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Russ College of Engineering and Technology
Stocker Center
Athens, OH 45701

Lonnie Welch

Lonnie Welch
Charles R. Jr. and Marilyn Stuckey Professor
Stocker Center 354
Biomedical Engineering
Electrical Engineering and Computer Science
welch@ohio.edu
740.593.1575

Professor Lonnie R. Welch is the Stuckey Professor of Electrical Engineering and Computer Science at 91探花, a member of the Graduate Faculties of the Biomedical Engineering Program and of the Molecular and Cellular Biology Program, director of the Bioinformatics Laboratory at 91探花, and the founder and Chair of the Great Lakes Bioinformatics Conference (an official conference of the International Society on Computational Biology). His research has been sponsored by the National Human Genome Research Institute, the Ohio Plant Biotechnology Consortium, NASA, the National Science Foundation, the Defense Advanced Research Projects Agency, and the Ohio Board of Regents. He is the principal investigator of the $9M Bioinformatics Program of the Ohio Board of Regents. Dr. Welch is founder and co-chair of the ISMB Special Interest Group on Bioinformatics for Regulatory Genomics (BioRegSIG).

Research Interests: Bioinformatics, Computational regulatory genomics, Machine learning, High performance computing

All Degrees Earned: Ph.D., 1990, M.S.1987, B.S. 1985, Computer and Information Science, the Ohio State University.

Patents:

  • Program Control For Resource Management Architecture and Corresponding Programs, US patent application 09/864821, US patent no. 7,096,248, patent issued 08-2006.
  • System for Monitoring and Reporting Performance of Hosts and Applications and Selectively Configuring Applications in a Resource Managed System, US patent application 09/864830, US patent number 7,051,098, patent issued 5-2006.
  • Resource Allocation Decision Function for Resource Management Architecture and Corresponding Programs, US patent application 09/864825, pending approval.

Awards:

  • 2010 Alumnus of the Year, Claymont High School (for demonstrated lifetime leadership and abilities in chosen field)
  • 2001 Stuckey Professorship, 91探花 (for outstanding accomplishments in research and teaching)
  • 1998 Outstanding Young Faculty Member, University of Texas at Arlington
  • 1998 Aegis Excellence Award, United States Navy (for contributions in dynamic resource management to the Navy's High Performance Distributed Computing (HiPer-D) and AdCon-21 projects)

Journal Article, Academic Journal (73)

