Journal articles on the topic 'Low-memory bioinformatics'
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Rizk, G., D. Lavenier, and R. Chikhi. "DSK: k-mer counting with very low memory usage." Bioinformatics 29, no. 5 (January 16, 2013): 652–53. http://dx.doi.org/10.1093/bioinformatics/btt020.
Full textChikhi, Rayan, Antoine Limasset, and Paul Medvedev. "Compacting de Bruijn graphs from sequencing data quickly and in low memory." Bioinformatics 32, no. 12 (June 15, 2016): i201—i208. http://dx.doi.org/10.1093/bioinformatics/btw279.
Full textKhan, Jamshed, and Rob Patro. "Cuttlefish: fast, parallel and low-memory compaction of de Bruijn graphs from large-scale genome collections." Bioinformatics 37, Supplement_1 (July 1, 2021): i177—i186. http://dx.doi.org/10.1093/bioinformatics/btab309.
Full textLi, Mulin Jun, Pak Chung Sham, and Junwen Wang. "FastPval: a fast and memory efficient program to calculate very low P-values from empirical distribution." Bioinformatics 26, no. 22 (September 21, 2010): 2897–99. http://dx.doi.org/10.1093/bioinformatics/btq540.
Full textStovner, Endre Bakken, and Pål Sætrom. "epic2 efficiently finds diffuse domains in ChIP-seq data." Bioinformatics 35, no. 21 (March 28, 2019): 4392–93. http://dx.doi.org/10.1093/bioinformatics/btz232.
Full textShi, Christina Huan, and Kevin Y. Yip. "A general near-exact k-mer counting method with low memory consumption enables de novo assembly of 106× human sequence data in 2.7 hours." Bioinformatics 36, Supplement_2 (December 2020): i625—i633. http://dx.doi.org/10.1093/bioinformatics/btaa890.
Full textSchulz, Tizian, Roland Wittler, Sven Rahmann, Faraz Hach, and Jens Stoye. "Detecting high-scoring local alignments in pangenome graphs." Bioinformatics 37, no. 16 (February 3, 2021): 2266–74. http://dx.doi.org/10.1093/bioinformatics/btab077.
Full textShimmura, Keisuke, Yuki Kato, and Yukio Kawahara. "Bivartect: accurate and memory-saving breakpoint detection by direct read comparison." Bioinformatics 36, no. 9 (January 27, 2020): 2725–30. http://dx.doi.org/10.1093/bioinformatics/btaa059.
Full textSaha, Subrata, Jethro Johnson, Soumitra Pal, George M. Weinstock, and Sanguthevar Rajasekaran. "MSC: a metagenomic sequence classification algorithm." Bioinformatics 35, no. 17 (January 14, 2019): 2932–40. http://dx.doi.org/10.1093/bioinformatics/bty1071.
Full textSater, Vincent, Pierre-Julien Viailly, Thierry Lecroq, Élise Prieur-Gaston, Élodie Bohers, Mathieu Viennot, Philippe Ruminy, Hélène Dauchel, Pierre Vera, and Fabrice Jardin. "UMI-VarCal: a new UMI-based variant caller that efficiently improves low-frequency variant detection in paired-end sequencing NGS libraries." Bioinformatics 36, no. 9 (January 27, 2020): 2718–24. http://dx.doi.org/10.1093/bioinformatics/btaa053.
Full textChen, Jun-Yu, Ya-Ru Sun, Tao Xiong, Guan-Nan Wang, and Qing Chang. "Identification of HIBCH as a Fatty Acid Metabolism-Related Biomarker in Aortic Valve Calcification Using Bioinformatics." Oxidative Medicine and Cellular Longevity 2022 (October 7, 2022): 1–24. http://dx.doi.org/10.1155/2022/9558713.
