@article{wimberley_heber_2020, title={PeakPass: Automating ChIP-Seq Blacklist Creation}, volume={27}, ISBN={1557-8666}, DOI={10.1089/cmb.2019.0295}, number={2}, journal={JOURNAL OF COMPUTATIONAL BIOLOGY}, author={Wimberley, Charles E. and Heber, Steffen}, year={2020}, pages={259–268} }
 @article{wimberley_heber_2019, series={Lecture Notes in Bioinformatics}, title={PeakPass: Automating ChIP-Seq Blacklist Creation}, volume={11490}, ISBN={1611-3349}, DOI={10.1007/978-3-030-20242-2_20}, journal={BIOINFORMATICS RESEARCH AND APPLICATIONS, ISBRA 2019}, author={Wimberley, Charles E. and Heber, Steffen}, year={2019}, pages={232–243}, collection={Lecture Notes in Bioinformatics} }
 @article{perkins_mazzoni-putman_stepanova_alonso_heber_2019, title={RiboStreamR: a web application for quality control, analysis, and visualization of Ribo-seq data}, volume={20}, ISBN={1471-2164}, DOI={10.1186/s12864-019-5700-7}, journal={BMC GENOMICS}, author={Perkins, Patrick and Mazzoni-Putman, Serina and Stepanova, Anna and Alonso, Jose and Heber, Steffen}, year={2019} }
 @article{tokarz_heffelfinger_jima_gerlach_shah_rodriguez-nunez_kortum_fletcher_nordone_law_et al._2017, title={Disruption of Trim9 function abrogates macrophage motility in vivo}, volume={102}, DOI={10.1189/jlb.1a0816-371r}, number={6}, journal={Journal of Leukocyte Biology}, author={Tokarz, D. A. and Heffelfinger, A. K. and Jima, D. D. and Gerlach, J. and Shah, R. N. and Rodriguez-Nunez, I. and Kortum, A. N. and Fletcher, A. A. and Nordone, S. K. and Law, J. M. and et al.}, year={2017}, pages={1371–1380} }
 @inproceedings{perkins_heber_2017, title={riboStreamR: A web application for quality control, analysis, and visualization of Ribo-seq data}, DOI={10.1109/iccabs.2017.8114317}, booktitle={International conference on computational advances in bio and medical}, author={Perkins, P. and Heber, Steffen}, year={2017} }
 @article{hu_merchante_stepanova_alonso_heber_2016, title={Genome-wide search for translated upstream open reading frames in Arabidopsis thaliana}, volume={15}, number={2}, journal={IEEE Transactions on Nanobioscience}, author={Hu, Q. W. and Merchante, C. and Stepanova, A. N. and Alonso, J. M. and Heber, S.}, year={2016}, pages={150–159} }
 @article{villarino_hu_manrique_flores-vergara_sehra_robles_brumos_stepanova_colombo_sundberg_et al._2016, title={Transcriptomic signature of the SHATTERPROOF2 expression domain reveals the meristematic nature of Arabidopsis gynoecial medial domain}, volume={171}, DOI={10.1104/pp.15.01845}, number={1}, journal={Plant Physiology}, author={Villarino, G. H. and Hu, Q. W. and Manrique, S. and Flores-Vergara, M. and Sehra, B. and Robles, L. and Brumos, J. and STEPANOVA, ANNA and Colombo, L. and Sundberg, E. and et al.}, year={2016}, pages={42–61} }
 @inbook{hu_merchante_stepanova_alonso_heber_2015, title={A Stacking-Based Approach to Identify Translated Upstream Open Reading Frames in Arabidopsis Thaliana}, ISBN={9783319190471 9783319190488}, ISSN={0302-9743 1611-3349}, url={http://dx.doi.org/10.1007/978-3-319-19048-8_12}, DOI={10.1007/978-3-319-19048-8_12}, booktitle={Bioinformatics Research and Applications}, publisher={Springer International Publishing}, author={Hu, Qiwen and Merchante, Catharina and Stepanova, Anna N. and Alonso, Jose M. and Heber, Steffen}, year={2015}, pages={138–149} }
 @inproceedings{hu_merchante_stepanova_alonso_heber_2015, title={A stacking-based approach to identify translated upstream open reading frames in Arabidopsis thaliana}, volume={9096}, booktitle={Bioinformatics research and applications (isbra 2015)}, author={Hu, Q. W. and Merchante, C. and Stepanova, A. N. and Alonso, J. M. and Heber, S.}, year={2015}, pages={138–149} }