  • Welch, L. An integrated bioinformatics approach to the discovery of cis-regulatory elements involved in plant gravitropic signal transduction, X. Liang, K. Shen, J. Lichtenberg, S.E. Wyatt, and L.R. Welch. International Journal of Computational Bioscience 1:33-54. 2010.
  • Lichtenberg, J., Yilmaz, A., Seaman, J., Liang, X., Lee, S., Ecker, K., Grotewold, E., Welch, L. The Word Landscape of the Arabidopsis Genome. BMC Genomics.
  • Welch, L., Welch, L., Drews, F. WordSeeker: Concurrent bioinformatics software for discovering genome-wide patterns and word-based genomic signatures. BMC Bioinformatics, 2010, 11(Suppl 12):S6.
  • Welch, L. 鈥淪calable parallel word search in multicore/multiprocessor systems,鈥 Frank Drews, Jens Lichtenberg, Lonnie Welch. The Journal of Supercomputing 51(1):58-75. 2010 Jan.
  • Welch, L., Baugher, C., Zhang, Y., Davis, T., Li, Y. (2023). Multiplex-GAM: genome-wide identification of chromatin contacts yields insights overlooked by Hi-C. 7. Nature Methods; 20: 1037-1047. .
  • Kilpatrick, A., Rahman, F., Anjum, A., Welch, L. (2022). Characterizing domain-specific open educational resources by linking ISCB Communities of Special Interest to Wikipedia. 38. Bioinformatics; i19-i27.
  • Winick-Ng, W., Kukalev, A., Harabula, I., Redondo, L., Szabo, D., Meijer, M., Serebreni, L., Zhang, Y., Bianco, S., Chiariello, A., others, . (2021). Cell-type specialization in the brain is encoded by specific long-range chromatin topologies. bioRxiv; 2020--04.
  • Beagrie, R., Thieme, C., Annunziatella, C., Baugher, C., Zhang, Y., Schueler, M., Kukalev, A., Kempfer, R., Chiariello, A., Bianco, S., others, . (2021). Multiplex-GAM: genome-wide identification of chromatin contacts yields insights not captured by Hi-C. bioRxiv; 2020--07.
  • Winick-Ng, W., Kukalev, A., Harabula, I., Zea-Redondo, L., Szab贸, D., Meijer, M., Serebreni, L., Zhang, Y., Bianco, S., Chiariello, A., Irastorza-Azcarate, I., Thieme, C., Sparks, T., Carvalho, S., Fiorillo, L., Musella, F., Irani, E., Triglia, E., Kolodziejczyk, A., Abentung, A., Apostolova, G., Paul, E., Franke, V., Kempfer, R., Akalin, A., Teichmann, S., Dechant, G., Ungless, M., Nicodemi, M., Welch, L., Castelo-Branco, G., Pombo, A. (2021). Cell-type specialization is encoded by specific chromatin topologies.. 7886. Nature; 599: 684-691.
  • Li , Y., Jaiswal, S., Kaur, R., Alsaadi, D., Liang, X., Drews, F., DeLoia, J., Krivak, T., Petrykowska, H., Gotea, V., Welch, L., Elnitski, L. (2021). Differential gene expression identifies a transcriptional regulatory network involving ER-alpha and PITX1 in invasive epithelial ovarian cancer.. 1. BMC cancer; 21: 768.
  • Li , Y., Mullin, M., Zhang, Y., Drews, F., Welch, L., Showalter, A. (2020). Identification of Cis-Regulatory Sequences Controlling Pollen-Specific Expression of Hydroxyproline-Rich Glycoprotein Genes in Arabidopsis thaliana.. 12. Plants (Basel, Switzerland); 9.
  • Grote, A., Li , Y., Liu, C., Voronin, D., Geber, A., Lustigman, S., Unnasch, T., Welch, L., Ghedin, E. (2020). Prediction pipeline for discovery of regulatory motifs associated with Brugia malayi聽molting.. 6. PLoS neglected tropical diseases; 14: e0008275.
  • Foster, J., Grote, A., Mattick, J., Tracey, A., Tsai, Y., Chung, M., Cotton, J., Clark, T., Geber, A., Holroyd, N., Korlach, J., Li , Y., Libro, S., Lustigman, S., Michalski, M., Paulini, M., Rogers, M., Teigen, L., Twaddle, A., Welch, L., Berriman, M., Dunning Hotopp, J., Ghedin, E. (2020). Sex chromosome evolution in parasitic nematodes of humans.. 1. Nature communications; 11: 1964.
  • Li , Y., Liu, Y., Juedes, D., Drews, F., Bunescu, R., Welch, L. (2020). Set cover-based methods for motif selection.. 4. Bioinformatics (Oxford, England); 36: 1044-1051.
  • Liu, X., McKenna, S., Welch, L., Showalter, A. (2020). Bioinformatic Identification of Plant Hydroxyproline-Rich Glycoproteins.. Methods in molecular biology (Clifton, N.J.); 2149: 463-481.
  • Williams, J., Drew, J., Galindo-Gonzalez, S., Robic, S., Dinsdale, E., Morgan, W., Triplett, E., Burnette, III, J., Donovan, S., Fowlks, E., Goodman, A., Grandgenett, N., Goller, C., Hauser, C., Jungck, J., Newman, J., Pearson, W., Ryder, E., Sierk, M., Smith, T., Tosado-Acevedo, R., Tapprich, W., Tobin, T., Toro-Mart铆nez, A., Welch, L., Wilson, M., Ebenbach, D., McWilliams, M., Rosenwald, A., Pauley, M. (2019). Barriers to integration of bioinformatics into undergraduate life sciences education: A national study of US life sciences faculty uncover significant barriers to integrating bioinformatics into undergraduate instruction. 11. Public Library of Science; 14: 1-19. .
  • Li, Y., Liu, Y., Juedes, D., Drews, F., Bunescu, R., Welch, L. (2019). Set cover-based methods for motif selection. . Bioinformatics/Oxford University Press.
  • Wilson Sayres, M., Hauser, C., Sierk, M., Robic, S., Rosenwald, A., Smith, T., Triplett, E., Williams, J., Dinsdale, E., Morgan, W., Burnette, III, J., Donovan, S., Drew, J., Elgin, S., Fowlks, E., Galindo-Gonzalez, S., Goodman, A., Grandgenett, N., Goller, C., Jungck, J., Newman, J., Pearson, W., Ryder, E., Tosado-Acevedo, R., Tapprich, W., Tobin, T., Toro-Mart铆nez, A., Welch, L., Wright, R., Barone, L., Ebenbach, D., McWilliams, M., Olney, K., Pauley, M. (2018). Bioinformatics core competencies for undergraduate life sciences education. 6. PLOS ONE; 13: 1-20. .
  • Spiller, S., Li, Y., Bl眉her, M., Welch, L., Hoffmann, R. (2018). Diagnostic Accuracy of Protein Glycation Sites in Long-Term Controlled Patients with Type 2 Diabetes Mellitus and Their Prognostic Potential for Early Diagnosis. Pharmaceuticals; 11: 38.
  • Mulder, N., Schwartz, R., Brazas, M., Brooksbank, C., Gaeta, B., Morgan, S., Pauley, M., Rosenwald, A., Rustici, G., Sierk, M., Warnow, T., Welch, L. (2018). The development and application of bioinformatics core competencies to improve bioinformatics training and education. 2. PLOS Computational Biology; 14: 1-14. .
  • Lee, K., Sharma, R., Gase, G., Ussar, S., Li , Y., Welch, L., Berryman, D., Kispert, A., Bluher, M., Kahn, C. (2017). Tbx15 Defines a Glycolytic Subpopulation and White Adipocyte Heterogeneity.. 11. Diabetes; 66: 2822-2829.
  • Welch, L., Lee, K., Sharma, R., Gase, G., Ussar, S., Li, Y., Berryman, D., Kispert, A., Bluher, M., Kahn, C. (2017). Tbx15 Defines a Glycolytic Subpopulation and White Adipocyte Heterogeneity. Diabetes; 2822-2829.
  • Welch, L., Spiller, S., Bluher, M., Li, Y., Hoffman, R. (2017). Glycated lysine-141 in haptoglobin improves the diagnostic accuracy for type 2 diabetes mellitus in combination with glycated hemoglobin HbA1c and fasting plasma glucose. Clin Proteomics.
  • Welch, L., Gaeta, B., J, D., Horton, P., Meysman, P., Mulder, N., Romano, P. (2017). Ten simple rules for forming a scientific professional society. PLoS Comput Biol.
  • Welch, L., Showalter, A., Keppler , B., Lichtenberg , J. (2016). Bioinformatic Identification and Analysis of Hydroxyproline-Rich Glycoproteins in Populus trichocarpa. Oct 21;16(1):229. BMC Plant Biol. 2016; Oct 21;16(1):229: .
  • Welch, L., Brooksbank , C., Schwartz, R., Morgan, S., Gaeta, B., Kilpatrick, A., Mietchen, D., Moore, B., Mulder, N., Pauley, M., Pearson, W., Radivojac, P., Rosenberg, N., Rosenwald, A., Rustici, G., Warnow, T. (2016). Applying, Evaluating and Refining Bioinformatics Core Competencies (An Update from the Curriculum Task Force of ISCB's Education Committee). 2016 May 13;12(5):e1004943. PLoS Comput Biol. 2016 May 13; 2016 May 13;12(5):e1004943: .
  • Welch, L., Hill, S., Heiser, L., Cokelaer, T., Unger, M., Nesser, N., Carlin, D., Zhang, Y., Sokolov, A., Paull, E., Wong, C., Graim, K., Bivol, B., Wang, H., Zhu, F., Afsari, B., Danilova, L., Favorov, A., Lee, W., Taylor, D., Hu, C., Long, B., Noren, D., Bisberg, A., Mills, G., Gray, J., Kellen, M., Norman, T., Friend, S., Qutub, A., Fertig, E., Guan, Y., Song, M., Stuart, J., Spellman, P., Koeppl, H., Stolobitzky, G., Saez-Rodriguez, J., Mukherjee, S. (2016). Inferring causal molecular networks: empirical assessment through a community-based effort. . 2016 Apr;13(4):310-8. Nat Methods; . 2016 Apr;13(4):310-8: .
  • Welch, L., Rosenwald, A., Pauley, M., Elgin, S., Wright, R., Blum, J. (2016). The CourseSource Bioinformatics Learning Framework. 2016 Spring;15(1):le2. CBE Life Sci Educ. 2016 Spring; 2016 Spring;15(1):le2: .
  • Welch, L., Liu, X., Wolfe, R., Domozych, D., Popper, Z., Showalter, A. (2016). Bioinformatic Identification and Analysis of Extensins in the Plant Kingdom. 2016 Feb 26;11(2):e0150177. PLoS One; 2016 Feb 26;11(2):e0150177: .
  • Benencia, F., Harshman, S., Duran-Ortiz, S., Lubbers, E., List, E., Householder, L., Al-Naeeli, M., Liang, X., Welch, L., Kopchick, J., Berryman, D. (2015). Male bovine GH transgenic mice have decreased adiposity with an adipose depot-specific increase in immune cell populations.. 5. Endocrinology; 156: 1794-803.
  • Welch, L. (2012). A Report of the Curriculum Task Force of the ISCB Education Committee. Bioinformatics/Oxford University Press.
