenberg J., QoS-based Management of Multiple Shared Resource in Dynamic Real-Time Systems, Workshop on Parallel and Distributed Real-Time Systems (WPDRTS), 2006, Rhodes (Greece)

 

2005

 

Marx Gómez, J., Lichtenberg, J., Development of an e-Election Application for University Purposes; Proceedings of XII Latin-Ibero-American Congress on Operations Research and Systems CLAIO'2004 – Havana (Cuba), 2005.

 

Lichtenberg, J., Marx Gómez, J., Intrusion Detection Management System for eCommerce Security; Proceedings of 29th Annual Conference of the German Classification Society (GfKl 2005) - From Data and Information Analysis to Knowledge Engineering, Magdeburg, Book of Abstracts, pp. 217-218.

 

Lichtenberg, J., Marx Gómez, J., Suppi, R., Multicast Based Client for Video-On-Demand Services; Proceedings of the IEEE SoutheastCon Conference 2005, Fort Lauderdale, (USA), 2005.

 

Lichtenberg, J., Marx Gómez, J., Intrusion Detection Management System for e-Commerce Security; Proceedings of the International Conference on Enterprise Information Systems - Workshop on Pattern Recognition in Information Systems (PRIS 2005), Miami (USA), 2005.

 

Marx Gómez, J., Lichtenberg, J., An eElection Application for University Purposes; Proceedings of the 4th Annual ISOneWorld Conference and Convention, Las Vegas, (USA), 2005

 

2004

 

Lichtenberg, J., Data Mining In Resource Management Systems, 1st Annual Symposium and Workshop on Resource Management, 2004, Athens, (USA).

 

2003

 

Lichtenberg, J., Marx Gómez, J., Stiefel, J.: Development and Implementation of an Internet-based Student Registration System using PHP/4 and a MySQL Database; in: Furnell, S., Dowland, P. (eds.): Proceedings of 8th Annual Scientific Conference on Web Technology, New Media, Communications and Telematics Theory, Methods, Tools and Applications (EUROMEDIA’2003), Plymouth (UK), pp. 208-218.

 

Poster Presentations

 

2008

 

Drews F., Ecker K., Kurz K., Lee S., Liang X., Lichtenberg J., Welch J., Welch L., WordSeeker: A High Performance Bioinformatics Pipeline for Computational Regulatory Genomics, Ohio Plant Biotechnology Consortium, 2008, Columbus (USA)

 

Drews F., Ecker K., Kurz K., Lee S., Liang X., Lichtenberg J., Welch J., Welch L., WordSeeker: A High Performance Bioinformatics Pipeline for Computational Regulatory Genomics, BioOhio, 2008, Dublin (USA)

 

Lichtenberg J., Jacox E., Welch J., Kurz K., Yang M.Q., Ecker K., Drews F., Elnitski L., Welch L., Word-based characterization of promoters from human DNA-repair pathways, Genome Informatics, 2008, Hinxton (UK)

 

Ecker K., Lichtenberg J., Welch L., The SiteSeeker Motif Discovery Tool, Biocomp, 2008, Las Vegas (USA)

 

2007

 

Lichtenberg J., Welch L., Design Pattern for Protein Identification, Ohio Collaborative Conference, 2007, Miami, Ohio (USA)

 

Lichtenberg J., Welch L., Kopchick J., Okada S., Sackmann-Sala L., Sankaran S., Post-translational Modification Analysis, Ohio Collaborative Conference, 2007, Miami, Ohio (USA)

 

Lichtenberg J., Welch L., Design Pattern for Protein Identification, Poster proceedings of the International Symposium on Bioinformatics Research and Applications, 2007, Atlanta, Georgia (USA)

 

Lichtenberg J., Welch L., Pattern Language for Biomarker Discovery, Ohio Mass Spectrometry Symposium, 2007, Columbus, Ohio (USA)

 

