Steffen Heber

Wimberley, C. E., & Heber, S. (2020, February 1). PeakPass: Automating ChIP-Seq Blacklist Creation. JOURNAL OF COMPUTATIONAL BIOLOGY, Vol. 27, pp. 259–268. https://doi.org/10.1089/cmb.2019.0295

Wimberley, C. E., & Heber, S. (2019). PeakPass: Automating ChIP-Seq Blacklist Creation. BIOINFORMATICS RESEARCH AND APPLICATIONS, ISBRA 2019, Vol. 11490, pp. 232–243. https://doi.org/10.1007/978-3-030-20242-2_20

Perkins, P., Mazzoni-Putman, S., Stepanova, A., Alonso, J., & Heber, S. (2019, June 6). RiboStreamR: a web application for quality control, analysis, and visualization of Ribo-seq data. BMC GENOMICS, Vol. 20. https://doi.org/10.1186/s12864-019-5700-7

Tokarz, D. A., Heffelfinger, A. K., Jima, D. D., Gerlach, J., Shah, R. N., Rodriguez-Nunez, I., … Yoder, J. A. (2017). Disruption of Trim9 function abrogates macrophage motility in vivo. Journal of Leukocyte Biology, 102(6), 1371–1380. https://doi.org/10.1189/jlb.1a0816-371r

Perkins, P., & Heber, S. (2017). riboStreamR: A web application for quality control, analysis, and visualization of Ribo-seq data. International conference on computational advances in bio and medical. https://doi.org/10.1109/iccabs.2017.8114317

Hu, Q. W., Merchante, C., Stepanova, A. N., Alonso, J. M., & Heber, S. (2016). Genome-wide search for translated upstream open reading frames in Arabidopsis thaliana. IEEE Transactions on Nanobioscience, 15(2), 150–159.

Villarino, G. H., Hu, Q., Manrique, S., Flores-Vergara, M., Sehra, B., Robles, L., … Franks, R. G. (2016). Transcriptomic Signature of the SHATTERPROOF2 Expression Domain Reveals the Meristematic Nature of Arabidopsis Gynoecial Medial Domain. PLANT PHYSIOLOGY, 171(1), 42–61. https://doi.org/10.1104/pp.15.01845

Hu, Q., Merchante, C., Stepanova, A. N., Alonso, J. M., & Heber, S. (2015). A Stacking-Based Approach to Identify Translated Upstream Open Reading Frames in Arabidopsis Thaliana. In Bioinformatics Research and Applications (Vol. 9096, pp. 138–149). https://doi.org/10.1007/978-3-319-19048-8_12

Hu, Q. W., Merchante, C., Stepanova, A. N., Alonso, J. M., & Heber, S. (2015). A stacking-based approach to identify translated upstream open reading frames in Arabidopsis thaliana. Bioinformatics research and applications (isbra 2015), 9096, 138–149.

Merchante, C., Brumos, J., Yun, J., Hu, Q., Spencer, K. R., Enriquez, P., … Alonso, J. M. (2015). Gene-Specific Translation Regulation Mediated by the Hormone-Signaling Molecule EIN2. CELL, 163(3), 684–697. https://doi.org/10.1016/j.cell.2015.09.036

Hu, Q. W., Merchante, C., STEPANOVA, A. N. N. A., Alonso, J., & Heber, S. (2015). Mining transcript features related to translation in Arabidopsis using LASSO and random forest. International conference on computational advances in bio and medical. https://doi.org/10.1109/iccabs.2015.7344713

Schreiner, D., Nguyen, T.-M., Russo, G., Heber, S., Patrignani, A., Ahrne, E., & Scheiffele, P. (2014). Targeted Combinatorial Alternative Splicing Generates Brain Region-Specific Repertoires of Neurexins. NEURON, 84(2), 386–398. https://doi.org/10.1016/j.neuron.2014.09.011

Howard, B. E., Hu, Q., Babaoglu, A. C., Chandra, M., Borghi, M., Tan, X., … Heber, S. (2013). High-Throughput RNA Sequencing of Pseudomonas-Infected Arabidopsis Reveals Hidden Transcriptome Complexity and Novel Splice Variants. PLOS ONE, 8(10). https://doi.org/10.1371/journal.pone.0074183

Heber, S., Mayr, R., & Stoye, J. (2011). Common Intervals of Multiple Permutations. ALGORITHMICA, 60(2), 175–206. https://doi.org/10.1007/s00453-009-9332-1