  • Yang, M., Laflamme, K., Gotea, V., Joiner, C., Seidel, N., Wong, C., Petrykowska, H., Lichtenburg, J., Lee, S., Welch, L., Gallagher, P., Bodine, D., Elnitski, L. (2011). Genome-wide detection of a TFIID localization element from an initial human disease mutation, Yang MQ, Laflamme K, Gotea V, Joiner CH, Seidel NE, Wong C, Petrykowska HM, Lichtenberg J, Lee S, Welch L, Gallagher PG, Bodine DM, Elnitski L. 6. Nucleic Acids Research; 39.
  • Welch, L., Yang, M., Laflamme, K., Gotea, V., Joiner, C., Seidel , N., Wong, C., Petrykowska, H., Lichtenberg, J., Lee, S., Gallagher, P., Bodine, D., Elnitski, L. (2011). Genome-wide detection of a TFIID localization element from an initial human disease mutation. . 6. Nucleic Acids Res.; 39.
  • Yilmaz, A., Mejia-Guerra, M., Kurz, K., Liang, X., Welch, L., Grotewold, E. (2011). AGRIS: the Arabidopsis Gene Regulatory Information Server, and update. databse issue. Nucleic Acids Res.; 39.
  • Showalter, A., Keppler, B., Lichtenberg, J., Gu, D., Welch, L. (2010). A bioinformatics approach to the identification, classification, and analysis of hydroxyproline-rich glycoproteins. Plant Physiology; 153: 485-513.
  • Liang, X., Shen, K., Lichtenberg, J., Wyatt, S., Welch, L. (2010). An integrated bioinformatics approach to the discovery of cis-regulatory elements involved in plant gravitropic signal transduction. 1. International Journal of Computational Bioscience; 1: 33-54.
  • Ecker, K., Lichtenberg, J., Welch, L. (2009). The SiteSeeker Motif Discovery Tool. 1. Silico Biology; 9: 11-22.
  • Lichtenberg, J., Jacox, E., Welch, J., Kurz, K., Liang, X., Yang, M., Drews, F., Ecker, K., Lee, S., Elnitski, L., Welch, L. (2009). Word-based Characterization of Promoters involved in Human DNA-repair Pathways. S1. BMC Genomics; 10.
  • Drews, F., Lichtenberg, J., Welch, L. (2009). Scalable Parallel Word Search in Multicore/Multiprocessor Systems. Journal of Supercomputing.
  • Gu, D., Welch, L., Drews, F., Ecker, K. (2007). Characterizing robustness in dynamic real-time systems. The Journal of Systems and Software; 80: 1005-1014.
  • Elnitski, L., Welch, L. (2007). New Frontiers in Computational Genomics: Identification of Novel Functional Elements and Genome-scale Pattern Analysis (an editorial). 3. Scalable Computing: Practice and Experience; 8: i-vii.
  • Tan, Z., Leal, W., Welch, L. (2007). Verification of instrumentation techniques for resource management of real-time systems. 80. The Journal of Systems and Software; 1015-1022.
  • List, E., Berryman, D., Palmer, A., Gosney, E., Okada, S., Kelder, B., Lichtenberg, J., Welch, L., Kopchick, J. (2007). Application of bioinformatics and scalable computing to perform proteomic analysis of stomach tissue from obese and diabetic mice. 2. Journal of Scalable Computing: Practice and Experience; 8: 173-183.
  • Huh, E., Welch, L. (2006). Adaptive resource management for dynamic distributed real-time applications. 38. Journal of Supercomputing; 127-142.
  • Juedes, D., Drews, F., Gu, D., Welch, L., Ecker, K., Schomann, S. (2006). Approximation Algorithm for Periodic Real-Time Tasks withWorkload -Dependant Running-. 3. Journal of Real-time Systems; 34: 173-194.
  • Sarnoff, S., Welch, L., Gradin, S., Sandell, K. (2004). Using a faculty in residence model to enhance curriculae in computer science and social work with writing and critical thinking. 3. Journal of Faculty Development; 19: 131-144.
  • Zhou, Q., Gillen, M., Parrot, D., Chelberg, D., Welch, L. (2004). Agent-based Computer Vision in a Dynamic, Real-time Environment. 4. Pattern Recognition, Elsevier Science; 37: 691-705.
  • Sandell, K., Welch, L. (2004). The Use of Group Testing for Formative and Summative Evaluation. 100. New Directions for Teaching and Learning, Wiley; 101-105.
  • Andrews, D., Vemuri, R., Chelberg, D., Fleeman, D., Parrott, D., Welch, L., Brandt, S. (2002). A Framework for Using Benefit Functions in Complex Real Time Systems. 1. Journal of Parallel and Distributed Computing Practices, Nova Science Publishers, Inc.; 5: 41-50.
  • Jain, S., Welch, L., Pfarr, B., Chelberg, D., Bruggeman, C., Fleeman, D., Parrot, D., Tan, Z., Shuler, C., McCoy, M. (2002). Management of QoS-level Adaptation for Real-time Systems. 1. Journal of Parallel and Distributed Computing Practices, Nova Science Publishers, Inc.; 5: 15-26.
  • Huh, E., Nelamegam, A., Welch, L., Park, H., Pfarr, B. (2002). Worst-Case Analysis for Real-Time Processes in Time-Sharing Environments. 1. Journal of Parallel and Distributed Computing Practices, Nova Science Publishers, Inc.; 5: 51-62.
  • Shirazi, B., Welch, L., Ravindran, B., Cavanaugh, C., Yanamula, B., Brucks, R., Huh, E. (2000). DynBench: A Benchmark Suite for Dynamic Real-Time Systems. 1. The Journal of Parallel and Distributed Computing Practices, Nova Science Publishers, Inc.; 3.
  • Welch, L., Werme, P., Shirazi, B., Cavanaugh, C., Fontenot, L., Huh, E., Masters, M. (2000). Load Balancing for Dynamic Real-Time Systems. 3. Cluster Computing; 125-138.
  • Ravindran, B., Welch, L., Shirazi, B. (2000). Resource Management Middleware for Dynamic, Dependable Real-Time Systems. 20. The Journal of Real-Time Systems, Kluwer Academic Press; 183-196.
  • Welch, L., Shirazi, B., Ravindran, B., Kamangar, F. (1999). Instrumentation Support for Dynamic Resource Management of Real-Time, Distributed Control Systems. 3. The International Journal of Parallel and Distributed Systems and Networks, ACTA Press; 2: 105-117.
  • Welch, L. (1997). COCOON: Creator Of Concurrent Object-OrieNted Systems. 6. Ada Letters, XVII, ACM Press; 32-38.
  • Welch, L. (1997). Prism: a Toolset for Reverse Engineering of Computer-Based Systems. 6. Ada Letters, XVII, ACM Press; 39-46.
  • Welch, L., Lankala, M., Farr, W., Hammer, D. (1996). Metrics for Quality and Concurrency in Object-Based Systems. 2. Annals of Software Engineering, J.C. Baltzer AG, Science Publishers; 93-119.
  • Welch, L., Yu, G., Ravindran, B., Kurfess, F., Henriques, J., Wilson, M., Masters, M., Samuel, A. (1996). Reverse Engineering of Computer-Based Control Systems. 4. International Journal of Software Engineering and Knowledge Engineering, World Scientific Publishing; 6: 531-547.
  • Verhoosel, J., Welch, L., Hammer, D., Luit, E. (1996). Incorporating Temporal Considerations During Assignment and Pre-run-time Scheduling of Objects and Processes. 1. Journal of Parallel and Distributed Computing, Academic Press; 36: 13-31.
  • Welch, L. (1996). A Metrics-Driven Process for Utilizing Concurrency in Object-Oriented Real-Time Systems. 1. Association for Computing Machinery (ACM) OOPS Messenger, ACM Press; 7: 70-77.
  • Welch, L. (1996). A Taxonomy for Distributed Object-Oriented Real-Time Systems. 1. Association for Computing Machinery (ACM) OOPS Messenger, ACM Press; 7: 78-85.
  • Welch, L., Yu, G., Verhoosel, J., Haney, J., Samuel, A., Ng, P. (1995). Metrics for Evaluating Concurrency in Reengineered Complex Systems. 1. Annals of Software Engineering, J.C. Baltzer AG, Science Publishers; 179-217.
  • Welch, L., Samuel, A., Masters, M., Harrison, R., Wilson, M., Caruso, J. (1995). Reengineering Complex Computer Systems for Enhanced Concurrency and Layering. 2. Journal of Systems and Software; 30: 45-70.
  • Welch, L., Stoyenko, A., Marlowe, T. (1995). Modeling Resource Contention Among Distributed Periodic Processes Specified in CaRT-Spec. 5. Control Engineering Practice; 3: 651-664.
  • Yu, G., Welch, L. (1995). A Novel Approach to Off-line Scheduling in Real-Time Systems. 1. Informatica; 19: 71-82.
  • Verhoosel, J., Welch, L., Hammer, D., Stoyenko, A., Luit, E. (1995). A Model for Scheduling of Object-Based, Distributed Real-Time Systems. 1. Journal of Real-Time Systems, Kluwer Academic Publishers; 8: 5-34.
  • Stoyenko, A., Welch, L., Cheng, B. (1994). Response Time Prediction in Object-Based, Parallel Embedded Systems. 40. Microprocessing and Microprogramming, Elsevier Science; 135-150.
  • Welch, L. (1994). Techniques for Complex Systems Development. Real-Time Computing 鈥揘ATO Advanced Study Institute on Real-Time Computing, NATO ASI Series, Series F, Computer and Systems Sciences, Springer-Verlag; 127.
  • Welch, L. (1994). The State-of-the-Art in Real-Time Computing. NATO ASI Series, Series F. Real-Time Computing 鈥揘ATO Advanced Study Institute on Real-Time Computing, NATO ASI Series, Series F, Computer and Systems Sciences, Springer-Verlag; 127.
  • Welch, L. (1994). A Parallel Virtual Machine for Programs Constructed from Abstract Data Types. 11. IEEE Transactions on Computers, IEEE Computer Society Press; 37: 1249-1261.
  • Marlowe, T., Stoyenko, A., Masticola, S., Welch, L. (1994). Schedulability-Analyzable Exception Handling for Responsive Languages. 2. Journal of Real-Time Systems, Kluwer Academic Publishers; 7: 183-212.
  • Sitaraman, M., Welch, L., Harms, D. (1993). On Specification of Reusable Software Components. 2. The International Journal of Software Engineering and Knowledge Engineering, World Scientific Publishers; 3: 207-229.