Lichtenberg J., Welch L., Design Pattern for Protein Identification, Ohio Mass Spectrometry Symposium, 2007, Columbus, Ohio (USA)

 

Lichtenberg J., Welch L., Kopchick J., Okada S., Sackmann-Sala L., Sankaran S., Post-translational Modification Analysis, Ohio Mass Spectrometry Symposium, 2007, Columbus, Ohio (USA)

 

2006

 

Lichtenberg J., Welch L., Conley T., Okada S., Sankaran S., Kopchick J., Analysis of Mass Spectrometry data based on different algorithms in a generic framework, Ohio Collaborative Conference, 2006, Athens, Ohio (USA)

 

Lichtenberg J., Welch L., Conley T., Okada S., Sankaran S., Kopchick J.: Analysis of Mass Spectrometry data based on different algorithms in a generic framework, Ohio Mass Spectrometry Symposium, 2006, Columbus (USA), pp. 48-49.

 

Reviewer

Published Reviews

 

ACM Computing Reviews

 

·         Design by evolution: Advances in Evolutionary Design (Jan. 28th 2009)

·         Life, information, entropy and time: vehicles for semantic inheritance (Apr. 23rd 2008)

·         Design of an irreversible DNA memory element (Feb. 22nd 2008)

·         Static and dynamic models of biological networks: research articles (Nov. 7th 2007)

·         Sharing mass spectrometry data in a grid-based distributed proteomics laboratory (Sep. 4th 2007)

·         Analysis of yearly variations in drug expenditure for one patient using data warehouse in a hospital (Aug. 1st 2007)

 

Peer Reviews

 

·         International Journal of Computers and Applications

·         Journal of Supercomputing

·         BMC Genomics

·         International Journal of Computational Science

·         Scalable Computing: Practice and Experience

·         IEEE Transactions on Computers

·         Elsevier Journal of Systems and Software

·         EUROMEDIA (WEBTEC) Conference

·         Ohio Collaborative Conference on Bioinformatics

 

Conference Activities, Committee Memberships and Other Professional Service

 

Inaugural President, Ohio Student Chapter of the International Society of Computational Biology (ISCB)

                Preparing the proposal for the acceptance of the Ohio Student Chapter

                Conducting activities

                Organizing chapter specific session at OCCBIO

                Supervising officer corps

 

Session Organizer, OCCBIO 2009

                Session name: Ohio Student Chapter of the International Society of Computational Biology (ISCB)

 

Publication Chair, BOSC 2009

 

Organizing Committee, BOSC 2009

 

Program Committee, EUROMEDIA (WEBTEC) 2009

 

Session Chair, BIOCOMP’08, 2008

                Session name: Metabolomics, Proteomic and Protein Function

 

Publication Chair, Ohio Collaborative Conference for Bioinformatics, 2008

                Abstract submission and review procedure,

EasyChair Management

 

Domain Expert, International Journal of Pattern, since 2007

                Domain: Bioinformatics, Proteomics

 

Session Chair, Ohio Collaborative Conference for Bioinformatics, 2007

                Session name: Disease Research

 

Publication Chair, Ohio Collaborative Conference for Bioinformatics, 2007

                Creation of Poster/Paper Award System and Judging

 

Student Volunteer, Ohio Collaborative Conference for Bioinformatics, 2006

 

Student Member, Institute of Electrical and Electronics Engineers

 

Professional Member, Association for Computing Machinery

 

Associate Member, Bioinformatics Organization

 

Member, bimatics – Bioinformatics (Open) Student Society

 

Member, O|B|F – Open Bioinformatics Foundation

 

Student Member, International Society of Computational Biology (ISCB)

 

 

On the Media

 

Number Crunch – Bioinformatics project harnesses computer power for research

 

CIDDS Newsletter: Spring 2005

 


[1] Equivalent to Master of Management Information Systems

[2] Equivalent to Bachelor of Management Information Systems