Proceedings of RECOMB-Seq

RECOMB-Seq Google Scholar Profile

Full Proceedings Papers

2025
  • Alignment-free detection of differences between sequencing data sets. Alessia Petescia, Luca Denti, Askar Gafurov, Viktória Hodorová, Jozef Nosek, Broňa Brejová and Tomas Vinar.
  • Tile-X: A vertex reordering approach for scalable long read assembly. Oieswarya Bhowmik and Ananth Kalyanaraman. bioRxiv 2025.04.21.649853, (2025)
  • Decoding the causal drivers of spatial cellular topology. Prannav Shankar, Huan Liang, Uthsav Chitra and Rohit Singh. bioRxiv 2025.03.19.644241, (2025)
  • Efficient trace reconstruction in DNA storage systems using Bidirectional Beam Search. Zhenhao Gu, Hongyi Xin, Puru Sharma, Gary Yipeng Goh, Limsoon Wong and Niranjan Nagarajan. bioRxiv 2025.04.16.644694, (2025)
  • Decoupling Hi-C matrices with non-negative matrix factorization to reveal assorted TADs. Zhao Ling, Shi Ying Li, Jingwan Wang, Xikang Feng, Bowen Tan and Shuai Cheng Li.
  • Run-length compressed metagenomic read classification with SMEM-finding and tagging. Lore Depuydt, Omar Y. Ahmed, Jan Fostier, Ben Langmead and Travis Gagie. bioRxiv 2025.02.25.640119, (2025)
  • De novo clustering of extensive long-read transcriptome datasets with isONclust3. Alexander Petri and Kristoffer Sahlin. overlay preprint
  • Multi-context seeds enable fast and high-accuracy read mapping. Ivan Tolstoganov, Marcel Martin and Kristoffer Sahlin. overlay preprint
  • GPU-accelerated homology search with MMseqs2. Felix Kallenborn, Alejandro Chacon, Christian Hundt, Hassan Sirelkhatim, Kieran Didi, Sooyoung Cha, Christian Dallago, Milot Mirdita, Bertil Schmidt and Martin Steinegger. overlay preprint
  • DeepMM: identify and correct metagenome misassemblies with deep learning. Yi Ding, Jin Xiao, Bohao Zou and Lu Zhang. overlay preprint
  • On the coverage required for diploid genome assembly. Daanish Mahajan, Chirag Jain and Navin Kashyap. overlay preprint
  • Pangenome graph augmentation from unassembled long reads. Luca Denti, Paola Bonizzoni, Brona Brejova, Rayan Chikhi, Thomas Krannich, Tomas Vinar and Fereydoun Hormozdiari. overlay preprint
2024
  • Movi: a fast and cache-efficient full-text pangenome index. Mohsen Zakeri, Nathaniel Brown, Omar Ahmed, Travis Gagie and Ben Langmead. iScience, 27 (12): 111464, (2024) S1 (2014)
  • Building a Pangenome Alignment Index via Recursive Prefix-Free Parsing. Eddie Ferro, Marco Oliva, Travis Gagie and Christina Boucher. iScience, 27 (10): 110933, (2024) S2 (2014)
  • The Backpack Quotient Filter: a dynamic and space-efficient data structure for querying k-mers with abundance. Victor Levallois, Pierre Peterlongo, Yoann Dufresne, Bertrand Le Gal and Francesco Andreace. iScience, 27 (12): 111435, (2024) S3 (2014)
  • Synthetic promoter design in Escherichia coli based on multinomial diffusion model. Qixiu Du, May Nee Poon, Xiaocheng Zeng, Pengcheng Zhang, Zheng Wei, Haochen Wang, Ye Wang, Lei Wei and Xiaowo Wang. iScience, 27 (11): 111207, (2024) S4 (2014)
  • Quick and effective approximation of in silico saturation mutagenesis experiments with first-order Taylor expansion. Alexander Sasse, Sara Mostafavi and Maria Chikina. iScience, 27 (9): 110807, (2024) S5 (2014)
  • Flowtigs: safety in flow decompositions for assembly graphs. Francisco Sena, Eliel Ingervo, Shahbaz Khan, Andrey Prjibelski, Sebastian Schmidt and Alexandru Tomescu. iScience, 27 (12): 111208, (2024) S6 (2014)
  • PLA-complexity of k-mer multisets. Md Hasin Abrar and Paul Medvedev. overlay preprint
