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Genetics and Biochemistry Profiles


Alex Feltus

Professor
Genetics and Biochemistry Department

Office: 302C Biosystems Research Complex, C
Phone: 864-656-3231
Email: ffeltus@clemson.edu
Personal Website: https://www.linkedin.com/pub/alex-feltus/3a/7/86a

 

 Educational Background

Ph.D. Cell Biology
Vanderbilt University 2000

B.Sc. Biochemistry
Auburn University 1992

 Courses Taught

Bioinformatics
Computational Genomics
Biomedical Informatics
Next-Generation Sequence Analysis
Special Topics in Advanced Biochemistry and Genetics (Network and Systems Genetics)
Essential Elements of Biochemistry
Issues in Research
Senior Seminar
Perl for Bioinformatics

 Profile

Dr. F. Alex Feltus received a B.Sc. in Biochemistry from Auburn University in 1992, served two years in the Peace Corps, and then completed advanced training in biomedical sciences at Vanderbilt and Emory. Since 2002, he has performed research in bioinformatics, high-performance computing, cyberinfrastructure, network biology, genome assembly, systems genetics, paleogenomics, and bioenergy feedstock genetics. Currently, Feltus is an Professor in Clemson University's Dept. of Genetics & Biochemistry, CEO of Allele Systems LLC, Core Faculty in the CU-MUSC Biomedical Data Science and Informatics (BDSI) program, member of the Center for Human Genetics, and serves on the Internet2 Board of Trustees as well as various "Advance Research Computing" engagement workgroups. Feltus has published numerous scientific articles in peer-reviewed journals, teaches undergrad and PhD students in bioinformatics, biochemistry, and genetics. At present, he is funded by multiple NSF grants and is engaged in tethering together extremely smart people from diverse technical backgrounds in an effort to propel genomics research from the Excel-scale towards the Exascale.

 Research Interests

Our group uses software engineering and computational biology techniques to make useful molecular discoveries in human and plant biological systems; We also engineer elastic advanced compute systems and technologies to run robust genomics workflows to enable small labs to perform innovative petascale computational biology. The lab also actively engaged in traditional PhD training and the development of a scalable asynchronous training platform for data-intensive computing including but not limited to computational biology.

My lifetime research goal is to reveal the genomic mechanisms underlying phenotype expression. A core aspect of this approach to identify biomarkers that are able to group interesting biological states (e.g. normal kidney verses renal tumor somatic mutation and/or transcriptome profiles). Given that most traits are under control by complex cellular control systems, we always seek to identify sets of functionally interacting genes (biomarker systems) that discriminate between biological states. My group focuses on the transcriptome layer (RNA) of gene expression but we are always seeking methods to integrate data from other genome information orbitals.
A staple data construct of our lab is the gene co-expression network (GCN) where an edge represents a statistically significant RNA expression correlation between two gene products (network nodes). We are active developers of a GCN discovery software application called KINC that is able to identify condition-specific edges from mixed input gene expression matrices (GEMs) (Ficklin et al. [2017]). KINC GCNs are made from GEMs in a bottom up approach where all gene pairs are tested for correlation. This approach is computationally intensive and is not be scalable to millions of samples. Further, traditional GCNs do not detect non-linear relationships missed by correlation tests and do not place genetic relationships in a gene expression intensity context. In response, we developed EdgeScaping (Husain and Feltus [2019]), which constructs and analyzes the pairwise gene intensity network in a holistic, top down approach where no edges are filtered. EdgeScaping uses a novel technique to convert traditional pairwise gene expression data into an image based format and allows for exploring non-linear relationships between genes by leveraging deep learning image analysis algorithms. We have applied EdgeScaping to a human tumor expression profiles candidate biomarker systems that exhibit conventional and non-conventional interdependent non-linear behavior associated with brain specific tumor sub-types. Edgescaping is open source and available at [https://github.com/bhusain/EdgeScaping].

We have been mining RNA expression profiles for biomarker systems from many NIH projects including GTEx and TCGA. We are also leveraging open and protected PsychENCODE (Akbarian et al. [2015]) and SPARK (Feliciano et al. [2018]) datasets to better understand normal and aberrant brain expression patterns. Once we detect biomarker systems using the techniques described above, we try to understand the gene regulatory networks underlying those systems. We are focusing on detection and understanding biomarker systems for three specific biomedical phenotypes: intellectual disability (e.g. autism spectrum disorder -- ASD), brain cancer, and renal cancer.

Genomics databases are swelling and larger compute systems are needed by my group and thousands of individual life science investigators. Soon, DNA sequencers will replace qPCR machines in research labs and everyone will need terascale/petascale compute systems. Towards this disruptive technological event on par with the roll out of molecular biology into labs in the 1980s, my group is actively engaged in several funded cyberinfrastructure projects: “CC*Data: National Cyberinfrastructure for Scientific Data Analysis at Scale (SciDAS).” NSF[1659300] (Feltus PI); “RCN: Advancing Research and Education Through a National Network of Campus Research Computing Infrastructures - The CaRC Consortium” NSF[1620695] (Feltus PI – Bottum Former PI); “Exposing the Potential of Information Centric Networks for the Life Sciences” Cisco Research (Feltus PI); “CC* NPEO: Toward the National Research Platform.” NSF[826967](Smarr PI, Feltus End User); “DIBBs: EI: SLATE and the Mobility of Capability” NSF[1724821] (Gardner PI, Feltus End User). Along with many others, I am linking these partnerships to help build larger democratized compute systems and scaling the training so people can actually use them. In addition to the workflow engineering outlined above, we are focusing efforts in these cutting edge three cyberinfrastructure areas: scaling out usage of Kubernetes based compute systems and moving genomics data from traditional data repositories into information centric network systems.