Journal Article, Professional Journal (3)

  • Al-Ouran, R., Schmidt, R., Naik, A., Jones, J., Drews, F., Juedes, D., Elnitski, L., Welch, L. (2015). Discovering Gene Regulatory Elements Using Coverage-based Heuristics. [Epub ahead of print] PubMed PMID: 26540692. IEEE/ACM Transactions on Computational Biology and Bioinformatics; October 30, 2015.
  • Welch, L., Benencia, F., Duran-Ortiz, S., Lubbers, E., List, E., Householder, L., Al-Naeeli, M., Liang, X., Kopchick, J., Berryman, D. (2015). Male bovine GH transgenic mice have decreased adiposity with an adipose depot-specific increase in immune cell populations. 156(5):1794-803. Endocrinology; May 2015.
  • Welch, L., Lewitter, F., Schwartz, R., Brooksbank, C., Radivojac, P., Gaeta, B., Schneider, M. (2014). Bioinformatics Curriculum Guidelines: Toward a Definition of Core Competencies. PLOS Computational Biology; .

Patent (4)

  • Welch, L. Resource Allocation Decision Function for Resource Management Architecture and Corresponding Programs.
  • Welch, L. Diabetes Biomarker Discovery.
  • Welch, L. Program Control For Resource Management Architecture and Corresponding Programs. US patent no. 7,096,248.
  • Welch, L. System for Monitoring and Reporting Performance of Hosts and Applications and Selectively Configuring Applications in a Resource Managed System. US patent number 7,051,098.

Book, Scholarly (2)

  • Welch, L. Genome-scale Pattern Analysis in the Post-ENCODE Era, Laura Elnitski, Helen Piontkivska and Lonnie Welch Editors. World Scientific Publishers, Hackensack, NJ, 2011.
  • Elnitski, L., Piontkivska, H., Welch, L. (2011). Advances In Genomic Sequence Analysis and Pattern Discovery (Science, Engineering, and Biology Inofrmatics). World Scientific Publishing Company.

Book, Chapter in Scholarly Book (11)

  • Linchtenberg, J., Yilmaz, A., Kurtz, K., Liang, X., Nelson, C., Bitterman, T., Stockinger, E., Grotewold, E., Welch, L. (2011). "Encyclopedieas of DNA Elements for Plant Genomes" in Advances in Genomic Sequence Analysis and Pattern Discovery. Hackensack, NJ: World Scientific Publishers; 159--178.
  • Welch, L., Koehly, L., Elnitski, L. (2011). Shared Regulatory Motifs in Promoters of Human DNA Repair Genes (Science, Engineering, and Biology Informatics). Rijeka: In Inna Kruman ; 67-84.
  • Liu, C., Atighetchi, M., Cross, J., DiPippo, L., Fay-Wolfe, V., Gill, C., Gupta, P., Heightland, T., James, J., Loyall, J., Murphy, M., Neihaus, D., Rubel, P., Schantz, R., Schmidt, D., Welch, L., Zhang, J., Zinky, J. (2009). Chapter 3: Resource Management Specification and Enforcement Patterns. Design Patterns for Distributed Real-time Systems, Real-Time Systems Series, Springer 2008.; 24.
  • DiPippo, L., Fay-Wolfe, V., Gill, C., Heightland, T., James, J., Niehaus, D., Subramonian, V., Welch, L., Zhang, W. (2008). Resource Management Actuation Patterns. Design Patterns for Distributed Real-time Systems, Real-Time Systems Series, Springer 2008; 24.
  • Atighetchi, M., DiPippo, L., Fay-Wolfe, V., Gill, C., Gupta, P., Heightland, T., James, J., Loyall, J., Murphy, M., Niehaus, D., Rubel, P., Schantz, R., Welch, L., Zhang, J., Zinky, J. (2008). Resource Management Monitoring Patterns. Design Patterns for Distributed Real-time Systems, Real-Time Systems Series, Springer 2008; 24.
  • Gu, D., Welch, L. (2008). Robust Allocation and Scheduling Heuristics for Dynamic, Distributed Real-time Systems. Meta-Heuristics for Scheduling, Volume 2 鈥 Distributed Computing Environments, (Series in Studies in Computational Intelligence), Springer; 2.
  • DiPippo, L., Fay-Wolfe, V., Gill, C., Heightland, T., Niehaus, D., Rubel, P., Shapiro, R., Welch, L., Zinky, J. (2008). System Engineering Patterns. Design Patterns for Distributed Real-time Systems, Real-Time Systems Series, Springer 2008; 24.
  • Welch, L., Masters, M., Madden, L., Werme, P., Marlow, D., Irey, P., Shirazi, B. (1999). A Distributed System Reference Architecture for Adaptive QoS and Resource Management. 1586. Lecture Notes in Computer Science, Springer-Verlag; 1316-1326.
  • Welch, L., Ravindran, B., Shirazi, B., Bruggeman, C. (1999). A Resource Management Model for Multidimensional, Dynamic Real-Time Systems. 1388. Lecture Notes in Computer Science, Springer-Verlag; 931-936.
  • Shirazi, B., Welch, L., Ravindran, B., Cavanaugh, C., Yanamula, B., Brucks, R., Huh, E. (1999). DynBench: A Dynamic Benchmark Suite for Distributed Real-Time Systems. 1586. Lecture Notes in Computer Science, Springer-Verlag; 1335-1349.
  • Welch, L., Shirolkar, P., Anwar, S., Sergeant, T., Shirazi, B., Bruggeman, C., Ravindran, B., Werme, P., Masters, M., Harrison, R., Mills, D., Do, T., Lafratta, J., Sharp, S., Bilowus, G., Swick, M., Hoppel, J., Caruso, J. (1999). Real-Time Resource Management Middleware: Open Systems and Applications. Upper Saddle River, New Jersey: High Performance Cluster Computing: Programming and Applications, Prentice Hall PTR; 2: 418-439.

Conference Proceeding (145)