  • Phasing Diploid Genome Assembly Graphs with Single-Cell Strand Sequencing. Mir Henglin, Maryam Ghareghani, William Harvey, David Porubsky, Sergey Koren, Evan Eichler, Peter Ebert and Tobias Marschall. overlay preprint
  • CNVeil enables accurate and robust tumor subclone identification and copy number estimation from single cell sequencing data. Weiman Yuan, Can Luo, Yunfei Hu, Liting Zhang, Zihang Wen, Yichen Henry Liu, Xian Mallory and Xin Maizie Zhou. overlay preprint
  • Quality assessment of splice site annotation based on conservation across multiple species. Ilia Minkin and Steven Salzberg. overlay preprint
  • MaskGraphene: Advancing joint embedding, clustering, and batch correction for spatial transcriptomics using graph-based self-supervised learning. Yunfei Hu, Yikang Li, Manfei Xie, Mingxing Rao, Yichen Henry Liu and Xin Maizie Zhou. overlay preprint
  • Investigating the performance of foundation models on human 3’UTR sequences. Sergey Vilov and Matthias Heinig. overlay preprint
2023
  • TreeTerminus - creating transcript trees using inferential replicate counts. Noor Pratap Singh, Michael I Love and Rob Patro. iScience, 26 (6): 106961, (2023)
  • DandD: efficient measurement of sequence growth and similarity. Jessica Bonnie, Omar Ahmed and Ben Langmead. iScience, 27 (3): 109054, (2024)
  • ADEPT: autoencoder with differentially expressed genes and imputation for a robust spatial transcriptomics clusterin. Yunfei Hu, Yuying Zhao, Curtis Schunk, Yingxiang Ma, Tyler Derr and Xin Maizie Zhou. iScience, 26 (6): 106792, (2023)
  • aKmerBroom: ancient oral DNA decontamination using Bloom filters on k-mer sets. Camila Duitama González, Riccardo Vicedomini, Hugues Richard and Rayan Chikhi. iScience, 26 (11): 108057, (2023)
  • Masked superstrings as a unified framework for textual k-mer set representations. Ondrej Sladky, Pavel Vesely and Karel Brinda. bioRxiv 2023.02.01.526717, (2023)
  • WGT: tools and algorithms for recognizing, visualizing and generating Wheeler graphs. Kuan-Hao Chao, Pei-Wei Chen, Sanjit A. Seshia and Ben Langmead. iScience, 26 (8): 107402, (2023)
  • Exploring high-quality microbial genomes by assembly of linked-reads with high barcode specificity using deep learning. Zhenmiao Zhang, Hongbo Wang, Chao Yang, Yufen Huang, Zhen Yue, Yang Chen, Lijuan Han, Aiping Lyu, Xiaodong Fang and Lu Zhang. overlay preprint
  • A safety framework for flow decomposition problems via integer linear programming. Fernando Hugo Cunha Dias, Manuel Caceres, Lucia Williams, Brendan Mumey and Alexandru I. Tomescu. overlay preprint
  • Coverage-preserving sparsification of overlap graphs for long-read assembly. Chirag Jain. overlay preprint
  • Predicting transcription factor activity using prior biological information. Joseph Estabrook, William Yashar, Hannah Holly, Julia Somers, Olga Nikolova, Ozgun Babur, Theodore Braun and Emek Demir. overlay preprint
  • On minimizers and convolutional filters: a partial justification for the effectiveness of CNNs in categorical sequence analysis. Yun William Yu. overlay preprint
  • TargetCall: eliminating the wasted computation in basecalling via pre-basecalling filtering. Meryem Banu Cavlak, Gagandeep Singh, Mohammed Alser, Can Firtina, Joël Lindegger, Mohammad Sadrosadati, Nika Mansouri Ghiasi, Can Alkan and Onur Mutlu. overlay preprint
  • An intrinsically interpretable neural network architecture for sequence to function learning. Ali Tugrul Balci, Mark Maher Ebeid, Panayiotis Benos, Dennis Kostka and Maria Chikina. overlay preprint
  • Scrooge: a fast and memory-frugal genomic sequence aligner for CPUs, GPUs, and ASICs. Joël Lindegger, Damla Senol Cali, Mohammed Alser, Juan Gómez-Luna, Nika Mansouri Ghiasi and Onur Mutlu. overlay preprint