Full textJing, Gongchao, Yufeng Zhang, Ming Yang, Lu Liu, Jian Xu, and Xiaoquan Su. "Dynamic Meta-Storms enables comprehensive taxonomic and phylogenetic comparison of shotgun metagenomes at the species level." Bioinformatics 36, no. 7 (December 3, 2019): 2308–10. http://dx.doi.org/10.1093/bioinformatics/btz910.
Full textLai, Qing, and Haifei Feng. "An Immune-Related Prognostic Risk Model in Colon Cancer by Bioinformatics Analysis." Evidence-Based Complementary and Alternative Medicine 2022 (August 27, 2022): 1–13. http://dx.doi.org/10.1155/2022/3640589.
Full textHajibaba, Majid, Mohsen Sharifi, and Saeid Gorgin. "The Influence of Memory-Aware Computation on Distributed BLAST." Current Bioinformatics 14, no. 2 (January 7, 2019): 157–63. http://dx.doi.org/10.2174/1574893613666180601080811.
Full textLi, Yu, Sheng Wang, Chongwei Bi, Zhaowen Qiu, Mo Li, and Xin Gao. "DeepSimulator1.5: a more powerful, quicker and lighter simulator for Nanopore sequencing." Bioinformatics 36, no. 8 (January 8, 2020): 2578–80. http://dx.doi.org/10.1093/bioinformatics/btz963.
Full textLi, Xiangtao, Shixiong Zhang, and Ka-Chun Wong. "Single-cell RNA-seq interpretations using evolutionary multiobjective ensemble pruning." Bioinformatics 35, no. 16 (December 28, 2018): 2809–17. http://dx.doi.org/10.1093/bioinformatics/bty1056.
Full textLuo, Zhiwen, and Xinyu Bi. "Recurrence after surgery for concurrent metastatic colorectal cancer: The perspective of bioinformatics and machine learning." Journal of Clinical Oncology 38, no. 15_suppl (May 20, 2020): 4043. http://dx.doi.org/10.1200/jco.2020.38.15_suppl.4043.
Full textTang, Deyou, Daqiang Tan, Weihao Xiao, Jiabin Lin, and Juan Fu. "KMC3 and CHTKC: Best Scenarios, Deficiencies, and Challenges in High-Throughput Sequencing Data Analysis." Algorithms 15, no. 4 (March 24, 2022): 107. http://dx.doi.org/10.3390/a15040107.
Full textJin, Hai, Hao Qi, Jin Zhao, Xinyu Jiang, Yu Huang, Chuangyi Gui, Qinggang Wang, et al. "Software Systems Implementation and Domain-Specific Architectures towards Graph Analytics." Intelligent Computing 2022 (October 29, 2022): 1–32. http://dx.doi.org/10.34133/2022/9806758.
Full textYook, Jang Soo, Randeep Rakwal, Junko Shibato, Kanako Takahashi, Hikaru Koizumi, Takeru Shima, Mitsushi J. Ikemoto, Leandro K. Oharomari, Bruce S. McEwen, and Hideaki Soya. "Leptin in hippocampus mediates benefits of mild exercise by an antioxidant on neurogenesis and memory." Proceedings of the National Academy of Sciences 116, no. 22 (May 13, 2019): 10988–93. http://dx.doi.org/10.1073/pnas.1815197116.
Full textChu, Justin, Hamid Mohamadi, Emre Erhan, Jeffery Tse, Readman Chiu, Sarah Yeo, and Inanc Birol. "Mismatch-tolerant, alignment-free sequence classification using multiple spaced seeds and multiindex Bloom filters." Proceedings of the National Academy of Sciences 117, no. 29 (July 8, 2020): 16961–68. http://dx.doi.org/10.1073/pnas.1903436117.
Full textHansson, Lotta, Hodjattallah Rabbani, Jan Fagerberg, Anders Österborg, and Håkan Mellstedt. "T-cell epitopes within the complementarity-determining and framework regions of the tumor-derived immunoglobulin heavy chain in multiple myeloma." Blood 101, no. 12 (June 15, 2003): 4930–36. http://dx.doi.org/10.1182/blood-2002-04-1250.
