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ORCIDBMC Bioinformatics, Volume 22
Volume 22, Number 1, December 2021
- Pedro M. Martins
, Lucianna Helene Santos, Diego C. B. Mariano, Felippe C. Queiroz, Luana L. Bastos, Isabela de Souza Gomes, Pedro H. C. Fischer, Rafael E. O. Rocha, Sabrina de Azevedo Silveira, Leonardo H. F. de Lima, Mariana T. Q. de Magalhães, Maria G. A. Oliveira, Raquel Cardoso de Melo Minardi:
Propedia: a database for protein-peptide identification based on a hybrid clustering algorithm. 1 - Panagiotis Moulos:
recoup: flexible and versatile signal visualization from next generation sequencing. 2 - Nick W. Smith, Paul R. Shorten, Eric Altermann, Nicole C. Roy, Warren C. McNabb:
Examination of hydrogen cross-feeders using a colonic microbiota model. 3 - Joaquim Aguirre-Plans, Alberto Meseguer, Ruben Molina-Fernandez, Manuel Alejandro Marín-López, Gaurav Jumde, Kevin Casanova, Jaume Bonet, Oriol Fornes, Narcis Fernandez-Fuentes, Baldo Oliva:
SPServer: split-statistical potentials for the analysis of protein structures and protein-protein interactions. 4 - Yan Zheng, Yuanke Zhong, Jialu Hu, Xuequn Shang:
SCC: an accurate imputation method for scRNA-seq dropouts based on a mixture model. 5 - Johanna Zoppi, Jean-François Guillaume, Michel Neunlist, Samuel Chaffron:
MiBiOmics: an interactive web application for multi-omics data exploration and integration. 6 - Yilin Ye, Jian Wang, Yunwan Xu, Yi Wang, Youdong Pan, Qi Song, Xing Liu, Ji Wan:
MATHLA: a robust framework for HLA-peptide binding prediction integrating bidirectional LSTM and multiple head attention mechanism. 7 - Badri Adhikari, Bikash Shrestha, Matthew Bernardini, Jie Hou, Jamie Lea:
DISTEVAL: a web server for evaluating predicted protein distances. 8 - Edwin A. Solares, Yuan Tao, Anthony D. Long, Brandon S. Gaut:
HapSolo: an optimization approach for removing secondary haplotigs during diploid genome assembly and scaffolding. 9 - Shuwei Yin, Xiao Tian, Jingjing Zhang, Peisen Sun, Guanglin Li:
PCirc: random forest-based plant circRNA identification software. 10 - Carlos A. Ruiz-Perez, Roth E. Conrad, Konstantinos T. Konstantinidis:
MicrobeAnnotator: a user-friendly, comprehensive functional annotation pipeline for microbial genomes. 11 - Bing Song, August E. Woerner, John Planz:
mixIndependR: a R package for statistical independence testing of loci in database of multi-locus genotypes. 12 - Jiaxing Lu, Ming Chen, Yufang Qin:
Drug-induced cell viability prediction from LINCS-L1000 through WRFEN-XGBoost algorithm. 13 - Changyong Li, Yongxian Fan, Xiaodong Cai:
PyConvU-Net: a lightweight and multiscale network for biomedical image segmentation. 14 - Joshua D. Mannheimer, Ashok Prasad, Daniel L. Gustafson:
Predicting chemosensitivity using drug perturbed gene dynamics. 15 - João Lobo, Rui Henriques, Sara C. Madeira:
G-Tric: generating three-way synthetic datasets with triclustering solutions. 16 - Shengqiao Gao, Lu Han, Dan Luo, Gang Liu, Zhiyong Xiao, Guangcun Shan, Yongxiang Zhang, Wenxia Zhou:
Modeling drug mechanism of action with large scale gene-expression profiles using GPAR, an artificial intelligence platform. 17 - Nan Zhou, Jinku Bao, Yuping Ning:
H2V: a database of human genes and proteins that respond to SARS-CoV-2, SARS-CoV, and MERS-CoV infection. 18 - Zhengfeng Wang, Xiujuan Lei:
Identifying the sequence specificities of circRNA-binding proteins based on a capsule network architecture. 19 - Jose Arturo Molina-Mora, Mariela Solano-Vargas:
Set-theory based benchmarking of three different variant callers for targeted sequencing. 20 - Pascal Holzheu, Ruth Großeholz, Ursula Kummer:
Impact of explicit area scaling on kinetic models involving multiple compartments. 21 - Mike Fang, Brian Richardson, Cheryl M. Cameron, Jean-Eudes J. Dazard, Mark J. Cameron:
Drug perturbation gene set enrichment analysis (dpGSEA): a new transcriptomic drug screening approach. 22 - Xinping Fan, Guanghao Luo, Yu S. Huang:
Accucopy: accurate and fast inference of allele-specific copy number alterations from low-coverage low-purity tumor sequencing data. 23 - Dipan Shaw, Hao Chen, Minzhu Xie, Tao Jiang:
DeepLPI: a multimodal deep learning method for predicting the interactions between lncRNAs and protein isoforms. 24 - Eliza Dhungel, Yassin Mreyoud, Ho-Jin Gwak, Ahmad Rajeh, Mina Rho, Tae-Hyuk Ahn:
MegaR: an interactive R package for rapid sample classification and phenotype prediction using metagenome profiles and machine learning. 25 - Mehrdad Kashefi, Mohammad Reza Daliri:
A stack LSTM structure for decoding continuous force from local field potential signal of primary motor cortex (M1). 26 - Lingpeng Kong, Yuanyuan Chen, Fengjiao Xu, Mingmin Xu, Zutan Li, Jingya Fang, Liangyun Zhang, Cong Pian:
Mining influential genes based on deep learning. 27 - Tamer N. Jarada, Jon G. Rokne, Reda Alhajj:
SNF-NN: computational method to predict drug-disease interactions using similarity network fusion and neural networks. 28 - Amber N. Habowski, T. J. Habowski, M. L. Waterman:
GECO: gene expression clustering optimization app for non-linear data visualization of patterns. 29 - Tianqi Wu, Zhiye Guo, Jie Hou, Jianlin Cheng:
DeepDist: real-value inter-residue distance prediction with deep residual convolutional network. 30 - Lili Jiang, Kaini Qiao, Chunlin Li:
Distance-based functional criticality in the human brain: intelligence and emotional intelligence. 32 - Akram Emdadi, Changiz Eslahchi:
Auto-HMM-LMF: feature selection based method for prediction of drug response via autoencoder and hidden Markov model. 33 - Shawn Gu, Tijana Milenkovic:
Data-driven biological network alignment that uses topological, sequence, and functional information. 34 - Tara Eicher, Jany Chan, Han Luu, Raghu Machiraju, Ewy A. Mathé:
Self-organizing maps with variable neighborhoods facilitate learning of chromatin accessibility signal shapes associated with regulatory elements. 35 - Takuma Nishimaki, Keiko Sato:
P*R*O*P: a web application to perform phylogenetic analysis considering the effect of gaps. 36 - Ana M. Vasconcelos, Maria Beatriz Carmo, Beatriz Ferreira, Inês Viegas, Margarida Gama-Carvalho, Antonio Ferreira, Andreia J. Amaral:
IsomiR_Window: a system for analyzing small-RNA-seq data in an integrative and user-friendly manner. 37 - Chen Chen, Jie Hou, Xiaowen Shi, Hua Yang, James A. Birchler, Jianlin Cheng:
DeepGRN: prediction of transcription factor binding site across cell-types using attention-based deep neural networks. 38 - Ryan B. Patterson-Cross, Ariel J. Levine, Vilas Menon:
Selecting single cell clustering parameter values using subsampling-based robustness metrics. 39 - Charlie M. Carpenter, Daniel N. Frank, Kayla Williamson, Jaron Arbet, Brandie D. Wagner, Katerina J. Kechris, Miranda Kroehl:
tidyMicro: a pipeline for microbiome data analysis and visualization using the tidyverse in R. 41 - Yulia M. Suvorova, Anastasya M. Kamionskaya, Eugene V. Korotkov:
Search for SINE repeats in the rice genome using correlation-based position weight matrices. 42 - Liangqun Lu, Kevin A. Townsend, Bernie J. Daigle Jr.:
GEOlimma: differential expression analysis and feature selection using pre-existing microarray data. 44 - Elisa Pischedda, Cristina Crava, Martina Carlassara, Susanna Zucca, Leila Gasmi, Mariangela Bonizzoni:
ViR: a tool to solve intrasample variability in the prediction of viral integration sites using whole genome sequencing data. 45 - Marcos José Andrade Viana, Adhemar Zerlotini, Maurício de Alvarenga Mudado:
Plant Co-expression Annotation Resource: a web server for identifying targets for genetically modified crop breeding pipelines. 46 - Jiarui Feng, Heming Zhang, Fuhai Li:
Investigating the relevance of major signaling pathways in cancer survival using a biologically meaningful deep learning model. 47 - Paulien Adamse, Emilie Dagand, Karen Bohmert-Tatarev, Daniela Wahler, Manoela Miranda, Esther J. Kok, Joachim Bendiek:
GMO Genetic Elements Thesaurus (GMO-GET): a controlled vocabulary for the consensus designation of introduced or modified genetic elements in genetically modified organisms. 48 - Daniella Vo, Shayal Charisma Singh, Sara Safa, Debashis Sahoo:
Boolean implication analysis unveils candidate universal relationships in microbiome data. 49 - Haohan Wang, Fen Pei, Michael M. Vanyukov, Ivet Bahar, Wei Wu, Eric P. Xing:
Coupled mixed model for joint genetic analysis of complex disorders with two independently collected data sets. 50 - Hayam Alamro, Mai Alzamel, Costas S. Iliopoulos, Solon P. Pissis, Steven Watts:
IUPACpal: efficient identification of inverted repeats in IUPAC-encoded DNA sequences. 51 - Hailin Chen, Zuping Zhang, Jingpu Zhang:
In silico drug repositioning based on the integration of chemical, genomic and pharmacological spaces. 52 - Ermanno Cordelli, Paolo Soda, Giulio Iannello:
Visual4DTracker: a tool to interact with 3D + t image stacks. 53 - Elma Akand, John M. Murray:
NGlyAlign: an automated library building tool to align highly divergent HIV envelope sequences. 54 - Nguyen P. Nguyen, Ilker Ersoy, Jacob Gotberg, Filiz Bunyak, Tommi A. White:
DRPnet: automated particle picking in cryo-electron micrographs using deep regression. 55 - Florent Grélard, David Legland, Mathieu Fanuel, Bastien Arnaud, Loïc Foucat, Hélène Rogniaux:
Esmraldi: efficient methods for the fusion of mass spectrometry and magnetic resonance images. 56 - Julia Åkesson, Zelmina Lubovac-Pilav, Rasmus Magnusson, Mika Gustafsson:
ComHub: Community predictions of hubs in gene regulatory networks. 58 - Oleksii Bryzghalov, Izabela Makalowska, Michal Wojciech Szczesniak:
lncEvo: automated identification and conservation study of long noncoding RNAs. 59 - Daniele Dall'Olio, Nico Curti, Eugenio Fonzi, Claudia Sala, Daniel Remondini, Gastone C. Castellani, Enrico Giampieri:
Impact of concurrency on the performance of a whole exome sequencing pipeline. 60 - William R. P. Denault, Astanand Jugessur:
Detecting differentially methylated regions using a fast wavelet-based approach to functional association analysis. 61 - Cesim Erten, Aissa Houdjedj, Hilal Kazan:
Ranking cancer drivers via betweenness-based outlier detection and random walks. 62 - Pengyu Liu, Jiangning Song, Chun-Yu Lin, Tatsuya Akutsu:
ReCGBM: a gradient boosting-based method for predicting human dicer cleavage sites. 63 - Angana Chakraborty, Burkhard Morgenstern, Sanghamitra Bandyopadhyay:
S-conLSH: alignment-free gapped mapping of noisy long reads. 64 - Truong Khanh Linh Dang, Thach Nguyen, Michael Habeck, Mehmet Gültas, Stephan Waack:
A graph-based algorithm for detecting rigid domains in protein structures. 66 - Alina Peluso, Robert C. Glen, Timothy M. D. Ebbels:
Multiple-testing correction in metabolome-wide association studies. 67 - Olga Permiakova, Romain Guibert, Alexandra Kraut, Thomas Fortin, Anne-Marie Hesse, Thomas Burger:
CHICKN: extraction of peptide chromatographic elution profiles from large scale mass spectrometry data by means of Wasserstein compressive hierarchical cluster analysis. 68 - Aseel Awdeh, Marcel Turcotte, Theodore J. Perkins:
WACS: improving ChIP-seq peak calling by optimally weighting controls. 69 - Ryan D. Crawford, Evan S. Snitkin:
cognac: rapid generation of concatenated gene alignments for phylogenetic inference from large, bacterial whole genome sequencing datasets. 70 - Moustafa Shokrof, C. Titus Brown, Tamer A. Mansour:
MQF and buffered MQF: quotient filters for efficient storage of k-mers with their counts and metadata. 71 - Grzegorz Bokota, Jacek Sroka, Subhadip Basu, Nirmal Das, Pawel Trzaskoma, Yana Yushkevich, Agnieszka Grabowska, Adriana Magalska, Dariusz Plewczynski:
PartSeg: a tool for quantitative feature extraction from 3D microscopy images for dummies. 72 - Momoko Imakubo, Jun Takayama, Hatsumi Okada, Shuichi Onami:
Statistical image processing quantifies the changes in cytoplasmic texture associated with aging in Caenorhabditis elegans oocytes. 73 - Damian Gola, Inke R. König:
Empowering individual trait prediction using interactions for precision medicine. 74 - Xiao Wen, Lin Gao, Tuo Song, Chaoqun Jiang:
CeNet Omnibus: an R/Shiny application to the construction and analysis of competing endogenous RNA network. 75 - Matteo Perini, Gherard Batisti Biffignandi, Domenico Di Carlo, Ajay Ratan Pasala, Aurora Piazza, Simona Panelli, Gianvincenzo Zuccotti, Francesco Comandatore:
MeltingPlot, a user-friendly online tool for epidemiological investigation using High Resolution Melting data. 76 - Christopher Paul Wardell, Cody Ashby, Michael Anton Bauer:
FiNGS: high quality somatic mutations using filters for next generation sequencing. 77 - Dörte Wittenburg, Michael Doschoris, Jan Klosa:
Grouping of genomic markers in populations with family structure. 79 - Janet C. Siebert, Martine Saint-Cyr, Sarah J. Borengasser, Brandie D. Wagner, Catherine A. Lozupone, Carsten Görg:
CANTARE: finding and visualizing network-based multi-omic predictive models. 80 - Snorre Sulheim, Fredrik A. Fossheim, Alexander Wentzel, Eivind Almaas:
Automatic reconstruction of metabolic pathways from identified biosynthetic gene clusters. 81 - Anna Maria Masci, Scott White, Ben Neely, Maryanne Ardini-Polaske, Carol B. Hill, Ravi S. Misra, Bruce J. Aronow, Nathan Gaddis, Lina Yang, Susan E. Wert, Scott M. Palmer, Cliburn Chan:
Ontology-guided segmentation and object identification for developmental mouse lung immunofluorescent images. 82 - Matthew N. Bernstein, Zijian Ni, Michael Collins, Mark E. Burkard, Christina Kendziorski, Ron M. Stewart:
CHARTS: a web application for characterizing and comparing tumor subpopulations in publicly available single-cell RNA-seq data sets. 83 - Vandhana Krishnan, Sowmithri Utiramerur, Zena Ng, Somalee Datta, Michael Snyder, Euan A. Ashley:
Benchmarking workflows to assess performance and suitability of germline variant calling pipelines in clinical diagnostic assays. 85 - Camilo Broc, Thérèse Truong, Benoit Liquet:
Penalized partial least squares for pleiotropy. 86 - Raíssa Lorena Silva da Silva, Kleber Padovani de Souza, Fabiana Rodrigues de Góes, Ronnie Alves:
geneRFinder: gene finding in distinct metagenomic data complexities. 87 - Octav Caldararu, Tom L. Blundell, Kasper P. Kepp:
A base measure of precision for protein stability predictors: structural sensitivity. 88 - Amra Omanovic, Hilal Kazan, Polona Oblak, Tomaz Curk:
Sparse data embedding and prediction by tropical matrix factorization. 89 - Titinunt Kitrungrotsakul, Yutaro Iwamoto, Satoko Takemoto, Hideo Yokota, Sari Ipponjima, Tomomi Nemoto, Lanfen Lin, Ruofeng Tong, Jingsong Li, Yen-Wei Chen:
Accurate and fast mitotic detection using an anchor-free method based on full-scale connection with recurrent deep layer aggregation in 4D microscopy images. 91 - Raul Rodriguez-Esteban:
Biomedical articles share annotations with their citation neighbors. 95 - Tongjun Gu, Xiwu Zhao, William Bradley Barbazuk, Ji-Hyun Lee:
miTAR: a hybrid deep learning-based approach for predicting miRNA targets. 96 - Yuqi Wen, Xinyu Song, Bowei Yan, Xiaoxi Yang, Lianlian Wu, Dongjin Leng, Song He, Xiaochen Bo:
Multi-dimensional data integration algorithm based on random walk with restart. 97 - Casey B. Bernhards, Matthew W. Lux, Sarah E. Katoski, Tyler D. P. Goralski, Alvin T. Liem, Henry S. Gibbons:
barCoder: a tool to generate unique, orthogonal genetic tags for qPCR detection. 98 - Zachary B. Abrams, Dwayne G. Tally, Lin Zhang, Caitlin E. Coombes, Philip R. O. Payne, Lynne V. Abruzzo, Kevin R. Coombes:
Pattern recognition in lymphoid malignancies using CytoGPS and Mercator. 100 - Sebastian M. Siegner, Mehmet E. Karasu, Markus S. Schröder, Zacharias Kontarakis, Jacob E. Corn:
PnB Designer: a web application to design prime and base editor guide RNAs for animals and plants. 101 - Umesh Kathad, Aditya Kulkarni, Joseph Ryan McDermott, Jordan Wegner, Peter Carr, Neha Biyani, Rama Modali, Jean-Philippe Richard, Panna Sharma, Kishor Bhatia:
A machine learning-based gene signature of response to the novel alkylating agent LP-184 distinguishes its potential tumor indications. 102 - Dominik Jens Elias Waibel, Sayedali Shetab Boushehri, Carsten Marr:
InstantDL: an easy-to-use deep learning pipeline for image segmentation and classification. 103 - Robert H. Dolin, Shaileshbhai R. Gothi, Aziz A. Boxwala, Bret S. E. Heale, Ammar Husami, James Jones, Himanshu Khangar, Shubham Londhe, Frank Naeymi-Rad, Soujanya Rao, Barbara Rapchak, James Shalaby, Varun Suraj, Ning Xie, Srikar Chamala, Gil Alterovitz:
vcf2fhir: a utility to convert VCF files into HL7 FHIR format for genomics-EHR integration. 104 - Jakob Willforss, Valentina Siino, Fredrik Levander:
OmicLoupe: facilitating biological discovery by interactive exploration of multiple omic datasets and statistical comparisons. 107 - Heeju Noh, Ziyi Hua, Panagiotis Chrysinas, Jason E. Shoemaker, Rudiyanto Gunawan:
DeltaNeTS+: elucidating the mechanism of drugs and diseases using gene expression and transcriptional regulatory networks. 108 - Marwan A. Hawari, Celine S. Hong, Leslie G. Biesecker:
SomatoSim: precision simulation of somatic single nucleotide variants. 109 - Mateusz Garbulowski, Klev Diamanti, Karolina Smolinska, Nicholas Baltzer, Patricia Stoll, Susanne Bornelöv, Aleksander Øhrn, Lars Feuk, Jan Komorowski:
R.ROSETTA: an interpretable machine learning framework. 110 - Fetulhak Abdurahman, Kinde Anlay Fante, Mohammed Aliy:
Malaria parasite detection in thick blood smear microscopic images using modified YOLOV3 and YOLOV4 models. 112 - Kevin De Angeli, Shang Gao, Mohammed M. Alawad, Hong-Jun Yoon, Noah Schaefferkoetter, Xiao-Cheng Wu, Eric B. Durbin, Jennifer A. Doherty, Antoinette Stroup, Linda Coyle, Lynne Penberthy, Georgia D. Tourassi:
Deep active learning for classifying cancer pathology reports. 113 - Hao Chen, Yan Lu, Dongsheng Lu, Shuhua Xu:
Y-LineageTracker: a high-throughput analysis framework for Y-chromosomal next-generation sequencing data. 114 - Eleanor F. Miller, Andrea Manica:
mtDNAcombine: tools to combine sequences from multiple studies. 115 - David Toubiana, Helena Maruenda:
Guidelines for correlation coefficient threshold settings in metabolite correlation networks exemplified on a potato association panel. 116 - Xiao Liang, Kyle Akers, Ishi Keenum, Lauren Wind, Suraj Gupta, Chaoqi Chen, Reem Aldaihani, Amy Pruden, Liqing Zhang, Katharine F. Knowlton, Kang Xia, Lenwood S. Heath:
AgroSeek: a system for computational analysis of environmental metagenomic data and associated metadata. 117 - Zachary Deng, Eric Delwart:
ContigExtender: a new approach to improving de novo sequence assembly for viral metagenomics data. 119 - Pierre-Julien Viailly, Vincent Sater, Mathieu Viennot, Élodie Bohers, Nicolas Vergne, Caroline Bérard, Hélène Dauchel, Thierry Lecroq, Alison Celebi, Philippe Ruminy, Vinciane Marchand, Marie-Delphine Lanic, Sydney Dubois, Dominique Penther, Hervé Tilly, Sylvain Mareschal, Fabrice Jardin:
Improving high-resolution copy number variation analysis from next generation sequencing using unique molecular identifiers. 120 - Elena Tea Russo, Alessandro Laio, Marco Punta:
Density Peak clustering of protein sequences associated to a Pfam clan reveals clear similarities and interesting differences with respect to manual family annotation. 121 - Richard M. Jiang, Arya A. Pourzanjani, Mitchell J. Cohen, Linda R. Petzold:
Associations of longitudinal D-Dimer and Factor II on early trauma survival risk. 122 - Lisa Amrhein, Christiane Fuchs:
stochprofML: stochastic profiling using maximum likelihood estimation in R. 123 - Samuel Martin, Richard M. Leggett:
Alvis: a tool for contig and read ALignment VISualisation and chimera detection. 124 - Katie L. Ovens, Farhad Maleki, B. Frank Eames, Ian McQuillan:
Juxtapose: a gene-embedding approach for comparing co-expression networks. 125 - Liangliang Zhang, Yushu Shi, Kim-Anh Do, Christine B. Peterson, Robert R. Jenq:
ProgPerm: Progressive permutation for a dynamic representation of the robustness of microbiome discoveries. 126 - Xiaopeng Ma, Ruiqi Huang, Xikun Wu, Pei Zhang:
Dualmarker: a flexible toolset for exploratory analysis of combinatorial dual biomarkers for clinical efficacy. 127 - Zhujie Gu, Said el Bouhaddani, Jiayi Pei, Jeanine J. Houwing-Duistermaat, Hae-Won Uh:
Statistical integration of two omics datasets using GO2PLS. 131 - Arika Fukushima, Masahiro Sugimoto, Satoru Hiwa, Tomoyuki Hiroyasu:
Bayesian approach for predicting responses to therapy from high-dimensional time-course gene expression profiles. 132 - Jingjing Wang, Yanpeng Zhao, Weikang Gong, Yang Liu, Mei Wang, Xiaoqian Huang, Jianjun Tan:
EDLMFC: an ensemble deep learning framework with multi-scale features combination for ncRNA-protein interaction prediction. 133 - Tuure Hameri, Georgios Fengos, Vassily Hatzimanikatis:
The effects of model complexity and size on metabolic flux distribution and control: case study in Escherichia coli. 134 - Yiqun Zhang, Fengju Chen, Chad Creighton:
SVExpress: identifying gene features altered recurrently in expression with nearby structural variant breakpoints. 135 - Zhuangwei Shi, Han Zhang, Chen Jin, Xiongwen Quan, Yanbin Yin:
A representation learning model based on variational inference and graph autoencoder for predicting lncRNA-disease associations. 136 - Christof Seiler, Anne-Maud Ferreira, Lisa M. Kronstad, Laura J. Simpson, Mathieu Le Gars, Elena Vendrame, Catherine A. Blish, Susan P. Holmes:
CytoGLMM: conditional differential analysis for flow and mass cytometry experiments. 137 - Yuting Dai, Aining Xu, Jianfeng Li, Liang Wu, Shanhe Yu, Jun Chen, Weili Zhao, Xiao-Jian Sun, Jinyan Huang:
CytoTree: an R/Bioconductor package for analysis and visualization of flow and mass cytometry data. 138 - Marius A. Wenzel, Berndt Müller, Jonathan Pettitt:
SLIDR and SLOPPR: flexible identification of spliced leader trans-splicing and prediction of eukaryotic operons from RNA-Seq data. 140 - Fumihiko Takeuchi, Norihiro Kato:
Nonlinear ridge regression improves cell-type-specific differential expression analysis. 141 - Ruiming Li, Chun-Yu Lin, Weifeng Guo, Tatsuya Akutsu:
Weighted minimum feedback vertex sets and implementation in human cancer genes detection. 143 - Umberto Ferraro Petrillo, Francesco Palini, Giuseppe Cattaneo, Raffaele Giancarlo:
FASTA/Q data compressors for MapReduce-Hadoop genomics: space and time savings made easy. 144 - Martin Lycka, Vratislav Peska, Martin Demko, Ioannis Spyroglou, Agata Kilar, Jirí Fajkus, Miloslava Fojtová:
WALTER: an easy way to online evaluate telomere lengths from terminal restriction fragment analysis. 145 - Silvia Madritsch, Agnes Burg, Eva M. Sehr:
Comparing de novo transcriptome assembly tools in di- and autotetraploid non-model plant species. 146 - Zhong Ren, Gundula Povysil, Joseph A. Hostyk, Hongzhu Cui, Nitin Bhardwaj, David B. Goldstein:
ATAV: a comprehensive platform for population-scale genomic analyses. 149 - Giulia Fiscon, Paola Paci:
SAveRUNNER: an R-based tool for drug repurposing. 150 - Linjun Zhou, Deling Fan, Wei Yin, Wen Gu, Zhen Wang, Jining Liu, Yanhua Xu, Lili Shi, Mingqing Liu, Guixiang Ji:
Comparison of seven in silico tools for evaluating of daphnia and fish acute toxicity: case study on Chinese Priority Controlled Chemicals and new chemicals. 151 - Jiani Ma, Lin Zhang, Jin Chen, Bowen Song, Chenxuan Zang, Hui Liu:
m7GDisAI: N7-methylguanosine (m7G) sites and diseases associations inference based on heterogeneous network. 152 - Xinyu Li, Wei Zhang, Jianming Zhang, Guang Li:
ModularBoost: an efficient network inference algorithm based on module decomposition. 153 - Shima Hadifar, Shayan Mostafaei, Ava Behrouzi, Abolfazl Fateh, Parisa Riahi, Seyed Davar Siadat, Farzam Vaziri:
Strain-specific behavior of Mycobacterium tuberculosis in A549 lung cancer cell line. 154 - Juming Pan:
Improved two-stage model averaging for high-dimensional linear regression, with application to Riboflavin data analysis. 155 - Danying Shao, Nabeel Ahmed, Nishant Soni, Edward P. O'Brien:
RiboA: a web application to identify ribosome A-site locations in ribosome profiling data. 156 - Andrew J. Kavran, Aaron Clauset:
Denoising large-scale biological data using network filters. 157 - Lidong Guo, Mengyang Xu, Wenchao Wang, Shengqiang Gu, Xia Zhao, Fang Chen, Ou Wang, Xun Xu, Inge Seim, Guangyi Fan, Li Deng, Xin Liu:
SLR-superscaffolder: a de novo scaffolding tool for synthetic long reads using a top-to-bottom scheme. 158 - Dawit A. Yohannes, Katri Kaukinen, Kalle Kurppa, Päivi Saavalainen, Dario Greco:
Clustering based approach for population level identification of condition-associated T-cell receptor β-chain CDR3 sequences. 159 - Jeremy Fan, Steven Huang, Samuel D. Chorlton:
BugSeq: a highly accurate cloud platform for long-read metagenomic analyses. 160 - Bailong Liu, Xiaoyan Zhu, Lei Zhang, Zhizheng Liang, Zhengwei Li:
Combined embedding model for MiRNA-disease association prediction. 161 - Jiefu Li, Jung-Youn Lee, Li Liao:
A new algorithm to train hidden Markov models for biological sequences with partial labels. 162 - Sondes Haddad-Boubaker, Houcemeddine Othman, Rabeb Touati, Kaouther Ayouni, Marwa Lakhal, Imen Ben Mustapha, Kais Ghedira, Maher Kharrat, Henda Triki:
In silico comparative study of SARS-CoV-2 proteins and antigenic proteins in BCG, OPV, MMR and other vaccines: evidence of a possible putative protective effect. 163 - The Tien Mai, Paul Turner, Jukka Corander:
Boosting heritability: estimating the genetic component of phenotypic variation with multiple sample splitting. 164 - Ming He, Chen Huang, Bo Liu, Yadong Wang, Junyi Li:
Factor graph-aggregated heterogeneous network embedding for disease-gene association prediction. 165 - Kishan KC, Sridevi K. Subramanya, Rui Li, Feng Cui:
Machine learning predicts nucleosome binding modes of transcription factors. 166 - Qinghong Dai, Tao Liu, Yongchao Gao, Honghao Zhou, Xiong Li, Wei Zhang:
Six genes involved in prognosis of hepatocellular carcinoma identified by Cox hazard regression. 167 - Emily R. Flynn, Annie Chang, Russ B. Altman:
Large-scale labeling and assessment of sex bias in publicly available expression data. 168 - Linyu Wang, Xiaodan Zhong, Shuo Wang, Hao Zhang, Yuanning Liu:
A novel end-to-end method to predict RNA secondary structure profile based on bidirectional LSTM and residual neural network. 169 - Mohammad A. Tabatabai, Stephanie Bailey, Zoran Bursac, Habib Tabatabai, Derek Wilus, Karan P. Singh:
An introduction to new robust linear and monotonic correlation coefficients. 170 - Yingxi Yang, Hui Wang, Wen Li, Xiaobo Wang, Shizhao Wei, Yulong Liu, Yan Xu:
Prediction and analysis of multiple protein lysine modified sites based on conditional wasserstein generative adversarial networks. 171 - Artur van Bemmelen van der Plaat, Rob van Treuren, Theo J. L. van Hintum:
Reliable genomic strategies for species classification of plant genetic resources. 173 - Trevor S. Frisby, Shawn J. Baker, Guillaume Marçais, Quang Minh Hoang, Carl Kingsford, Christopher J. Langmead:
Harvestman: a framework for hierarchical feature learning and selection from whole genome sequencing data. 174 - Rong Zhu, Yong Wang, Jin-Xing Liu, Ling-Yun Dai:
IPCARF: improving lncRNA-disease association prediction using incremental principal component analysis feature selection and a random forest classifier. 175 - Beatriz Galindo-Prieto, Paul Geladi, Johan Trygg:
Multiblock variable influence on orthogonal projections (MB-VIOP) for enhanced interpretation of total, global, local and unique variations in OnPLS models. 176 - Adrià Antich, Creu Palacin, Owen S. Wangensteen, Xavier Turon:
To denoise or to cluster, that is not the question: optimizing pipelines for COI metabarcoding and metaphylogeography. 177 - Yi Chen, Fons J. Verbeek, Katherine Wolstencroft:
Establishing a consensus for the hallmarks of cancer based on gene ontology and pathway annotations. 178 - Gnanendra Shanmugam, Song Hee Lee, Junhyun Jeon:
EzMAP: Easy Microbiome Analysis Platform. 179 - James M. Kunert-Graf, Nikita A. Sakhanenko, David J. Galas:
Optimized permutation testing for information theoretic measures of multi-gene interactions. 180 - Jeffrey N. Dudley, Celine S. Hong, Marwan A. Hawari, Jasmine Shwetar, Julie C. Sapp, Justin Lack, Henoke Shiferaw, Jennifer J. Johnston, Leslie G. Biesecker:
Low-level variant calling for non-matched samples using a position-based and nucleotide-specific approach. 181 - Aleksandra Gruca, Joanna Ziemska-Legiecka, Patryk Jarnot, Elzbieta Sarnowska, Tomasz J. Sarnowski, Marcin Grynberg:
Common low complexity regions for SARS-CoV-2 and human proteomes as potential multidirectional risk factor in vaccine development. 182 - Haipeng Xing, Yingru Wu, Michael Q. Zhang, Yong Chen:
Deciphering hierarchical organization of topologically associated domains through change-point testing. 183 - Yang Wang, Zhanchao Li, Yanfei Zhang, Yingjun Ma, Qixing Huang, Xingyu Chen, Zong Dai, Xiaoyong Zou:
Performance improvement for a 2D convolutional neural network by using SSC encoding on protein-protein interaction tasks. 184 - Tao Zhou, Libin Chen, Jing Guo, Mengmeng Zhang, Yanrui Zhang, Shanbo Cao, Feng Lou, Haijun Wang:
MSIFinder: a python package for detecting MSI status using random forest classifier. 185 - Bobby Ranjan, Florian Schmidt, Wenjie Sun, Jinyu Park, Mohammad Amin Honardoost, Joanna Tan, Nirmala Arul Rayan, Shyam Prabhakar:
scConsensus: combining supervised and unsupervised clustering for cell type identification in single-cell RNA sequencing data. 186 - Khushnood Abbas, Alireza Abbasi, Shi Dong, Niu Ling, Laihang Yu, Bolun Chen, Shi-Min Cai, Qambar Hasan:
Application of network link prediction in drug discovery. 187 - Xinshan Zhu, Jiayu Wang, Biao Sun, Chao Ren, Ting Yang, Jie Ding:
An efficient ensemble method for missing value imputation in microarray gene expression data. 188 - Stefan Gerber, Gerhard Schratt, Pierre-Luc Germain:
Streamlining differential exon and 3′ UTR usage with diffUTR. 189 - Baptiste Colcombet-Cazenave, Karen Druart, Crystel Bonnet, Christine Petit, Olivier Sperandio, Julien Guglielmini, Nicolas Wolff:
Phylogenetic analysis of Harmonin homology domains. 190 - Chengshu Xie, Shaurya Jauhari, Antonio Mora:
Popularity and performance of bioinformatics software: the case of gene set analysis. 191 - Eu-Tteum Baek, Hyung Jeong Yang, Soo-Hyung Kim, Guee-Sang Lee, In-Jae Oh, Sae-Ryung Kang, Jung-Joon Min:
Survival time prediction by integrating cox proportional hazards network and distribution function network. 192 - Xi Chen, Xu Shi, Andrew F. Neuwald, Leena Hilakivi-Clarke, Robert Clarke, Jianhua Xuan:
ChIP-BIT2: a software tool to detect weak binding events using a Bayesian integration approach. 193 - Harold P. Frisch, Allan Sprau, Virginia F. McElroy, James D. Turner, Laura R. E. Becher, Wendy K. Nevala, Alexey A. Leontovich, Svetomir N. Markovic:
Cancer immune control dynamics: a clinical data driven model of systemic immunity in patients with metastatic melanoma. 197 - Muhammad Muneeb, Andreas Henschel:
Eye-color and Type-2 diabetes phenotype prediction from genotype data using deep learning methods. 198 - Snorre Sulheim, Fredrik A. Fossheim, Alexander Wentzel, Eivind Almaas:
Correction to: Automatic reconstruction of metabolic pathways from identified biosynthetic gene clusters. 199 - Neel Patel, William S. Bush:
Modeling transcriptional regulation using gene regulatory networks based on multi-omics data sources. 200 - An Zheng, Michael Lamkin, Yutong Qiu, Kevin Ren, Alon Goren, Melissa Gymrek:
A flexible ChIP-sequencing simulation toolkit. 201 - Jesse T. Chao, Calvin D. Roskelley, Christopher J. R. Loewen:
MAPS: machine-assisted phenotype scoring enables rapid functional assessment of genetic variants by high-content microscopy. 202 - Marvin van Aalst, Oliver Ebenhöh, Anna Matuszynska:
Constructing and analysing dynamic models with modelbase v1.2.3: a software update. 203 - Seyedeh Zahra Sajadi, Mohammad Ali Zare Chahooki, Sajjad Gharaghani, Karim Abbasi:
AutoDTI++: deep unsupervised learning for DTI prediction by autoencoders. 204 - Sagnik Banerjee, Priyanka Bhandary, Margaret Woodhouse, Taner Z. Sen, Roger P. Wise, Carson M. Andorf:
FINDER: an automated software package to annotate eukaryotic genes from RNA-Seq data and associated protein sequences. 205 - Henry E. Miller, Alexander J. R. Bishop:
Correlation AnalyzeR: functional predictions from gene co-expression correlations. 206 - Xueyuan Cao, Stan Pounds:
Gene-set distance analysis (GSDA): a powerful tool for gene-set association analysis. 207 - Suzanne M. Paley, Peter D. Karp:
The BioCyc Metabolic Network Explorer. 208 - Nicola Licheri, Vincenzo Bonnici, Marco Beccuti, Rosalba Giugno:
GRAPES-DD: exploiting decision diagrams for index-driven search in biological graph databases. 209 - Qing Ning, Dali Wang, Fei Cheng, Yuheng Zhong, Qi Ding, Jing You:
Predicting rifampicin resistance mutations in bacterial RNA polymerase subunit beta based on majority consensus. 210 - Zechuan Chen, Zeruo Yang, Xiaojun Yuan, Xiaoming Zhang, Pei Hao:
scSensitiveGeneDefine: sensitive gene detection in single-cell RNA sequencing data by Shannon entropy. 211 - Markos N. Xenakis, Dimos Kapetis, Yang Yang, Monique M. Gerrits, Jordi Heijman, Stephen G. Waxman, Giuseppe Lauria, Catharina G. Faber, Ronald L. Westra, Patrick J. Lindsey, Hubert J. M. Smeets:
Hydropathicity-based prediction of pain-causing NaV1.7 variants. 212 - Sayed Asaduzzaman, Md. Raihan Ahmed, Hasin Rehana, Setu Chakraborty, Md. Shariful Islam, Touhid Bhuiyan:
Machine learning to reveal an astute risk predictive framework for Gynecologic Cancer and its impact on women psychology: Bangladeshi perspective. 213 - Michael Wybrow, Peter Rodgers, Fadi K. Dib:
Euler diagrams drawn with ellipses area-proportionally (Edeap). 214 - Jose Francisco Sanchez Herrero, Raquel Pluvinet, Antonio Luna de Haro, Lauro Sumoy:
Paired-end small RNA sequencing reveals a possible overestimation in the isomiR sequence repertoire previously reported from conventional single read data analysis. 215 - Yun Zuo, Jianyuan Lin, Xiangxiang Zeng, Quan Zou, Xiangrong Liu:
CarSite-II: an integrated classification algorithm for identifying carbonylated sites based on K-means similarity-based undersampling and synthetic minority oversampling techniques. 216 - Shiming Yang, Yaping Zhou, Xiangxin Zhang, Lu Wang, Jianfeng Fu, Xiaotong Zhao, Liu Yang:
The prognostic value of an autophagy-related lncRNA signature in hepatocellular carcinoma. 217 - Maria Zanti, Kyriaki Michailidou, Maria Loizidou, Christina Machattou, Panagiota Pirpa, Kyproula Christodoulou, George M. Spyrou, Kyriacos Kyriacou, Andreas Hadjisavvas:
Performance evaluation of pipelines for mapping, variant calling and interval padding, for the analysis of NGS germline panels. 218 - Dayun Liu, Yibiao Huang, Wenjuan Nie, Jiaxuan Zhang, Lei Deng:
SMALF: miRNA-disease associations prediction based on stacked autoencoder and XGBoost. 219 - Jeongmin Bae, Hajin Jeon, Min-Soo Kim:
GPrimer: a fast GPU-based pipeline for primer design for qPCR experiments. 220 - Rahi Jain, Wei Xu:
Dynamic model updating (DMU) approach for statistical learning model building with missing data. 221 - Witold Dyrka, Marlena Gasior-Glogowska, Monika Szefczyk, Natalia Szulc:
Searching for universal model of amyloid signaling motifs using probabilistic context-free grammars. 222 - Jin Li, Wenjie Liu, Huang Li, Feng Chen, Haoran Luo, Peihua Bao, Yanzhao Li, Hailong Jiang, Yue Gao, Hong Liang, Shiaofen Fang:
Genome-wide variant-based study of genetic effects with the largest neuroanatomic coverage. 223 - Nicholas J. Eagles, Emily E. Burke, Jacob Leonard, Brianna K. Barry, Joshua M. Stolz, Louise Huuki, BaDoi N. Phan, Violeta Larios Serrato, Everardo Gutiérrez-Millán, Israel Aguilar-Ordoñez, Andrew E. Jaffe, Leonardo Collado-Torres:
SPEAQeasy: a scalable pipeline for expression analysis and quantification for R/bioconductor-powered RNA-seq analyses. 224 - Ben Bettisworth, Alexandros Stamatakis:
Root Digger: a root placement program for phylogenetic trees. 225 - Charles C. David, Chris S. Avery, Donald J. Jacobs:
JEDi: java essential dynamics inspector - a molecular trajectory analysis toolkit. 226 - Samuel M. Gerner, Alexandra B. Graf, Thomas Rattei:
Tamock: simulation of habitat-specific benchmark data in metagenomics. 227 - Sarah S. Ji, Christopher A. German, Kenneth Lange, Janet S. Sinsheimer, Hua Zhou, Jin Zhou, Eric M. Sobel:
Modern simulation utilities for genetic analysis. 228 - Andreas Krämer, Jean-Noel Billaud, Stuart Tugendreich, Dan Shiffman, Martin Jones, Jeff Green:
The Coronavirus Network Explorer: mining a large-scale knowledge graph for effects of SARS-CoV-2 on host cell function. 229 - Pål V. Johnsen, Signe Riemer-Sørensen, Andrew Thomas DeWan, Megan E. Cahill, Mette Langaas:
A new method for exploring gene-gene and gene-environment interactions in GWAS with tree ensemble methods and SHAP values. 230 - Xiaoyun Yang, Liyuan Zhao, Fang Wei, Jing Li:
DeepNetBim: deep learning model for predicting HLA-epitope interactions based on network analysis by harnessing binding and immunogenicity information. 231 - Oliver Tills, John I. Spicer, Ziad Ibbini, Simon Rundle:
Spectral phenotyping of embryonic development reveals integrative thermodynamic responses. 232 - Michal R. Grzadkowski, Hannah D. Holly, Julia Somers, Emek Demir:
Systematic interrogation of mutation groupings reveals divergent downstream expression programs within key cancer genes. 233 - Bjørn André Bredesen, Marc Rehmsmeier:
MOCCA: a flexible suite for modelling DNA sequence motif occurrence combinatorics. 234 - Reto Gerber, Mark D. Robinson:
Censcyt: censored covariates in differential abundance analysis in cytometry. 235 - Steffen Klasberg, Alexander H. Schmidt, Vinzenz Lange, Gerhard Schöfl:
DR2S: an integrated algorithm providing reference-grade haplotype sequences from heterozygous samples. 236 - Michael A. Roth, Pranjal Jain, Jinkyu Koo, Somali Chaterji:
Simultaneous learning of individual microRNA-gene interactions and regulatory comodules. 237 - Cong Xu, Ting Liang, Fangrong Zhang, Jing Liu, Yunfeng Fu:
tRNA-derived fragments as novel potential biomarkers for relapsed/refractory multiple myeloma. 238 - Kyle Boone, Cate Wisdom, Kyle V. Camarda, Paulette Spencer, Candan Tamerler:
Combining genetic algorithm with machine learning strategies for designing potent antimicrobial peptides. 239 - Adrien Rougny, Loïc Paulevé, Michèle Teboul, Franck Delaunay:
A detailed map of coupled circadian clock and cell cycle with qualitative dynamics validation. 240 - Milad Mostavi, Yu-Chiao Chiu, Yidong Chen, Yufei Huang:
CancerSiamese: one-shot learning for predicting primary and metastatic tumor types unseen during model training. 244 - Aimeric Bruno, Jean-Marc Aury, Stefan Engelen:
BoardION: real-time monitoring of Oxford Nanopore sequencing instruments. 245 - Ying Li, Hang Sun, Shiyao Feng, Qi Zhang, Siyu Han, Wei Du:
Capsule-LPI: a LncRNA-protein interaction predicting tool based on a capsule network. 246 - Sanket Desai, Aishwarya Rane, Asim Joshi, Amit Dutt:
IPD 2.0: To derive insights from an evolving SARS-CoV-2 genome. 247 - Jiancheng Zhong, Chao Tang, Wei Peng, Minzhu Xie, Yusui Sun, Qiang Tang, Qiu Xiao, Jiahong Yang:
A novel essential protein identification method based on PPI networks and gene expression data. 248 - Yin Zhang, Fei Wang:
SSBER: removing batch effect for single-cell RNA sequencing data. 249 - Pietro Pinoli, Sriganesh Srihari, Limsoon Wong, Stefano Ceri:
Identifying collateral and synthetic lethal vulnerabilities within the DNA-damage response. 250 - Dongbin Park, Yoonsoo Hahn:
Rapid protein sequence evolution via compensatory frameshift is widespread in RNA virus genomes. 251 - Alexander Partin, Thomas S. Brettin, Yvonne A. Evrard, Yitan Zhu, Hyun Seung Yoo, Fangfang Xia, Songhao Jiang, Austin Clyde, Maulik Shukla, Michael Fonstein, James H. Doroshow, Rick L. Stevens:
Learning curves for drug response prediction in cancer cell lines. 252 - Emily A. King, Fengjiao Dunbar, Justin Wade Davis, Jacob F. Degner:
Estimating colocalization probability from limited summary statistics. 254 - Yuanyuan Li, Ping Luo, Yi Lu, Fang-Xiang Wu:
Identifying cell types from single-cell data based on similarities and dissimilarities between cells. 255 - Teresita M. Porter, Mehrdad Hajibabaei:
Profile hidden Markov model sequence analysis can help remove putative pseudogenes from DNA barcoding and metabarcoding datasets. 256 - Yiqing Yan, Nimisha Chaturvedi, Raja Appuswamy:
Accel-Align: a fast sequence mapper and aligner based on the seed-embed-extend method. 257 - Janka Puterová, Tomás Martínek:
digIS: towards detecting distant and putative novel insertion sequence elements in prokaryotic genomes. 258 - In-Hee Lee, Yufei Lin, William Jefferson Alvarez, Carles Hernandez-Ferrer, Kenneth D. Mandl, Sek Won Kong:
WEScover: selection between clinical whole exome sequencing and gene panel testing. 259 - David Borland, Carolyn M. McCormick, Niyanta K. Patel, Oleh Krupa, Jessica T. Mory, Alvaro A. Beltran, Tala M. Farah, Carla F. Escobar-Tomlienovich, Sydney S. Olson, Minjeong Kim, Guorong Wu, Jason L. Stein:
Segmentor: a tool for manual refinement of 3D microscopy annotations. 260 - Farshid Shirafkan, Sajjad Gharaghani, Karim Rahimian, Reza Hasan Sajedi, Javad Zahiri:
Moonlighting protein prediction using physico-chemical and evolutional properties via machine learning methods. 261 - Kai Kang, Caizhi Huang, Yuanyuan Li, David M. Umbach, Leping Li:
CDSeqR: fast complete deconvolution for gene expression data from bulk tissues. 262 - Ege Ülgen, Osman Ugur Sezerman:
driveR: a novel method for prioritizing cancer driver genes using somatic genomics data. 263 - Gilad Ben Or, Isana Veksler-Lublinsky:
Comprehensive machine-learning-based analysis of microRNA-target interactions reveals variable transferability of interaction rules across species. 264 - Zachary D. Wallen:
Comparison study of differential abundance testing methods using two large Parkinson disease gut microbiome datasets derived from 16S amplicon sequencing. 265 - Dimitra Sarantopoulou, Thomas G. Brooks, Soumyashant Nayak, Antonijo Mrcela, Nicholas F. Lahens, Gregory R. Grant:
Comparative evaluation of full-length isoform quantification from RNA-Seq. 266 - Gwenaëlle G. Lemoine, Marie-Pier Scott-Boyer, Bathilde Ambroise, Olivier Périn, Arnaud Droit:
GWENA: gene co-expression networks analysis and extended modules characterization in a single Bioconductor package. 267 - Jing Tian, Jianping Zhao, Chunhou Zheng:
Clustering of cancer data based on Stiefel manifold for multiple views. 268 - Sejin Park, Jihee Soh, Hyunju Lee:
Super.FELT: supervised feature extraction learning using triplet loss for drug response prediction with multi-omics data. 269 - Gezheng Xu, Wenge Rong, Yanmeng Wang, Yuanxin Ouyang, Zhang Xiong:
External features enriched model for biomedical question answering. 272 - Kshitij Srivastava, Anne-Sophie Fratzscher, Bo Lan, Willy Albert Flegel:
Cataloguing experimentally confirmed 80.7 kb-long ACKR1 haplotypes from the 1000 Genomes Project database. 273 - Kevin Chappell, Stefan Graw, Charity L. Washam, Aaron J. Storey, Chris Bolden, Eric C. Peterson, Stephanie D. Byrum:
PTMViz: a tool for analyzing and visualizing histone post translational modification data. 275 - William R. P. Denault, Astanand Jugessur:
Correction to: Detecting differentially methylated regions using a fast wavelet-based approach to functional association analysis. 276 - John Anders, Hannes Petruschke, Nico Jehmlich, Sven-Bastiaan Haange, Martin von Bergen, Peter F. Stadler:
A workflow to identify novel proteins based on the direct mapping of peptide-spectrum-matches to genomic locations. 277 - Giovanni Scala, Antonio Federico, Dario Greco:
CpGmotifs: a tool to discover DNA motifs associated to CpG methylation events. 278 - Swapna Vidhur Daulatabad, Rajneesh Srivastava, Sarath Chandra Janga:
Lantern: an integrative repository of functional annotations for lncRNAs in the human genome. 279 - Madalina Ciortan, Matthieu Defrance:
Contrastive self-supervised clustering of scRNA-seq data. 280 - Jindan Guo, Erli Pang, Hongtao Song, Kui Lin:
A tri-tuple coordinate system derived for fast and accurate analysis of the colored de Bruijn graph-based pangenomes. 282 - Mengya Liu, Yun Xu:
An effective method to resolve ambiguous bisulfite-treated reads. 283 - Chengyuan Sha, Miroslava Cuperlovic-Culf, Ting Hu:
SMILE: systems metabolomics using interpretable learning and evolution. 284 - Nicola De Maio, Alexander V. Alekseyenko, William J. Coleman-Smith, Fabio Pardi, Marc A. Suchard, Asif U. Tamuri, Jakub Truszkowski, Nick Goldman:
A phylogenetic approach for weighting genetic sequences. 285 - Yu Wan, Zhuo Wang, Tzong-Yi Lee:
Incorporating support vector machine with sequential minimal optimization to identify anticancer peptides. 286 - Song Feng, Emily Heath, Brett A. Jefferson, Cliff A. Joslyn, Henry Kvinge, Hugh D. Mitchell, Brenda Praggastis, Amie J. Eisfeld, Amy C. Sims, Larissa B. Thackray, Shufang Fan, Kevin B. Walters, Peter J. Halfmann, Danielle Westhoff-Smith, Qing Tan, Vineet D. Menachery, Timothy P. Sheahan, Adam S. Cockrell, Jacob F. Kocher, Kelly G. Stratton, Natalie C. Heller, Lisa M. Bramer, Michael S. Diamond, Ralph S. Baric, Katrina M. Waters, Yoshihiro Kawaoka, Jason E. McDermott, Emilie Purvine:
Hypergraph models of biological networks to identify genes critical to pathogenic viral response. 287 - Lin Zhang, Gangshen Li, Xiuyu Li, Honglei Wang, Shutao Chen, Hui Liu:
EDLm6APred: ensemble deep learning approach for mRNA m6A site prediction. 288 - Shiyang Zeng, Yuwei Hua, Yong Zhang, Guifen Liu, Chengchen Zhao:
GLEANER: a web server for GermLine cycle Expression ANalysis and Epigenetic Roadmap visualization. 289 - Maxim Ivanov, Albin Sandelin, Sebastian Marquardt:
TrancriptomeReconstructoR: data-driven annotation of complex transcriptomes. 290 - Daniele Dall'Olio, Nico Curti, Eugenio Fonzi, Claudia Sala, Daniel Remondini, Gastone C. Castellani, Enrico Giampieri:
Correction to: Impact of concurrency on the performance of a whole exome sequencing pipeline. 292 - Gulden Olgun, Afshan Nabi, Öznur Tastan:
NoRCE: non-coding RNA sets cis enrichment tool. 294 - Huiwei Zhou, Zhe Liu, Chengkun Lang, Yibin Xu, Yingyu Lin, Junjie Hou:
Improving the recall of biomedical named entity recognition with label re-correction and knowledge distillation. 295 - Lindsay M. W. Piel, Codie J. Durfee, Stephen N. White:
Proteome-wide analysis of Coxiella burnetii for conserved T-cell epitopes with presentation across multiple host species. 296 - Zengchao Mu, Ting Yu, Xiaoping Liu, Hongyu Zheng, Leyi Wei, Juntao Liu:
FEGS: a novel feature extraction model for protein sequences and its applications. 297 - Alessandro La Ferlita, Salvatore Alaimo, Sebastiano Di Bella, Emanuele Martorana, Georgios I. Laliotis, Francesco Bertoni, Luciano Cascione, Philip N. Tsichlis, Alfredo Ferro, Roberta Bosotti, Alfredo Pulvirenti:
RNAdetector: a free user-friendly stand-alone and cloud-based system for RNA-Seq data analysis. 298 - Juanjuan Chen, Anqi Wang, Qi Wang:
Dysbiosis of the gut microbiome is a risk factor for osteoarthritis in older female adults: a case control study. 299 - Xiaomei Li, Buu Minh Thanh Truong, Taosheng Xu, Lin Liu, Jiuyong Li, Thuc Duy Le:
Uncovering the roles of microRNAs/lncRNAs in characterising breast cancer subtypes and prognosis. 300 - Thomas E. Bartlett:
Fusion of single-cell transcriptome and DNA-binding data, for genomic network inference in cortical development. 301 - Rachel Nadeau, Anastasiia Byvsheva, Mathieu Lavallée-Adam:
PIGNON: a protein-protein interaction-guided functional enrichment analysis for quantitative proteomics. 302 - Nadège Guiglielmoni, Antoine Houtain, Alessandro Derzelle, Karine Van Doninck, Jean-François Flot:
Overcoming uncollapsed haplotypes in long-read assemblies of non-model organisms. 303 - Yunfeng Wang, Haoliang Xue, Christine Pourcel, Yang Du, Daniel Gautheret:
2-kupl: mapping-free variant detection from DNA-seq data of matched samples. 304 - Jia-You Lin, Bao-Rong Juo, Yu-Hsuan Yeh, Shu-Hsuan Fu, Yi-Ting Chen, Chien-Lun Chen, Kun-Pin Wu:
Putative markers for the detection of early-stage bladder cancer selected by urine metabolomics. 305 - Zong-Lan Zuo, Rui-Fen Cao, Pi-Jing Wei, Jun-Feng Xia, Chun-Hou Zheng:
Double matrix completion for circRNA-disease association prediction. 307 - Andrea Tangherloni, Federico Ricciuti, Daniela Besozzi, Pietro Liò, Ana Cvejic:
Analysis of single-cell RNA sequencing data based on autoencoders. 309 - Theo R. Allnutt, Alexandra J. Roth-Schulze, Leonard C. Harrison:
Expanding the taxonomic range in the fecal metagenome. 312 - Hugo Talibart, François Coste:
PPalign: optimal alignment of Potts models representing proteins with direct coupling information. 317 - Qichao Luo, Shenglong Mo, Yunfei Xue, Xiangzhou Zhang, Yuliang Gu, Lijuan Wu, Jia Zhang, Linyan Sun, Mei Liu, Yong Hu:
Novel deep learning-based transcriptome data analysis for drug-drug interaction prediction with an application in diabetes. 318 - Muhammad Muneeb, Andreas Henschel:
Correction to: Eye‑color and Type‑2 diabetes phenotype prediction from genotype data using deep learning methods. 319 - Javier López-Ibáñez, Florencio Pazos, Monica Chagoyen:
Predicting biological pathways of chemical compounds with a profile-inspired approach. 320 - Xiaolan Chen, Hui Yang, Guifen Liu, Yong Zhang:
NUCOME: A comprehensive database of nucleosome organization referenced landscapes in mammalian genomes. 321 - Hiroaki Kato, Mitsuhiro Shimizu, Takeshi Urano:
Chemical map-based prediction of nucleosome positioning using the Bioconductor package nuCpos. 322 - Arnaud Liehrmann, Guillem Rigaill, Toby Dylan Hocking:
Increased peak detection accuracy in over-dispersed ChIP-seq data with supervised segmentation models. 323 - Christopher A. Mela, Yang Liu:
Application of convolutional neural networks towards nuclei segmentation in localization-based super-resolution fluorescence microscopy images. 325 - Lanlan Wu, Fei Liu, Hongmin Cai:
IOAT: an interactive tool for statistical analysis of omics data and clinical data. 326 - Mohammad A. Tabatabai, Stephanie Bailey, Zoran Bursac, Habib Tabatabai, Derek Wilus, Karan P. Singh:
Correction to: An introduction to new robust linear and monotonic correlation coefficients. 328 - Cody Glickman, Jo Hendrix, Michael Strong:
Simulation study and comparative evaluation of viral contiguous sequence identification tools. 329 - Dongyan Ding, Tingyuan Lang, Dongling Zou, Jiawei Tan, Jia Chen, Lei Zhou, Dong Wang, Rong Li, Yunzhe Li, Jingshu Liu, Cui Ma, Qi Zhou:
Machine learning-based prediction of survival prognosis in cervical cancer. 331 - Lin Yuan, Jing Zhao, Tao Sun, Zhen Shen:
A machine learning framework that integrates multi-omics data predicts cancer-related LncRNAs. 332 - Alvaro Ras-Carmona, Marta Gomez-Perosanz, Pedro A. Reche:
Prediction of unconventional protein secretion by exosomes. 333 - Shaya Akbarinejad, Mostafa Hadadian Nejad Yousefi, Maziar Goudarzi:
SVNN: an efficient PacBio-specific pipeline for structural variations calling using neural networks. 335 - Håkon Tjeldnes, Kornel Labun, Yamila N. Torres cleuren, Katarzyna Chyzynska, Michal Swirski, Eivind Valen:
ORFik: a comprehensive R toolkit for the analysis of translation. 336 - Leili Zhang, Giacomo Domeniconi, Chih-Chieh Yang, Seung-gu Kang, Ruhong Zhou, Guojing Cong:
CASTELO: clustered atom subtypes aided lead optimization - a combined machine learning and molecular modeling method. 338 - Richard M. Jiang, Fredrik Wrede, Prashant Singh, Andreas Hellander, Linda R. Petzold:
Accelerated regression-based summary statistics for discrete stochastic systems via approximate simulators. 339 - Wan Kin Au Yeung, Osamu Maruyama, Hiroyuki Sasaki:
A convolutional neural network-based regression model to infer the epigenetic crosstalk responsible for CG methylation patterns. 341 - Prabina Kumar Meher, Anil Rai, Atmakuri Ramakrishna Rao:
mLoc-mRNA: predicting multiple sub-cellular localization of mRNAs using random forest algorithm coupled with feature selection via elastic net. 342 - Jordi Martorell-Marugan, Raúl López-Domínguez, Adrián García-Moreno, Daniel Toro-Domínguez, Juan Antonio Villatoro-García, Guillermo Barturen, Adoración Martín-Gómez, Kevin Troulé, Gonzalo Gómez-López, Fátima Al-Shahrour, Víctor González-Rumayor, María Peña-Chilet, Joaquín Dopazo, Julio Sáez-Rodríguez, Marta E. Alarcón-Riquelme, Pedro Carmona-Saez:
A comprehensive database for integrated analysis of omics data in autoimmune diseases. 343 - Yingbo Cui, Zihang Wang, Johannes Köster, Xiangke Liao, Shaoliang Peng, Tao Tang, Chun Huang, Canqun Yang:
VISPR-online: a web-based interactive tool to visualize CRISPR screening experiments. 344 - Dominik Drees, Aaron Scherzinger, René Hägerling, Friedemann Kiefer, Xiaoyi Jiang:
Scalable robust graph and feature extraction for arbitrary vessel networks in large volumetric datasets. 346 - Ittai B. Muller, Stijn Meijers, Peter Kampstra, Steven van Dijk, Michel van Elswijk, Marry Lin, Anna M. Wojtuszkiewicz, Gerrit Jansen, Robert de Jonge, Jacqueline Cloos:
Computational comparison of common event-based differential splicing tools: practical considerations for laboratory researchers. 347 - Miao Zhang, Yiwen Liu, Hua Zhou, Joseph Watkins, Jin Zhou:
A novel nonlinear dimension reduction approach to infer population structure for low-coverage sequencing data. 348 - Léa Pradier, Tazzio Tissot, Anna-Sophie Fiston-Lavier, Stéphanie Bedhomme:
PlasForest: a homology-based random forest classifier for plasmid detection in genomic datasets. 349 - Ching-Yu Shih, Amrita Chattopadhyay, Chien-Hui Wu, Yu-Wen Tien, Tzu-Pin Lu:
Transcript annotation tool (TransAT): an R package for retrieving annotations for transcript-specific genetic variants. 350 - Siyuan Liu, Tong Wang, Qijiang Xu, Bin Shao, Jian Yin, Tie-Yan Liu:
Complementing sequence-derived features with structural information extracted from fragment libraries for protein structure prediction. 351 - Zaynab Mousavian, Mehran Khodabandeh, Ali Sharifi-Zarchi, Alireza Nadafian, Alireza Mahmoudi:
StrongestPath: a Cytoscape application for protein-protein interaction analysis. 352 - Tianqi Wu, Zhiye Guo, Jie Hou, Jianlin Cheng:
Correction to: DeepDist: real‑value inter‑residue distance prediction with deep residual convolutional network. 354 - Luna L. Sánchez-Reyes, Martha Kandziora, Emily Jane McTavish:
Physcraper: a Python package for continually updated phylogenetic trees using the Open Tree of Life. 355 - Ruifeng Cui, Xiaoge Wang, Waqar Afzal Malik, Xuke Lu, Xiugui Chen, Delong Wang, Junjuan Wang, Shuai Wang, Chao Chen, Lixue Guo, Quanjia Chen, Wuwei Ye:
Genome-wide identification and expression analysis of Raffinose synthetase family in cotton. 356 - Qiang Yang, Xiaokun Li:
BiGAN: LncRNA-disease association prediction based on bidirectional generative adversarial network. 357 - Xue-Jun Chen, Xin-Yun Hua, Zhen-Ran Jiang:
ANMDA: anti-noise based computational model for predicting potential miRNA-disease associations. 358 - Lior Galanti, Dennis E. Shasha, Kristin C. Gunsalus:
Pheniqs 2.0: accurate, high-performance Bayesian decoding and confidence estimation for combinatorial barcode indexing. 359 - Marilisa Montemurro, Elena Grassi, Carmelo Gabriele Pizzino, Andrea Bertotti, Elisa Ficarra, Gianvito Urgese:
PhyliCS: a Python library to explore scCNA data and quantify spatial tumor heterogeneity. 360 - Galadriel Brière, Élodie Darbo, Patricia Thébault, Raluca Uricaru:
Consensus clustering applied to multi-omics disease subtyping. 361 - Emily Goren, Chong Wang, Zhulin He, Amy M. Sheflin, Dawn Chiniquy, Jessica E. Prenni, Susannah Tringe, Daniel P. Schachtman, Peng Liu:
Feature selection and causal analysis for microbiome studies in the presence of confounding using standardization. 362 - Ian Leifer, Mishael Sánchez-Pérez, Cecilia Ishida, Hernán A. Makse:
Predicting synchronized gene coexpression patterns from fibration symmetries in gene regulatory networks in bacteria. 363 - Tianyu Wang, Jun Bai, Sheida Nabavi:
Single-cell classification using graph convolutional networks. 364 - Justin Y. Lee, Britney Nguyen, Carlos Orosco, Mark P. Styczynski:
SCOUR: a stepwise machine learning framework for predicting metabolite-dependent regulatory interactions. 365 - Farshid Shirafkan, Sajjad Gharaghani, Karim Rahimian, Reza Hasan Sajedi, Javad Zahiri:
Correction to: Moonlighting protein prediction using physico‑chemical and evolutional properties via machine learning methods. 366 - Verônica R. de Melo Costa, Julianus Pfeuffer, Annita Louloupi, Ulf A. V. Ørom, Rosario M. Piro:
SPLICE-q: a Python tool for genome-wide quantification of splicing efficiency. 368 - Maxim Ivanov, Albin Sandelin, Sebastian Marquardt:
Publisher Correction to: TrancriptomeReconstructoR: data‑driven annotation of complex transcriptomes. 370 - Ruth Kristianingsih, Dan MacLean:
Accurate plant pathogen effector protein classification ab initio with deepredeff: an ensemble of convolutional neural networks. 372 - Phuoc Thien Truong Nguyen, Ilya Plyusnin, Tarja Sironen, Olli Vapalahti, Ravi Kant, Teemu Smura:
HAVoC, a bioinformatic pipeline for reference-based consensus assembly and lineage assignment for SARS-CoV-2 sequences. 373 - Dayne L. Filer, Fengshen Kuo, Alicia T. Brandt, Christian R. Tilley, Piotr A. Mieczkowski, Jonathan S. Berg, Kimberly Robasky, Yun Li, Chris Bizon, Jeffery L. Tilson, Bradford C. Powell, Darius M. Bost, Clark D. Jeffries, Kirk C. Wilhelmsen:
Pre-capture multiplexing provides additional power to detect copy number variation in exome sequencing. 374 - Alexandre Souvorov, Richa Agarwala:
SAUTE: sequence assembly using target enrichment. 375 - Natalja Kurbatova, Rowan Swiers:
Disease ontologies for knowledge graphs. 377 - Jinlong Hu, Lijie Cao, Tenghui Li, Shoubin Dong, Ping Li:
GAT-LI: a graph attention network based learning and interpreting method for functional brain network classification. 379 - Daishin Ueno, Harunori Kawabe, Shotaro Yamasaki, Taku Demura, Ko Kato:
Feature selection for RNA cleavage efficiency at specific sites using the LASSO regression model in Arabidopsis thaliana. 380 - Nicholas J. Eagles, Emily E. Burke, Jacob Leonard, Brianna K. Barry, Joshua M. Stolz, Louise Huuki, BaDoi N. Phan, Violeta Larios Serrato, Everardo Gutiérrez-Millán, Israel Aguilar-Ordoñez, Andrew E. Jaffe, Leonardo Collado-Torres:
Correction to: SPEAQeasy: a scalable pipeline for expression analysis and quantification for R/bioconductor‑powered RNA‑seq analyses. 381 - Ting Sun, Yufei He, Wendong Li, Guang Liu, Lin Li, Lu Wang, Zixuan Xiao, Xiaohan Han, Hao Wen, Yong Liu, Yifan Chen, Haoyu Wang, Jing Li, Yubo Fan, Wei Zhang, Jing Zhang:
neoDL: a novel neoantigen intrinsic feature-based deep learning model identifies IDH wild-type glioblastomas with the longest survival. 382 - Glen van Ginkel, Lukás Pravda, Jose M. Dana, Mihaly Varadi, Peter A. Keller, Stephen Anyango, Sameer Velankar:
PDBeCIF: an open-source mmCIF/CIF parsing and processing package. 383 - Shade Horn, Jacky L. Snoep, David D. van Niekerk:
Uncovering the effects of heterogeneity and parameter sensitivity on within-host dynamics of disease: malaria as a case study. 384 - Raziyeh Masumshah, Rosa Aghdam, Changiz Eslahchi:
A neural network-based method for polypharmacy side effects prediction. 385 - Yance Feng, Lei M. Li:
MUREN: a robust and multi-reference approach of RNA-seq transcript normalization. 386 - Tetsu Sakamoto, José Miguel Ortega:
Taxallnomy: an extension of NCBI Taxonomy that produces a hierarchically complete taxonomic tree. 388 - Onkar Singh, Wen-Lian Hsu, Emily Chia-Yu Su:
Co-AMPpred for in silico-aided predictions of antimicrobial peptides by integrating composition-based features. 389 - Santiago Redondo-Salvo, Roger Bartomeus-Peñalver, Luis Vielva, Kaitlin A. Tagg, Hattie E. Webb, Raúl Fernández-López, Fernando de la Cruz:
COPLA, a taxonomic classifier of plasmids. 390 - Sergio Marco Salas, Daniel Gyllborg, Christoffer Mattsson Langseth, Mats Nilsson:
Matisse: a MATLAB-based analysis toolbox for in situ sequencing expression maps. 391 - Audrey Hulot, Denis Laloë, Florence Jaffrézic:
A unified framework for the integration of multiple hierarchical clusterings or networks from multi-source data. 392 - Gulden Olgun, Afshan Nabi, Öznur Tastan:
Correction to: NoRCE: non‑coding RNA sets cis enrichment tool. 393 - Jingyi Liu, Ross Mawhorter, Nuo Liu, Santi Santichaivekin, Eliot C. Bush, Ran Libeskind-Hadas:
Maximum parsimony reconciliation in the DTLOR model. 394 - Erica Ponzi, Magne Thoresen, Therese Haugdahl Nøst, Kajsa Møllersen:
Integrative, multi-omics, analysis of blood samples improves model predictions: applications to cancer. 395 - Yang Xu, Rachel Patton McCord:
CoSTA: unsupervised convolutional neural network learning for spatial transcriptomics analysis. 397 - Jorge Oliveira, Miguel Antunes, Cláudia P. Godinho, Miguel C. Teixeira, Isabel Sá-Correia, Pedro T. Monteiro:
From a genome assembly to full regulatory network prediction: the case study of Rhodotorula toruloides putative Haa1-regulon. 399 - Alejandro A. Schäffer, Richard McVeigh, Barbara Robbertse, Conrad L. Schoch, Anjanette Johnston, Beverly A. Underwood, Ilene Karsch-Mizrachi, Eric P. Nawrocki:
Ribovore: ribosomal RNA sequence analysis for GenBank submissions and database curation. 400 - Cindy Perscheid:
Comprior: facilitating the implementation and automated benchmarking of prior knowledge-based feature selection approaches on gene expression data sets. 401 - Jochen Bathke, Gesine Lühken:
OVarFlow: a resource optimized GATK 4 based Open source Variant calling workFlow. 402 - Anand Ramachandran, Steven S. Lumetta, Eric W. Klee, Deming Chen:
HELLO: improved neural network architectures and methodologies for small variant calling. 404 - Hesham ElAbd, Frauke Degenhardt, Tomás Koudelka, Ann-Kristin Kamps, Andreas Tholey, Petra Bacher, Tobias L. Lenz, Andre Franke, Mareike Wendorff:
Immunopeptidomics toolkit library (IPTK): a python-based modular toolbox for analyzing immunopeptidomics data. 405 - Peter Michael Schwarz, Bernd Freisleben:
NOREC4DNA: using near-optimal rateless erasure codes for DNA storage. 406 - Lélia Polit, Gwenneg Kerdivel, Sebastian Gregoricchio, Michela Esposito, Christel Guillouf, Valentina Boeva:
CHIPIN: ChIP-seq inter-sample normalization based on signal invariance across transcriptionally constant genes. 407 - Kalyani Dhusia, Yinghao Wu:
Classification of protein-protein association rates based on biophysical informatics. 408 - James G. Lefevre, Yvette W. H. Koh, Adam A. Wall, Nicholas D. Condon, Jennifer L. Stow, Nicholas A. Hamilton:
LLAMA: a robust and scalable machine learning pipeline for analysis of large scale 4D microscopy data: analysis of cell ruffles and filopodia. 410 - John J. Cole, Bekir A. Faydaci, David McGuinness, Robin Shaw, Rose A. Maciewicz, Neil A. Robertson, Carl S. Goodyear:
Searchlight: automated bulk RNA-seq exploration and visualisation using dynamically generated R scripts. 411 - Andreas Untergasser, Jan Ruijter, Vladimir Benes, Maurice J. B. van den Hoff:
Web-based LinRegPCR: application for the visualization and analysis of (RT)-qPCR amplification and melting data. 398 - Kyriakos Schwarz, Ahmed Allam, Nicolas Andres Perez Gonzalez, Michael Krauthammer:
AttentionDDI: Siamese attention-based deep learning method for drug-drug interaction predictions. 412 - Tilman Mehl, Michael Gruenstaeudl:
airpg: automatically accessing the inverted repeats of archived plastid genomes. 413 - Tianzhong Yang, Jingbo Niu, Han Chen, Peng Wei:
Estimation of total mediation effect for high-dimensional omics mediators. 414 - Leila Baghaarabani, Sama Goliaei, Mohammad-Hadi Foroughmand-Araabi, Seyed Peyman Shariatpanahi, Bahram Goliaei:
Conifer: clonal tree inference for tumor heterogeneity with single-cell and bulk sequencing data. 416 - Tim W. McInerney, Brian Fulton-Howard, Christopher Patterson, Devashi Paliwal, Lars S. Jermiin, Hardip R. Patel, Judy Pa, Russell H. Swerdlow, Alison M. Goate, Simon Easteal, Shea J. Andrews:
A globally diverse reference alignment and panel for imputation of mitochondrial DNA variants. 417 - Yang Yue, Shan He:
DTI-HeNE: a novel method for drug-target interaction prediction based on heterogeneous network embedding. 418 - Xin Wang, Jie Zheng:
Velo-Predictor: an ensemble learning pipeline for RNA velocity prediction. 419 - Xiaoxiao Zhao, Jianghuai Ji, Shijia Wang, Rendong Wang, Qiuhong Yu, Dongguo Li:
The regulatory pattern of target gene expression by aberrant enhancer methylation in glioblastoma. 420 - Siyu Xiong, Guoqing Wu, Xitian Fan, Xuan Feng, Zhongcheng Huang, Wei Cao, Xuegong Zhou, Shijin Ding, Jinhua Yu, Lingli Wang, Zhifeng Shi:
MRI-based brain tumor segmentation using FPGA-accelerated neural network. 421 - Ryan Ehrlich, Larisa Kamga, Anna Gil, Katherine Luzuriaga, Liisa K. Selin, Dario Ghersi:
SwarmTCR: a computational approach to predict the specificity of T cell receptors. 422 - Tusharkanti Ghosh, Daisy Philtron, Weiming Zhang, Katerina J. Kechris, Debashis Ghosh:
Reproducibility of mass spectrometry based metabolomics data. 423 - Victor Bernal, Rainer Bischoff, Peter Horvatovich, Victor Guryev, Marco Grzegorczyk:
The 'un-shrunk' partial correlation in Gaussian graphical models. 424 - Hui-Yi Lin, Po-Yu Huang, Tung-Sung Tseng, Jong Y. Park:
SNPxE: SNP-environment interaction pattern identifier. 425 - Leonardo Alexandre, Rafael S. Costa, Rui Henriques:
DI2: prior-free and multi-item discretization of biological data and its applications. 426 - M. Elena Garcia-Pardo, Jeremy C. Simpson, Niamh C. O'sullivan:
A novel automated image analysis pipeline for quantifying morphological changes to the endoplasmic reticulum in cultured human cells. 427 - Ting Zhou, Huiwen Wang, Chen Zeng, Yunjie Zhao:
RPocket: an intuitive database of RNA pocket topology information with RNA-ligand data resources. 428 - Yongxue Huo, Yikun Zhao, Liwen Xu, Hongmei Yi, Yunlong Zhang, Xianqing Jia, Han Zhao, Jiuran Zhao, Fengge Wang:
An integrated strategy for target SSR genotyping with toleration of nucleotide variations in the SSRs and flanking regions. 429 - Shiyuan Li, Zhen Zhang, Xueyong Li, Yihong Tan, Lei Wang, Zhiping Chen:
An iteration model for identifying essential proteins by combining comprehensive PPI network with biological information. 430 - Chengkun Wu, Xinyi Xiao, Canqun Yang, Jinxiang Chen, Jiacai Yi, Yanlong Qiu:
Mining microbe-disease interactions from literature via a transfer learning model. 432 - David R. Stirling, Madison J. Swain-Bowden, Alice M. Lucas, Anne E. Carpenter, Beth A. Cimini, Allen Goodman:
CellProfiler 4: improvements in speed, utility and usability. 433 - Zhaorui Zuo, Penglei Wang, Xiaowei Chen, Li Tian, Hui Ge, Dahong Qian:
SWnet: a deep learning model for drug response prediction from cancer genomic signatures and compound chemical structures. 434 - Mohammad Shahedul Islam, Md. Abul Kashem Mia, Mohammad Shamsur Rahman, Mohammad Shamsul Arefin, Pranab Kumar Dhar, Takeshi Koshiba:
Frequent contiguous pattern mining over biological sequences of protein misfolded diseases. 435 - Nikolaos Pappas, Bas E. Dutilh:
Finding functional associations between prokaryotic virus orthologous groups: a proof of concept. 438 - Lupeng Kong, Fusong Ju, Haicang Zhang, Shiwei Sun, Dongbo Bu:
FALCON2: a web server for high-quality prediction of protein tertiary structures. 439 - Rasmus Magnusson, Zelmina Lubovac-Pilav:
TFTenricher: a python toolbox for annotation enrichment analysis of transcription factor target genes. 440 - Christian Staerk, Andreas Mayr:
Randomized boosting with multivariable base-learners for high-dimensional variable selection and prediction. 441 - Stephen Kotiang, Ali Eslami:
Boolean factor graph model for biological systems: the yeast cell-cycle network. 442 - Jimena Solana, Emilio Garrote-Sánchez, Rosario Gil:
DELEAT: gene essentiality prediction and deletion design for bacterial genome reduction. 444 - Mattia Prosperi, Simone Marini, Christina Boucher:
Fast and exact quantification of motif occurrences in biological sequences. 445 - Liang-Chin Huang, Rahil Taujale, Nathan Gravel, Aarya Venkat, Wayland Yeung, Dominic P. Byrne, Patrick A. Eyers, Natarajan Kannan:
KinOrtho: a method for mapping human kinase orthologs across the tree of life and illuminating understudied kinases. 446 - Linyu Wang, Xiaodan Zhong, Shuo Wang, Yuanning Liu:
ncDLRES: a novel method for non-coding RNAs family prediction based on dynamic LSTM and ResNet. 447 - Ewan Carr, Mathieu Carrière, Bertrand Michel, Frédéric Chazal, Raquel Iniesta:
Identifying homogeneous subgroups of patients and important features: a topological machine learning approach. 449 - Qi Wei, Stephen A. Ramsey:
Predicting chemotherapy response using a variational autoencoder approach. 453 - Francisco Carrillo-Perez, Juan Carlos Morales, Daniel Castillo-Secilla, Yésica Molina-Castro, Alberto Guillén, Ignacio Rojas, Luis Javier Herrera:
Non-small-cell lung cancer classification via RNA-Seq and histology imaging probability fusion. 454 - Edward J. Martin, Thomas R. Meagher, Daniel Barker:
Using sound to understand protein sequence data: new sonification algorithms for protein sequences and multiple sequence alignments. 456 - Matin Fathollahi, Anwar Fathollahi, Hamid Motamedi, Jale Moradi, Amirhooshang Alvandi, Ramin Abiri:
In silico vaccine design and epitope mapping of New Delhi metallo-beta-lactamase (NDM): an immunoinformatics approach. 458 - Yong Wang, Shiya Song, Joshua G. Schraiber, Alisa Sedghifar, Jake K. Byrnes, David A. Turissini, Eurie L. Hong, Catherine A. Ball, Keith Noto:
Ancestry inference using reference labeled clusters of haplotypes. 459 - Quentin Ferré, Jeanne Chèneby, Denis Puthier, Cécile Capponi, Benoît Ballester:
Anomaly detection in genomic catalogues using unsupervised multi-view autoencoders. 460 - Edwin J. C. G. van den Oord, Lin Y. Xie, Charles J. Tran, Min Zhao, Karolina A. Åberg:
A targeted solution for estimating the cell-type composition of bulk samples. 462 - François Chevenet, Denis Fargette, Stéphane Guindon, Anne-Laure Bañuls:
EvoLaps: a web interface to visualize continuous phylogeographic reconstructions. 463 - Jan Geryk, Alzbeta Zinkova, Iveta Zedníková, Halina Simková, Vlastimil Stenzl, Marie Korabecna:
Improving structural variant clustering to reduce the negative effect of the breakpoint uncertainty problem. 464 - Koya Sakuma, Shintaro Minami:
Enumeration and comprehensive in-silico modeling of three-helix bundle structures composed of typical αα-hairpins. 465 - Oliviero Carugo:
Decline of protein structure rigidity with interatomic distance. 466 - Hong Zeng, Reza Rohani, Wei E. Huang, Aidong Yang:
Understanding and mathematical modelling of cellular resource allocation in microorganisms: a comparative synthesis. 467 - Manon Geerts, Achim Schnaufer, Frederik Van den Broeck:
rKOMICS: an R package for processing mitochondrial minicircle assemblies in population-scale genome projects. 468 - Silvia D'Angelo, Isobel Claire Gormley, Aoife E. McNamara, Lorraine Brennan:
multiMarker: software for modelling and prediction of continuous food intake using multiple biomarkers measurements. 469 - Jonas Meisner, Anders Albrechtsen, Kristian Hanghøj:
Detecting selection in low-coverage high-throughput sequencing data using principal component analysis. 470 - Kaikai Shen, Yuqing Wei, Tangfeng Lv, Yong Song, Xiaogan Jiang, Zhiwei Lu, Ping Zhan, Xianghai Wang, Meng Fan, Weihua Lu:
The expression landscape of JAK1 and its potential as a biomarker for prognosis and immune infiltrates in NSCLC. 471 - Ralf C. Mueller, Nicolai Mallig, Jacqueline Smith, Lél Eöery, Richard I. Kuo, Robert H. S. Kraus:
Correction to: Avian Immunome DB: an example of a user‑friendly interface for extracting genetic information. 472 - Clémentine Decamps, Alexis Arnaud, Florent Petitprez, Mira Ayadi, Aurélia Baurès, Lucile Armenoult, Sergio Escalera, Isabelle Guyon, Rémy Nicolle, Richard Tomasini, Aurélien de Reyniès, Jérôme Cros, Yuna Blum, Magali Richard:
DECONbench: a benchmarking platform dedicated to deconvolution methods for tumor heterogeneity quantification. 473 - Christopher T. Lee, Manolis Maragkakis:
SamQL: a structured query language and filtering tool for the SAM/BAM file format. 474 - Lianxin Zhong, Qingfang Meng, Yuehui Chen, Lei Du, Peng Wu:
A laminar augmented cascading flexible neural forest model for classification of cancer subtypes based on gene expression data. 475 - S. Olaechea-Lázaro, I. García-Santisteban, José R. Pineda, Iker Badiola, Santos Alonso, Jose Ramon Bilbao, Nora Fernandez-Jimenez:
shinyCurves, a shiny web application to analyse multisource qPCR amplification data: a COVID-19 case study. 476 - Rogia Kpanou, Mazid Abiodoun Osseni, Prudencio Tossou, François Laviolette, Jacques Corbeil:
On the robustness of generalization of drug-drug interaction models. 477 - Ronan Duchesne, Anissa Guillemin, Olivier Gandrillon, Fabien Crauste:
Practical identifiability in the frame of nonlinear mixed effects models: the example of the in vitro erythropoiesis. 478 - Liqian Zhou, Zhao Wang, Xiongfei Tian, Lihong Peng:
LPI-deepGBDT: a multiple-layer deep framework based on gradient boosting decision trees for lncRNA-protein interaction identification. 479 - Mira Park, Hoe-Bin Jeong, Jong-Hyun Lee, Taesung Park:
Spatial rank-based multifactor dimensionality reduction to detect gene-gene interactions for multivariate phenotypes. 480 - Benjamin Nordick, Tian Hong:
Identification, visualization, statistical analysis and mathematical modeling of high-feedback loops in gene regulatory networks. 481 - Nícia Rosário-Ferreira, Victor Guimarães, Vítor Santos Costa, Irina S. Moreira:
SicknessMiner: a deep-learning-driven text-mining tool to abridge disease-disease associations. 482 - William R. P. Denault, Håkon K. Gjessing, Julius Juodakis, Bo Jacobsson, Astanand Jugessur:
Wavelet Screening: a novel approach to analyzing GWAS data. 484 - Shiqing Yu, Mathias Drton, Daniel E. L. Promislow, Ali Shojaie:
CorDiffViz: an R package for visualizing multi-omics differential correlation networks. 486 - Joel Gustafsson, Peter Norberg, Jan R. Qvick-Wester, Alexander Schliep:
Fast parallel construction of variable-length Markov chains. 487 - Gwenna Breton, Anna C. V. Johansson, Per Sjödin, Carina M. Schlebusch, Mattias Jakobsson:
Comparison of sequencing data processing pipelines and application to underrepresented African human populations. 488 - Weize Xu, Quan Zhong, Da Lin, Ya Zuo, Jinxia Dai, Guoliang Li, Gang Cao:
CoolBox: a flexible toolkit for visual analysis of genomics data. 489 - Teng-Ruei Chen, Yen-Cheng Lin, Yu-Wei Huang, Chih-Chieh Chen, Wei-Cheng Lo:
CirPred, the first structure modeling and linker design system for circularly permuted proteins. 494 - Dat Thanh Nguyen, Quang Thinh Trac, Thi-Hau Nguyen, Ha-Nam Nguyen, Nir Ohad, Yudi Pawitan, Trung-Nghia Vu:
Circall: fast and accurate methodology for discovery of circular RNAs from paired-end RNA-sequencing data. 495 - Xianrui Wang, Ting-Ting Cao, Cong Min Jia, Xuemei Tian, Yun Wang:
Quantitative prediction model for affinity of drug-target interactions based on molecular vibrations and overall system of ligand-receptor. 497 - Camilla Lingjærde, Tonje Lien, Ørnulf Borgan, Helga Bergholtz, Ingrid Kristine Glad:
Tailored graphical lasso for data integration in gene network reconstruction. 498 - Elias Oziolor, Seda Arat, Matthew Martin:
Annotation depth confounds direct comparison of gene expression across species. 499 - Morteza Pourreza Shahri, Indika Kahanda:
Deep semi-supervised learning ensemble framework for classifying co-mentions of human proteins and phenotypes. 500 - Bradley T. Martin, Tyler K. Chafin, Marlis R. Douglas, Michael E. Douglas:
ClineHelpR: an R package for genomic cline outlier detection and visualization. 501 - Qihua Liang, Stefano Lonardi:
Reference-agnostic representation and visualization of pan-genomes. 502 - Tzu-Hsien Yang, Sheng-Cian Shiue, Kuan-Yu Chen, Yan Yuan Tseng, Wei-Sheng Wu:
Identifying piRNA targets on mRNAs in C. elegans using a deep multi-head attention network. 503 - Tomasz Wozniak, Malgorzata Sajek, Jadwiga Jaruzelska, Marcin Piotr Sajek:
RNAlign2D: a rapid method for combined RNA structure and sequence-based alignment using a pseudo-amino acid substitution matrix. 504 - Hayato Takihara, Nobuaki Miura, Kiyoko F. Aoki-Kinoshita, Shujiro Okuda:
Functional glyco-metagenomics elucidates the role of glycan-related genes in environments. 505 - Rui Zhang, Chang Liu, Kai Yuan, Xumin Ni, Yuwen Pan, Shuhua Xu:
AdmixSim 2: a forward-time simulator for modeling complex population admixture. 506 - Mengqi Luo, Zhongyan Li, Shangfu Li, Tzong-Yi Lee:
A representation and deep learning model for annotating ubiquitylation sentences stating E3 ligase - substrate interaction. 507 - Brianna Sierra Chrisman, Kelley M. Paskov, Nate Tyler Stockham, Jae-Yoon Jung, Maya Varma, Peter Washington, Christine A. Tataru, Shoko Iwai, Todd Z. DeSantis, Maude M. David, Dennis P. Wall:
Improved detection of disease-associated gut microbes using 16S sequence-based biomarkers. 509 - Johannes Linder, Georg Seelig:
Fast activation maximization for molecular sequence design. 510 - Takayuki Osabe, Kentaro Shimizu, Koji Kadota:
Differential expression analysis using a model-based gene clustering algorithm for RNA-seq data. 511 - Huiqing Wang, Jian Zhao, Hong Zhao, Haolin Li, Juan Wang:
CL-ACP: a parallel combination of CNN and LSTM anticancer peptide recognition model. 512 - Adam Voshall, Sairam Behera, Xiangjun Li, Xiao-Hong Yu, Kushagra Kapil, Jitender S. Deogun, John Shanklin, Edgar B. Cahoon, Etsuko N. Moriyama:
A consensus-based ensemble approach to improve transcriptome assembly. 513 - Amelia Villegas-Morcillo, Victoria E. Sánchez, Angel M. Gomez:
FoldHSphere: deep hyperspherical embeddings for protein fold recognition. 490 - Yiyi Pu, Chao Li, Haining Yuan, Xiaoju Wang:
Identification of prostate cancer specific methylation biomarkers from a multi-cancer analysis. 492 - Daniel P. Dacey, Frédéric J. J. Chain:
Concatenation of paired-end reads improves taxonomic classification of amplicons for profiling microbial communities. 493 - Kun Yu, Weidong Xie, Linjie Wang, Wei Li:
ILRC: a hybrid biomarker discovery algorithm based on improved L1 regularization and clustering in microarray data. 514 - Qi Li, Khalique Newaz, Tijana Milenkovic:
Improved supervised prediction of aging-related genes via weighted dynamic network analysis. 520 - Ye-Cheng Wang, Zhen-Bo Tian, Xu-Qing Tang:
Bioinformatics screening of biomarkers related to liver cancer. 521 - Jing Hu, Longwei Zhou, Bo Li, Xiaolong Zhang, Nansheng Chen:
Improve hot region prediction by analyzing different machine learning algorithms. 522 - Patrik Waldmann:
A proximal LAVA method for genome-wide association and prediction of traits with mixed inheritance patterns. 523 - Hongyu Li, Biqing Zhu, Zhichao Xu, Taylor Adams, Naftali Kaminski, Hongyu Zhao:
A Markov random field model for network-based differential expression analysis of single-cell RNA-seq data. 524 - Ramin Hasibi, Tom Michoel:
A Graph Feature Auto-Encoder for the prediction of unobserved node features on biological networks. 525 - L. F. Signorini, T. Almozlino, Roded Sharan:
ANAT 3.0: a framework for elucidating functional protein subnetworks using graph-theoretic and machine learning approaches. 526 - Ariele Viacava Follis:
Centrality of drug targets in protein networks. 527 - Anna Paola Muntoni, Andrea Pagnani, Martin Weigt, Francesco Zamponi:
adabmDCA: adaptive Boltzmann machine learning for biological sequences. 528 - Rosa Barcelona-Cabeza, Walter Sanseverino, Riccardo Aiese Cigliano:
isoCNV: in silico optimization of copy number variant detection from targeted or exome sequencing data. 530 - Athanasios D. Balomenos, Victoria Stefanou, Elias S. Manolakos:
Analytics and visualization tools to characterize single-cell stochasticity using bacterial single-cell movie cytometry data. 531 - Peng Chen, Tianjiazhi Bao, Xiaosheng Yu, Zhongtu Liu:
A drug repositioning algorithm based on a deep autoencoder and adaptive fusion. 532 - Bin Huang, Guozheng Wei, Bing Wang, Fusong Ju, Yi Zhong, Zhuozheng Shi, Shiwei Sun, Dongbo Bu:
Filling gaps of genome scaffolds via probabilistic searching optical maps against assembly graph. 533 - Lauren Coombe, Janet X. Li, Theodora Lo, Johnathan Wong, Vladimir Nikolic, René L. Warren, Inanç Birol:
LongStitch: high-quality genome assembly correction and scaffolding using long reads. 534 - Youri Hoogstrate, Guido Jenster, Harmen J. G. van de Werken:
FASTAFS: file system virtualisation of random access compressed FASTA files. 535 - Xiangxin Zhang, Liu Yang, Ming Kong, Jian Ma, Yutao Wei:
Development of a prognostic signature of patients with esophagus adenocarcinoma by using immune-related genes. 536 - Ayyüce Begüm Bektas, Mehmet Gönen:
PrognosiT: Pathway/gene set-based tumour volume prediction using multiple kernel learning. 537 - Jianwei Li, Jianing Li, Mengfan Kong, Duanyang Wang, Kun Fu, Jiangcheng Shi:
SVDNVLDA: predicting lncRNA-disease associations by Singular Value Decomposition and node2vec. 538 - Yiran Zhang, Kellie J. Archer:
Bayesian variable selection for high-dimensional data with an ordinal response: identifying genes associated with prognostic risk group in acute myeloid leukemia. 539 - Sergey Senkin:
MSA: reproducible mutational signature attribution with confidence based on simulations. 540 - Camila Riccio-Rengifo, Jorge Finke, Camilo Rocha:
Identifying stress responsive genes using overlapping communities in co-expression networks. 541 - Sangmin Seo, Jonghwan Choi, Sanghyun Park, Jaegyoon Ahn:
Binding affinity prediction for protein-ligand complex using deep attention mechanism based on intermolecular interactions. 542 - Andreas Ruscheinski, Anna Lena Reimler, Roland Ewald, Adelinde M. Uhrmacher:
VPMBench: a test bench for variant prioritization methods. 543 - Zhixia Teng, Zitong Zhang, Zhen Tian, Yanjuan Li, Guohua Wang:
ReRF-Pred: predicting amyloidogenic regions of proteins based on their pseudo amino acid composition and tripeptide composition. 545 - Jonathan K. Kayondo, Alfred Ssekagiri, Grace Nabakooza, Nicholas Bbosa, Deogratius Ssemwanga, Pontiano Kaleebu, Samuel Mwalili, John Mango Magero, Andrew J. Leigh Brown, Roberto A. Saenz, Ronald Galiwango, John M. Kitayimbwa:
Employing phylogenetic tree shape statistics to resolve the underlying host population structure. 546 - Bianca A. Buchner, Jürgen Zanghellini:
EFMlrs: a Python package for elementary flux mode enumeration via lexicographic reverse search. 547 - Hsuan-Lin Her, Po-Ting Lin, Yu-Wei Wu:
PangenomeNet: a pan-genome-based network reveals functional modules on antimicrobial resistome for Escherichia coli strains. 548 - Hossein Khabbaz, Mohammad Hossein Karimi-Jafari, Ali Akbar Saboury, Bagher BabaAli:
Prediction of antimicrobial peptides toxicity based on their physico-chemical properties using machine learning techniques. 549 - Pengyue Lin, Siyuan Xia, Jiang Yi, Wen Yang, Xiaoning Liu, Guohua Geng, Shixiong Wang:
ANINet: a deep neural network for skull ancestry estimation. 550 - Zhihao Ma, Zhufang Kuang, Lei Deng:
CRPGCN: predicting circRNA-disease associations using graph convolutional network based on heterogeneous network. 551 - Tao Jiang, Shiqi Liu, Shuqi Cao, Yadong Liu, Zhe Cui, Yadong Wang, Hongzhe Guo:
Long-read sequencing settings for efficient structural variation detection based on comprehensive evaluation. 552 - Ruixue Hou, Lewis E. Tomalin, Mayte Suárez-Fariñas:
cosinoRmixedeffects: an R package for mixed-effects cosinor models. 553 - Shitao Zhao, Michiaki Hamada:
Multi-resBind: a residual network-based multi-label classifier for in vivo RNA binding prediction and preference visualization. 554 - Ali Ghanbari Sorkhi, Zahra Abbasi, Majid Iranpour Mobarakeh, Jamshid Pirgazi:
Drug-target interaction prediction using unifying of graph regularized nuclear norm with bilinear factorization. 555 - Wendell J. Pereira, Felipe Marques Almeida, D. Conde, K. M. Balmant, P. M. Triozzi, H. W. Schmidt, C. Dervinis, Georgios Joannis Pappas Jr., M. Kirst:
Asc-Seurat: analytical single-cell Seurat-based web application. 556 - Saptarshi Bej, Anne-Marie Galow, Robert David, Markus Wolfien, Olaf Wolkenhauer:
Automated annotation of rare-cell types from single-cell RNA-sequencing data through synthetic oversampling. 557 - Irene Zorzan, Simone Del Favero, Alberto Giaretta, Riccardo Manganelli, Barbara Di Camillo, Luca Schenato:
Mathematical modelling of SigE regulatory network reveals new insights into bistability of mycobacterial stress response. 558 - Dustin B. Miller, Stephen R. Piccolo:
trioPhaser: using Mendelian inheritance logic to improve genomic phasing of trios. 559 - Rhys A. Farrer:
HaplotypeTools: a toolkit for accurately identifying recombination and recombinant genotypes. 560 - Nicolas Scalzitti, Arnaud Kress, Romain Orhand, Thomas Weber, Luc Moulinier, Anne Jeannin-Girardon, Pierre Collet, Olivier Poch, Julie Dawn Thompson:
Spliceator: multi-species splice site prediction using convolutional neural networks. 561 - Dongju Chen, Minghui Shao, Pei Meng, Chunli Wang, Qi Li, Yuhang Cai, Chengcheng Song, Xi Wang, Taiping Shi:
GSA: an independent development algorithm for calling copy number and detecting homologous recombination deficiency (HRD) from target capture sequencing. 562 - Alice R. Owens, Caitríona E. McInerney, Kevin M. Prise, Darragh G. McArt, Anna Jurek-Loughrey:
Novel deep learning-based solution for identification of prognostic subgroups in liver cancer (Hepatocellular carcinoma). 563 - Wei Bai, Mei Dong, Longhai Li, Cindy Feng, Wei Xu:
Randomized quantile residuals for diagnosing zero-inflated generalized linear mixed models with applications to microbiome count data. 564 - Jiyu Chen, Nicholas Geard, Justin Zobel, Karin Verspoor:
Automatic consistency assurance for literature-based gene ontology annotation. 565 - Lars Gabriel, Katharina Jasmin Hoff, Tomás Bruna, Mark Borodovsky, Mario Stanke:
TSEBRA: transcript selector for BRAKER. 566 - Xiujin Wu, Wenhua Zeng, Fan Lin, Xiuze Zhou:
NeuRank: learning to rank with neural networks for drug-target interaction prediction. 567 - Liqian Zhou, Qi Duan, Xiongfei Tian, He Xu, Jianxin Tang, Lihong Peng:
LPI-HyADBS: a hybrid framework for lncRNA-protein interaction prediction integrating feature selection and classification. 568 - Dengfeng Guan, Shane A. McCarthy, Zemin Ning, Guohua Wang, Yadong Wang, Richard Durbin:
Efficient iterative Hi-C scaffolder based on N-best neighbors. 569 - Madolyn L. MacDonald, Kelvin H. Lee:
EvalDNA: a machine learning-based tool for the comprehensive evaluation of mammalian genome assembly quality. 570 - Chiara Regondi, Maddalena Fratelli, Giovanna Damia, Federica Guffanti, Monica Ganzinelli, Matteo Matteucci, Marco Masseroli:
Predictive modeling of gene expression regulation. 571 - Thi Ngan Dong, Graham Brogden, Gisa Gerold, Megha Khosla:
A multitask transfer learning framework for the prediction of virus-human protein-protein interactions. 572 - Feng Zhou, Meng-Meng Yin, Cui-Na Jiao, Zhen Cui, Jing-Xiu Zhao, Jin-Xing Liu:
Bipartite graph-based collaborative matrix factorization method for predicting miRNA-disease associations. 573 - Neeraj Sinha, Evert M. van Schothorst, Guido J. E. K. Hooiveld, Jaap Keijer, Vítor A. P. Martins dos Santos, María Suárez-Diez:
Exploring the associations between transcript levels and fluxes in constraint-based models of metabolism. 574 - Pegah Mavaie, Lawrence Holder, Daniel Beck, Michael K. Skinner:
Predicting environmentally responsive transgenerational differential DNA methylated regions (epimutations) in the genome using a hybrid deep-machine learning approach. 575 - Leonardo Morelli, Valentina Giansanti, Davide Cittaro:
Nested Stochastic Block Models applied to the analysis of single cell data. 576 - Junwei Luo, Hongyu Ding, Jiquan Shen, Haixia Zhai, Zhengjiang Wu, Chaokun Yan, Huimin Luo:
BreakNet: detecting deletions using long reads and a deep learning approach. 577 - Junpeng Zhang, Lin Liu, Taosheng Xu, Wu Zhang, Chunwen Zhao, Sijing Li, Jiuyong Li, Nini Rao, Thuc Duy Le:
Exploring cell-specific miRNA regulation with single-cell miRNA-mRNA co-sequencing data. 578 - Marc Pereyra, Armin Drusko, Franziska Krämer, Frederic Strobl, Ernst H. K. Stelzer, Franziska Matthäus:
QuickPIV: Efficient 3D particle image velocimetry software applied to quantifying cellular migration during embryogenesis. 579 - Xiaolong Li, Hengchao Zhang, Jingjing Liu, Ping Li, Yi Sun:
Five crucial prognostic-related autophagy genes stratified female breast cancer patients aged 40-60 years. 580 - Zao Liu, Zhiwei Chen, Kan Song:
SpinSPJ: a novel NMR scripting system to implement artificial intelligence and advanced applications. 581 - Chenyang Xu, Lei Cai, Jingyang Gao:
An efficient scRNA-seq dropout imputation method using graph attention network. 582 - Linyu Wang, Xiaodan Zhong, Shuo Wang, Yuanning Liu:
Correction to: ncDLRES: a novel method for non‑coding RNAs family prediction based on dynamic LSTM and ResNet. 583 - John Luke McConn, Cameron R. Lamoureux, Saugat Poudel, Bernhard O. Palsson, Anand V. Sastry:
Optimal dimensionality selection for independent component analysis of transcriptomic data. 584 - Xi Yang, Chengkun Wu, Goran Nenadic, Wei Wang, Kai Lu:
Correction to: Mining a stroke knowledge graph from literature. 585 - Katrin Madjar, Manuela Zucknick, Katja Ickstadt, Jörg Rahnenführer:
Combining heterogeneous subgroups with graph-structured variable selection priors for Cox regression. 586 - Ruya Sun, Yuan Zhou, Qinghua Cui:
Comparative analysis of aneurysm subtypes associated genes based on protein-protein interaction network. 587 - Nastaran Maus Esfahani, Daniel R. Catchpoole, Javed Khan, Paul J. Kennedy:
MCKAT: a multi-dimensional copy number variant kernel association test. 588 - Li-Ming Xiao, Yun-Qi Wan, Zhen-Ran Jiang:
AttCRISPR: a spacetime interpretable model for prediction of sgRNA on-target activity. 589 - Xingwang Li, Yijia Zhang, Faiz ul Islam, Deshi Dong, Hao Wei, Mingyu Lu:
JLAN: medical code prediction via joint learning attention networks and denoising mechanism. 590 - Ying Hu, Chunhua Yan, Qingrong Chen, Daoud M. Meerzaman:
gcMECM: graph clustering of mutual exclusivity of cancer mutations. 592 - Chiara E. Cotroneo, Isobel Claire Gormley, Denis C. Shields, Michael Salter-Townshend:
Computational modelling of chromosomally clustering protein domains in bacteria. 593 - David Chardin, Olivier Humbert, Caroline Bailleux, Fanny Burel-Vandenbos, Valerie Rigau, Thierry Pourcher, Michel Barlaud:
Primal-dual for classification with rejection (PD-CR): a novel method for classification and feature selection - an application in metabolomics studies. 594 - Nanette Christie, Chanaka Mannapperuma, Raphael Ployet, Karen van der Merwe, Niklas Mähler, Nicolas Delhomme, Sanushka Naidoo, Eshchar Mizrachi, Nathaniel Street, Alexander A. Myburg:
qtlXplorer: an online systems genetics browser in the Eucalyptus Genome Integrative Explorer (EucGenIE). 595 - William F. Anjos, Gabriel C. Lanes, Vasco A. Azevedo, Anderson Santos:
GENPPI: standalone software for creating protein interaction networks from genomes. 596 - Junhua Ye, Shunfang Wang, Xin Yang, Xianjun Tang:
Gene prediction of aging-related diseases based on DNN and Mashup. 597 - Mayla Boguslav, Negacy D. Hailu, Michael Bada, William A. Baumgartner Jr., Lawrence E. Hunter:
Concept recognition as a machine translation problem. 598 - Pilar López-Úbeda, Manuel Carlos Díaz-Galiano, Luis Alfonso Ureña López, María Teresa Martín Valdivia:
Combining word embeddings to extract chemical and drug entities in biomedical literature. 599 - Ying Xiong, Shuai Chen, Buzhou Tang, Qingcai Chen, Xiaolong Wang, Jun Yan, Yi Zhou:
Improving deep learning method for biomedical named entity recognition by using entity definition information. 600 - Renzo M. Rivera Zavala, Paloma Martínez:
Analyzing transfer learning impact in biomedical cross-lingual named entity recognition and normalization. 601 - Cong Sun, Zhihao Yang, Lei Wang, Yin Zhang, Hongfei Lin, Jian Wang:
Deep learning with language models improves named entity recognition for PharmaCoNER. 602 - Joe Wandy, Rónán Daly:
GraphOmics: an interactive platform to explore and integrate multi-omics data. 603 - Fadilla Wahyudi, Farhang A. Aghakhanian, Sadequr Rahman, Yik-Ying Teo, Michal Szpak, Jasbir Dhaliwal, Qasim Ayub:
Prioritising positively selected variants in whole-genome sequencing data using FineMAV. 604 - Federico Martinez-Seidel, Yin-Chen Hsieh, Dirk Walther, Joachim Kopka, Alexandre Augusto Pereira Firmino:
COSNeti: ComplexOme-Structural Network Interpreter used to study spatial enrichment in metazoan ribosomes. 605 - Minhyeok Cho, Albert No:
FCLQC: fast and concurrent lossless quality scores compressor. 606 - João Victor da Silva Guerra, Helder Veras Ribeiro filho, Gabriel Ernesto Jara, Leandro Oliveira Bortot, José Geraldo de Carvalho Pereira, Paulo Sérgio Lopes-de-Oliveira:
pyKVFinder: an efficient and integrable Python package for biomolecular cavity detection and characterization in data science. 607 - Shu-Hong Lin, Rohit Thakur, Mitchell J. Machiela:
LDexpress: an online tool for integrating population-specific linkage disequilibrium patterns with tissue-specific expression data. 608 - Yu Zhang, Yahui Long, Chee Keong Kwoh:
Class similarity network for coding and long non-coding RNA classification. 609 - Federico Marini, Annekathrin Ludt, Jan Linke, Konstantin Strauch:
GeneTonic: an R/Bioconductor package for streamlining the interpretation of RNA-seq data. 610 - Meifang Qi, Utthara Nayar, Leif S. Ludwig, Nikhil Wagle, Esther Rheinbay:
cDNA-detector: detection and removal of cDNA contamination in DNA sequencing libraries. 611 - J. L. Weissman, Sonia Dogra, Keyan Javadi, Samantha Bolten, Rachel Flint, Cyrus Davati, Jess Beattie, Keshav Dixit, Tejasvi Peesay, Shehar Awan, Peter Thielen, Florian P. Breitwieser, Philip L. F. Johnson, David K. Karig, William F. Fagan, Sharon Bewick:
Exploring the functional composition of the human microbiome using a hand-curated microbial trait database. 306 - Dengfeng Guan, Shane A. McCarthy, Zemin Ning, Guohua Wang, Yadong Wang, Richard Durbin:
Correction to: Efficient iterative Hi-C scaffolder based on N-best neighbors. 612
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