 Extension and Outreach

Dr. F. Alex Feltus is developing systems genetics software for anyone including plant breeders.

 Publications

1. Raúl Herranz, Joshua P Vandenbrink, Alicia Villacampa, Aranzazu Manzano, William Poehlman, Frank Alex Feltus, John Z Kiss, Francisco Javier Medina. "RNAseq analysis of Arabidopsis thaliana gradual response to fractional gravity under positive blue-light stimulation during spaceflight." Frontiers in Plant Science (in press)
2. Benjamin T. Shealy, Josh J.R. Burns, Melissa C. Smith, F. Alex Feltus, and Stephen P. Ficklin. "GPU Implementation of Pairwise Gaussian Mixture Models for Multi-Modal Gene Co-Expression Networks” IEEE Access. (in press), 2019.
3. (Conference Proceedings) Colin Targonski, Benjamin T. Shealy, Melissa C. Smith, F. Alex Feltus. “Cellular State Transformations Using Generative Adversarial Networks” NeurIPS ML4H 2019. (in press), 2019.
4. William Poehlman, Elise Schnabel, Suchitra Chavan, Julia Alice Frugoli, Frank Alex Feltus*. “Identifying Temporally Regulated Root Nodulation Biomarkers Using Time Series Gene Co-expression Network Analysis”. Frontiers in Plant Science (in press), 2019.
5. (Conference Proceedings) Coleman McKnight, Alexandra L. Poulos, M. Reed Bender, F. Alex Feltus, Jon C. Calhoun.” Exploring Lossy Compression of Gene Expression Matrices.” The 5th International Workshop on Data Analysis and Reduction for Big Scientific Data (DRBSD-5) at SC19.(SC19) (in press), 2019.
6. Joshua P. Vandenbrink, Raul Herranz, William Poehlman, F. Alex Feltus, Alicia Villacampa, Malgorzata Ciska, F. Javier Medina, and John Z. Kiss*. "RNAseq analyses of Arabidopsis seedlings after exposure to blue-light phototropic stimuli in microgravity." American Journal of Botany (in press), 2019.
7. Spoor S, Cheng CH, Sanderson LA, Condon B, Almsaeed A, Chen M, Bretaudeau A, Rasche H, Jung S, Main D, Bett K, Staton M, Wegrzyn JL, Feltus FA, Ficklin SP. "Tripal v3: an ontology-based toolkit for construction of FAIR biological community databases." Database (Oxford). pii: baz077. doi: 10.1093/database/baz077, 2019.
8. C Targonski, BT Shealy, MC Smith, FA Feltus* “Cellular State Transformations using Generative Adversarial Networks.” arXiv preprint arXiv:1907.00118, 2019.
9. Benafsh Husain and F. Alex Feltus* “EdgeScaping: Mapping the spatial distribution of gene edge expression levels.” PLOS ONE 14 (8), e0220279. https://doi.org/10.1371/journal.pone.0220279 , 2019.
10. Colin A. Targonski, Courtney A. Shearer, Ben T. Shealy, Melissa C. Smith, and F. Alex Feltus*. “Uncovering biomarker genes with enriched classification potential from Hallmark gene sets.” Scientific Reports. Scientific reports 9 (1), 9747, 2019.
11. (Conference Proceedings) Susmit Shannigrahi, Chengyu Fan, Christos Papadopoulos, and Alex Feltus. "NDN-SCI for Managing Large Scale Genomics Data." ICN ’18. pp 204-205. https://doi.org/10.1145/3267955.3269022, 2018.
12. Nicholas Mills, Ethan M. Bensman, William L. Poehlman, Walter B. Ligon III, and F. Alex Feltus*. “Moving Just Enough Deep Sequencing Data to Get the Job Done.” Bioinformatics and Biology Insights. https://doi.org/10.1177/1177932219856359, 2019.
13. (Conference Proceedings) Mats Rynge, Karan Vahi, Anirban Mandal, Omkar Bhide, Randy Heiland, Von Welch, Raquel Hill, Ilya Baldin, Ewa Deelman, William L. Poehlman and F. Alex Feltus. “Integrity Protection for Scientific Workflow Data: Motivation and Initial Experiences.” PEARC2019. v17. https://doi.org/10.1145/3332186.3332222, 2019.
14. M. A. Greene, J. L. Britt, R. Reigers Powell, F. A. Feltus, W. C. Bridges Jr., T. Bruce, J. L. Klot, M. F. Miller Jr., and S. K. Duckett. “Ergot Alkaloid Exposure During Gestation Alters: 3. Fetal Growth, Muscle Fiber Development and miRNA Transcriptome.” Journal of Animal Science. https://doi.org/10.1093/jas/skz15 (2019).
15. Emily L. Casanova, Allison Hickman, Andrew E. Switala, Srini Dandamudi, Joshua Vandenbrink, Julia L. Sharp, F. Alex Feltus, Manuel F. Casanova. “Autism Risk Genes Are Evolutionarily Ancient and Maintain a Unique Feature Landscape that Echoes Their Function.” Autism Research. https://doi.org/10.1002/aur.2112 (2019).