2022
  • Sequence-based pangenomic core detection. Tizian Schulz, Roland Wittler and Jens Stoye. iScience, 25 (6): 104413, (2022)
  • scTagger: Fast and accurate matching of cellular barcodes across short- and long-reads of single-cell RNA-seq experiments. Ghazal Ebrahimi, Baraa Orabi, Meghan Robinson, Cedric Chauve, Ryan Flannigan and Faraz Hach. iScience, 25 (7): 104530, (2022)
  • Genetic polyploid phasing from low-depth progeny samples. Sven Schrinner, Rebecca Serra Mari, Richard Finkers, Paul Arens, Björn Usadel, Tobias Marschall and Gunnar W. Klau. iScience, 25 (6): 104461, (2022)
  • BOA: a partitioned view of genome assembly . Priyanka Ghosh, Xiaojing An, Patrick Keppler, Sureyya Emre Kurt, Umit Catalyurek, Sriram Krishnamoorthy, Ponnuswamy Sadayappan, Aravind Sukumaran Rajam and Ananth Kalyanaraman. iScience, 25 (11): 105273, (2022)
  • Mapping-friendly sequence reductions: going beyond homopolymer compression. Luc Blassel, Paul Medvedev and Rayan Chikhi. iScience, 25 (11): 105305, (2022)
  • BinSPreader: refine binning results for fuller MAG reconstruction . Ivan Tolstoganov, Yury Kamenev, Roman Kruglikov, Sofia Ochkalova and Anton Korobeynikov. iScience, 25 (8): 104770, (2022)
  • Flexible seed size enables ultra-fast and accurate read alignment. Kristoffer Sahlin. overlay preprint
  • Sparse and skew hashing of k-mers. Giulio Ermanno Pibiri. overlay preprint
  • Metagenome assembly of high-fidelity long reads with hifiasm-meta. Xiaowen Feng, Haoyu Cheng, Daniel Portik and Heng Li. overlay preprint
  • Scalable sequence database search using Partitioned Aggregated Bloom Comb-Trees. Camille Marchet and Antoine Limasset. overlay preprint
  • Improved structural variant discovery in hard-to-call regions using sample-specific string detection from accurate long reads. Luca Denti, Parsoa Khorsand, Paola Bonizzoni, Fereydoun Hormozdiari and Rayan Chikhi. overlay preprint
  • The minimizer Jaccard estimator is biased and inconsistent. Mahdi Belbasi, Antonio Blanca, Robert S. Harris, David Koslicki and Paul Medvedev. overlay preprint
2021
  • Dynamic partitioning of search patterns for approximate pattern matching using search schemes. Luca Renders, Kathleen Marchal and Jan Fostier. iScience, 24 (7): 102687, (2021)
  • Linearization of genome sequence graphs revisited. Anna Lisiecka and Norbert Dojer. iScience, 24 (7): 102755, (2021)
  • Pan-genomic matching statistics for targeted nanopore sequencing. Omar Ahmed, Massimiliano Rossi, Sam Kovaka, Michael Schatz, Travis Gagie, Christina Boucher and Ben Langmead. iScience, 24 (6): 102696, (2021)
  • A molecular taxonomy of tumors independent of tissue-of-origin. Peter Nguyen, Simon Coetzee, Daniel Lakeland and Dennis Hazelett . iScience, 24 (10): 103084, (2021)
  • A reference-free approach for cell type classification with scRNA-seq. Qi Sun, Yifan Peng and Jinze Liu. iScience, 24 (8): 102855, (2021)
  • Accurate spliced alignment of long RNA sequencing reads. Kristoffer Sahlin and Veli Mäkinen. overlay preprint
  • Algorithms and complexity on indexing founder graphs. Massimo Equi, Tuukka Norri, Jarno Alanko, Bastien Cazaux, Alexandru I. Tomescu and Veli Mäkinen. overlay preprint
  • HolistIC: leveraging Hi-C and whole genome shotgun sequencing for double minute chromosome discovery. Matthew Hayes, Angela Nguyen, Rahib Islam, Caryn Butler, Ethan Tran, Derrick Mullins and Chindo Hicks. overlay preprint
  • CONSULT: Accurate contamination removal usinglocality-sensitive hashing. Eleonora Rachtman, Vineet Bafna and Siavash Mirarab. overlay preprint