Chang, K.-Y., Georgianna, D. R., Heber, S., Payne, G. A., & Muddiman, D. C. (2010). Detection of Alternative Splice Variants at the Proteome Level in Aspergillus flavus. Journal of Proteome Research, 9(3), 1209–1217. https://doi.org/10.1021/pr900602d

Cholewa, J., Mantey, S., Heber, S., & Hollweg, W. (2010). Developmental surface and phonological dysgraphia in German 3rd graders. Reading and Writing, 23(1), 97–127. https://doi.org/10.1007/S11145-008-9153-7

Shi, R., Sun, Y.-H., Li, Q., Heber, S., Sederoff, R., & Chiang, V. L. (2010). [Review of Towards a Systems Approach for Lignin Biosynthesis in Populus trichocarpa: Transcript Abundance and Specificity of the Monolignol Biosynthetic Genes]. PLANT AND CELL PHYSIOLOGY, 51(1), 144–163. https://doi.org/10.1093/pcp/pcp175

Howard, B. E., & Heber, S. (2010). Towards reliable isoform quantification using RNA-SEQ data. BMC BIOINFORMATICS, Vol. 11. https://doi.org/10.1186/1471-2105-11-s3-s6

Zhao, S., Kim, J., & Heber, S. (2009). Analysis of Cis-Regulatory Motifs in Cassette Exons by Incorporating Exon Skipping Rates. In Bioinformatics Research and Applications (pp. 272–283). https://doi.org/10.1007/978-3-642-01551-9_27

Kim, J., Zhao, S., Howard, B. E., & Heber, S. (2009). Mining of cis-Regulatory Motifs Associated with Tissue-Specific Alternative Splicing. In Bioinformatics Research and Applications (pp. 260–271). https://doi.org/10.1007/978-3-642-01551-9_26

Howard, B. E., Sick, B., & Heber, S. (2009). Practical Quality Assessment of Microarray Data by Simulation of Differential Gene Expression. In Bioinformatics Research and Applications (pp. 18–27). https://doi.org/10.1007/978-3-642-01551-9_3

Wheeler, B. M., Heimberg, A. M., Moy, V. N., Sperling, E. A., Holstein, T. W., Heber, S., & Peterson, K. J. (2009). The deep evolution of metazoan microRNAs. EVOLUTION & DEVELOPMENT, 11(1), 50–68. https://doi.org/10.1111/j.1525-142X.2008.00302.x

Howard, B. E., Sick, B., & Heber, S. (2009). Unsupervised assessment of microarray data quality using a Gaussian mixture model. BMC BIOINFORMATICS, 10. https://doi.org/10.1186/1471-2105-10-191

Zhi, D., Keich, U., Pevzner, P., Heber, S., & Tang, H. (2007). Correcting base-assignment errors in repeat regions of shotgun assembly. IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, 4(1), 54–64. https://doi.org/10.1109/TCBB.2007.1005

Li, L., Andersen, M. E., Heber, S., & Zhang, Q. (2007). Non-monotonic dose-response relationship in steroid hormone receptor-mediated gene expression. JOURNAL OF MOLECULAR ENDOCRINOLOGY, 38(5-6), 569–585. https://doi.org/10.1677/JME-07-0003

Frahm, J. L., Howard, B. E., Heber, S., & 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. JOURNAL OF MASS SPECTROMETRY, 41(3), 281–288. https://doi.org/10.1002/jms.1024

Heber, S., & Savage, C. D. (2005). Common intervals of trees. INFORMATION PROCESSING LETTERS, 93(2), 69–74. https://doi.org/10.1016/j.ipl.2004.09.016

Psarros, M., Heber, S., Sick, M., Thoppae, G., Harshman, K., & Sick, B. (2005). RACE: Remote Analysis Computation for gene Expression data. NUCLEIC ACIDS RESEARCH, 33, W638–W643. https://doi.org/10.1093/nar/gki490

Leipzig, J., Pevzner, P., & Heber, S. (2004). The  alternative splicing gallery (ASG): bridging the gap between genome and transcriptome. Nucleic Acids Research, 32(13), 3977–3983. https://doi.org/10.1039/nar/gkh731

Heber, S., & Stoye, J. (2001). Finding All Common Intervals of k Permutations. In Combinatorial Pattern Matching (pp. 207–218). https://doi.org/10.1007/3-540-48194-x_19