 @article{merchante_brumos_yun_hu_spencer_enriquez_binder_heber_stepanova_alonso_2015, title={Gene-specific translation regulation mediated by the hormone-signaling molecule EIN2}, volume={163}, DOI={10.1016/j.cell.2015.09.036}, number={3}, journal={Cell}, author={Merchante, C. and Brumos, J. and Yun, J. and Hu, Q. W. and Spencer, K. R. and Enriquez, P. and Binder, B. M. and Heber, Steffen and STEPANOVA, ANNA and Alonso, Jose}, year={2015}, pages={684–697} }
 @inproceedings{hu_merchante_stepanova_alonso_heber_2015, title={Mining transcript features related to translation in Arabidopsis using LASSO and random forest}, DOI={10.1109/iccabs.2015.7344713}, booktitle={International conference on computational advances in bio and medical}, author={Hu, Q. W. and Merchante, C. and STEPANOVA, ANNA and Alonso, Jose and Heber, Steffen}, year={2015} }
 @article{schreiner_nguyen_russo_heber_patrignani_ahrne_scheiffele_2014, title={Targeted combinatorial alternative splicing generates brain region-specific repertoires of neurexins}, volume={84}, DOI={10.1016/j.neuron.2014.09.011}, number={2}, journal={Neuron (Cambridge, Mass.)}, author={Schreiner, D. and Nguyen, T. M. and Russo, G. and Heber, Steffen and Patrignani, A. and Ahrne, E. and Scheiffele, P.}, year={2014}, pages={386–398} }
 @article{howard_hu_babaoglu_chandra_borghi_tan_he_winter-sederoff_gassmann_veronese_et al._2013, title={High-throughput RNA sequencing of pseudomonas-infected arabidopsis reveals hidden transcriptome complexity and novel splice variants}, volume={8}, DOI={10.1371/journal.pone.0074183}, number={10}, journal={PLoS One}, author={Howard, B. E. and Hu, Q. W. and Babaoglu, A. C. and Chandra, M. and Borghi, M. and Tan, X. P. and He, L. Y. and Winter-Sederoff, H. and Gassmann, W. and Veronese, P. and et al.}, year={2013} }
 @article{heber_mayr_stoye_2011, title={Common intervals of multiple permutations}, volume={60}, DOI={10.1007/s00453-009-9332-1}, number={2}, journal={Algorithmica}, author={Heber, Steffen and Mayr, R. and Stoye, J.}, year={2011}, pages={175–206} }
 @article{shi_sun_li_heber_sederoff_chiang_2010, title={Towards a systems approach for lignin biosynthesis in populus trichocarpa: transcript abundance and specificity of the monolignol biosynthetic genes}, volume={51}, DOI={10.1093/pcp/pcp175}, number={1}, journal={Plant and Cell Physiology}, author={Shi, R. and Sun, Y. H. and Li, Q. Z. and Heber, Steffen and Sederoff, R. and Chiang, V. L.}, year={2010}, pages={144–163} }
 @inproceedings{howard_heber_2010, title={Towards reliable isoform quantification using RNA-SEQ data}, volume={11}, DOI={10.1186/1471-2105-11-s3-s6}, booktitle={BMC Bioinformatics}, author={Howard, B. E. and Heber, Steffen}, year={2010} }
 @inbook{zhao_kim_heber_2009, title={Analysis of Cis-Regulatory Motifs in Cassette Exons by Incorporating Exon Skipping Rates}, ISBN={9783642015502 9783642015519}, ISSN={0302-9743 1611-3349}, url={http://dx.doi.org/10.1007/978-3-642-01551-9_27}, DOI={10.1007/978-3-642-01551-9_27}, booktitle={Bioinformatics Research and Applications}, publisher={Springer Berlin Heidelberg}, author={Zhao, Sihui and Kim, Jihye and Heber, Steffen}, year={2009}, pages={272–283} }
 @inbook{kim_zhao_howard_heber_2009, title={Mining of cis-Regulatory Motifs Associated with Tissue-Specific Alternative Splicing}, ISBN={9783642015502 9783642015519}, ISSN={0302-9743 1611-3349}, url={http://dx.doi.org/10.1007/978-3-642-01551-9_26}, DOI={10.1007/978-3-642-01551-9_26}, booktitle={Bioinformatics Research and Applications}, publisher={Springer Berlin Heidelberg}, author={Kim, Jihye and Zhao, Sihui and Howard, Brian E. and Heber, Steffen}, year={2009}, pages={260–271} }
