Anna Stepanova Department of Plant and Microbial Biology, North Carolina State University, USA
1 protocol

Jose Alonso Department of Plant and Microbial Biology, North Carolina State University, USA
1 protocol

Qiwen Hu Department of Computer Science, North Carolina State University, USA
1 protocol

Catharina Merchante Instituto de Hortofruticultura Subtropical y Mediterranea (IHSM)-UMA-CSIC, Departamento de Biología Molecular y Bioquímica, Universidad de Málaga, Spain
1 protocol

Steffen Heber
  • Department of Computer Science, North Carolina State University, USA
  • 1 Author merit


Ph.D., Mathematics, University of Heidelberg, Heidelberg, Germany, 2001

Current position

Associate Professor, NC State University, Department of Computer Science, NC
Joint appointment with College of Physical and Mathematical Sciences to support the Bioinformatics Research Center at NC State University


  1. Villarino, G. H., Hu, Q., Manrique, S., Flores-Vergara, M., Sehra, B., Robles, L., Brumos, J., Stepanova, A. N., Colombo, L., Sundberg, E., Heber, S. and Franks, R. G. (2016). Transcriptomic Signature of the SHATTERPROOF2 Expression Domain Reveals the Meristematic Nature of Arabidopsis Gynoecial Medial Domain. Plant Physiol 171(1): 42-61.

  2. Hu, Q., Merchante, C., Stepanova, A. N., Alonso, J. M. and Heber, S. (2016). Genome-Wide Search for Translated Upstream Open Reading Frames in Arabidopsis Thaliana. IEEE Trans Nanobioscience 15(2): 148-157.

  3. Merchante, C., Brumos, J., Yun, J., Hu, Q., Spencer, K. R., Enriquez, P., Binder, B. M., Heber, S., Stepanova, A. N. and Alonso, J. M. (2015). Gene-specific translation regulation mediated by the hormone-signaling molecule EIN2. Cell 163(3): 684-697.

  4. Schreiner, D., Nguyen, T. M., Russo, G., Heber, S., Patrignani, A., Ahrne, E. and Scheiffele, P. (2014). Targeted combinatorial alternative splicing generates brain region-specific repertoires of neurexins. Neuron 84(2): 386-398.

  5. Howard, B. E., Hu, Q., Babaoglu, A. C., Chandra, M., Borghi, M., Tan, X., He, L., Winter-Sederoff, H., Gassmann, W., Veronese, P. and Heber, S. (2013). High-throughput RNA sequencing of pseudomonas-infected Arabidopsis reveals hidden transcriptome complexity and novel splice variants. PLoS One 8(10): e74183.

  6. Howard, B. E. and Heber, S. (2010). Towards reliable isoform quantification using RNA-SEQ data. BMC Bioinformatics 11 Suppl 3: S6.

  7. Chang, K. Y., Georgianna, D. R., Heber, S., Payne, G. A. and Muddiman, D. C. (2010). Detection of alternative splice variants at the proteome level in Aspergillus flavus. J Proteome Res 9(3): 1209-1217.

  8. Shi, R., Sun, Y. H., Li, Q., Heber, S., Sederoff, R. and Chiang, V. L. (2010). Towards a systems approach for lignin biosynthesis in Populus trichocarpa: transcript abundance and specificity of the monolignol biosynthetic genes. Plant Cell Physiol 51(1): 144-163.

  9. Heber, S., Mayr, R. and Stoye, J. (2009). Common Intervals of Multiple Permutations. Algorithmica 60(2): 175-206.

  10. Howard, B. E., Sick, B. and Heber, S. (2009). Unsupervised assessment of microarray data quality using a Gaussian mixture model. BMC Bioinformatics 10: 191.

  11. Wang, T., Furey, T. S., Connelly, J. J., Ji, S., Nelson, S., Heber, S., Gregory, S. G. and Hauser, E. R. (2009). A general integrative genomic feature transcription factor binding site prediction method applied to analysis of USF1 binding in cardiovascular disease. Hum Genomics 3(3): 221-235.

  12. Wheeler, B. M., Heimberg, A. M., Moy, V. N., Sperling, E. A., Holstein, T. W., Heber, S. and Peterson, K. J. (2009). The deep evolution of metazoan microRNAs. Evol Dev 11(1): 50-68.

  13. Li, L., Andersen, M. E., Heber, S. and Zhang, Q. (2007). Non-monotonic dose-response relationship in steroid hormone receptor-mediated gene expression. J Mol Endocrinol 38(5): 569-585.

  14. Zhi, D., Keich, U., Pevzner, P., Heber, S. and Tang, H. (2007). Correcting base-assignment errors in repeat regions of shotgun assembly. IEEE/ACM Trans Comput Biol Bioinform 4(1): 54-64.

  15. Heber, S. and Sick, B. (2006). Quality assessment of Affymetrix GeneChip data. OMICS 10(3): 358-368.

  16. Saha, S. and Heber, S. (2006). In silico prediction of yeast deletion phenotypes. Genet Mol Res 5(1): 224-232.

  17. Frahm, J. L., Howard, B. E., Heber, S. and Muddiman, D. C. (2006). Accessible proteomics space and its implications for peak capacity for zero-, one- and two-dimensional separations coupled with FT-ICR and TOF mass spectrometry. J Mass Spectrom 41(3): 281-288.

  18. Psarros, M., Heber, S., Sick, M., Thoppae, G., Harshman, K. and Sick, B. (2005). RACE: Remote Analysis Computation for gene Expression data. Nucleic Acids Res 33(Web Server issue): W638-643.

  19. Heber, S. and Savage, C. (2005). Common Intervals of Trees. Information Processing Letters 93(2), 69-74.

1 Protocol published
A Ribosome Footprinting Protocol for Plants
Authors:  Catharina Merchante, Qiwen Hu, Steffen Heber, Jose Alonso and Anna N. Stepanova, date: 11/05/2016, view: 1927, Q&A: 0
Ribosome footprinting, or Ribo-seq, has revolutionized the studies of translation. It was originally developed for yeast and mammalian cells in culture (Ingolia et al., 2009). Herein, we describe a plant-optimized hands-on ribosome ...