Full textSun, Heng, Bowen Sui, Yu Li, Jun Yan, Mingming Cao, Lijia Zhang, and Songjiang Liu. "Analysis of the Significance of Immune Cell Infiltration and Prognosis of Non-Small-Cell Lung Cancer by Bioinformatics." Journal of Healthcare Engineering 2021 (September 22, 2021): 1–8. http://dx.doi.org/10.1155/2021/3284186.
Full textFan, Wei, Jun Ding, Shushu Liu, and Wei Zhong. "Development and validation of novel prognostic models based on RNA-binding proteins in breast cancer." Journal of International Medical Research 50, no. 6 (June 2022): 030006052211062. http://dx.doi.org/10.1177/03000605221106285.
Full textDezordi, Filipe Zimmer, Antonio Marinho da Silva Neto, Túlio de Lima Campos, Pedro Miguel Carneiro Jeronimo, Cleber Furtado Aksenen, Suzana Porto Almeida, and Gabriel Luz Wallau. "ViralFlow: A Versatile Automated Workflow for SARS-CoV-2 Genome Assembly, Lineage Assignment, Mutations and Intrahost Variant Detection." Viruses 14, no. 2 (January 23, 2022): 217. http://dx.doi.org/10.3390/v14020217.
Full textStrycharz, Justyna, Ewa Świderska, Adam Wróblewski, Marta Podolska, Piotr Czarny, Janusz Szemraj, Aneta Balcerczyk, Józef Drzewoski, Jacek Kasznicki, and Agnieszka Śliwińska. "Hyperglycemia Affects miRNAs Expression Pattern during Adipogenesis of Human Visceral Adipocytes—Is Memorization Involved?" Nutrients 10, no. 11 (November 15, 2018): 1774. http://dx.doi.org/10.3390/nu10111774.
Full textXiao, Gong, Qiongjing Yuan, and Wei Wang. "The Prognostic Value of the m6A Score in Multiple Myeloma Based on Machine Learning." BioMedInformatics 1, no. 3 (September 27, 2021): 77–87. http://dx.doi.org/10.3390/biomedinformatics1030006.
Full textLi, Chunzhen, Weizheng Zhou, Ji Zhu, Qi Shen, Guangjie Wang, Ling Chen, and Tiejun Zhao. "Identification of an Immune-Related Gene Signature Associated with Prognosis and Tumor Microenvironment in Esophageal Cancer." BioMed Research International 2022 (December 23, 2022): 1–22. http://dx.doi.org/10.1155/2022/7413535.
Full textZhaoran, Su, and Jia Weidong. "INSC Is a Prognosis-Associated Biomarker Involved in Tumor Immune Infiltration in Colon Adenocarcinoma." BioMed Research International 2022 (September 12, 2022): 1–9. http://dx.doi.org/10.1155/2022/5794150.
Full textDong, Gaifang, Xueliang Fu, Honghui Li, and Xu Pan. "An Accurate Sequence Assembly Algorithm for Livestock, Plants and Microorganism Based on Spark." International Journal of Pattern Recognition and Artificial Intelligence 31, no. 08 (May 9, 2017): 1750024. http://dx.doi.org/10.1142/s0218001417500240.
Full textFan, Yunjian, Jie Zhang, Jiayu Shi, Lin Chen, Jiazhen Long, Shuqi Zhang, and Shuguang Liu. "Genetic Cross-Talk between Oral Squamous Cell Carcinoma and Type 2 Diabetes: The Potential Role of Immunity." Disease Markers 2022 (May 19, 2022): 1–24. http://dx.doi.org/10.1155/2022/6389906.
Full textMüller, Robert, and Markus Nebel. "On the use of sequence-quality information in OTU clustering." PeerJ 9 (August 16, 2021): e11717. http://dx.doi.org/10.7717/peerj.11717.