  • Welch, L., Al-Ouran, R., Schmidt, R., Naik, A., Jones, J., Juedes, D., Elnitski, L., Drews, F. (2015). Discovering Gene Regulatory Elements Using Coverage-based Heuristics. Potomac, Maryland: ENCODE 2015: Research Applications and Users Meeting, National Institutes of Health, Potomac, Maryland.
  • Welch, L., Al-Ouran, R., Schmidt, R., Naik, A., Jones, J., Juedes, D., Elnitski, L., Drews, F. (2015). Discovering Gene Regulatory Elements Using Coverage-based Heuristics. West Lafayette, IN: 10th Great Lakes Bioinformatics Conference, International Society for Computational Biology, Purdue University.
  • Welch, L., Duran Ortiz, S., Jara, A., Liang, X., Brooks, N., Lubbers, E., List, E., Benencia, F., Kopchick, J., Berryman, D. (2015). Impact of Growth Hormone on Angiogenesis and Intracellular Signaling Pathways in Subcutaneous and Visceral Adipose Tissue from Wild Type and Bovine Growth Hormone Transgenic Mice. San Diego, California: ENDO 2015 (The Endocrine Society鈥檚 97th Annual Meeting and Expo).
  • Nau, L., Drews, F., Welch, L. (2011). A scalable multicore Implementation of the TEIRESIAS Algorithm . Vienna, Austria: 12th Bioinformatics Open Source Conference.
  • Welch, L., Schwartz, R., Lewitter, F. (2011). Report from the ISCB Education Committee: A Draft Curriculum for Bioinformatics. Vienna, Austria: Third Annual RECOMB Conference on Bioinformatics Education (RECOMB-BE), an ISMB/ECCB 2011 Satellite Meeting.
  • Lichtenberg, J., Alam, K., Bitterman, T., Drews, F., Ecker, K., Elnitski, L., Evans, S., Grotewold, E., Gu, D., Jacox, E., Kurz, K., Lee, S., Liang, X., Majmudar, P., Morris, P., Nelson, C., Stockinger, E., Welch, J., Wyatt, S., Yilmaz, A., Welch, L. (2009). Construction of Genomic Regulatory Encyclopedias: Strategies and Case Studies. Proceedings of the Ohio Collaborative Conference on Bioinformatics, IEEE Computer Society press.
  • Lichtenberg, J., Jacox, E., Yang, M., Elnitski, L., Welch, L. (2008). Word-Based Characterization of Promoters from Human DNA Repair Pathways. Hinxton, UK: GENOME INFORMATICS, Cold Spring Harbor Laboratory/Wellcome Trust Joint Conference.
  • Lichtenberg, J., Morris, P., Ecker, K., Welch, L. (2008). Discovery of Regulatory Elements in Oomycete Orthologs. Las Vegas, NV: The 2008 International Conference on Bioinformatics and Computational Biology (BIOCOMP'08).
  • Drews, F., Petri, E., Lichtenberg, J., Welch, L. (2008). Scalable Parallel Word Search in Multi-Core/Multiprocessor Systems . Las Vegas, NV: The 2008 International Conference on Bioinformatics and Computational Biology (BIOCOMP'08).
  • Ecker, K., Welch, L. (2008). The SiteSeeker Motif Discovery Tool. Las Vegas, NV: The 2008 International Conference on Bioinformatics and Computational Biology (BIOCOMP'08).
  • Lichtenberg, J., Jacox, E., Yang, M., Elnitski, L., Welch, L. (2008). Word-based Characterization of the Bidirectional Promoters from the Human DNA-repair Pathways. Las Vegas, NV: The 2008 International Conference on Bioinformatics and Computational Biology (BIOCOMP'08).
  • Lichtenberg, J., Welch, L. (2008). Clustering of Motif Discovery Data to Identify Transcription Factor Binding Sites. Toledo, Ohio: Ohio Collaborative Conference on Bioinformatics.
  • Shen, K., Wyatt, S., Welch, L. (2008). Finding cis-regulatory elements involved in plant gravitropic signal transduction. Toledo, Ohio: Ohio Collaborative Conference on Bioinformatics.
  • Wyatt, S., Shen, K., Welch, L. (2008). Grappling with the Gravity Box. Toledo, Ohio: Ohio Collaborative Conference on Bioinformatics.
  • Nelson, C., Welch, L., Stockinger, E. (2008). Using WordSeeker to identify regulatory elements in CBF genes from the Triticeae. Toledo, Ohio: Ohio Collaborative Conference on Bioinformatics.
  • Morris, P., Lichtenberg, J., Welch, L. (2008). In Silico Identification of Regulatory Elements in Oomycete Genomes using WordSeeker. Birnam, UK: Oomycete Molecular Genetics Workshop.
  • Ecker, K., Gu, D., Welch, L. (2007). SiteSeeker 鈥 A Motif Discovery Tool. Boston, MA: 7th IEEE International Conference on Bioinformatics and Bioengineering.
  • Welch, L., Petri, E., Gu, D. (2007). WordSeeker: Discovering Genome-wide Patterns. Miami, Ohio: Ohio Collaborative Conference on Bioinformatics.
  • Lichtenberg, J., Welch, L. (2007). Design Pattern for Protein Identification. Columbus, Ohio: 4th Annual Ohio Mass Spectrometry Symposium.
  • Lichtenberg, J., Welch, L., Kopchick, J., Okada, S., Sackmann-Sala, L., Sankaran, S. (2007). Post-translational Modification Analysis. Columbus, Ohio: 4th Annual Ohio Mass Spectrometry Symposium.
  • Slaby, J., Welch, L., Work, P. (2006). Toward Certification of Adaptive Distributed Systems. Arlington, VA: OMG's Workshop on Distributed Object Computing for Real-time and Embedded Systems.
  • Showalter, A., Yerardi, J., Conley, T., Keppler, B., Welch, L. (2006). A Bioinformatics-Based Approach to the Identification, Classification, and Expression of Genes Encoding Plant Cell Wall Hydroxyproline-Rich Glycoproteins (HRGPs). Athens, OH: Ohio Collaborative Conference on Bioinformatics.
  • Lichtenberg, J., Welch, L., Conley, T., Okada, S., Sankaran, S., Kopchick, J. (2006). Bioinformatics Tools for Analysis of Mass Spectrometry Data. Columbus, Ohio: 3rd Annual Ohio Mass Spectrometry Symposium.
  • Gu, D., Yang, L., Welch, L. (2005). A Predictive, Decentralized Load Balancing Approach. 13th International Workshop on Parallel and Distributed Real-time Systems.
  • Gu, D., Drews, F., Welch, L. (2005). Robust Task Allocation for Dynamic Distributed Real-time Systems Subject to Multiple Environmental Parameters. The 25th International Conference on Distributed Computing Systems.
  • Zhao, H., Gu, D., Welch, L., Drews, F. (2005). Stable Allocations in Distributed Real-time Systems with Multiple Environmental Parameters and Replicable Applications. 13th International Workshop on Parallel and Distributed Real-time Systems.
  • Liu, C., Sandell, K., Welch, L. (2005). Teaching Communication Skills in Software Engineering Courses. Portland, Oregon: 2005 ASEE Annual Conference and Exposition.
  • Judd, R., Drews, F., Lawrence, D., Juedes, D., Leal, W., Deshpande, J., Welch, L. (2005). QoS-Based Resource Allocation in Dynamic Real-Time Systems. Portland, OR: Proceedings of the 2005 American Control Conference; 1745 鈥 1751.
  • Bryan, K., DiPippo, L., Fay-Wolfe, V., Murphy, M., Zhang, J., Fleeman, D., Juedes, D., Liu, C., Welch, L., Niehaus, D., Gill, C. (2005). Integrated CORBA Scheduling and Resource Management for Distributed Real-Time Embedded Systems. San Francisco, CA: Proceeding of 11th IEEE Real-Time and Embedded Technology and Applications Symosium (RTAS 2005), IEEE Computer Society Press; 374-384.
  • Gu, D., Drews, F., Welch, L. (2004). A Characterization of Task Allocation Problems for Distributed Real-time Systems. Parallel and Distributed Computing and Systems (PDCS).
  • Welch, L., Fleeman, D., Juedes, D., Liu, C. (2004). Adaptive Resource Management Services in CORBA. The Object Management Group (OMG) Workshop on Distributed Object Computing for Real-time and Embedded Systems.
  • Delaney, M., Welch, L. (2004). RMBench: CORBA Benchmarking Services for Resource Management Middleware. The Object Management Group (OMG) Workshop on Distributed Object Computing for Real-time and Embedded Systems.
  • Bryan, K., DiPippo, L., Fay-Wolfe, V., Fleeman, D., Gill, C., Juedes, D., Liu, C., Murphy, M., Niehaus, D., Subramonian, V., Welch, L., Zhang, J. (2004). Towards Integrated CORBA Scheduling and Resource Management Services for Distributed Real-Time and Embedded Systems. Arlington, VA: 4th Annual Workshop on TAO and CIAO.
  • Aber, E., Drews, F., Gu, D., Juedes, D., Lenharth, A., Parrott, D., Welch, L., Zhao, H., Fleeman, D. (2004). Experimental Comparison of Heuristic and Optimal Resource Allocation Algorithms for Maximizing Allowable Workload in Dynamic, Distributed Real-Time Systems. WTR 2004 - 6th Brazilian Workshop on Real-Time Systems.
  • Campbell, R., Daley, R., Dasarathy, B., Lardieri, P., Orner, B., Schantz, R., Coleburn, R., Welch, L., Work, P. (2004). Toward an Approach for Specification of QoS and Resource Information for Dynamic Resource Management. Workshop on Model-based Development of Embedded Systems.
  • Juedes, D., Drews, F., Welch, L. (2004). Workload Functions: A New Paradigm for Real-Time Computing. In Proceedings of the RTAS Work-In-Progress Session.
  • Liu, C., Fleeman, D., Aber, E., Welch, L., Juedes, D. (2004). Model-Driven Resource Management for Distributed Real-Time and Embedded Systems. 2nd RTAS Workshop on Model-Driven Embedded Systems (MoDES '04.
  • Leal, W., Drews, F., Liu, C., Welch, L. (2004). Toward Model-Based Verification of Adaptive Allocation Managers. Proceedings of the 2nd RTAS Workshop on Model-Driven Embedded Systems (MoDES '04).
  • Juedes, D., Drews, F., Welch, L., Fleeman, D. (2004). Heuristic Resource Allocation Algorithms for Maximizing Allowable Workload in Dynamic, Distributed Real-Time Systems. 12th International Workshop on Parallel and Distributed Real-time Systems, IEEE Computer Society Press.
  • Fleeman, D., Gillen, M., Lenharth, A., Delaney, M., Welch, L., Juedes, D., Liu, C. (2004). Quality-based Adaptive Resource Management Architecture (QARMA): A CORBA Resource Management Service, IEEE Press. 12th International Workshop on Parallel and Distributed Real-time Systems, IEEE Computer Society Press.
  • Drews, F., Welch, L., Juedes, D., Fleeman, D., Bruening, A., Ecker, K., Hoefer, M. (2004). Utility-Function based Resource Allocation for Adaptable Applications in Dynamic Distributed Real-Time Systems. 12th International Workshop on Parallel and Distributed Real-time Systems, IEEE Computer Society Press.
  • Fleeman, D., Gillen, M., Lenharth, A., Delaney, M., Welch, L., Juedes, D., Liu, C. (2004). Quality-based Adaptive Resource Management Architecture (QARMA): A CORBA Resource Management Service. Santa Fe, New Mexico: Workshop on Parallel and Distributed Real-Time Systems 2004 (WPDRTS04).
  • Heightland, T., Welch, L. (2004). Characterization and Engineering Real-Time Systems. Carefree, AZ: ChiliPLOP.
  • Stewart, C., Welch, L., Gradin, S. (2004). Improving Graduate Students鈥 Writing Through Thesis-Writing Workshops. Spotlight on Learning.
  • Yang, L., Welch, L., Liu, J., Cavanaugh, C. (2003). A Robust QoS Forecasting Technique For Dynamic Distributed Real-Time Testbed. New Orleans, LA: IEEE CAMP 2003 International Workshop on Computer Architectures for Machine Perception.