16. William L. Poehlman, James J. Hsieh, F. Alex Feltus*. “Linking Binary Gene Relationships to Drivers of Renal Cell Carcinoma Reveals Convergent Function in Alternate Tumor Progression Paths.” Scientific Reports.9(1):2899. https://doi.org/10.1038/s41598-019-39875-y (2019).
17. Emily L. Casanova, Zachary Gerstner, Julia L. Sharp, Manuel F. Casanova, F. Alex Feltus. “Widespread Genotype-Phenotype Correlations in Intellectual Disability.” Frontiers in Psychiatry. 29;9:535. https://doi.org/10.3389/fpsyt.2018.00535, 2018.
18. Falk, T., Herndon, N., Grau E., Buehler S., Richter P., Zaman S., Baker E.M., Ramnath R., Ficklin S., Staton M., Feltus F.A., Jung S., Main D., Wegrzyn J.L. “Growing and cultivating the forest genomics database, TreeGenes” Database. 1: bay084. https://doi.org/10.1093/database/bay084, 2018.
19. Kimberly E. Roche, Marvin Weinstein, Leland Dunwoodie, William L. Poehlman, and Frank A. Feltus*. "Sorting Five Human Tumor Types Reveals Specific Biomarkers and Background Classification Genes” Scientific Reports,. 8(1):8180. https://doi.org/10.1038/s41598-018-26310-x, 2018.
20. Nicholas Mills, F. Alex Feltus*, Walter B. Ligon III. “Maximizing the Performance of Scientific Data Transfer by Optimizing the Interface Between Parallel File Systems and Advanced Research Networks.” Future Generation Computer Systems. 79: 190-198. https://doi.org/10.1016/j.future.2017.04.030, 2018.
21. Leland J. Dunwoodie, William L. Poehlman, Stephen P. Ficklin, F. Alex Feltus*. “Discovery and Validation of a Glioblastoma Co-expressed Gene Module.” Oncotarget 9(13):10995-11008. doi:10.18632/oncotarget.24228, 2018.
22. (Conference Proceedings) Terrell Russell, Michael Stealey, Jason Coposky, Ben Keller, Claris Castillo, Ray Idaszak, Alex Feltus. “Distributing the iRODS Catalog: A Way Forward.” iRODS UGM 2017 Proceedings. Page 35, 2017.
23. Donald Livingstone III, Conrad Stack, Guiliana Mustiga, Dayana Rodezno, Carmen Suarez, Freddy Amores, F. Alex Feltus, Keithanne Mockaitis, Omar Cornejo, Juan Carlos Motamayor. "A Larger Chocolate Chip - Development of a 15K Theobroma cacao L. SNP Array to create high density linkage maps." Frontiers Plant Science. 8:2008, 2017.
24. (Conference Proceedings) William Poehlman, Mats Rynge, Balamurugan Desinghu, Nicholas Mills, and Frank Feltus*. OSG-KINC: High-Throughput Gene Co-Expression Network Construction Using the Open Science Grid. IEEE BIBM 2017 Proceedings. Pages 1827-1831, 2017.
25. Stephen P. Ficklin, Leland J. Dunwoodie, William L. Poehlman, Christopher Watson, Kimberly Roche, F. Alex Feltus. Discovering Condition-Specific Gene Co-Expression Patterns Using Gaussian Mixture Models: A Cancer Case Study. Scientific Reports 7: 8617. doi: 10.1038/s41598-017-09094-42017, Published online 17 Aug, 2017.
26. Kimberly Roche, F. Alex Feltus, Jang Pyo Park, Marie-May Coissieux, Chenyan Chang, Vera B.S. Chan, Mohamed Bentires-Alj, and Brian W. Booth. Cancer Cell Redirection Biomarker Discovery Using a Mutual Information Approach. PLOS ONE 12(6):e0179265. doi: 10.1371/journal.pone.0179265, 2017.
27. Hannah Schmucker, Jang Pyo Park, Marie-May Coissieux, Kerri Kwist, Mohamed Bentires-Alj, F. Alex Feltus, and Brian W. Booth. RNA expression profiling reveal differentially regulated growth factor and receptor expression in redirected cancer cells. Stem Cells and Development May 1;26(9):646-655. doi: 10.1089/scd.2016.0340, 2017.
28. Nick A. Watts and Frank A. Feltus. Big Data Smart Socket (BDSS): A Tool that Abstracts Data Transfer Habits from End Users. Bioinformatics 33(4):627-628. doi: 10.1093/bioinformatics/btw679, 2017.
29. William L. Poehlman, Mats Rynge, Chris Branton, D. Balamurugan, and Frank A. Feltus. "OSG-GEM: Gene Expression Matrix Construction Using the Open Science Grid." Bioinformatics and Biology Insights 10:133, 2016. TC#6455.
30. Yupeng Wang, Stephen P. Ficklin, Xiyin Wang, Frank A. Feltus, Andrew H. Paterson. Large-scale gene relocations following an ancient genome triplication associated with the diversification of core eudicots. PLOS ONE. 11(5):e0155637. doi: 10.1371/journal.pone.0155637, 2016.