Full textKovjazin, Riva, David Shitrit, Rachel Preiss, Ilanit Haim, Lev Triezer, Leonardo Fuks, Abdel Rahman Nader, et al. "Characterization of Novel Multiantigenic Vaccine Candidates with Pan-HLA Coverage against Mycobacterium tuberculosis." Clinical and Vaccine Immunology 20, no. 3 (January 2, 2013): 328–40. http://dx.doi.org/10.1128/cvi.00586-12.
Full textChen, Peixin, Lishu Zhao, Hao Wang, Liping Zhang, Wei Zhang, Jun Zhu, Jia Yu, et al. "Human leukocyte antigen class II-based immune risk model for recurrence evaluation in stage I–III small cell lung cancer." Journal for ImmunoTherapy of Cancer 9, no. 8 (August 2021): e002554. http://dx.doi.org/10.1136/jitc-2021-002554.
Full textА.Р., Дягель,, Зарубин, А.А., Назаренко, М.С., and Слепцов, А.А. "Single-cell RNA Sequencing Data Analysis Reveals Structural Diversity of T-lymphocyte and Macrophage Infiltration in Atherosclerosis." Nauchno-prakticheskii zhurnal «Medicinskaia genetika, no. 7 (July 29, 2022): 43–45. http://dx.doi.org/10.25557/2073-7998.2022.07.43-45.
Full textNuthikattu, Saivageethi, Dragan Milenkovic, John C. Rutledge, and Amparo C. Villablanca. "Sex-Dependent Molecular Mechanisms of Lipotoxic Injury in Brain Microvasculature: Implications for Dementia." International Journal of Molecular Sciences 21, no. 21 (October 31, 2020): 8146. http://dx.doi.org/10.3390/ijms21218146.
Full textDupont, Marine, Paco Derouault, Virginie Pascal, Charlotte Rivière, Benjamin Ganne, Mélanie Boulin, Sophie Perron, et al. "Comparison with Private and Public Clonotypes Reveals That, While CLL Type Stereotyped BCR Are Produced in 90% of Healthy Subjects from 18 to 78 Years, They Are Not Accumulated and Are Mostly Found in Immature and Naïve B-Cells." Blood 138, Supplement 1 (November 5, 2021): 2621. http://dx.doi.org/10.1182/blood-2021-152714.
Full textAttaf, Noudjoud, Inaki Cervera-Marzal, Laurine Gil, Chuang Dong, Jean-Marc Navarro, Lionel Spinelli, Bertrand Nadel, and Pierre Milpied. "Single-Cell RNA Sequencing Identifies a Pseudo-Immune Differentiation Axis As the Main Source of Functional Heterogeneity in Follicular Lymphoma B-Cells." Blood 134, Supplement_1 (November 13, 2019): 548. http://dx.doi.org/10.1182/blood-2019-125718.
Full textAlmeida, Diogo, Ida Skov, Jesper Lund, Afsaneh Mohammadnejad, Artur Silva, Fabio Vandin, Qihua Tan, Jan Baumbach, and Richard Röttger. "Jllumina - A comprehensive Java-based API for statistical Illumina Infinium HumanMethylation450 and Infinium MethylationEPIC BeadChip data processing." Journal of Integrative Bioinformatics 13, no. 4 (October 1, 2016): 24–32. http://dx.doi.org/10.1515/jib-2016-294.
Full textWang, Zhihuai, Adeel Ur Rehman, Xihu Qin, Chunfu Zhu, and Siyuan Wu. "PI3K/AKT/mTOR Pathway-Associated Genes Reveal a Putative Prognostic Signature Correlated with Immune Infiltration in Hepatocellular Carcinoma." Disease Markers 2022 (May 9, 2022): 1–18. http://dx.doi.org/10.1155/2022/7545666.