  • Welch, L. (2003). An Approach for On-line Performance Certification. Nice, France: International Workshop on Parallel and Distributed Real-time Systems.
  • Gu, D., Welch, L., Shelly, R., Bruggeman, C. (2003). Decentralized Resource Management for Dynamic Distributed Real-time Systems with Pavlov Strategy. Las Vegas, Nevada: The 2003 International Conference on Security and Management.
  • Gu, D., Welch, L., Bruggeman, C., Shelly, R. (2003). The Applicability of Social Models for Self-Organizing Real-Time Systems. Workshop on Parallel and Distributed Real-time Systems.
  • Drews, F., Welch, L. (2003). An Architecture and a General Optimization Framework for Resource Management in Dynamic, Distributed Real-Time Systems. Capri, Italy: IEEE International Workshop on Object-oriented Real-time Dependable Systems.
  • Marinucci, T., Welch, L. (2003). Patterns for Characterization and Engineering of Adaptive, Distributed Real-Time Systems. Monticello, Illinois: 10th Conference on Pattern Languages of Programs (PLoP 2003).
  • Chelberg, D., Drews, F., Fleeman, D., Welch, L., Marquart, J., Pfarr, B. (2003). Obtaining the Greatest Scientific Benefit from Observational Platforms by Consideration of the Relative Benefit of Observations. Pasadena, CA: International Conference on Space Mission Challenges for Information Technology (SMC-IT).
  • Welch, L., Chelberg, D., Pfarr, B. (2003). Adaptive Resource Management Technology for NASA Computing Systems. The Third Earth Science Technology Conference (ESTC-2003).
  • Tan, Z., Welch, L., Bruggeman, C., Chelberg, D., Fleeman, D., Parrott, D. (2003). Automatic Profiling Architecture for Dynamic, Distributed Real-time Systems. Las Vegas, Nevada: International Conference on Parallel and Distributed Processing Techniques and Applications (PDPTA).
  • Parrott, D., Fleeman, D., Welch, L., Chelberg, D., Bruggeman, C., Drews, F., Tan, Z. (2003). Autonomous Satellite Systems Operating in Dynamic, Real-Time Environments. Las Vegas, Nevada: International Conference of Artificial Intelligence.
  • Yang, L., Liu, J., Cavanaugh, C., Welch, L. (2003). A L2E-Based QoS Forecasting Algorithm for a Dynamic, Distributed Real-Time Systems. Las Vegas, NV: The 2003 International Conference on Parallel and Distributed Processing Techniques and Applications (PDPTA'03); 424-429.
  • Ecker, K., Drews, F., Juedes, D., Welch, L., Chelberg, D., Fleeman, D., Parrott, D. (2003). An Optimization Framework for Dynamic, Distributed Real-Time Systems. Nice, France: 11th International Workshop on Parallel and Distributed Real-Time Systems.
  • Brooks-Rather, R., Welch, L., Gradin, S. (2003). The Lecture is Over, Now it鈥檚 Time to Learn: A Pilot Study on Writing in a Computer Science Course. Spotlight on Learning Conference.
  • Masters, M., Welch, L. (2002). Open Architectures for Mission-Critical Real-Time Systems. Workshop on Large Scale Real-Time and Embedded Systems, in conjunction with RTSS (Real-Time Systems Symposium).
  • Govindaswamy, V., Welch, L., Shirazi, B. (2002). Preparing Dependable, Dynamic Real-time Application Systems for an Adaptive Resource Management Environment. IEEE Canadian Conference on Electrical and Computer Engineering.
  • Marinucci, T., Welch, L., Masters, M., Werme, P. (2002). A Pattern Language for Engineering Dynamic Real-Time Applications. Workshop on Patterns in Distributed Real-time and Embedded Systems (affiliated with OOPSLA 2002).
  • Gill, C., Niehaus, D., DiPippo, L., Wolfe, V., Welch, L. (2002). Mapping a Multi-Level Scheduling Pattern Language to Distributed Real-Time Embedded Applications. Workshop on Patterns in Distributed Real-time and Embedded Systems (affiliated with OOPSLA 2002).
  • Welch, L., Gradin, S., Sandell, K. (2002). Enhancing Engineering Education with Writing-to-learn and Cooperative Learning: Experiences from a Software Engineering Course. Berlin, Germany: The American Society for Engineering Education (ASEE) in collaboration with the Eurpoean Society for Engineering Education (SEFI) and the Technical University Berlin (TUB), the 2002 ASEE/SEFI/TUB International Colloquium, "Global Changes in Engineering Education".
  • Gradin, S., Kovalchick, A., Sarnoff, S., Welch, L. (2002). Using a Faculty in Residence Model to Enhance Curriculae in Computer Science and Social Work with Writing and Critical Thinking. International Conference of the Society for Exploring Teaching Alternatives.
  • Welch, L., Marinucci, T., Masters, M., Werme, P. (2002). Dynamic Resource Management Architecture Patterns. 9th Conference on Pattern Languages of Programs.
  • Welch, L., Shah, P., Jain, S. (2002). Hybrid Resource Management Middleware for Dynamic Real-Time Systems. DARPA ITO Workshop on Real-time and Embedded Distributed Object Computing.
  • Welch, L., Fleeman, D. (2002). The ACE ORB and Distributed Resource Management. 2nd Workshop on The ACE ORB (TAO).
  • Welch, L., Tjaden, B., Pfarr, B. (2002). Adaptive Resource Management Technology . NASA Earth Science Technology Conference.
  • Welch, L., Gradin, S., Sandell, K. (2002). Enhancing Engineering Education with Writing-to-learn and Cooperative Learning: Experiences from a Software Engineering Course. Annual Conference of the American Society of Engineering Education.
  • Welch, L., Gradin, S., Sandell, K. (2002). Enhancing Engineering Education with Writing-to-learn and Cooperative Learning: Experiences from a Software Engineering Course. Spotlight on Learning Conference.
  • Jain, S., Welch, L., Chelberg, D., Tan, Z., Fleeman, D., Parrott, D., Pfarr, B., Liu, M., Shuler, C. (2002). A Collaborative Problem Solving Agent for On-Board Real-time Systems. The 10th Workshop on Parallel and Distributed Real-Time Systems.
  • Andrews, D., Welch, L., Chelberg, D., Brandt, S. (2002). A Framework for Using Benefit Functions in Complex Real-Time Systems. The 10th Workshop on Parallel and Distributed Real-Time Systems.
  • Huh, E., Welch, L. (2002). An Efficient Schedulability Analysis Policing Technique for Periodic, Dynamic Real-Time Applications. The 10th Workshop on Parallel and Distributed Real-Time Systems.
  • Chen, H., Tjaden, B., Welch, L., Bruggerman, C., Tong, L., Pfarr, B. (2002). Monitoring Network QoS in a Dynamic Real-Time System. The 10th Workshop on Parallel and Distributed Real-Time Systems.
  • Huh, E., Welch, L. (2002). Real-time Performance Analysis for Dynamic, Distributed Real-time Systems. International Conference on Computational Science.
  • Lakshmikumar, D., Chelberg, D., Gillen, M., Marling, C., Tomko, M., Welch, L. (2002). A Hybrid, Hierarchical Schema-Based Architecture for Distributed Autonomous Agents. The American Association for Artificial Intelligence (AAAI) Spring Symposium on Intelligent Embedded and Distributed Systems.
  • Welch, L., Masters, M. (2001). Challenges for Building Complex Real-time Computing Systems. Software Design and Productivity Coordinating Group Workshop on New Visions for Software Design and Productivity: Research and Applications.
  • Welch, L., Masters, M. (2001). Characterizing Patterns for Real-Time Systems and Their Environments. ACM OOPSLA Workshop: Towards Patterns and Pattern Languages for OO Distributed Real-time and Embedded Systems.
  • Anwar, S., Welch, L. (2001). Experience With TAO for Development of Adaptive Resource Management Middleware. 1st Workshop on The ACE ORB (TAO).
  • Marinucci, T., Neelamegam, A., Tjaden, B., Tong, L., Welch, L., Goldman, B., Greer, G., Kaul, D., Pfarr, B. (2001). Sensor Web Adaptive Resource Manager. NASA Earth Science Technology Conference (ESTC-2001).
  • Tong, L., Bruggeman, C., Tjaden, B., Chen, H., Welch, L. (2001). Specification and Modeling of Network Resources in Dynamic, Distributed Real-time System. ISCA 14th International Conference on Parallel and Distributed Computing Systems.
  • Shah, P., Bruggeman, C., Welch, L. (2001). A Novel Paradigm for Mission Critical Systems. 2001 International Conference on Parallel and Distributed Processing Techniques and Applications (PDPTA 2001); 1428-1433.
  • Neelamagem, ., Bruggeman, C., Welch, L. (2001). Modeling Multiple and Heterogeneous Streams for Resource Management. 2001 International Conference on Parallel and Distributed Processing Techniques and Applications (PDPTA 2001); 1434-1438.
  • Chelberg, D., Welch, L., Marling, C. (2001). A Dynamic, Real-Time Testbed for Resource Management Technology. 10th HETEROGENEOUS COMPUTING WORKSHOP (HCW 2001).
  • Lawrence, D., Guan, J., Mehta, S., Welch, L. (2001). Adaptive Scheduling via Feedback Control for Dynamic Real-Time Systems. Phoenix, Arizona: Proceedings of the 2001 IEEE International Performance, Computing, and Communications Conference; 373-378.
  • Lawrence, D., Guan, J., Mehta, S., Welch, L. (2001). Adaptive Scheduling via Feedback Control for Dynamic Real-Time Systems. 20th IEEE International Performance, Computing, And Communications Conference (IPCCC 2001).
  • Zhou, Y., Welch, L., Huh, E., Alexander, C., Lawrence, D. (2001). Execution Time Analysis for Dynamic, Periodic Processes. The 9th Workshop on Parallel and Distributed Real-Time Systems.
  • Welch, L., Brandt, S. (2001). The Value of Benefit in Real-Time Computing. The 9th Workshop on Parallel and Distributed Real-Time Systems.
  • Cavanaugh, C., Welch, L., Shirazi, B. (2001). Towards a Characterization of QoS Management Approaches in Distributed, Real-Time Systems. The 9th Workshop on Parallel and Distributed Real-Time Systems.
  • Chelberg, D., Welch, L., Lakshmikumar, A., Gillen, M., Zhou, Q. (2001). 91探花鈥檚 RoboCup Team: Combining Resource Management with Distributed Agents. The 33rd Southeastern Symposium on System Theory.
  • Kumar, ., Das, S., Shirazi, B., Levine, D., Marquis, J., Welch, L. (2001). Pervasive Information Community Organization (PICO) of Camileuns and Delegents for Future Global Networking. Vienna, VA: Large Scale Networking (LSN) Workshop.
  • Cavanaugh, C., Welch, L., Shirazi, B. (2000). Diagnosing End-To-End Paths in Dynamic, Distributed Real-Time Systems. The IEEE Real-Time Systems Symposium.
  • Welch, L., Lawrence, D., Alexander, D. (2000). Feedback Control Resource Management Using A Posteriori Workload Characterizations. The 39th IEEE Conference on Decision and Control.
  • Alexander, D., Lawrence, D., Welch, L. (2000). Feedback Control Resource Management using A Posteriori Workload Characterizations. Sydney, Australia: Proceedings of the 39th IEEE Conference on Decision and Control; 2222-2227.
  • Tjaden, B., Welch, L., Ostermann, S., Chelberg, D., Balupari, R., Bykova, M., Mitchell, A., Tong, L. (2000). Secure-RM: Security and Resource Management for Distributed Real-Time Mission Critical Systems. The Southern Conference on Computing (SCC 2000).