31. Frank A. Feltus, Joe Breen, Juan Deng, Ryan Izard, Christopher A Konger, Walt Ligon, Don Preuss, Kuangching Wang. The Widening Gulf Between Genomics Data Generation and Consumption- A Practical Guide To Big Data Transfer Technology. Bioinformatics and Biology Insights Suppl. 1 9-19, 2015.
32. Clyde Phelix and F. Alex Feltus. Plant Stress Biomarkers from Biosimulations: The Transcriptome-To-Metabolometm (TTMtm) Technology. Effects of drought stress on rice. Plant Biology17 (1), 63-73, 2015.
33. (Book Chapter) Saski CA, Feltus FA, Parida L, Haiminen N. "BAC Sequencing Using Pooled Methods." Methods in Molecular Biology. 1227:55-67. doi: 10.1007/978-1-4939-1652-8_3, 2015.
34. (Technical paper) Feltus FA Big Data Inventory at Clemson University. Presented to the CIO and VPR (October 2015)
35. Feltus FA Systems Genetics: A Paradigm to Improve Discovery of Candidate Genes and Mechanisms Underlying Complex Traits. Plant Science 223, 45-48, 2014.
36. Roger N. Hilten, Joshua P. Vandenbrink, Andrew H. Paterson, F. Alex Feltus, and Keshav C. Das. Linking isoconversional pyrolysis kinetics to compositional characteristics for multiple Sorghum bicolor genotypes. Thermochimica Acta 577, 46-52, 2014. TC#6176.
37. Yannick Pauchet, Christopher A. Saski, Frank A. Feltus, Isabelle Luyten, Hadi Quesneville, and David G. Heckel. Studying the organization of genes encoding plant cell wall degrading enzymes in Chrysomela tremulae provides insights into a leaf beetle genome. Insect Molecular Biology 23(3):286-300, 2014.
38. Nadia Shakoor, Ramesh Nair, Oswald Crasta, Geoffrey Morris, Alex Feltus and Stephen Kresovich A Sorghum bicolor expression atlas reveals dynamic genotype-specific expression profiles for vegetative tissues of grain, sweet and bioenergy sorghums. BMC Plant Biology 14(1):35, 2014.
39. (Technical paper) Dmitriy Beloslyudtsev, Dmitry Bulgakov, Joseph Bernard, Mike Cannon, Edward B. Duffy, Frank A. Feltus*, Corey Ferrier, Frank Gao, Christopher A Konger, Blaine Lee, Yang Li, Kathryn Mace, Dierdre Odom, Brian Parker, Jim Pepin, Don Preuss, Robert Schwartzkopf, Kuangching Wang. Configuring a 100Gbit Internet2 Connection Between Two Institutions: Practical Advice and Prospects. Internet2 Case Study. http://www.internet2.edu/research-solutions/case-studies/accelerating-genomic-research-advanced-networking-collaborations., August 2014.
40. Sanderson LA, Ficklin SP, Cheng CH, Jung S, Bett KE, Feltus FA, Main D Tripal 1.1: a Standards-based Platform for Construction of Online Genetic, Genomic and Biological Databases. Database (Oxford) doi: 10.1093/database/bat075, 2013.
41. Joshua P. Vandenbrink, Ryan E Hammonds, Andrew H. Paterson, KC Das, J Michael Henson, Roger N. Hilten, and F. Alex Feltus. Tissue specific analysis of hydrolysis related traits and pretreatment efficacy in the bioenergy grass Sorghum bicolor. Industrial Crops & Products 50:118-130, 2013. TC#6018.
42. Joshua P. Vandenbrink, Andrew H. Paterson, Lori Goff, Wenqian Kong, Huizhe Jin and F. Alex Feltus. Identification of Bioconversion Quantitative Trait Loci in the Interspecific Bioenergy Grass Cross Sorghum bicolor x Sorghum propinquum. Theoretical and Applied Genetics 126(9):2367-80, 2013. TC#6096.
43. Stephen P. Ficklin and F. Alex Feltus. A Systems-Genetics Approach and Data Mining Tool For the Discovery of Genes Underlying Complex Traits in Oryza Sativa. PloS ONE 8(7): e68551, 2013.
44. F. Alex Feltus, Stephen P. Ficklin, Scott M Gibson, and Melissa C. Smith. Maximizing Capture of Gene Co-expression Relationships Through Pre-Clustering of Input Expression Samples: An Arabidopsis Case Study. BMC Systems Biology 7:44, doi:10.1186/1752-0509-7-44, 2013.
45. Jacob B Spangler and F. Alex Feltus. Conserved Noncoding Sequences are Associated with Rates of mRNA Decay in Arabidopsis. Frontiers in Plant Science. doi:10.3389/fpls.2013.00129, 2013.
46. Juan C Motamayor, Keithanne Mockaitis, Jeremy Schmutz, Niina Haiminen, Donald Livingstone, Omar Cornejo, Seth D Findley, Ping Zheng, Filippo Utro, Stefan Royaert, Christopher Saski, Jerry Jenkins, Ram Podicheti, Meixia Zhao, Brian E Scheffler, Joseph C Stack, Frank A Feltus, Guiliana M Mustiga, Freddy Amores, Wilbert Phillips, Jean Philippe Marelli, Gregory D May, Howard Shapiro, Jianxin Ma, Carlos D Bustamante, Raymond J Schnell, Dorrie Main, Don Gilbert, Laxmi Parida and David N Kuhn. The genome sequence of the most widely cultivated cacao type and its use to identify candidate genes regulating pod color. Genome Biology 14(6):R53 doi:10.1186/gb-2013-14-6-r532013, 2013.