Full textCoscia, Marta, Candida Vitale, Silvia Peola, Chiara Riganti, Daniela Angelini, Myriam Foglietta, Francesca Pantaleoni, et al. "The Defective Proliferation of Vgamma9Vdelta2 T Cells to Zoledronic Acid In Chronic Lymphocytic Leukemia (CLL) Is a Powerful Time to First Treatment (TFT) Predictor Associated with the IGHV Mutational Status." Blood 116, no. 21 (November 19, 2010): 3602. http://dx.doi.org/10.1182/blood.v116.21.3602.3602.
Full textAwad, Mark, David Spigel, Edward Garon, Saiama Waqar, Aaron Lisberg, Melissa Moles, Jennifer Tepper, et al. "364 A personal neoantigen vaccine NEO-PV-01 in combination with chemotherapy and pembrolizumab induces broad de novo immune responses in first line, non-squamous NSCLC." Journal for ImmunoTherapy of Cancer 8, Suppl 3 (November 2020): A389. http://dx.doi.org/10.1136/jitc-2020-sitc2020.0364.
Full textVergani, Stefano, Davide Bagnara, Andrea Nicola Mazzarello, Gerardo Ferrer, Sophia Yancopoulos, Kostas Stamatopoulos, and Nicholas Chiorazzi. "CLL Stereotyped IGHV-D-J Rearrangements Can Be Detected Throughout Normal B-Cell Developmental Stages in Aged People When Using Ultra-Deep, Next Generation Sequencing Techniques." Blood 128, no. 22 (December 2, 2016): 2028. http://dx.doi.org/10.1182/blood.v128.22.2028.2028.
Full textKatsuta, Eriko, Tao Dai, Abhisha Sawant Dessai, and Subhamoy Dasgupta. "Abstract P5-06-12: Extracellular adenosine synthesis genes regulated by estrogen signaling are associated with cancer aggressiveness and poor prognosis in estrogen receptor (ER)-positive breast cancer." Cancer Research 82, no. 4_Supplement (February 15, 2022): P5–06–12—P5–06–12. http://dx.doi.org/10.1158/1538-7445.sabcs21-p5-06-12.
Full textXing, Fei, Yi Ping Yao, Zhi Wen Jiang, and Bing Wang. "Fine-Grained Parallel and Distributed Spatial Stochastic Simulation of Biological Reactions." Advanced Materials Research 345 (September 2011): 104–12. http://dx.doi.org/10.4028/www.scientific.net/amr.345.104.
Full textMarchet, Camille, Mael Kerbiriou, and Antoine Limasset. "BLight: efficient exact associative structure for k-mers." Bioinformatics, April 3, 2021. http://dx.doi.org/10.1093/bioinformatics/btab217.
Full textBenoit, Gaëtan, Mahendra Mariadassou, Stéphane Robin, Sophie Schbath, Pierre Peterlongo, and Claire Lemaitre. "SimkaMin: fast and resource frugal de novo comparative metagenomics." Bioinformatics, September 3, 2019. http://dx.doi.org/10.1093/bioinformatics/btz685.
Full textPeng, Xiyu, and Karin S. Dorman. "AmpliCI: a high-resolution model-based approach for denoising Illumina amplicon data." Bioinformatics, July 22, 2020. http://dx.doi.org/10.1093/bioinformatics/btaa648.
Full textKim, Jeremie S., Can Firtina, Meryem Banu Cavlak, Damla Senol Cali, Can Alkan, and Onur Mutlu. "FastRemap: A Tool for Quickly Remapping Reads between Genome Assemblies." Bioinformatics, August 17, 2022. http://dx.doi.org/10.1093/bioinformatics/btac554.
Full textLu, Chengqian, Min Zeng, Fang-Xiang Wu, Min Li, and Jianxin Wang. "Improving circRNA-disease association prediction by sequence and ontology representations with convolutional and recurrent neural networks." Bioinformatics, December 26, 2020. http://dx.doi.org/10.1093/bioinformatics/btaa1077.
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