  • Detter, R., Welch, L., Pfarr, B., Tjaden, B., Huh, E. (2000). Adaptive Management of Computing and Network Resources for Spacecraft Systems. The 3rd Annual Military and Aerospace Applications of Programmable Devices and Technologies Conference (MAPLD 2000).
  • Tjaden, B., Welch, L., Ostermann, S., Balupari, R., Bykova, M., Delaney, M., Mitchell, A., Li, S., Lissitsyn, D., Tong, L. (2000). INBOUNDS: The Integrated Network-Based 91探花 Network Detective Service. 1. The 4th World Multiconference on Systemics, Cybernetics and Informatics (SCI'2000); 395-400.
  • Huh, E., Welch, L., Shirazi, B., Tjaden, B., Cavanaugh, C. (2000). Accommodating QoS Prediction in an Adaptive Resource Management Framework. The 5th International Workshop on Embedded/Distributed HPC Systems and Applications (EHPC 2000).
  • Huh, E., Welch, L., Shirazi, B., Cavanaugh, C., Anwar, S. (2000). Heterogeneous Resource Management for Dynamic Real-Time Systems. The 9th Heterogeneous Computing Workshop; 287-296.
  • Islam, K., Shirazi, B., Welch, L., Tjaden, B., Cavanaugh, C., Anwar, S. (2000). Network Load Monitoring in Distributed Systems. The 5th International Workshop on Embedded/Distributed HPC Systems and Applications (EHPC 2000).
  • Cavanaugh, C., Welch, L., Shirazi, B., Huh, E. (2000). Quality of Service Negotiation for Distributed Dynamic Real-Time Systems. The 8th Workshop on Parallel and Distributed Real-Time Systems.
  • Welch, L., Huh, E. (2000). Toward Dynamic Schedulability Analysis for Dynamic Real-Time Systems. The IEEE Real-Time Technology and Application Symposium.
  • Cavanaugh, C., Welch, L., Kamangar, F., Shirazi, B. (1999). Quality of Service Forecasting for Distributed, Dynamic Real-Time Systems. Work-in-Progress - The IEEE Real-Time Systems Symposium; 6-10.
  • Welch, L., Shirazi, B. (1999). A Dynamic Real-Time Benchmark for Assessment of QoS and Resource Management Technology. The IEEE Real-Time Technology and Applications Symposium; 36-45.
  • Masters, M., Werme, P., Welch, L., Madden, L., Marlow, D., Irey, IV, P., Shirazi, B. (1999). A Reference Architecture for Adaptive Resource Management. Work-in Progress - the IEEE Real-Time Technology and Applications Symposium; 23-26.
  • Welch, L., Werme, P., Fontenot, L., Masters, M., Shirazi, B., Ravindran, B., Mills, D. (1999). Adaptive QoS and Resource Management Using A Posteriori Workload Characterizations. The IEEE Real-Time Technology and Applications Symposium; 266-275.
  • Welch, L., Ravindran, B., Werme, P., Masters, M., Shirazi, B., Shirolkar, P., Harrison, R., Mills, W., Do, T., Lafratta, J., Anwar, S., Sergeant, T., Sharp, S., Bilowus, G., Swick, M., Hoppel, J., Caruso, J. (1999). Distributed, Scalable, Dependable, Real-Time Systems: Middleware Services and Applications. The International Parallel Processing Symposium (IPPS)/Symposium on Parallel and Distributed Processing (SPDP), IEEE Computer Society Press; 297-301.
  • Welch, L., Ravindran, B., Shirazi, B., Bruggeman, C. (1998). Specification and Modeling Of Dynamic, Distributed Real-Time Systems. The IEEE Real-Time Systems Symposium, IEEE Computer Society Press; 72-81.
  • Welch, L., Shirazi, B., Ravindran, B., Bruggeman, C. (1998). DeSiDeRaTa: QoS Management Technology For Dynamic, Scalable, Dependable, Real-Time Systems. The 15th Symposium on Distributed Computer Control Systems (DCCS鈥98); 7-12.
  • Welch, L., Shirolkar, P., Anwar, S., Sargeant, T., Shirazi, B., Ravindran, B. (1998). Adaptive Resource Management for Scalable, Dependable Real-Time Systems: Middleware Services and Applications to Shipboard Computing Systems. Work-in-Progress - The IEEE Real-Time Technology and Applications Symposium.
  • Welch, L., Shirazi, B. (1997). DeSiDeRaTa: QoS Management Tools for Dynamic, Scalable, Dependable Real-Time Systems. The IEEE Workshop on Middleware for Distributed Real-Time Systems and Services; 164-178.
  • Welch, L. (1997). Architectures of Large-Grain, Distributed Real-Time Systems. The Fifth Workshop on Parallel and Distributed Real-Time Systems, IEEE Computer Society Press.
  • Kurfess, F., Lankala, M., Vantipalli, A., Welch, L. (1997). A Toolset for the Reengineering of Complex Computer Systems. The IEEE Conference on Engineering of Computer-Based Systems, IEEE Computer Society Press; 97-104.
  • Ravindran, B., Welch, L., Kelling, C. (1997). Building Distributed, Scalable, Dependable Real-Time Systems. The IEEE Conference on Engineering of Computer-Based Systems, IEEE Computer Society Press; 452-459.
  • Ravindran, B., Welch, L. (1996). Exploiting Parallelism in High Performance Embedded System Scheduling. The High Performance Computing Conference, IEEE Computer Society Press.
  • Welch, L., Ravindran, B., Harrison, R., Madden, L., Masters, M., Mills, D. (1996). Challenges in Engineering Distributed Shipboard Control Systems. Work-in-progress - The IEEE Real-Time Systems Symposium.
  • Welch, L., LeGore, E., Harrison, R., Masters, M. (1996). Instrumentation and Visualization of Large-Grain Distributed Control Systems. Workshop on Instrumentation and Visualization.
  • Welch, L., Kurfess, F. (1996). A Toolset For Reverse Engineering Of Computer-Based Control Systems. 8th Annual Software Technology Conference.
  • Welch, L., Wilson, M. (1996). Tools For Automatic Partitioning And Assignment Of Object-Based Concurrent Programs. 8th Annual Software Technology Conference.
  • Hammer, D., Welch, L., van Roosmalen, O. (1996). A Taxonomy for Object-Oriented Real-Time Systems: Classifying the Ada95 and Deal Languages. IEEE Symposium on Engineering of Computer-Based Systems.
  • Kurfess, F., Welch, L. (1996). Categorization of Programs Using Neural Networks. IEEE Symposium on Engineering of Computer-Based Systems.
  • Welch, L., Ravindran, B., Henriques, J., Hammer, D. (1995). Metrics and Techniques for Automatic Partitioning and Assignment of Object-based Concurrent Programs. Seventh IEEE Symposium on Parallel and Distributed Processing.
  • Welch, L., Haney, J., Samuel, A., Harrison, R., Lynch, J., Masters, M., Moffit, T., Ravindran, B., Sam, E., Wright, W. (1995). Reengineering of Legacy Systems: Toward an Automated Approach. The Fifth Systems Reengineering Technology Workshop.
  • Welch, L., Toda, K. (1994). Architectural Support for Real-Time Systems: Issues and Tradeoffs. International Workshop on Real-Time Computing Systems and Applications.
  • Verhoosel, J., Welch, L., Hammer, D., Stoyenko, A. (1994). Assignment and Pre-Run-Time Scheduling of Object-Based, Parallel Real-Time Processes. IEEE Symposium on Parallel and Distributed Processing; 638-645.
  • Yu, G., Welch, L. (1994). Program Dependence Analysis for Concurrency Exploitation in Programs Composed of Abstract Data Type Modules. IEEE Symposium on Parallel and Distributed Processing; 66-73.
  • Verhoosel, J., Yu, G., Welch, L., Hammer, D. (1994). Pre-Run-Time Scheduling for Object-Based, Concurrent Real-Time Applications. IEEE Real-Time Applications Workshop.
  • Rossak, W., Welch, L. (1994). A Concept for Hybrid Human-Machine Interaction in Retrieving Reusable Software Components. The 12th European Meeting on Cybernetics and Systems Research.
  • Welch, L., Samuel, A., Masters, M., Harrison, R., Stoyenko, A., Caruso, J. (1994). A Framework for Automated Reengineering of Complex Computer Systems. The Fourth Systems Reengineering Technology Workshop.
  • Welch, L. (1993). Cloning ADT Modules to Increase Parallelism: Rationale and Techniques. The Fifth IEEE Symposium on Parallel and Distributed Processing; 430-437.
  • Stoyenko, A., Welch, L., Laplante, P., Marlowe, T. (1993). A Platform for Complex Real-Time Applications. Complex Systems Engineering Synthesis and Assessment Workshop; 172-177.
  • Marlowe, T., Stoyenko, A., Welch, L., Laplante, P. (1993). Incremental Analysis for Reuse and Change in a Software Development Environment for Hard-Real-Time Systems. The 10th IEEE Workshop on Real-Time Operating Systems and Software.
  • Steigerwald, R., Welch, L. (1993). Reusable Component Retrieval for Real-Time Applications. IEEE Workshop on Real-Time Applications.
  • Welch, L., Stoyenko, A., Chen, S. (1993). Assigning ADT Modules with Random Neural Networks. The Hawaii International Conference on System Sciences, IEEE Computer Society Press; 546-555.
  • Welch, L., Stoyenko, A., Marlowe, T. (1992). Modeling Resource Contention for Distributed Periodic Processes. The Fourth IEEE Symposium on Parallel and Distributed Computing.
  • Yu, G., Welch, L., Rossak, W., Stoyenko, A. (1992). Automatic Retrieval of Formally Specified Real-Time Software Components. The 5th Annual Workshop on Software Reuse.
  • Rossak, W., Stoyenko, A., Welch, L. (1992). The Component Manager: Supporting Interactive and Automated Retrieval of Real-Time Software Components. The Complex Systems Engineering Synthesis and Assessment Technology Workshop; 591-608.
  • Welch, L. (1992). An Integrated System for Real-Time Software. The International Conference on Systems Integration, IEEE Computer Society Press.
  • Stoyenko, A., Welch, L., Marlowe, T. (1992). Schedulability Analysis and Timing Tools. The 9th IEEE Workshop on Real-Time Operating Systems and Software.
  • Welch, L. (1992). Assignment of ADT Modules to Processors. The IEEE International Parallel Processing Symposium; 72-75.
  • Welch, L., Stoyenko, A. (1991). A Multicomputer for Real-Time Software Constructed From Reusable Components. Workshop on Architectural Aspects of Real-Time Systems.
  • Stoyenko, A., Welch, L. (1991). Towards a System for Teaching and Research in Predictable Real-Time Systems. Work-in-progress - The 12th IEEE Symposium on Real-Time Systems.
  • Welch, L. (1991). Architectural Support for Dynamic Data Distribution and Dynamic Scheduling. The Sixth Distributed Memory Computing Conference, IEEE Computer Society Press; 83-89.
  • Welch, L., Weide, B. (1990). Avoiding Deadlock when Mapping Reusable Software Components onto the ARC Parallel Processor. The International Conference on Parallel and Distributed Computing, and Systems, International Society for Mini and Microcomputers; 224-225.
  • Welch, L., Weide, B. (1990). Mapping Reusable Software Components onto the ARC Parallel Processor. The Third Symposium on the Frontiers of Massively Parallel Computation, IEEE Computer Society Press; 499-502.
  • Welch, L., Weide, B. (1990). Architectural Support for Efficient Execution of Reusable Software Components. The Fifth Distributed Memory Computing Conference, IEEE Computer Society Press; 1082-1087.