47. Joshua P. Vandenbrink, Andrew H. Paterson, KC Das, Roger N. Hilten, and F. Alex Feltus. Quantitative Models of Hydrolysis Conversion Efficiency and Biomass Crystallinity Index for Plant Breeding. Plant Breeding, 132(3): 252–258, 2013. TC#6060.
48. Scott M. Gibson, Stephen P. Ficklin, Sven Isaacson, Feng Luo, F. Alex Feltus, Melissa C. Smith. Massive-Scale Gene Co-expression Network Construction and Robustness Testing using Random Matrix Theory. PLoS ONE (2), e55871, 2013.
49. (Book Chapter) Milton Yutaka Nishiyama-Jr, Fabio Vicente, Paloma Mieko Sato, Savio Siqueira Ferreira, Frank Alex Feltus and Glaucia M Souza. The Saccharinae transcriptome. In Plant Genetics and Genomics: Crops and Models, Vol. 11: Genetics and Genomics of the Saccharinae. Paterson, Andrew H. (Ed). Springer, New York. ISBN: 978-1-4419-5946-1, 2013.
50. (Book Chapter) A Gingle and FA Feltus. Saccharinae bioinformatics resources. in Genomics of the Saccharinae. In Plant Genetics and Genomics: Crops and Models, Vol. 11: Genetics and Genomics of the Saccharinae. Paterson, Andrew H. (Ed). Springer, New York. ISBN: 978-1-4419-5946-1, 2013.
51. F. Alex Feltus and Joshua P. Vandenbrink. Bioenergy Grass Feedstock: Current options and prospects for improvement using emerging genetic, genomic, and systems biology toolkits. Biotechnology for Biofuels Nov 2;5(1):80, 2012. TC#6038.
52. Jacob B. Spangler, Stephen P. Ficklin, Feng Luo, Michael Freeling and F. Alex Feltus. Conserved Non-Coding Regulatory Signatures in Arabidopsis Co-expressed Gene Modules. PLoS ONE 7(9): e45041. doi:10.1371/journal.pone.0045041, 2012.
53. Jianping Wang, Jong-Kuk Na, Qingyi Yu, Andrea Gschwend, Jennifer Han, Fanchang Zeng, Rishi Aryal, Robert VanBuren, Jan E. Murray, Wenli Zhang, Rafael Navajas Pérez, F. Alex Feltus, Cornelia Lemke, Eric J. Tong, Cuixia Chen, Ching Man Wai, Ratnesh Singh, Ming-Li Wang, Xiangjia Min, Maqsudul Alam, Deborah Charlesworth, Paul H. Moore, Jiming Jiang, Andrew H. Paterson, Ray Ming. Sequencing papaya X and Yh chromosomes reveals molecular basis of incipient sex chromosome evolution. Proceedings of the National Academy of Sciences USA, Aug 21;109(34):13710-5, 2012.
54. Jong-Kuk Na, Jianping Wang, Jan E Murray, Andrea R Gschwend, Wenli Zhang, Qingyi Yu, Rafael N Pérez, F. Alex Feltus, Cuixia Chen, Zdenek Kubat, Paul H Moore, Jiming Jiang, Andrew H Paterson and Ray Ming. Construction of physical maps for the sex-specific regions of papaya sex chromosomes. BMC Genomics, 13:176, 2012.
55. Spangler, Jacob; Subramaniam, Sabarinath; Freeling, Michael, and F. Alex Feltus. Evidence of Function for Conserved Non-coding Sequence in Arabidopsis thaliana. New Phytologist, 193(1):241-252, 2012.
56. Yupeng Wang, Xiyin Wang, Haibao Tang, Xu Tan, Stephen Ficklin, F. Alex Feltus and Andrew H Paterson. Modes of gene duplication contribute differently to genetic novelty and redundancy, but show parallels across divergent angiosperms. PLoS ONE, 6(12): e28150, 2011.
57. David N. Kuhn, Don Livingstone III, Dorrie Main, Ping Zheng, Chris Saski, F. Alex Feltus, Keithanne Mockaitis, Andrew D. Farmer, Gregory D. May, Raymond J. Schnell, and Juan C. Motamayor. Identification and mapping of conserved ortholog set (COS) II sequences of cacao and their conversion to SNP markers for marker-assisted selection in Theobroma cacao and comparative genomics studies. Tree Genetics & Genomes, 8(1):97-111, 2012.
58. Joshua P. Vandenbrink, Roger N. Hilten, K.C. Das, Andrew H. Paterson, and F. Alex Feltus. Analysis of Crystallinity Index and Hydrolysis Rates in the Bioenergy Crop Sorghum bicolor. BioEnergy Research, 5(2):387-397, 2012. TC#5906.
59. Christopher A. Saski, Frank A Feltus, Margaret E Staton, Barbara P Blackmon, Stephen P Ficklin, David N Kuhn, Ray Schnell, Howard Shapiro, Juan Carlos Motamayor. A genetically anchored physical framework for Theobroma cacao (cv. Matina 1-6). BMC Genomics. 12:413, 2011.