  • DeepDRIM: a deep neural network to reconstruct cell-type-specific gene regulatory network using single-cell RNA-seq data. Jiaxing Chen, Chinwang Cheong, Liang Lan, Xin Zhou, Jiming Liu, Aiping Lyu, William K Cheung and Lu Zhang. overlay preprint
  • Conditional resampling improves calibration and sensitivity in single-cell CRISPR screen analysis. Timothy Barry, Xuran Wang, Kathryn Roeder and Eugene Katsevich. overlay preprint
  • Accel-Align: a fast sequence mapper and aligner based on the seed–embed–extend method. Yiqing Yan, Nimisha Chaturvedi and Raja Appuswamy. overlay preprint
  • BiTSC2: Bayesian inference of tumor clonal tree by joint analysis of single-cell SNV and CNA data. Ziwei Chen, Fuzhou Gong, Lin Wan and Liang Ma. overlay preprint
  • Automated strain separation in low-complexity metagenomes using long reads. Riccardo Vicedomini, Christopher Quince, Aaron Darling and Rayan Chikhi. overlay preprint
  • Real-time, direct classification of nanopore signals with SquiggleNet. Yuwei Bao, Jack Wadden, John Erb-Downward, Piyush Ranjan, Robert Dickson, David Blaauw and Joshua Welch. overlay preprint
  • Population-scale detection of non-reference sequence variants using colored de Bruijn graphs. Thomas Krannich, W. Timothy J. White, Sebastian Niehus, Guillaume Holley, Bjarni V. Halldorsson and Birte Kehr. overlay preprint
  • Ariadne: barcoded linked-read deconvolution using de Bruijn graphs. Lauren Mak, Dmitry Meleshko, David C. Danko, Waris Barakzai, Natan Belchikov and Iman Hajirasouliha. overlay preprint
  • ACTIVA: realistic single-cell RNA-seq generation with automatic cell-type identification using introspective variational autoencoders. A. Ali Heydari, Oscar Davalos, Lihong Zhao, Katrina Hoyer and Suzanne Sindi. overlay preprint
2020
  • Spherical thresholding improves sketching of single-cell transcriptomic heterogeneity. Van Hoan Do, Khaled Elbassioni and Stefan Canzar. iScience, 23(6): 101126, 2020 S1 (2014)
  • HASLR: Fast Hybrid Assembly of Long Reads. Ehsan Haghshenas, Hossein Asghari, Jens Stoye, Cedric Chauve and Faraz Hach. iScience, 23(8): 101389, 2020 S2 (2014)
  • BATMAN: fast and accurate integration of single-cell RNA-Seq datasets via minimum-weight matching. Igor Mandric, Brian Hill, Malika Freund, Michael Thompson and Eran Halperin. iScience 23(6): 101185, 2020 S3 (2014)
  • Scalable pairwise whole-genome homology mapping of large genomes with BubbZ. Ilia Minkin and Paul Medvedev. iScience 23(6): 101224, 2020 S4 (2014)
  • Hierarchically labeled database indexing allows scalable characterization of microbiomes. Filippo Utro, Niina Haiminen, Enrico Siragusa, Laura-Jayne Gardiner, Edward Seabolt, Ritesh Krishna, James Kaufman and Laxmi Parida. iScience 23(4): 100988, 2020 S5 (2014)
  • Maximal Perfect Haplotype Blocks with Wildcards. Lucia Williams and Brendan Mumey. iScience 23(6): 101149, 2020 S6 (2014)
  • CONNET: Accurate Diploid Genome Consensus in de novo Assembly of Nanopore Sequencing Data via Deep Learning. Yifan Zhang, Chi-Man Liu, Henry Cm Leung, Ruibang Luo and Tak-Wah Lam. iScience 23(5): 101128, 2020 S7 (2014)
  • TALC: Transcription-aware long read correction. Lucile Broseus, Aubin Thomas and William Ritchie. overlay preprint
  • Metalign: Efficient alignment-based metagenomic profiling via containment min hash. Nathan Lapierre, Mohammed Alser, Eleazar Eskin, David Koslicki and Serghei Mangul. overlay preprint
  • SCAPP: An algorithm for improved plasmid assembly in metagenomes. David Pellow, Maraike Probst, Ori Furman, Alvah Zorea, Arik Segal, Itzik Mizrahi and Ron Shamir. overlay preprint
2019