Online Article (3)

  • Loof, G., Szabo, D., Welch, L., Hadjantonakis, A., Pombo, A. (2022). 3D genome topologies distinguish pluripotent epiblast and primitive endoderm cells in the mouse blastocyst. BioRxiv (the pre-print server for biology); .
  • Welch, L. (2020). Multiplex-GAM: genome-wide identification of chromatin contacts yields insights not captured by Hi-C. bioRxiv; .
  • Welch, L. (2020). Single-cell analysis of the 3D topologies of genomic loci using genome architecture mapping. bioRxiv; .

Other (3)

  • Li, Y., Jaiswal, S., Kaur, R., Alsaadi, D., Liang, X., Drews, F., DeLoia, J., Krivak, T., Petrykowska, H., Gotea, V., others, . (2021). Differential gene expression identifies a transcriptional regulatory network involving ESR1and PITX1 in invasive epithelial ovarian cancer. American Association for Cancer Research.
  • Kilpatrick, A., Anjum, A., Welch, L. (2020). Ten simple rules for designing learning experiences that involve enhancing computational biology Wikipedia articles.. 5. PLoS computational biology; 16: e1007868.
  • Welch, L. (2019). Prediction pipeline for discovery of regulatory motifs associated with Brugia malayi molting. Cold Spring Harbor Laboratory.

Regular Column in Journal or Newspaper (2)

  • Frenkel-Morgenstern, M. (2018). Art in Science Competition invites artworks to the annual exhibition on ISMB 2018 in Chicago. 5. PLoS Comput Biol; 14.
  • Welch, L. (2018). Art in Science Competition invites artworks to the annual exhibition on ISMB 2018 in Chicago. F1000Res; ISCB Comm J-337.