60. Frank A. Feltus, Chris A. Saski, Keithanne Mockaitis, Niina Haiminen, Laxmi Parida, Zachary Smith, James Ford, Margaret E. Staton, Stephen P. Ficklin, Barbara P. Blackmon, Ray J. Schnell, David N. Kuhn, Juan-Carlos Motamayor. Sequencing of a QTL-rich Region of the Theobroma cacao Genome using Pooled BACs and the Identification of Trait Specific Candidate Genes. BMC Genomics, 12(1):379, 2011.
61. Christopher A. Saski, Zhigang Li, Frank A. Feltus, Hong Luo. New genomic resources for switchgrass: a bacterial artificial chromosome library (BAC) and comparative analysis of a homoeologous genomic region harboring bioenergy traits. BMC Genomics, 12:369, 2011.
62. Xumeng Li, F. Alex Feltus, Xiaoqian Sun, Zijun Wang and Feng Luo. Identifying Differentially Expressed Genes in Cancer Patients using A Non-parameter Ising Model. Proteomics, 11(19):3845-52, 2011.
63. Stephen P. Ficklin and F. Alex Feltus. Gene Co-Expression Network Alignment and Conservation of Gene Modules Between Two Grass Species: Maize (Zea mays) and Rice (Oryza sativa). Plant Physiology 156(3):1244-56, 2011.
64. Niina Haiminen, F. Alex Feltus, Laxmi Parida. Assessing Pooled BAC and Whole Genome Shotgun Strategies for Assembly of Complex Genomes. BMC Genomics 12:194, 2011.
65. Stephen P. Ficklin, Feng Luo, and F. Alex Feltus. The Association of Multiple Interacting Genes with Specific Phenotypes in Rice Using Gene Coexpression Networks. Plant Physiology 154(1):13-24, 2010.
66. Mahendar Thudi, Senapathi Senthilvel, Andrew Bottley, C. Tom Hash, Arjula R. Reddy, Alex Feltus, Andrew H. Paterson, David A. Hoisington, Rajeev K. Varshney. A comparative assessment of the utility of PCR-based marker systems in pearl millet. Euphytica 174(2):253-260, 2010.
67. Joshua P. Vandenbrink, Maria P. Delgado, Jim R. Frederick, and F. Alex Feltus. A Sorghum Diversity Panel Biofuel Feedstock Screen for Genotypes with High Hydrolysis Yield Potential. Industrial Crops and Products 31(3):444-448, 2010. TC#5759.
68. Xumeng Li, F. Alex Feltus, Xiaoqian Sun, Zijun Wang, and Feng Luo. A Non-parameter Ising Model for Network-based Identification of Differentially Expressed Genes in Recurrent Breast Cancer Patients. IEEE International Conference on Bioinformatics and Biomedicine (18-21):214-217, 2010.
69. Junkang Rong, Frank A. Feltus, Limei Liu, Lifeng Lin, Andrew H. Paterson. Gene copy number evolution during tetraploid cotton radiation. Heredity 105:463–472, 2010.
70. (Conference Proceedings) Bo Li, James Z. Wang, F. Alex Feltus, Feng Luo. Effectively integrating information content and structural relationship to improve the GO-based similarity measure between proteins. BIOCOMP'10 Conference Proceedings (July 12, 2010).
71. Shin Sato, F. Alex Feltus, Prashanti Iyer, and Ming Tien. The first genome-level transcriptome of the wood-degrading fungus Phanerochaete chrysosporium grown on red oak. Current Genetics. 55(3):273-86, 2009. TC#5685.
72. J. A. Buggs, N. Doust, R., J. A. Tate, J. Koh, K. Soltis, F. A. Feltus, A. H. Paterson, P. S. Soltis, D. E. Soltis. Gene Loss and Silencing in Tragopogon miscellus (Asteraceae): Comparison of Natural and Synthetic Allotetraploids. Heredity. (1) 1-9, 2009.
73. Andrew H. Paterson, John E. Bowers, Remy Bruggmann, Inna Dubchak, Jane Grimwood, Heidrun Gundlach, Georg Haberer, Uffe Hellsten, Therese Mitros, Alexander Poliakov, Jeremy Schmutz, Manuel Spannagl, Haibao Tang, Xiyin Wang, Thomas Wicker, Arvind K. Bharti, Jarrod Chapman, F. Alex Feltus, Udo Gowik, Eric Lyons, Christopher Maher, Mihaela Martis, Apurva Narechania, Bryan Penning, Yu Wang, Lifang Zhang, Nicholas C. Carpita, Michael Freeling, Alan R. Gingle, C. Thomas Hash, Beat Keller, Patricia Klein, Stephen Kresovich, Maureen C. McCann, Ray Ming, Daniel G. Peterson, Mehboob ur-Rahman, Doreen Ware, Peter Westhoff, Klaus F.X. Mayer, Joachim Messing, Daniel S. Rokhsar. The Sorghum bicolor genome and the diversification of grasses. Nature. 457(7229):551-6, 2009.