  • GenMap: Fast and Exact Computation of Genome Mappability. Christopher Pockrandt, Mai Alzamel, Costas Iliopoulos and Knut Reinert. Bioinformatics, 36(12): 3687-3692, 2020
  • Samovar: Single-sample mosaic SNV calling with linked reads. Charlotte A. Darby, James R. Fitch, Patrick J. Brennan, Benjamin J. Kelly, Natalie Bir, Vincent Magrini, Jeffrey Leonard, Catherine E. Cottrell, Julie M. Gastier-Foster, Richard K. Wilson, Elaine R. Mardis, Peter White, Ben Langmead and Michael C. Schatz . iScience, 18: 1-10, 2019
  • PathRacer: racing profile HMM paths on assembly graph. Alexander Shlemov and Anton Korobeynikov. bioRxiv 562579
  • Accurate and Efficient Mapping of the Cross-linked microRNA-mRNA Duplex Reads. Cuncong Zhong and Shaojie Zhang. iScience, 18: 11-19, 2019
  • MALVA: genotyping by Mapping-free ALlele detection of known VAriants. Giulia Bernardini, Paola Bonizzoni, Luca Denti, Marco Previtali and Alexander Schönhuth. iScience, 18: 20-27, 2019
  • Kevlar: a mapping-free framework for accurate discovery of de novo variants. Daniel Standage, C. Titus Brown and Fereydoun Hormozdiari. iScience, 18: 28-36, 2019
  • Parallel decompression of gzip-compressed files and random access to DNA sequences. Maël Kerbiriou and Rayan Chikhi. overlay preprint
  • Indexing De Bruijn graphs with minimizers. Camille Marchet, Maël Kerbiriou and Antoine Limasset. overlay preprint
  • CONSENT: Scalable self-correction of long reads with multiple sequence alignment. Pierre Morisse, Camille Marchet, Antoine Limasset, Thierry Lecroq and Arnaud Lefebvre. overlay preprint
  • Graph analysis of fragmented long-read bacterial genome assemblies. Pierre Marijon, Rayan Chikhi and Jean-Stéphane Varré. overlay preprint
  • Improved Representation of Sequence Bloom Trees. Robert S. Harris and Paul Medvedev. overlay preprint
  • Scalable multiple whole-genome alignment and locally collinear block construction with SibeliaZ. Ilia Minkin and Paul Medvedev. overlay preprint
  • Nebula: Ultra-efficient mapping free structural variant genotyper. Parsoa Khorsand and Fereydoun Hormozdiari. overlay preprint
2018
  • Full-length de novo viral quasispecies assembly through variation graph construction. Jasmijn Baaijens, Bastiaan van der Roest, Johannes Koster, Leen Stougie and Alexander Schoenhuth. Bioinformatics, 35 (24): 5086-5094, (2019)
  • Alignment-free clustering of barcode (UMI) tagged DNA molecules. Baraa Orabi, Emre Erhan, Brian McConeghy, Stanislav V. Volik, Stephane Le Bihan, Collin C. Collins, Cedric Chauve and Faraz Hach. Bioinformatics, 35 (11): 1829-1836, (2019)
  • Toward perfect reads: self-correction of short reads via mapping on de Bruijn graphs. Antoine Limasset, Jean-François Flot and Pierre Peterlongo. Bioinformatics, 36 (5): 1374-1381, (2020)
  • TNER: a novel background error suppression method for mutation detection in circulating tumor DNA. Shibing Deng, Maruja Lira, Donghui Huang, Kai Wang, Crystal Valdez, Jennifer Kinong, Paul Rejto, Jadwiga Bienkowska, James Hardwick and Tao Xie. BMC Bioinformatics, 18: 387, (2018)
  • Optimum search schemes for approximate string matching using bidirectional FM-Index. Kiavash Kianfar, Christopher Pockrandt, Bahman Torkamandi, Haochen Luo and Knut Reinert. bioRxiv 301085, (2018)
  • Resistome SNP calling via read colored de Bruijn graphs . Bahar Alipanahi, Martin Muggli, Musa Jundi, Noelle Noyes and Christina Boucher. Bioinformatics, 36 (22-23): 5275-5281, (2021)
  • Deconvoluting the diversity of within-host pathogen strains in a Multi-Locus Sequence Typing framework. Guo Liang Gan, Elijah Willie, Cedric Chauve and Leonid Chindelevitch. BMC Bioinformatics, 20: 637, (2019)
2017