 @inbook{howard_sick_heber_2009, title={Practical Quality Assessment of Microarray Data by Simulation of Differential Gene Expression}, ISBN={9783642015502 9783642015519}, ISSN={0302-9743 1611-3349}, url={http://dx.doi.org/10.1007/978-3-642-01551-9_3}, DOI={10.1007/978-3-642-01551-9_3}, booktitle={Bioinformatics Research and Applications}, publisher={Springer Berlin Heidelberg}, author={Howard, Brian E. and Sick, Beate and Heber, Steffen}, year={2009}, pages={18–27} }
 @article{wheeler_heimberg_moy_sperling_holstein_heber_peterson_2009, title={The deep evolution of metazoan microRNAs}, volume={11}, DOI={10.1111/j.1525-142X.2008.00302.x}, number={1}, journal={Evolution & Development}, author={Wheeler, B. M. and Heimberg, A. M. and Moy, V. N. and Sperling, E. A. and Holstein, T. W. and Heber, Steffen and Peterson, K. J.}, year={2009}, pages={50–68} }
 @article{howard_sick_heber_2009, title={Unsupervised assessment of microarray data quality using a Gaussian mixture model}, volume={10}, DOI={10.1186/1471-2105-10-191}, journal={BMC Bioinformatics}, author={Howard, B. E. and Sick, B. and Heber, Steffen}, year={2009} }
 @article{zhi_keich_pevzner_heber_tang_2007, title={Correcting base-assignment errors in repeat regions of shotgun assembly}, volume={4}, DOI={10.1109/TCBB.2007.1005}, number={1}, journal={IEEE/ACM Transactions on Computational Biology and Bioinformatics}, author={Zhi, D. G. and Keich, U. and Pevzner, P. and Heber, Steffen and Tang, H. X.}, year={2007}, pages={54–64} }
 @article{li_andersen_heber_zhang_2007, title={Non-monotonic dose-response relationship in steroid hormone receptor-mediated gene expression}, volume={38}, DOI={10.1677/JME-07-0003}, number={5-6}, journal={Journal of Molecular Endocrinology}, author={Li, L. and Andersen, M. E. and Heber, Steffen and Zhang, Q.}, year={2007}, pages={569–585} }
 @article{frahm_howard_heber_muddiman_2006, title={Accessible proteomics space and its implications for peak capacity for zero-, one- and two-dimensional separations coupled with FT-ICR and TOF mass spectrometry}, volume={41}, DOI={10.1002/jms.1024}, number={3}, journal={Journal of Mass Spectrometry}, author={Frahm, J. L. and Howard, B. E. and Heber, Steffen and Muddiman, D. C.}, year={2006}, pages={281–288} }
 @article{heber_savage_2005, title={Common intervals of trees}, volume={93}, DOI={10.1016/j.ipl.2004.09.016}, number={2}, journal={Information Processing Letters}, author={Heber, Steffen and Savage, C. D.}, year={2005}, pages={69–74} }
 @article{psarros_heber_sick_thoppae_harshman_sick_2005, title={RACE: Remote Analysis Computation for gene Expression data}, volume={33}, DOI={10.1093/nar/gki490}, journal={Nucleic Acids Research}, author={Psarros, M. and Heber, Steffen and Sick, M. and Thoppae, G. and Harshman, K. and Sick, B.}, year={2005}, pages={W638–643} }
 @article{leipzig_pevzner_heber_2004, title={The  alternative splicing gallery (ASG): bridging the gap between genome and transcriptome}, volume={32}, DOI={10.1039/nar/gkh731}, number={13}, journal={Nucleic Acids Research}, author={Leipzig, J. and Pevzner, P. and Heber, Steffen}, year={2004}, pages={3977–3983} }
 @inbook{heber_stoye_2001, title={Finding All Common Intervals of k Permutations}, ISBN={9783540422716 9783540481942}, ISSN={0302-9743 1611-3349}, url={http://dx.doi.org/10.1007/3-540-48194-x_19}, DOI={10.1007/3-540-48194-x_19}, booktitle={Combinatorial Pattern Matching}, publisher={Springer Berlin Heidelberg}, author={Heber, Steffen and Stoye, Jens}, year={2001}, pages={207–218} }