74. Ksenija Gasic, Delkin Gonzalez, Jyothi Thimmapuram, Mickael Malnoy, George Gong, Yuepeng Han, Lila O Vodkin, Lei Liu, Herb S Aldwinckle, Natalie J Carroll, Kathryn S Orvis, Peter Goldsbrough, Sandra Clifton, Deana Pape, Lucinda Fulton, John Martin, Brenda Theising, Michael E. Wisniewski, Gennaro Fazio, F. Alex Feltus, Schuyler S Korban. Analysis and Functional Annotation of a Large Expressed Sequence Tag Collection of Apple. The Plant Genome. (2)23–38, 2009.
75. Andrew H. Paterson, John E. Bowers, Frank A. Feltus, Haibao Tang, Xiyin Wang. Comparative genomics of the grasses: Promising a bountiful harvest. Plant Physiology 149(1):125-31, Jan. 2009.
76. Chansoo Kim, Cheol Sang Kim, Terry L. Kamps, Jon R. Robertson, Frank A. Feltus, Andrew H. Paterson. Transcriptome analysis of leaf tissue from Bermuda grass (Cynodon dactylon L.) by a normalized cDNA library. Functional Plant Biology 35(7):585-596, 2008.
77. Ray Ming, Shaobin Hou, Yun Feng, Qingyi Yu, Alexandre Dionne-Laporte, J.H. Saw, Pavel Senin, Wei Wang, Benjamin V. Ly, Kanako L. T. Lewis, Steven L. Salzberg, Lu Feng, Meghan R. Jones, Rachel L. Skelton, Jan E. Murray, Cuixia Chen, Wubin Qian, Junguo Shen, Peng Du, Moriah Eustice, Eric Tong, Haibao Tang, Eric Lyons, Robert E. Paull, Todd P. Michael, Kerr Wall, Danny Rice, Henrik Albert, Ming-Li Wang, Yun J. Zhu, Michael Schatz, Niranjan Nagarajan, Ricelle Agbayani, Peizhu Guan, Andrea Blas, Ching Man Wai, Christine M. Ackerman, Yan Ren, Chao Liu, Jianmei Wang, Jianping Wang, Jong-Kuk Na, Eugene V Shakirov, Brian Haas, Jyothi Thimmapuram, David Nelson, Xiyin Wang, John E. Bowers, Andrea R. Gschwend, Arthur L. Delcher, Ratnesh Singh, Jon Y. Suzuki, Savarni Tripathi, Kabi Neupane, Hairong Wei, Beth Irikura, Maya Paidi, Ning Jiang, Wenli Zhang, Gernot Presting, Aaron Windsor, Rafael Navajas Pérez, Manuel J. Torres, F. Alex Feltus, Brad Porter, Yingjun Li, A. Max Burroughs, Ming-Cheng Luo, Lei Liu, David A. Christopher, Stephen M. Mount, Paul H. Moore, Tak Sugimura, Jiming Jiang, Mary A. Schuler, V. Friedman, Thomas Mitchell-Olds, Dorothy Shippen, Claude W. dePamphilis, J.D. Palmer, Michael Freeling, Andrew H. Paterson, Dennis Gonsalves, Lei Wang, Maqsudul Alam. Genome of the transgenic tropical fruit tree papaya (Carica papaya L.). Nature 452(7190):991-6, Apr. 2008.
78. Qingyi Yu, Shaobin Hou, F. Alex Feltus, Meghan R. Jones, Jan E. Murray, Olivia Veatch, Cornelia Lemke, Jimmy H. Saw, Richard C. Moore, Jyothi Thimmapuram, Lei Liu, Paul H. Moore, Maqsudul Alam, Jiming Jiang, Andrew H. Paterson, Ray Ming. Low X/Y divergence in four pairs of papaya sex linked genes. The Plant Journal, 53(1):124-32, Jan. 2008.
79. (Book Chapter) Paterson AH, JE Bowers, FA Feltus. Genomics of Sorghum, a Semi-Arid Cereal and Emerging Model for Tropical Grass Genomics. in Moore, P. H. and R. Ming, Genomics of Tropical Crops. Springer, New York. pages 469-482. ISBN: 978-0-387-71219-2, 2008.
80. Wang X, Tang H, Bowers JE, Feltus FA, Paterson AH. Extensive concerted evolution of rice paralogs and the road to regaining independence. Genetics. 177(3):1753-63, Nov. 2007.
81. Bacon CD, Feltus FA, Paterson AH, and Bailey CD. Novel nuclear intron-spanning primers for Arecaceae evolutionary biology. Molecular Ecology Resources 8, 211–214, 2008.
82. Mei HW, Feng FJ, Lu BR, Wen WW, Paterson AH, Cai XX, Chen L, Feltus FA, Xu XY, Wili JH, Yu XQ, Chen HW, Li Y, and Luo LJ. Experimental validation of inter-subspecific genetic. diversity in rice represented by the differences between the DNA sequences of 'Nipponbare' and '93-11'. Chinese Science Bulletin 52(10):1327-1337, 2007.
83. Junkang Rong, F. Alex Feltus, Vijay N. Waghmare, Gary J. Pierce, Peng W. Chee,Xavier Draye, Yehoshua Saranga, Robert J. Wright, Thea A. Wilkins, O. Lloyd May, C. Wayne Smith, John R. Gannaway, Jonathan F. Wendel, Andrew H. Paterson. Meta-analysis of polyploid cotton QTLs shows unequal contributions of subgenomes to a complex network of genes and gene clusters implicated in lint fiber development. Genetics 176(4):2577-88, Aug. 2007.
84. Qingyi Yu, Shaobin Hou, Roman Hobza, F. Alex Feltus, Xiue Wang, Weiwei Jin, Rachel L. Skelton, Andrea Blas, Cornelia Lemke, Jimmy H. Saw, Paul H. Moore, Maqsudul Alam, Jiming Jiang, Andrew H. Paterson, Boris Vyskot, Ray Ming. Chromosomal location and gene paucity of the male specific region on papaya Y chromosome. Molecular Genetics and Genomics 278(2):177-85, 2007.