  • QUENTIN: accurate reconstruction of disease transmissions from viral quasispecies genomic data. Pavel Skums, Alex Zelikovsky, Sergey Knyazev, Igor Mandric, Zoya Dimitrova, Sumathi Ramachandran, David Stiven Campo Rendon, Leonid Bunimovich, Elizabeth Costenbader, Connie Sexton, Siobhan O’Connor, Guo-Liang Xia and Yury Khudyakov. Bioinformatics, 34 (1): 163-170, (2018)
  • An accurate algorithm for the detection of DNA fragments from dilution pool sequencing experiments. Vikas Bansal. Bioinformatics, 34 (1): 155-162, (2018)
  • A novel data structure to support ultra-fast taxonomic classification of metagenomic sequences with k-mer signatures. Xinan Liu, Ye Yu, Jinpeng Liu, Chen Qian and Jinze Liu. Bioinformatics, 34 (1): 171-178, (2018)
  • DIMM-SC: A Dirichlet mixture model for clustering droplet-based single cell transcriptomic data. Zhe Sun, Ting Wang, Ke Deng, Xiao-Feng Wang, Robert Lafyatis, Ying Ding, Ming Hu and Wei Chen. Bioinformatics, 34 (1): 139-146, (2018)
  • Transcription factor-8mer glossary with GENRE genomic background enables precise identification of lineage-specific co-regulators. Luca Mariani, Kathryn Weinand, Anastasia Vedenko, Luis A Barrera and Martha L Bulyk. Cell Systems, 5 (3):187-201.e7, (2017)
  • In-silico read normalization using set multicover optimization. Dilip Durai and Marcel Schulz. Bioinformatics, 34 (19): 3273-3280, (2018)
  • Repeat-aware evaluation of scaffolding tools. Igor Mandric, Sergey Knyazev and Alex Zelikovsky. Bioinformatics, 34 (15): 2530-2537, (2018)
  • Faucet: streaming de novo assembly graph construction. Roye Rozov, Gil Goldshlager, Ron Shamir and Eran Halperin. Bioinformatics, 34 (1): 147-154, (2018)
2016
  • Accurate self correction of errors in long reads using de Bruijn graphs. Leena Salmela, Riku Walve, Eric Rivals and Esko Ukkonen. Bioinformatics, 33 (6): 799–806
  • Designing robust watermark barcodes for multiplex long-read sequencing. Joaquín Ezpeleta, Flavia J. Krsticevic, Pilar Bulacio and Elizabeth Tapia. Bioinformatics, 33 (6): 807-813
  • COCACOLA: binning metagenomic contigs using sequence COmposition, read CoverAge, CO-alignment, and paired-end read LinkAge. Yang Lu, Ting Chen, Jed Fuhrman and Fengzhu Sun. Bioinformatics, 33 (6): 791-798
2015
  • PopIns: population-scale detection of novel sequence insertions. Birte Kehr, Pall Melsted and Bjarni Halldorsson. Bioinformatics, 32 (7): 961-967, (2016)
  • BMix: probabilistic modeling of occurring substitutions in PAR-CLIP data. Monica Golumbeanu, Pejman Mohammadi and Niko Beerenwinkel. Bioinformatics, 32 (7): 976-983, (2016)
  • SV-Bay: structural variant detection in cancer genomes using a Bayesian approach with correction for GC-content and read mappability. Daria Iakovishina, Isabelle Janoueix-Lerosey, Emmanuel Barillot, Mireille Regnier and Valentina Boeva. Bioinformatics, 32 (7): 984-992, (2016)
  • Inference of Markovian properties of molecular sequences from NGS data and applications to comparative genomics. Jie Ren, Kai Song, Minghua Deng, Gesine Reinert, Chuck Cannon and Fengzhu Sun. Bioinformatics, 32 (7): 993-1000, (2016)
  • Utilizing de Bruijn graph of metagenome assembly for metatranscriptome analysis. Yuzhen Ye and Haixu Tang . Bioinformatics, 32 (7): 1001-1008, (2016)
  • OPTIMA: index-based map-to-sequence alignment in large eukaryotic genomes. Davide Verzotto, Audrey S.M. Teo, Axel Hillmer and Niranjan Nagarajan. GigaScience, 5 (1): s13742-016-0110-0, (2016)
  • Rank regularized RNA-seq. Nicolas Bray and Lior Pachter.
2014
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2012
2011
Short Talks Selected from Abstracts and Posters