85. (Co-First Authors: Lohithaswa HC, Feltus FA), Singh, HP, Bacon CD, Bailey CD, and Paterson AH. Leveraging the Rice Genome Sequence for Monocot Comparative and Translational Genomics. Theoretical and Applied Genetics 115(2):237-43, 2007.
86. Paterson AH, Chapman BA, Kissinger JC, Bowers JE, Feltus FA, and JC Estill. Many gene/domain families have convergent fates following independent whole-genome duplication events in Arabidopsis, Oryza, Saccharomyces, and Tetraodon. Trends in Genetics 22(11):597-602, 2006.
87. Feltus FA, Singh HP, Lohithaswa HC, Schulze SR, Silva TD, and AH Paterson. A Comparative Genomics Strategy for Targeted Discovery of SNPs and Conserved Non-coding Sequences in Orphan Crops. Plant Physiology 140(4):1183-91, 2006.
88. Feltus FA, Hart GE, Schertz KF, Casa AM, Kresovich S, Abraham S, Klein PE, Brown PJ and AH Paterson Alignment of Genetic Maps and QTLs Between Inter-and Intra-specific Sorghum Populations. Theoretical and Applied Genetics 112(7):1295-305, 2006.
89. Feltus FA, Lee EK, Costello JF, Plass C, and Vertino PM DNA Motifs Associated with CpG Island Methylation. Genomics 87(5):572-9, 2006.
90. Chapman B, Bowers J, Feltus FA, Paterson AH. Buffering of crucial functions by paleologous duplicated genes may contribute cyclicality to angiosperm genome duplication. Proceedings of the National Academy of Sciences USA 103(8):2730-2735, 2006.
91. Gorantla M, Babu PR, Lachagari VBR, Feltus FA, Paterson AH, and Reddy AR. Functional Genomics of Drought Stress Response in Rice: Transcript Mapping of Annotated Unigenes of an Indica Rice (Oryza Sativa L. cv. Nagina 22). Current Science 89(3):496-514, 2005
92. Simard J, Ricketts ML, Gingras S, Soucy P, Feltus FA, Melner MH. Molecular biology of the 3?-hydroxysteroid dehydrogenase?5-?4 isomerase gene family. Endocrine Reviews 26(4):525-82, 2005.
93. Wicker T, Robertson JS, Schulze SR, Feltus FA, Magrini V, Morrison JA, Mardis ER, Wilson RK, Peterson DG, Paterson AH, Ivarie R. The Repetitive Landscape of the Chicken Genome. Genome Research 15(1):126-36, 2005.
94. Feltus FA, Wan J, Schulze SR, Estill JC, Paterson AH. An SNP Resource for Rice Genetics and Breeding Based on Subspecies Indica and Japonica Genome Alignments. Genome Research 14:1812-1819, 2004.
95. (Conference Proceedings) HP Singh, FA Feltus, SR Schulze, Silva T, and AH Paterson. Search for molecular markers in cereals: An approach by intron scanning and genome complexity reduction using DOP-PCR. In Resilient crops for water limited environments: proceedings of a Rockefeller Foundation workshop held at Cuernavaca, Mexico, 24-28. May 2004, pages 70-71.
96. Feltus FA, Lee EK, Costello JF, Plass C, Vertino PM. Predicting Aberrant CpG Island Methylation. Proceedings of the National Academy of Sciences USA 100(21):12253-8, 2003.
97. Feltus FA, Kovacs WJ, Nicholson W, Silva CM, Nagdas SK, Ducharme NA, Melner MH. Epidermal Growth Factor Increases Cortisol Production and Type II 3?-Hydroxysteroid Dehydrogenase/?5-?4 Isomerase Expression in Human Adrenocortical Carcinoma Cells: Evidence for a Stat5 Dependent Mechanism. Endocrinology 144(5):1847-53, 2003.
98. Feltus FA, Cote S, Simard J, Gingras S, Kovacs WJ, Nicholson WE, Clark BJ, Melner MH Glucocorticoids enhance activation of the human type II 3?-hydroxysteroid dehydrogenase/?5–?4 isomerase gene. Journal of Steroid Biochemistry and Molecular Biology 82(1):55-63, 2002.
99. Osteen KG, Keller NR, Feltus FA, Melner MH Paracrine Regulation of Matrix Metalloproteinase Expression in the Normal Human Endometrium. Obstetric and Gynecologic Investigation 48(suppl 1): 2-13, 1999.
100. Melner MH and Feltus FA Autoimmune Premature Ovarian Failure: Endocrine Aspects of a T-cell Disease. Endocrinology 140(8): 3401-3403, 1999.
101. Feltus FA, Groner B, Melner MH Stat5-Mediated Regulation of the Human Type II 3beta-Hydroxysteroid Dehydrogenase/?5-?4 Isomerase Gene: Activation by Prolactin. Molecular Endocrinology 13:1084-1093, 1999.
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