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ORCIDBMC Bioinformatics, Volume 21
Volume 21, Number 1, December 2020
- Melanie Fachet, Carina Witte, Robert J. Flassig
, Liisa K. Rihko-Struckmann, Zaid McKie-Krisberg, Jürgen E. W. Polle, Kai Sundmacher:
Reconstruction and analysis of a carbon-core metabolic network for Dunaliella salina. 1 - Mehran Aflakparast, Geert Geeven, Mathisca C. M. de Gunst:
Bayesian mixture regression analysis for regulation of Pluripotency in ES cells. 3 - Robert Esch, Rainer Merkl:
Conserved genomic neighborhood is a strong but no perfect indicator for a direct interaction of microbial gene products. 5 - Rita Torres Sousa, Sara Silva, Catia Pesquita:
Evolving knowledge graph similarity for supervised learning in complex biomedical domains. 6 - Xihui Lin, Paul C. Boutros:
Optimization and expansion of non-negative matrix factorization. 7 - Feixiao Long:
Microscopy cell nuclei segmentation with enhanced U-Net. 8 - Attila Csala, Aeilko H. Zwinderman, Michel H. Hof:
Multiset sparse partial least squares path modeling for high dimensional omics data analysis. 9 - Hiroyuki Fukuda, Kentaro Tomii:
DeepECA: an end-to-end learning framework for protein contact prediction from a multiple sequence alignment. 10 - Takoua Jendoubi, Timothy M. D. Ebbels:
Integrative analysis of time course metabolic data and biomarker discovery. 11 - Yan Li, Dayou Liu, Tengfei Li, Yungang Zhu:
Bayesian differential analysis of gene regulatory networks exploiting genetic perturbations. 12 - Sarah M. Kim, Matthew I. Peña, Mark Moll, George N. Bennett, Lydia E. Kavraki:
Improving the organization and interactivity of metabolic pathfinding with precomputed pathways. 13 - Theresa A. Alexander, Mitchell J. Machiela:
LDpop: an interactive online tool to calculate and visualize geographic LD patterns. 14 - Martin Raden, Teresa Müller, Stefan Mautner, Rick Gelhausen, Rolf Backofen:
The impact of various seed, accessibility and interaction constraints on sRNA target prediction- a systematic assessment. 15 - Clémentine Decamps, Florian Privé, Raphael Bacher, Daniel Jost, Arthur Waguet, Eugene Andres Houseman, Eugene Lurie, Pavlo Lutsik, Aleksandar Milosavljevic, Michael Scherer, Michael G. B. Blum, Magali Richard:
Guidelines for cell-type heterogeneity quantification based on a comparative analysis of reference-free DNA methylation deconvolution software. 16 - Xueming Zheng, Xingli Fu, Kaicheng Wang, Meng Wang:
Deep neural networks for human microRNA precursor detection. 17 - Maxime Folschette, Vincent Legagneux, Arnaud Poret, Lokmane Chebouba, Carito Guziolowski, Nathalie Théret:
A pipeline to create predictive functional networks: application to the tumor progression of hepatocellular carcinoma. 18 - Pavlos Stephanos Bekiaris, Steffen Klamt:
Automatic construction of metabolic models with enzyme constraints. 19 - Yichen He, Xiujuan Zhou, Ziyan Chen, Xiangyu Deng, Andrew Gehring, Hongyu Ou, Lida Zhang, Xianming Shi:
PRAP: Pan Resistome analysis pipeline. 20 - Thevaa Chandereng, Anthony Gitter:
Lag penalized weighted correlation for time series clustering. 21 - Defne Surujon, Tim van Opijnen:
ShinyOmics: collaborative exploration of omics-data. 22 - Antoine Buetti-Dinh, Malte Herold, Stephan Christel, Mohamed El Hajjami, Francesco Delogu, Olga Ilie, Sören Bellenberg, Paul Wilmes, Ansgar Poetsch, Wolfgang Sand, Mario Vera, Igor V. Pivkin, Ran Friedman, Mark Dopson:
Reverse engineering directed gene regulatory networks from transcriptomics and proteomics data of biomining bacterial communities with approximate Bayesian computation and steady-state signalling simulations. 23 - Louis Ranjard, Thomas K. F. Wong, Allen G. Rodrigo:
Correction to: Effective machine-learning assembly for next-generation amplicon sequencing with very low coverage. 24 - Rudolf Jagdhuber, Michel Lang, Arnulf Stenzl, Jochen Neuhaus, Jörg Rahnenführer:
Cost-Constrained feature selection in binary classification: adaptations for greedy forward selection and genetic algorithms. 26 - Simon Memmel, Dmitri Sisario, Heiko Zimmermann, Markus Sauer, Vladimir L. Sukhorukov, Cholpon S. Djuzenova, Michael Flentje:
FocAn: automated 3D analysis of DNA repair foci in image stacks acquired by confocal fluorescence microscopy. 27 - Bin Liu, Patrick Lindner, Adan Chari Jirmo, Ulrich Maus, Thomas Illig, David S. DeLuca:
A comparison of curated gene sets versus transcriptomics-derived gene signatures for detecting pathway activation in immune cells. 28 - Jin-Woo Chung, Wonsuk Yang, Jong-Chan Park:
Unsupervised inference of implicit biomedical events using context triggers. 29 - Arran K. Turnbull, Cigdem Selli, Carlos Martinez-Perez, Anu Fernando, Lorna Renshaw, Jane Keys, Jonine Figueroa, Xiaping He, Maki Tanioka, Alison F. Munro, Lee Murphy, Angie Fawkes, Richard Clark, Audrey Coutts, Charles M. Perou, Lisa A. Carey, Michael J. Dixon, Andrew H. Sims:
Unlocking the transcriptomic potential of formalin-fixed paraffin embedded clinical tissues: comparison of gene expression profiling approaches. 30 - Jianwei Li, Yan Huang, Qinghua Cui, Yuan Zhou:
m6Acorr: an online tool for the correction and comparison of m6A methylation profiles. 31 - Junpeng Zhang, Vu Viet Hoang Pham, Lin Liu, Taosheng Xu, Buu Minh Thanh Truong, Jiuyong Li, Nini Rao, Thuc Duy Le:
Correction to: Identifying miRNA synergism using multiple-intervention causal inference. 32 - Satya Nanda Vel Arjunan, Atsushi Miyauchi, Kazunari Iwamoto, Koichi Takahashi:
pSpatiocyte: a high-performance simulator for intracellular reaction-diffusion systems. 33 - Mikolaj Rybinski, Simon Möller, Mikael Sunnåker, Claude Lormeau, Jörg Stelling:
TopoFilter: a MATLAB package for mechanistic model identification in systems biology. 34 - Huiwei Zhou, Shixian Ning, Zhe Liu, Chengkun Lang, Zhuang Liu, Bizun Lei:
Knowledge-enhanced biomedical named entity recognition and normalization: application to proteins and genes. 35 - Miriam Sieg, Gesa Richter, Arne S. Schaefer, Jochen Kruppa:
Detection of suspicious interactions of spiking covariates in methylation data. 36 - Samuel E. Barnett, Daniel H. Buckley:
Simulating metagenomic stable isotope probing datasets with MetaSIPSim. 37 - Junhua Zhou, Minqiong Zhao, Zefang Sun, Feilong Wu, Yucong Liu, Xianghua Liu, Zuping He, Quan-Ze He, Quan-Yuan He:
BCREval: a computational method to estimate the bisulfite conversion ratio in WGBS. 38 - Samuel T. Westreich, Maria Nattestad, Christopher Meyer:
BigTop: a three-dimensional virtual reality tool for GWAS visualization. 39 - Tomasz Zok, Mariusz Popenda, Marta Szachniuk:
ElTetrado: a tool for identification and classification of tetrads and quadruplexes. 40 - Zhiqiang Yan, Xiaohui Zhu, Yuqian Wang, Yanli Nie, Shuo Guan, Ying Kuo, Di Chang, Rong Li, Jie Qiao, Liying Yan:
scHaplotyper: haplotype construction and visualization for genetic diagnosis using single cell DNA sequencing data. 41 - Lachlan Coff, Jeffrey Chan, Paul A. Ramsland, Andrew J. Guy:
Identifying glycan motifs using a novel subtree mining approach. 42 - Xudong Zhao, Qing Jiao, Hangyu Li, Yiming Wu, Hanxu Wang, Shan Huang, Guohua Wang:
ECFS-DEA: an ensemble classifier-based feature selection for differential expression analysis on expression profiles. 43 - Laurent S. V. Thomas, Jochen Gehrig:
Multi-template matching: a versatile tool for object-localization in microscopy images. 44 - Izaak Coleman, Giacomo Corleone, James Arram, Ho-Cheung Ng, Luca Magnani, Wayne Luk:
GeDi: applying suffix arrays to increase the repertoire of detectable SNVs in tumour genomes. 45 - Valentino Palombo, Marco Milanesi, Gabriella Sferra, Stefano Capomaccio, Sandy Sgorlon, Mariasilvia D'Andrea:
PANEV: an R package for a pathway-based network visualization. 46 - Lvxing Zhu, Haoran Zheng:
Biomedical event extraction with a novel combination strategy based on hybrid deep neural networks. 47 - Kun Gao, Jonathan Miller:
Primary orthologs from local sequence context. 48 - Konstantinos Pliakos, Celine Vens:
Drug-target interaction prediction with tree-ensemble learning and output space reconstruction. 49 - Junwei Luo, Mengna Lyu, Ranran Chen, Xiaohong Zhang, Huimin Luo, Chaokun Yan:
Correction to: SLR: a scaffolding algorithm based on long reads and contig classification. 50 - Qiaoyue Liu, Xiang Cheng, Gan Liu, Bohao Li, Xiuqin Liu:
Deep learning improves the ability of sgRNA off-target propensity prediction. 51 - Sinead E. Morris, Luise Dziobek-Garrett, Andrew J. Yates:
ushr: Understanding suppression of HIV in R. 52 - S. K. Hong, Jae-Gil Lee:
DTranNER: biomedical named entity recognition with deep learning-based label-label transition model. 53 - Mattia Chiesa, Giada Maioli, Gualtiero I. Colombo, Luca Piacentini:
GARS: Genetic Algorithm for the identification of a Robust Subset of features in high-dimensional datasets. 54 - Jia Li, Yue Yin, Mutian Zhang, Jie Cui, Zhenhai Zhang, Zhiyong Zhang, Deqiang Sun:
GsmPlot: a web server to visualize epigenome data in NCBI. 55 - Gaurav Kumar, Adam Ertel, George Feldman, Joan Kupper, Paolo Fortina:
iSeqQC: a tool for expression-based quality control in RNA sequencing. 56 - Zhen Yang, Xueqing Deng, Yang Liu, Weikang Gong, Chunhua Li:
Analyses on clustering of the conserved residues at protein-RNA interfaces and its application in binding site identification. 57 - Celine Everaert, Pieter-Jan Volders, Annelien Morlion, Olivier Thas, Pieter Mestdagh:
SPECS: a non-parametric method to identify tissue-specific molecular features for unbalanced sample groups. 58 - Marta B. Lopes, Susana Vinga:
Tracking intratumoral heterogeneity in glioblastoma via regularized classification of single-cell RNA-Seq data. 59 - Hai-Cheng Yi, Zhu-Hong You, Mei-Neng Wang, Zhen-Hao Guo, Yan-Bin Wang, Ji-Ren Zhou:
RPI-SE: a stacking ensemble learning framework for ncRNA-protein interactions prediction using sequence information. 60 - Zhen Gao, Yu-Tian Wang, Qing-Wen Wu, Jian-Cheng Ni, Chun-Hou Zheng:
Graph regularized L2, 1-nonnegative matrix factorization for miRNA-disease association prediction. 61 - Mrinmoy Das, Tarini Shankar Ghosh, Ian B. Jeffery:
IPCO: Inference of Pathways from Co-variance analysis. 62 - Eugene Lin, Sudipto Mukherjee, Sreeram Kannan:
A deep adversarial variational autoencoder model for dimensionality reduction in single-cell RNA sequencing analysis. 64 - Vasudha Sharma, Sharmistha Majumdar:
Comparative analysis of ChIP-exo peak-callers: impact of data quality, read duplication and binding subtypes. 65 - Ksenia Khelik, Geir Kjetil Sandve, Alexander Johan Nederbragt, Torbjørn Rognes:
NucBreak: location of structural errors in a genome assembly by using paired-end Illumina reads. 66 - Gong-Hua Li, Shaoxing Dai, Feifei Han, Wenxin Li, Jingfei Huang, Wenzhong Xiao:
FastMM: an efficient toolbox for personalized constraint-based metabolic modeling. 67 - Yu-Chuan Chang, June-Tai Wu, Ming-Yi Hong, Yi-An Tung, Ping-Han Hsieh, Sook Wah Yee, Kathleen M. Giacomini, Yen-Jen Oyang, Chien-Yu Chen:
GenEpi: gene-based epistasis discovery using machine learning. 68 - Ricardo Andrade, Mahdi Doostmohammadi, João L. Santos, Marie-France Sagot, Nuno P. Mira, Susana Vinga:
MOMO - multi-objective metabolic mixed integer optimization: application to yeast strain engineering. 69 - Emanuele Pio Barracchia, Gianvito Pio, Domenica D'Elia, Michelangelo Ceci:
Prediction of new associations between ncRNAs and diseases exploiting multi-type hierarchical clustering. 70 - Ying Xin, Bree Cummins, Tomás Gedeon:
Multistability in the epithelial-mesenchymal transition network. 71 - Anna Jaeschke, Hagen Eckert, Laura J. Bray:
proMAD: semiquantitative densitometric measurement of protein microarrays. 72 - Mark R. Segal, Kipper Fletez-Brant:
Assessing stationary distributions derived from chromatin contact maps. 73 - Michelle L. Treiber, Diana H. Taft, Ian Korf, David A. Mills, Danielle G. Lemay:
Pre- and post-sequencing recommendations for functional annotation of human fecal metagenomes. 74 - Lucile Mégret, Satish Sasidharan Nair, Julia Dancourt, Jeff Aaronson, Jim Rosinski, Christian Néri:
Combining feature selection and shape analysis uncovers precise rules for miRNA regulation in Huntington's disease mice. 75 - Xingyu Zheng, Christopher I. Amos, H. Robert Frost:
Comparison of pathway and gene-level models for cancer prognosis prediction. 76 - Robert A. Dromms, Justin Y. Lee, Mark P. Styczynski:
LK-DFBA: a linear programming-based modeling strategy for capturing dynamics and metabolite-dependent regulation in metabolism. 93 - Lotte B. Romijn, Axel A. Almet, Chin Wee Tan, James M. Osborne:
Modelling the effect of subcellular mutations on the migration of cells in the colorectal crypt. 95 - Nicholas Stoler, Barbara Arbeithuber, Gundula Povysil, Monika Heinzl, Renato Salazar, Kateryna D. Makova, Irene Tiemann-Boege, Anton Nekrutenko:
Family reunion via error correction: an efficient analysis of duplex sequencing data. 96 - Lanling Zhao, Han Liu, Xiguo Yuan, Kun Gao, Junbo Duan:
Comparative study of whole exome sequencing-based copy number variation detection tools. 97 - David Soong, Jeran Stratford, Herve Avet-Loiseau, Nizar Bahlis, Faith Davies, Angela Dispenzieri, A. Kate Sasser, Jordan M. Schecter, Ming Qi, Chad Brown, Wendell D. Jones, Jonathan J. Keats, Daniel Auclair, Christopher Chiu, Jason Powers, Michael Schaffer:
CNV Radar: an improved method for somatic copy number alteration characterization in oncology. 98 - Jianbo Zhang, Dilip R. Panthee:
PyBSASeq: a simple and effective algorithm for bulked segregant analysis with whole-genome sequencing data. 99 - Daniel Jordan de Abreu Santos, John B. Cole, George E. Liu, Paul M. Vanraden, Li Ma:
Gamevar.f90: a software package for calculating individual gametic diversity. 100 - Hung-Ching Chang, Chiao-Pei Chu, Shu-Ju Lin, Chuhsing Kate Hsiao:
Network hub-node prioritization of gene regulation with intra-network association. 101 - Robin Kobus, José Manuel Abuín, André Müller, Sören Lukas Hellmann, Juan Carlos Pichel, Tomás F. Pena, Andreas Hildebrandt, Thomas Hankeln, Bertil Schmidt:
A big data approach to metagenomics for all-food-sequencing. 102 - Yiqian Zhang, Michiaki Hamada:
MoAIMS: efficient software for detection of enriched regions of MeRIP-Seq. 103 - Zoltán Dezsö, Michele Ceccarelli:
Machine learning prediction of oncology drug targets based on protein and network properties. 104 - Tsunglin Liu, Chen-Yu Chen, An Chen-Deng, Yi-Lin Chen, Jiu-Yao Wang, Yung-I Hou, Min-Ching Lin:
Joining Illumina paired-end reads for classifying phylogenetic marker sequences. 105 - Du Zhang, Qi Hu, Xinxing Liu, Kai Zou, Emmanuel Konadu Sarkodie, Xueduan Liu, Fei Gao:
AllEnricher: a comprehensive gene set function enrichment tool for both model and non-model species. 106 - Jonas Reeb, Theresa Wirth, Burkhard Rost:
Variant effect predictions capture some aspects of deep mutational scanning experiments. 107 - Joshua J. Levy, Alexander J. Titus, Curtis L. Petersen, Youdinghuan Chen, Lucas A. Salas, Brock C. Christensen:
MethylNet: an automated and modular deep learning approach for DNA methylation analysis. 108 - Jiabing Fu, Bixin Ke, Shoubin Dong:
LCQS: an efficient lossless compression tool of quality scores with random access functionality. 109 - Xiaokang Zhang, Inge Jonassen:
RASflow: an RNA-Seq analysis workflow with Snakemake. 110 - Cheng Yan, Fang-Xiang Wu, Jianxin Wang, Guihua Duan:
PESM: predicting the essentiality of miRNAs based on gradient boosting machines and sequences. 111 - Lei Cui, Hansheng Li, Wenli Hui, Sitong Chen, Lin Yang, Yuxin Kang, Qirong Bo, Jun Feng:
A deep learning-based framework for lung cancer survival analysis with biomarker interpretation. 112 - Martin Lewinski, Yannik Bramkamp, Tino Köster, Dorothee Staiger:
SEQing: web-based visualization of iCLIP and RNA-seq data in an interactive python framework. 113 - Gianluca Ascolani, Timothy M. Skerry, Damien Lacroix, Enrico Dall'Ara, Aban Shuaib:
Revealing hidden information in osteoblast's mechanotransduction through analysis of time patterns of critical events. 114 - Konrad Grosser, Dirk Metzler:
Modeling methylation dynamics with simultaneous changes in CpG islands. 115 - Monica J. Quinzo, Esther M. Lafuente, Pilar Zuluaga, Darren R. Flower, Pedro A. Reche:
Correction to: Computational assembly of a human Cytomegalovirus vaccine upon experimental epitope legacy. 116 - Qiaofeng Ou, Jiabing Xiao, Lei Yu, Kaizhi Wu, Bangshu Xiong:
2D electrophoresis image brightness correction based on gradient interval histogram. 117 - Anna M. Nia, Tianlong Chen, Brooke L. Barnette, Kamil Khanipov, Robert L. Ullrich, Suresh K. Bhavnani, Mark R. Emmett:
Efficient identification of multiple pathways: RNA-Seq analysis of livers from 56Fe ion irradiated mice. 118 - Aaron M. Smith, Jonathan R. Walsh, John Long, Craig B. Davis, Peter Henstock, Martin R. Hodge, Mateusz Maciejewski, Xinmeng Jasmine Mu, Stephen Ra, Shanrong Zhao, Daniel Ziemek, Charles K. Fisher:
Standard machine learning approaches outperform deep representation learning on phenotype prediction from transcriptomics data. 119 - Audrey Hulot, Julien Chiquet, Florence Jaffrézic, Guillem Rigaill:
Fast tree aggregation for consensus hierarchical clustering. 120 - Guang-Hui Fu, Yuan-Jiao Wu, Min-Jie Zong, Jianxin Pan:
Hellinger distance-based stable sparse feature selection for high-dimensional class-imbalanced data. 121 - Yahya Bokhari, Areej Alhareeri, Tomasz Arodz:
QuaDMutNetEx: a method for detecting cancer driver genes with low mutation frequency. 122 - Ajay Abisheck Paul George, Mauricio Lacerda, Benjamin Franz Syllwasschy, Marie-Thérèse Hopp, Amelie Wißbrock, Diana Imhof:
HeMoQuest: a webserver for qualitative prediction of transient heme binding to protein motifs. 124 - Zhiheng Li, Zhihao Yang, Yang Xiang, Ling Luo, Yuanyuan Sun, Hongfei Lin:
Exploiting sequence labeling framework to extract document-level relations from biomedical texts. 125 - Dengju Yao, Xiaojuan Zhan, Xiaorong Zhan, Chee Keong Kwoh, Peng Li, Jinke Wang:
A random forest based computational model for predicting novel lncRNA-disease associations. 126 - Leilei Wu, Qinfang Deng, Ze Xu, Songwen Zhou, Chao Li, Yi-Xue Li:
A novel virtual barcode strategy for accurate panel-wide variant calling in circulating tumor DNA. 127 - Jessada Thutkawkorapin, Jesper Eisfeldt, Emma Tham, Daniel Nilsson:
pyCancerSig: subclassifying human cancer with comprehensive single nucleotide, structural and microsatellite mutational signature deconstruction from whole genome sequencing. 128 - Katja Ovchinnikova, Vitaly Kovalev, Lachlan Stuart, Theodore Alexandrov:
OffsampleAI: artificial intelligence approach to recognize off-sample mass spectrometry images. 129 - Lea Buchweitz, James T. Yurkovich, Christoph Blessing, Veronika Kohler, Fabian Schwarzkopf, Zachary A. King, Laurence Yang, Freyr Jóhannsson, Ólafur E. Sigurjónsson, Ottar Rolfsson, Julian Heinrich, Andreas Dräger:
Visualizing metabolic network dynamics through time-series metabolomic data. 130 - Siqi Chen, Sudhir Ghandikota, Yadu Gautam, Tesfaye B. Mersha:
MI-MAAP: marker informativeness for multi-ancestry admixed populations. 131 - Sergey Shityakov, Elena Bencurova, Carola Förster, Thomas Dandekar:
Modeling of shotgun sequencing of DNA plasmids using experimental and theoretical approaches. 132 - Di Shao, Wenzhi Mao, Yaoguang Xing, Haipeng Gong:
RDb2C2: an improved method to identify the residue-residue pairing in β strands. 133 - Rezvan Ehsani, Finn Drabløs:
Enhanced identification of significant regulators of gene expression. 134 - José María Martínez-Otzeta, Itziar Irigoien, Basilio Sierra, Concepción Arenas:
ORdensity: user-friendly R package to identify differentially expressed genes. 135 - Ruth Veevers, Gavin C. Cawley, Steven Hayward:
Investigation of sequence features of hinge-bending regions in proteins with domain movements using kernel logistic regression. 137 - Christian Ponte-Fernández, Jorge González-Domínguez, Antonio Carvajal-Rodríguez, María J. Martín:
Toxo: a library for calculating penetrance tables of high-order epistasis models. 138 - Guannan Wang, Dong-Ha Oh, Maheshi Dassanayake:
GOMCL: a toolkit to cluster, evaluate, and extract non-redundant associations of Gene Ontology-based functions. 139 - Mojtaba Tefagh, Stephen P. Boyd:
SWIFTCORE: a tool for the context-specific reconstruction of genome-scale metabolic networks. 140 - Eun Jeong Min, Qi Long:
Sparse multiple co-Inertia analysis with application to integrative analysis of multi -Omics data. 141 - Tania Timmermann, Bernardo González, Gonzalo A. Ruz:
Reconstruction of a gene regulatory network of the induced systemic resistance defense response in Arabidopsis using boolean networks. 142 - Felippe C. Queiroz, Adriana M. P. Vargas, Maria G. A. Oliveira, Giovanni V. Comarela, Sabrina de Azevedo Silveira:
ppiGReMLIN: a graph mining based detection of conserved structural arrangements in protein-protein interfaces. 143 - Cody Ashby, Michael W. Rutherford, Michael A. Bauer, Erich A. Peterson, Yan Wang, Eileen M. Boyle, Christopher Paul Wardell, Brian A. Walker:
TarPan: an easily adaptable targeted sequencing panel viewer for research and clinical use. 144 - Samuel E. Norton, Julia Koehler Leman, Tiffany Khong, Andrew Spencer, Barbara Fazekas de St Groth, Helen M. McGuire, Roslyn A. Kemp:
Brick plots: an intuitive platform for visualizing multiparametric immunophenotyped cell clusters. 145 - Amina Lemsara, Salima Ouadfel, Holger Fröhlich:
PathME: pathway based multi-modal sparse autoencoders for clustering of patient-level multi-omics data. 146 - Ahmed Ibrahim S. Khalil, Costerwell Khyriem, Anupam Chattopadhyay, Amartya Sanyal:
Hierarchical discovery of large-scale and focal copy number alterations in low-coverage cancer genomes. 147 - Zhongming Zhao, Yulin Dai, Chi Zhang, Ewy A. Mathé, Lai Wei, Kai Wang:
Correction to: The International Conference on Intelligent Biology and Medicine (ICIBM) 2019: bioinformatics methods and applications for human diseases. 148 - Adam H. Freedman, John M. Gaspar, Timothy B. Sackton:
Short paired-end reads trump long single-end reads for expression analysis. 149 - Pu Wang, Xiaotong Huang, Wangren Qiu, Xuan Xiao:
Identifying GPCR-drug interaction based on wordbook learning from sequences. 150 - Thomas Hütter, Maximilian H. Ganser, Manuel Kocher, Merima Halkic, Sabine Agatha, Nikolaus Augsten:
DeSignate: detecting signature characters in gene sequence alignments for taxon diagnoses. 151 - Tomás M. Coronado, Arnau Mir, Francesc Rosselló, Lucía Rotger:
On Sackin's original proposal: the variance of the leaves' depths as a phylogenetic balance index. 154 - Xingheng Yu, Xinqi Gong, Hao Jiang:
Heterogeneous multiple kernel learning for breast cancer outcome evaluation. 155 - Ali Foroughi Pour, Maciej Pietrzak, Lori A. Dalton, Grzegorz A. Rempala:
High dimensional model representation of log-likelihood ratio: binary classification with expression data. 156 - Jianquan Ouyang, Ningqiao Huang, Yunqi Jiang:
A single-model quality assessment method for poor quality protein structure. 157 - Rui Dong, Guo-Cheng Yuan:
GiniClust3: a fast and memory-efficient tool for rare cell type identification. 158 - Rui Kong, Xinnan Xu, Xiaoqing Liu, Pingan He, Michael Q. Zhang, Qi Dai:
2SigFinder: the combined use of small-scale and large-scale statistical testing for genomic island detection from a single genome. 159 - Ohgew Kweon, Seong-Jae Kim, Jae Hyun Kim, Seong Won Nho, Dongryeoul Bae, Jungwhan Chon, Mark Hart, Dong-Heon Baek, Young-Chang Kim, Wenjun Wang, Sung-Kwan Kim, John B. Sutherland, Carl Cerniglia:
CYPminer: an automated cytochrome P450 identification, classification, and data analysis tool for genome data sets across kingdoms. 160 - Joseph Bergenstråhle, Ludvig Bergenstråhle, Joakim Lundeberg:
SpatialCPie: an R/Bioconductor package for spatial transcriptomics cluster evaluation. 161 - Nathan Mih, Jonathan M. Monk, Xin Fang, Edward Catoiu, David Heckmann, Laurence Yang, Bernhard O. Palsson:
Adaptations of Escherichia coli strains to oxidative stress are reflected in properties of their structural proteomes. 162 - Chathuri Daluwatte, Peter Schotland, David G. Strauss, Keith Burkhart, Rebecca Racz:
Predicting potential adverse events using safety data from marketed drugs. 163 - Simona Aufiero, Yolan J. Reckman, Anke J. Tijsen, Yigal M. Pinto, Esther E. Creemers:
circRNAprofiler: an R-based computational framework for the downstream analysis of circular RNAs. 164 - James Fodor, Michael Brand, Rebecca J. Stones, Ashley M. Buckle:
Intrinsic limitations in mainstream methods of identifying network motifs in biology. 165 - Julian Schwanbeck, Ines Oehmig, Jerôme Dretzke, Andreas E. Zautner, Uwe Gross, Wolfgang Bohne:
YSMR: a video tracking and analysis program for bacterial motility. 166 - Matthias Gietzelt, Christian Karmen, Petra Knaup-Gregori, Matthias Ganzinger:
vivaGen - a survival data set generator for software testing. 167 - Bishnu Sarker, David W. Ritchie, Sabeur Aridhi:
GrAPFI: predicting enzymatic function of proteins from domain similarity graphs. 168 - Marius Wöste, Elsa Leitão, Sandra Laurentino, Bernhard Horsthemke, Sven Rahmann, Christopher Schröder:
wg-blimp: an end-to-end analysis pipeline for whole genome bisulfite sequencing data. 169 - Jad Abbass, Jean-Christophe Nebel:
Enhancing fragment-based protein structure prediction by customising fragment cardinality according to local secondary structure. 170 - Xu Ren, Pei Fen Kuan:
Negative binomial additive model for RNA-Seq data analysis. 171 - Jianjun Zhang, Xuan Guo, Samantha Gonzales, Jingjing Yang, Xuexia Wang:
TS: a powerful truncated test to detect novel disease associated genes using publicly available gWAS summary data. 172 - Xinpei Yi, Fuzhou Gong, Yan Fu:
Transfer posterior error probability estimation for peptide identification. 173 - Chun-Hsi Tso, Jen-Leih Wu, Ming-Wei Lu:
Blast2Fish: a reference-based annotation web tool for transcriptome analysis of non-model teleost fish. 174 - Soobok Joe, Hojung Nam:
Prediction model construction of mouse stem cell pluripotency using CpG and non-CpG DNA methylation markers. 175 - Hailin Chen, Ruiyu Guo, Guanghui Li, Wei Zhang, Zuping Zhang:
Comparative analysis of similarity measurements in miRNAs with applications to miRNA-disease association predictions. 176 - Xiaotian Dai, Guifang Fu, Randall Reese:
Detecting PCOS susceptibility loci from genome-wide association studies via iterative trend correlation based feature screening. 177 - Afrah Shafquat, Ronald G. Crystal, Jason G. Mezey:
Identifying novel associations in GWAS by hierarchical Bayesian latent variable detection of differentially misclassified phenotypes. 178 - Matthew Merski, Krzysztof Mlynarczyk, Jan Ludwiczak, Jakub Skrzeczkowski, Stanislaw Dunin-Horkawicz, Maria W. Górna:
Self-analysis of repeat proteins reveals evolutionarily conserved patterns. 179 - Qianqian Yuan, Xingli Guo, Yang Ren, Xiao Wen, Lin Gao:
Cluster correlation based method for lncRNA-disease association prediction. 180 - Joungmin Choi, Heejoon Chae:
methCancer-gen: a DNA methylome dataset generator for user-specified cancer type based on conditional variational autoencoder. 181 - Lei Li, Deborah Chang, Lei Han, Xiaojian Zhang, Joseph Zaia, Xiu-Feng Wan:
Multi-task learning sparse group lasso: a method for quantifying antigenicity of influenza A(H1N1) virus using mutations and variations in glycosylation of Hemagglutinin. 182 - Yi Zhou, Siu-wai Leung, Shosuke Mizutani, Tatsuya Takagi, Yu-Shi Tian:
MEPHAS: an interactive graphical user interface for medical and pharmaceutical statistical analysis with R and Shiny. 183 - Yue Hu, Xi Xi, Qian Yang, Xuegong Zhang:
SCeQTL: an R package for identifying eQTL from single-cell parallel sequencing data. 184 - Mikang Sim, Jongin Lee, Daehwan Lee, Daehong Kwon, Jaebum Kim:
TAMA: improved metagenomic sequence classification through meta-analysis. 185 - Michael D. Olp, Kelsey S. Kalous, Brian C. Smith:
ICEKAT: an interactive online tool for calculating initial rates from continuous enzyme kinetic traces. 186 - Lu Cao, Andries D. van der Meer, Fons J. Verbeek, Robert Passier:
Automated image analysis system for studying cardiotoxicity in human pluripotent stem cell-Derived cardiomyocytes. 187 - Halil Kilicoglu, Graciela Rosemblat, Marcelo Fiszman, Dongwook Shin:
Broad-coverage biomedical relation extraction with SemRep. 188 - Maya Galili, Tamir Tuller:
CSN: unsupervised approach for inferring biological networks based on the genome alone. 190 - H. Atakan Ekiz, Christopher J. Conley, W. Zac Stephens, Ryan M. O'Connell:
CIPR: a web-based R/shiny app and R package to annotate cell clusters in single cell RNA sequencing experiments. 191 - Hector Sanz, Ferran Reverter, Clarissa Valim:
Enhancing SVM for survival data using local invariances and weighting. 193 - Abdullah El-Kurdi, Ghiwa Ali Khalil, Georges Khazen, Pierre H. Khoueiry:
fcScan: a versatile tool to cluster combinations of sites using genomic coordinates. 194 - Yiru Zhao, Yifan Zhou, Yuan Liu, Yinyi Hao, Menglong Li, Xuemei Pu, Chuan Li, Zhining Wen:
Uncovering the prognostic gene signatures for the improvement of risk stratification in cancers by using deep learning algorithm coupled with wavelet transform. 195 - Hersh D. Ravkin, Ofer Givton, David B. Geffen, Eitan Rubin:
Direct comparison shows that mRNA-based diagnostics incorporate information which cannot be learned directly from genomic mutations. 196 - Noel Cabañas, Arturo Becerra, David Romero, Tzipe Govezensky, Jesús Javier Espinosa-Aguirre, Rafael Camacho-Carranza:
Repetitive DNA profile of the amphibian mitogenome. 197 - Lianbo Yu, Soledad Fernandez, Guy N. Brock:
Power analysis for RNA-Seq differential expression studies using generalized linear mixed effects models. 198 - David Gerard:
Data-based RNA-seq simulations by binomial thinning. 206 - Michael Gruenstaeudl, Nils Jenke:
PACVr: plastome assembly coverage visualization in R. 207 - Azree Nazri, Olalekan Agbolade, Razali Yaakob, Abdul Azim Abdul Ghani, Yoke Kqueen Cheah:
A novel investigation of the effect of iterations in sliding semi-landmarks for 3D human facial images. 208 - Patrick Kunzmann, Benjamin E. Mayer, Kay Hamacher:
Substitution matrix based color schemes for sequence alignment visualization. 209 - Hiroki Takizawa, Junichi Iwakiri, Kiyoshi Asai:
RintC: fast and accuracy-aware decomposition of distributions of RNA secondary structures with extended logsumexp. 210 - Alejandro A. Schäffer, Eneida Hatcher, Linda Yankie, Lara Shonkwiler, J. Rodney Brister, Ilene Karsch-Mizrachi, Eric P. Nawrocki:
VADR: validation and annotation of virus sequence submissions to GenBank. 211 - Lei Du, Qingfang Meng, Yuehui Chen, Peng Wu:
Subcellular location prediction of apoptosis proteins using two novel feature extraction methods based on evolutionary information and LDA. 212 - Zhijing Li, Yuchen Lian, Xiaoyong Ma, Xiangrong Zhang, Chen Li:
Bio-semantic relation extraction with attention-based external knowledge reinforcement. 213 - Samuel J. Roth, Sven Heinz, Christopher Benner:
ARTDeco: automatic readthrough transcription detection. 214 - Collin Giguere, Harsh Vardhan Dubey, Vishal Kumar Sarsani, Hachem Saddiki, Shai He, Patrick Flaherty:
SCSIM: Jointly simulating correlated single-cell and bulk next-generation DNA sequencing data. 215 - Kitsuchart Pasupa, Wanthanee Rathasamuth, Sissades Tongsima:
Discovery of significant porcine SNPs for swine breed identification by a hybrid of information gain, genetic algorithm, and frequency feature selection technique. 216 - Emily K. Mallory, Matthieu de Rochemonteix, Alexander Ratner, Ambika Acharya, Christopher Ré, Roselie A. Bright, Russ B. Altman:
Extracting chemical reactions from text using Snorkel. 217 - Elisabetta Sauta, Andrea Demartini, Francesca Vitali, Alberto Riva, Riccardo Bellazzi:
A Bayesian data fusion based approach for learning genome-wide transcriptional regulatory networks. 219 - William S. Pearman, Nikki E. Freed, Olin K. Silander:
Testing the advantages and disadvantages of short- and long- read eukaryotic metagenomics using simulated reads. 220 - Pirunthan Perampalam, Frederick A. Dick:
BEAVR: a browser-based tool for the exploration and visualization of RNA-seq data. 221 - Cheng Ye, Alberto Paccanaro, Mark Gerstein, Koon-Kiu Yan:
The corrected gene proximity map for analyzing the 3D genome organization using Hi-C data. 222 - Ali Haisam Muhammad Rafid, Md. Toufikuzzaman, Mohammad Saifur Rahman, M. Sohel Rahman:
CRISPRpred(SEQ): a sequence-based method for sgRNA on target activity prediction using traditional machine learning. 223 - David R. Espeso, Elena Algar, Esteban Martínez-García, Víctor de Lorenzo:
Exploiting geometric similarity for statistical quantification of fluorescence spatial patterns in bacterial colonies. 224 - Tiantian Liu, Hongyu Zhao, Tao Wang:
An empirical Bayes approach to normalization and differential abundance testing for microbiome data. 225 - Paul Müller, Gheorghe Cojoc, Jochen R. Guck:
DryMass: handling and analyzing quantitative phase microscopy images of spherical, cell-sized objects. 226 - William Meyerson, John Leisman, Fabio C. P. Navarro, Mark Gerstein:
Origins and characterization of variants shared between databases of somatic and germline human mutations. 227 - Tong Wang, Ping Xuan, Zonglin Liu, Tiangang Zhang:
Assistant diagnosis with Chinese electronic medical records based on CNN and BiLSTM with phrase-level and word-level attentions. 230 - Mohammad Asif Emon, Daniel Domingo-Fernández, Charles Tapley Hoyt, Martin Hofmann-Apitius:
PS4DR: a multimodal workflow for identification and prioritization of drugs based on pathway signatures. 231 - Fangjun Li, Mu Yang, Yunhe Li, Mingqiang Zhang, Wenjuan Wang, Dongfeng Yuan, Dongqi Tang:
An improved clear cell renal cell carcinoma stage prediction model based on gene sets. 232 - Alexis Robitaille, Rosario N. Brancaccio, Sankhadeep Dutta, Dana E. Rollison, Marcis Leja, Nicole Fischer, Adam Grundhoff, Tarik Gheit, Massimo Tommasino, Magali Olivier:
PVAmpliconFinder: a workflow for the identification of human papillomaviruses from high-throughput amplicon sequencing. 233 - Hesham ElAbd, Yana Bromberg, Adrienne Hoarfrost, Tobias Lenz, Andre Franke, Mareike Wendorff:
Amino acid encoding for deep learning applications. 235 - Jianwei Li, Xiaoyu Ma, Xichuan Li, Junhua Gu:
PPAI: a web server for predicting protein-aptamer interactions. 236 - Wei Du, Yu Sun, Gaoyang Li, Huansheng Cao, Ran Pang, Ying Li:
CapsNet-SSP: multilane capsule network for predicting human saliva-secretory proteins. 237 - Kenneth E. Westerman, Sean Harrington, José M. Ordovás, Laurence D. Parnell:
PhyteByte: identification of foods containing compounds with specific pharmacological properties. 238 - Yang Qi, Yang Guo, Huixin Jiao, Xuequn Shang:
A flexible network-based imputing-and-fusing approach towards the identification of cell types from single-cell RNA-seq data. 240 - Mihály Koltai, Vincent Noel, Andrei Yu. Zinovyev, Laurence Calzone, Emmanuel Barillot:
Exact solving and sensitivity analysis of stochastic continuous time Boolean models. 241 - Peter Hönigschmid, Stephan Breimann, Martina Weigl, Dmitrij Frishman:
AllesTM: predicting multiple structural features of transmembrane proteins. 242 - Raúl Aguirre-Gamboa, Niek de Klein, Jennifer di Tommaso, Annique Claringbould, Monique G. P. van der Wijst, Dylan de Vries, Harm Brugge, Roy Oelen, Urmo Võsa, Maria M. Zorro, Xiaojin Chu, Olivier B. Bakker, Zuzanna Borek, Isis Ricaño-Ponce, Patrick Deelen, Cheng-Jiang Xu, Morris A. Swertz, Iris Jonkers, Sebo Withoff, Irma Joosten, Serena Sanna, Vinod Kumar, Hans J. P. M. Koenen, Leo A. B. Joosten, Mihai G. Netea, Cisca Wijmenga, Lude Franke, Yang Li:
Deconvolution of bulk blood eQTL effects into immune cell subpopulations. 243 - Duc-Hau Le, Trang T. H. Tran:
RWRMTN: a tool for predicting disease-associated microRNAs based on a microRNA-target gene network. 244 - Vincent Laville, Timothy Majarian, Paul S. de Vries, Amy R. Bentley, Mary F. Feitosa, Yun J. Sung, D. C. Rao, Alisa Manning, Hugues Aschard:
Deriving stratified effects from joint models investigating gene-environment interactions. 251 - Zhi-Hui Luo, Meng-Wei Shi, Zhuang Yang, Hong-Yu Zhang, Zhen-Xia Chen:
pyMeSHSim: an integrative python package for biomedical named entity recognition, normalization, and comparison of MeSH terms. 252 - Sina Majidian, Mohammad Hossein Kahaei, Dick de Ridder:
Hap10: reconstructing accurate and long polyploid haplotypes using linked reads. 253 - Christopher S. Anderson, Mark Y. Sangster, Hongmei Yang, Thomas J. Mariani, Sidhartha Chaudhury, David J. Topham:
Implementing sequence-based antigenic distance calculation into immunological shape space model. 256 - Silas Kieser, Joseph Brown, Evgeny M. Zdobnov, Mirko Trajkovski, Lee Ann McCue:
ATLAS: a Snakemake workflow for assembly, annotation, and genomic binning of metagenome sequence data. 257 - Shintaro Kato, Takayoshi Ono, Hirotaka Minagawa, Katsunori Horii, Ikuo Shiratori, Iwao Waga, Koichi Ito, Takafumi Aoki:
FSBC: fast string-based clustering for HT-SELEX data. 263 - Louis-Marie Bobay:
CoreSimul: a forward-in-time simulator of genome evolution for prokaryotes modeling homologous recombination. 264 - Ayman Yousif, Nizar Drou, Jillian Rowe, Mohammed Khalfan, Kristin C. Gunsalus:
NASQAR: a web-based platform for high-throughput sequencing data analysis and visualization. 267 - Pietro Di Lena, Claudia Sala, Andrea Prodi, Christine Nardini:
Methylation data imputation performances under different representations and missingness patterns. 268 - Xiaoying Chen, Bo Zhang, Ting Wang, Azad Bonni, Guoyan Zhao:
Robust principal component analysis for accurate outlier sample detection in RNA-Seq data. 269 - Tristan Zindler, Helge Frieling, Alexandra Neyazi, Stefan Bleich, Eva Friedel:
Simulating ComBat: how batch correction can lead to the systematic introduction of false positive results in DNA methylation microarray studies. 271 - Fangzhen Li, Zhi-E. Liu, Xiu-Yuan Li, Li-Mei Bu, Hong-Xia Bu, Hui Liu, Cai-ming Zhang:
Chromatin 3D structure reconstruction with consideration of adjacency relationship among genomic loci. 272 - Måns Magnusson, Jesper Eisfeldt, Daniel Nilsson, Adam Rosenbaum, Valtteri Wirta, Anna Lindstrand, Anna Wedell, Henrik Stranneheim:
Loqusdb: added value of an observations database of local genomic variation. 273 - Stefan Niebler, André Müller, Thomas Hankeln, Bertil Schmidt:
RainDrop: Rapid activation matrix computation for droplet-based single-cell RNA-seq reads. 274 - José Renato M. S. Barroso, Diego C. B. Mariano, Sandro R. Dias, Rafael E. O. Rocha, Lucianna Helene Santos, Ronaldo Alves Pinto Nagem, Raquel Cardoso de Melo Minardi:
Proteus: An algorithm for proposing stabilizing mutation pairs based on interactions observed in known protein 3D structures. 275 - Shaima Belhechmi, Riccardo De Bin, Federico Rotolo, Stefan Michiels:
Accounting for grouped predictor variables or pathways in high-dimensional penalized Cox regression models. 277 - Khaled Mohamad Almustafa:
Prediction of heart disease and classifiers' sensitivity analysis. 278 - Johanna Vielhaben, Markus Wenzel, Wojciech Samek, Nils Strodthoff:
USMPep: universal sequence models for major histocompatibility complex binding affinity prediction. 279 - Minhua Qiu, Bin Zhou, Frederick Lo, Steven Cook, Jason Chyba, Doug Quackenbush, Jason Matzen, Zhizhong Li, Puiying Annie Mak, Kaisheng Chen, Yingyao Zhou:
A cell-level quality control workflow for high-throughput image analysis. 280 - Jing Zhang, Jason Liu, Donghoon Lee, Shaoke Lou, Zhanlin Chen, Gamze Gürsoy, Mark Gerstein:
DiNeR: a Differential graphical model for analysis of co-regulation Network Rewiring. 281 - Haileab Hilafu, Sandra E. Safo, Lillian Haine:
Sparse reduced-rank regression for integrating omics data. 283 - Julie Hurel, Sophie Schbath, Stéphanie Bougeard, Mathieu Rolland, Mauro Petrillo, Fabrice Touzain:
DUGMO: tool for the detection of unknown genetically modified organisms with high-throughput sequencing data for pure bacterial samples. 284 - Miika Leinonen, Leena Salmela:
Optical map guided genome assembly. 285 - Chao Li, Jun Sun, Vasile Palade:
Diversity-guided Lamarckian random drift particle swarm optimization for flexible ligand docking. 286 - Lisardo Fernández, Mariano Pérez, Ricardo Olanda, Juan M. Orduña, Joan Marquez-Molins:
HPG-DHunter: an ultrafast, friendly tool for DMR detection and visualization. 287 - Youngchul Kim, Daewon Kim, Biwei Cao, Rodrigo Carvajal, Minjung Kim:
PDXGEM: patient-derived tumor xenograft-based gene expression model for predicting clinical response to anticancer therapy in cancer patients. 288 - Xiaolei Zhu, Ling Liu, Jingjing He, Ting Fang, Yi Xiong, Julie C. Mitchell:
iPNHOT: a knowledge-based approach for identifying protein-nucleic acid interaction hot spots. 289 - Stephanie Heinen, Nick Schulze, Bernd Franke, Florian Klein, Clara Lehmann, Maria J. G. T. Vehreschild, Claas Gloistein, Melanie Stecher, Jörg Janne Vehreschild:
HEnRY: a DZIF LIMS tool for the collection and documentation of biomaterials in multicentre studies. 290 - Joel Tellinghuisen:
Critique of the pairwise method for estimating qPCR amplification efficiency: beware of correlated data! 291 - Natay Aberra, Aswathy Sebastian, Aaron P. Maloy, Christopher B. Rees, Meredith L. Bartron, István Albert:
Bioinformatics recipes: creating, executing and distributing reproducible data analysis workflows. 292 - Javier Calvelo, Hernán Juan, Héctor Musto, Uriel Koziol, Andrés Iriarte:
SLFinder, a pipeline for the novel identification of splice-leader sequences: a good enough solution for a complex problem. 293 - Yong Zhang, Yongsheng Chen, Huixin Xu, Junbin Fang, Zijian Zhao, Weipeng Hu, Xiaoqin Yang, Jia Ye, Yun Cheng, Jiayin Wang, Weiqiang Sun, Jian Wang, Huanming Yang, Jing Yan, Lin Fang:
SOAPTyping: an open-source and cross-platform tool for sequence-based typing for HLA class I and II alleles. 295 - Alex J. Washburn, Ward C. Wheeler:
Efficient implied alignment. 296 - Avi Kumar, Jack Mitchener, Zachary A. King, Christian M. Metallo:
Escher-Trace: a web application for pathway-based visualization of stable isotope tracing data. 297 - Xia Jiang, Alan Wells, Adam Brufsky, Darshan Shetty, Kahmil Shajihan, Richard E. Neapolitan:
Leveraging Bayesian networks and information theory to learn risk factors for breast cancer metastasis. 298 - Jane Hung, Allen Goodman, Deepali Ravel, Stefanie Lopes, Gabriel Rangel, Odailton A. Nery, Benoit Malleret, Francois Nosten, Marcus V. G. Lacerda, Marcelo U. Ferreira, Laurent Rénia, Manoj Duraisingh, Fabio T. M. Costa, Matthias Marti, Anne E. Carpenter:
Keras R-CNN: library for cell detection in biological images using deep neural networks. 300 - Matthew D. Koslovsky, Marina Vannucci:
MicroBVS: Dirichlet-tree multinomial regression models with Bayesian variable selection - an R package. 301 - Dries Debeer, Carolin Strobl:
Conditional permutation importance revisited. 307 - Dandan Che, Shun Guo, Qingshan Jiang, Lifei Chen:
PFBNet: a priori-fused boosting method for gene regulatory network inference. 308 - Prasannavenkatesh Durai, Young-Joon Ko, Cheol-Ho Pan, Keunwan Park:
Evolutionary chemical binding similarity approach integrated with 3D-QSAR method for effective virtual screening. 309 - Alexander Coulton, Keith J. Edwards:
AutoCloner: automatic homologue-specific primer design for full-gene cloning in polyploids. 311 - Di Zhao, Jian Wang, Yi-Jia Zhang, Xin Wang, Hongfei Lin, Zhihao Yang:
Incorporating representation learning and multihead attention to improve biomedical cross-sentence n-ary relation extraction. 312 - Yosef Masoudi-Sobhanzadeh, Ali Masoudi-Nejad:
Synthetic repurposing of drugs against hypertension: a datamining method based on association rules and a novel discrete algorithm. 313 - Cinque S. Soto, Jessica A. Finn, Jordan R. Willis, Samuel B. Day, Robert S. Sinkovits, Taylor Jones, Samuel Schmitz, Jens Meiler, Andre Branchizio, James E. Crowe Jr.:
PyIR: a scalable wrapper for processing billions of immunoglobulin and T cell receptor sequences using IgBLAST. 314 - Hyoung-Kyu Song, Ebrahim Al Alkeem, Jaewoong Yun, Tae-Ho Kim, Hyerin Yoo, Dasom Heo, Myungsu Chae, Chan Yeob Yeun:
Deep user identification model with multiple biometric data. 315 - Chin-Rur Yang, Chwan-Chuen King, Li-Yu Daisy Liu, Chia-Chi Ku:
FluConvert and IniFlu: a suite of integrated software to identify novel signatures of emerging influenza viruses with increasing risk. 316 - Maria Osmala, Harri Lähdesmäki:
Enhancer prediction in the human genome by probabilistic modelling of the chromatin feature patterns. 317 - Seyed Amir Malekpour, Amir Reza Alizad-Rahvar, Mehdi Sadeghi:
LogicNet: probabilistic continuous logics in reconstructing gene regulatory networks. 318 - Kellen Garrison Cresswell, John C. Stansfield, Mikhail G. Dozmorov:
SpectralTAD: an R package for defining a hierarchy of topologically associated domains using spectral clustering. 319 - Migle Gabrielaite, Rasmus L. Marvig:
GenAPI: a tool for gene absence-presence identification in fragmented bacterial genome sequences. 320 - Rongshan Yu, Wenxian Yang, Shun Wang:
Performance evaluation of lossy quality compression algorithms for RNA-seq data. 321 - Wei Wang, Hehe Lv, Yuan Zhao:
Predicting DNA binding protein-drug interactions based on network similarity. 322 - Fang Yang, Kunjie Fan, Dandan Song, Huakang Lin:
Graph-based prediction of Protein-protein interactions with attributed signed graph embedding. 323 - Archit Verma, Barbara E. Engelhardt:
A robust nonlinear low-dimensional manifold for single cell RNA-seq data. 324 - Vincent Henry, Fatiha Saïs, Olivier Inizan, Elodie Marchadier, Juliette Dibie, Anne Goelzer, Vincent Fromion:
BiPOm: a rule-based ontology to represent and infer molecule knowledge from a biological process-centered viewpoint. 327 - Arne Kutzner, Pok-Son Kim, Markus Schmidt:
A performant bridge between fixed-size and variable-size seeding. 328 - Nivedita Singh, Martin Eberhardt, Olaf Wolkenhauer, Julio Vera, Shailendra K. Gupta:
An integrative network-driven pipeline for systematic identification of lncRNA-associated regulatory network motifs in metastatic melanoma. 329 - Chunyan Tang, Cheng Zhong, Danyang Chen, Jianyi Wang:
Drug-target interactions prediction using marginalized denoising model on heterogeneous networks. 330 - Zhenhua Yu, Fang Du, Rongjun Ban, Yuanwei Zhang:
SimuSCoP: reliably simulate Illumina sequencing data based on position and context dependent profiles. 331 - Marcelo Zoccoler, Pedro Xavier de Oliveira:
METROID: an automated method for robust quantification of subcellular fluorescence events at low SNR. 332 - Joachim Theilhaber, Marielle Chiron, Jennifer Dreymann, Donald Bergstrom, Jack Pollard:
Construction and optimization of gene expression signatures for prediction of survival in two-arm clinical trials. 333 - Yi Yue, Hao Huang, Zhao Qi, Hui-Min Dou, Xin-Yi Liu, Tian-Fei Han, Yue Chen, Xiang-Jun Song, You-Hua Zhang, Jian Tu:
Evaluating metagenomics tools for genome binning with real metagenomic datasets and CAMI datasets. 334 - Behrend Heeren, Stefan Paulus, Heiner E. Goldbach, Heiner Kuhlmann, Anne-Katrin Mahlein, Martin Rumpf, Benedikt Wirth:
Statistical shape analysis of tap roots: a methodological case study on laser scanned sugar beets. 335 - Henri Riihimäki, Wojciech Chachólski, Jakob Theorell, Jan Hillert, Ryan Ramanujam:
A topological data analysis based classification method for multiple measurements. 336 - Steven M. Mussmann, Marlis R. Douglas, Tyler K. Chafin, Michael E. Douglas:
AdmixPipe: population analyses in Admixture for non-model organisms. 337 - Anthony R. Soltis, Clifton L. Dalgard, Harvey B. Pollard, Matthew D. Wilkerson:
MutEnricher: a flexible toolset for somatic mutation enrichment analysis of tumor whole genomes. 338 - Wenwen Fan, Junliang Shang, Feng Li, Yan Sun, Shasha Yuan, Jin-Xing Liu:
IDSSIM: an lncRNA functional similarity calculation model based on an improved disease semantic similarity method. 339 - Fajin Li, Xudong Xing, Zhengtao Xiao, Gang Xu, Xuerui Yang:
RiboMiner: a toolset for mining multi-dimensional features of the translatome with ribosome profiling data. 340 - Ze-Gang Wei, Shao-Wu Zhang, Fei Liu:
smsMap: mapping single molecule sequencing reads by locating the alignment starting positions. 341 - Ji-Hye Choi, Hye In Kim, Hyun Goo Woo:
scTyper: a comprehensive pipeline for the cell typing analysis of single-cell RNA-seq data. 342 - Hasindu Gamaarachchi, Wai Chun Lam, Gihan Jayatilaka, Hiruna Samarakoon, Jared T. Simpson, Martin A. Smith, Sri Parameswaran:
GPU accelerated adaptive banded event alignment for rapid comparative nanopore signal analysis. 343 - Stevenn Volant, Pierre Lechat, Perrine Woringer, Laurence Motreff, Pascal Campagne, Christophe Malabat, Sean Kennedy, Amine Ghozlane:
SHAMAN: a user-friendly website for metataxonomic analysis from raw reads to statistical analysis. 345 - Michelle B. Atallah, Varun Tandon, Kamir J. Hiam, Hunter Boyce, Michelle Hori, Waleed Atallah, Matthew H. Spitzer, Edgar Engleman, Parag Mallick:
ImmunoGlobe: enabling systems immunology with a manually curated intercellular immune interaction network. 346 - Bihai Zhao, Zhihong Zhang, Meiping Jiang, Sai Hu, Yingchun Luo, Lei Wang:
NPF: network propagation for protein function prediction. 355 - Min Woo Sun, Stefano Moretti, Kelley M. Paskov, Nate Tyler Stockham, Maya Varma, Brianna Sierra Chrisman, Peter Yigitcan Washington, Jae-Yoon Jung, Dennis P. Wall:
Game theoretic centrality: a novel approach to prioritize disease candidate genes by combining biological networks with the Shapley value. 356 - Hongwei Sun, Yuehua Cui, Hui Wang, Haixia Liu, Tong Wang:
Comparison of methods for the detection of outliers and associated biomarkers in mislabeled omics data. 357 - Fernando Puente-Sánchez, Natalia García-García, Javier Tamames:
SQMtools: automated processing and visual analysis of 'omics data with R and anvi'o. 358 - Zhen Yao, Frank M. You, Amidou N'Diaye, Ron E. Knox, Curt McCartney, Colin W. Hiebert, Curtis Pozniak, Wayne Xu:
Evaluation of variant calling tools for large plant genome re-sequencing. 360 - Michael Sekula, Jeremy T. Gaskins, Susmita Datta:
A sparse Bayesian factor model for the construction of gene co-expression networks from single-cell RNA sequencing count data. 361 - Yulia Kondratenko, Anton I. Korobeynikov, Alla L. Lapidus:
Correction to: CDSnake: Snakemake pipeline for retrieval of annotated OTUs from paired-end reads using CD-HIT utilities. 362 - Bruna Piereck, Marx Oliveira-Lima, Ana Maria Benko-Iseppon, Sarah Diehl, Reinhard Schneider, Ana Christina Brasileiro-Vidal, Adriano Barbosa-Silva:
LAITOR4HPC: A text mining pipeline based on HPC for building interaction networks. 365 - Fangli Dong, Yong He, Tao Wang, Dong Han, Hui Lu, Hongyu Zhao:
Predicting viral exposure response from modeling the changes of co-expression networks using time series gene expression data. 370 - Hector Sanz, Ferran Reverter, Clarissa Valim:
Correction to: Enhancing SVM for survival data using local invariances and weighting. 371 - Faranak Kazerouni, Azadeh Bayani, Farkhondeh Asadi, Leyla Saeidi, Nasrin Parvizi, Zahra Mansoori:
Type2 diabetes mellitus prediction using data mining algorithms based on the long-noncoding RNAs expression: a comparison of four data mining approaches. 372 - Kellen Garrison Cresswell, John C. Stansfield, Mikhail G. Dozmorov:
Correction to: SpectralTAD: an R package for defining a hierarchy of topologically associated domains using spectral clustering. 373 - Samir Rachid Zaim, Colleen Kenost, Joanne Berghout, Wesley Chiu, Liam Wilson, Hao Helen Zhang, Yves A. Lussier:
binomialRF: interpretable combinatoric efficiency of random forests to identify biomarker interactions. 374 - Brian Vestal, Camille M. Moore, Elizabeth Wynn, Laura M. Saba, Tasha Fingerlin, Katerina J. Kechris:
MCMSeq: Bayesian hierarchical modeling of clustered and repeated measures RNA sequencing experiments. 375 - Manuel Mauricio Goez, Maria C. Torres-Madronero, Sarah Röthlisberger, Edilson Delgado-Trejos:
Joint pre-processing framework for two-dimensional gel electrophoresis images based on nonlinear filtering, background correction and normalization techniques. 376 - Yuan Zhang, Fei Ye, Dapeng Xiong, Xieping Gao:
LDNFSGB: prediction of long non-coding rna and disease association using network feature similarity and gradient boosting. 377 - Mariam Quiñones, David Liou, Conrad Shyu, Wongyu Kim, Ivan Vujkovic-Cvijin, Yasmine Belkaid, Darrell E. Hurt:
"METAGENOTE: a simplified web platform for metadata annotation of genomic samples and streamlined submission to NCBI's sequence read archive". 378 - Siqi Jiang, Zhengyu Pan, Zhao Feng, Yue Guan, Miao Ren, Zhangheng Ding, Shangbin Chen, Hui Gong, Qingming Luo, Anan Li:
Skeleton optimization of neuronal morphology based on three-dimensional shape restrictions. 395 - Peng Xu, Qian Wu, Deyang Lu, Jian Yu, Yongsheng Rao, Zheng Kou, Gang Fang, Wenbin Liu, Henry Han:
A systematic study of critical miRNAs on cells proliferation and apoptosis by the shortest path. 396 - Moustafa Shokrof, Mohamed Abouelhoda:
IonCRAM: a reference-based compression tool for ion torrent sequence files. 397 - Zhenzhen Xue, Yanxia Wu, Qing-Zu Gao, Liang Zhao, Ying-Ying Xu:
Automated classification of protein subcellular localization in immunohistochemistry images to reveal biomarkers in colon cancer. 398 - Sinuo Liu, Xiaojuan Ban, Xiangrui Zeng, Fengnian Zhao, Yuan Gao, Wenjie Wu, Hongpan Zhang, Feiyang Chen, Thomas Hall, Xin Gao, Min Xu:
A unified framework for packing deformable and non-deformable subcellular structures in crowded cryo-electron tomogram simulation. 399 - Babak Khorsand, Abdorreza Savadi, Mahmoud Naghibzadeh:
Comprehensive host-pathogen protein-protein interaction network analysis. 400 - Bo-Ya Ji, Zhu-Hong You, Zhan-Heng Chen, Leon Wong, Hai-Cheng Yi:
NEMPD: a network embedding-based method for predicting miRNA-disease associations by preserving behavior and attribute information. 401 - Aranka Steyaert, Pieter Audenaert, Jan Fostier:
Accurate determination of node and arc multiplicities in de bruijn graphs using conditional random fields. 402 - Muaaz G. Awan, Jack Deslippe, Aydin Buluç, Oguz Selvitopi, Steven A. Hofmeyr, Leonid Oliker, Katherine A. Yelick:
ADEPT: a domain independent sequence alignment strategy for gpu architectures. 406 - Jan Klosa, Noah Simon, Pål O. Westermark, Volkmar Liebscher, Dörte Wittenburg:
Seagull: lasso, group lasso and sparse-group lasso regularization for linear regression models via proximal gradient descent. 407 - Dmytro Fishman, Ivan Kuzmin, Priit Adler, Jaak Vilo, Hedi Peterson:
PAWER: protein array web exploreR. 411 - Zhengqiao Zhao, Alexandru Cristian, Gail Rosen:
Keeping up with the genomes: efficient learning of our increasing knowledge of the tree of life. 412 - Juncheng Guo, Min Jin, Yuanyuan Chen, Jianxiao Liu:
An embedded gene selection method using knockoffs optimizing neural network. 414 - Lucas Coppens, Rob Lavigne:
SAPPHIRE: a neural network based classifier for σ70 promoter prediction in Pseudomonas. 415 - Adam Diehl, Alan P. Boyle:
MapGL: inferring evolutionary gain and loss of short genomic sequence features by phylogenetic maximum parsimony. 416 - Hayato Anzawa, Hitoshi Yamagata, Kengo Kinoshita:
Theoretical characterisation of strand cross-correlation in ChIP-seq. 417 - Jessica Henning, Rob Smith:
A web-based system for creating, viewing, and editing precursor mass spectrometry ground truth data. 418 - Yue-Hua Feng, Shaowu Zhang, Jian-Yu Shi:
DPDDI: a deep predictor for drug-drug interactions. 419 - Maria Th. Kotouza, Katerina Gemenetzi, Chrysi Galigalidou, Elisavet Vlachonikola, Nikolaos Pechlivanis, Andreas Agathangelidis, Raphael Sandaltzopoulos, Pericles A. Mitkas, Kostas Stamatopoulos, Anastasia Chatzidimitriou, Fotis E. Psomopoulos:
TRIP - T cell receptor/immunoglobulin profiler. 422 - Michael T. Ganger, Geoffrey D. Dietz, Patrick Headley, Sarah J. Ewing:
Application of the common base method to regression and analysis of covariance (ANCOVA) in qPCR experiments and subsequent relative expression calculation. 423 - Marouen Ben Guebila:
VFFVA: dynamic load balancing enables large-scale flux variability analysis. 424 - Szymon Grabia, Urszula Smyczynska, Konrad Pagacz, Wojciech Fendler:
NormiRazor: tool applying GPU-accelerated computing for determination of internal references in microRNA transcription studies. 425 - Weiya Chen, Chun Yao, Yingzhong Guo, Yan Wang, Zhidong Xue:
pmTM-align: scalable pairwise and multiple structure alignment with Apache Spark and OpenMP. 426 - Lili Blumenberg, Kelly V. Ruggles:
Hypercluster: a flexible tool for parallelized unsupervised clustering optimization. 428 - David E. Hufnagel, Matthew B. Hufford, Arun S. Seetharam:
SequelTools: a suite of tools for working with PacBio Sequel raw sequence data. 429 - Elisabetta Manduchi, Weixuan Fu, Joseph D. Romano, Stefano Ruberto, Jason H. Moore:
Embedding covariate adjustments in tree-based automated machine learning for biomedical big data analyses. 430 - Moustafa Shokrof, Mohamed Abouelhoda:
Correction to: IonCRAM: a reference-based compression tool for ion torrent sequence files. 435 - Marco Berghoff, Jakob Rosenbauer, Felix Hoffmann, Alexander Schug:
Cells in Silico - introducing a high-performance framework for large-scale tissue modeling. 436 - Dirk Zeckzer, Alrik Hausdorf, Nicole Hinzmann, Lydia Müller, Daniel Wiegreffe:
Masakari: visualization supported statistical analysis of genome segmentations. 437 - Erik N. Bergstrom, Mark Barnes, Iñigo Martincorena, Ludmil B. Alexandrov:
Generating realistic null hypothesis of cancer mutational landscapes using SigProfilerSimulator. 438 - Shisheng Wang, Hongwen Zhu, Hu Zhou, Jingqiu Cheng, Hao Yang:
MSpectraAI: a powerful platform for deciphering proteome profiling of multi-tumor mass spectrometry data by using deep neural networks. 439 - Chunxiang Wang, Xin Gao, Juntao Liu:
Impact of data preprocessing on cell-type clustering based on single-cell RNA-seq data. 440 - Ulrich Lautenschlager, Florian Wagner, Christoph Oberprieler:
AllCoPol: inferring allele co-ancestry in polyploids. 441 - Pasan C. Fernando, Paula M. Mabee, Erliang Zeng:
Integration of anatomy ontology data with protein-protein interaction networks improves the candidate gene prediction accuracy for anatomical entities. 442 - Ewoud Ewing, Nuria Planell-Picola, Maja Jagodic, David Gomez-Cabrero:
GeneSetCluster: a tool for summarizing and integrating gene-set analysis results. 443 - Dandan Liang, Quan Liu, Kejun Zhou, Wei Jia, Guoxiang Xie, Tianlu Chen:
IP4M: an integrated platform for mass spectrometry-based metabolomics data mining. 444 - Liang-Rui Ren, Ying-Lian Gao, Jin-Xing Liu, Junliang Shang, Chun-Hou Zheng:
Correntropy induced loss based sparse robust graph regularized extreme learning machine for cancer classification. 445 - S. Momsen Reincke, Harald Prüss, Jakob Kreye:
Brain antibody sequence evaluation (BASE): an easy-to-use software for complete data analysis in single cell immunoglobulin cloning. 446 - Lin Zhang, Shutao Chen, Jingyi Zhu, Jia Meng, Hui Liu:
REW-ISA: unveiling local functional blocks in epi-transcriptome profiling data via an RNA expression-weighted iterative signature algorithm. 447 - Stefania Alexandra Iakab, Lluc Sementé, María García-Altares, Xavier Correig, Pere Ràfols:
Raman2imzML converts Raman imaging data into the standard mass spectrometry imaging format. 448 - Toby Kenney, Junqiu Gao, Hong Gu:
Application of OU processes to modelling temporal dynamics of the human microbiome, and calculating optimal sampling schemes. 450 - Qiangwei Zhou, Ze Wang, Jing Li, Wing-Kin Sung, Guoliang Li:
MethHaplo: combining allele-specific DNA methylation and SNPs for haplotype region identification. 451 - Jiajun Qiu, Dmitrii Nechaev, Burkhard Rost:
Protein-protein and protein-nucleic acid binding residues important for common and rare sequence variants in human. 452 - Thomas Sherman, Tiger Gao, Elana J. Fertig:
CoGAPS 3: Bayesian non-negative matrix factorization for single-cell analysis with asynchronous updates and sparse data structures. 453 - Tian-Ru Wu, Meng-Meng Yin, Cui-Na Jiao, Ying-Lian Gao, Xiang-Zhen Kong, Jin-Xing Liu:
MCCMF: collaborative matrix factorization based on matrix completion for predicting miRNA-disease associations. 454 - Xiangwen Ji, Chunmei Cui, Qinghua Cui:
smORFunction: a tool for predicting functions of small open reading frames and microproteins. 455 - Joran Deschamps, Jonas Ries:
EMU: reconfigurable graphical user interfaces for Micro-Manager. 456 - Shaoke Lou, Tianxiao Li, Daniel Spakowicz, Xiting Yan, Geoffrey Lowell Chupp, Mark Gerstein:
Latent-space embedding of expression data identifies gene signatures from sputum samples of asthmatic patients. 457 - Jonathan Louis Golob, Samuel Schwartz Minot:
In silico benchmarking of metagenomic tools for coding sequence detection reveals the limits of sensitivity and precision. 459 - Wim De Mulder, Martin Kuiper:
A foundation for reference models for drug combinations with an application to Loewe's reference model. 460 - You Tang, Zhuo Li, Chao Wang, Yuxin Liu, Helong Yu, Aoxue Wang, Yao Zhou:
LDkit: a parallel computing toolkit for linkage disequilibrium analysis. 461 - Eugenio Azpeitia, Eugenio P. Balanzario, Andreas Wagner:
Signaling pathways have an inherent need for noise to acquire information. 462 - Xingyu Liao, Xin Gao, Xiankai Zhang, Fang-Xiang Wu, Jianxin Wang:
RepAHR: an improved approach for de novo repeat identification by assembly of the high-frequency reads. 463 - Arnaud Céol, Piero Montanari, Ilaria Bartolini, Stefano Ceri, Paolo Ciaccia, Marco Patella, Marco Masseroli:
Search and comparison of (epi)genomic feature patterns in multiple genome browser tracks. 464 - Henry Löffler-Wirth, Jasmin Reikowski, Siras Hakobyan, Jonas Wagner, Hans Binder:
oposSOM-Browser: an interactive tool to explore omics data landscapes in health science. 465 - Swati Sinha, Andrew M. Lynn, Dhwani K. Desai:
Implementation of homology based and non-homology based computational methods for the identification and annotation of orphan enzymes: using Mycobacterium tuberculosis H37Rv as a case study. 466 - Xingyu Zheng, Christopher I. Amos, H. Robert Frost:
Cancer prognosis prediction using somatic point mutation and copy number variation data: a comparison of gene-level and pathway-based models. 467 - Van-Kien Bui, Chaochun Wei:
CDKAM: a taxonomic classification tool using discriminative k-mers and approximate matching strategies. 468 - Akram Yazdani, Raul Mendez-Giraldez, Azam Yazdani, Michael R. Kosorok, Panos Roussos:
Differential gene regulatory pattern in the human brain from schizophrenia using transcriptomic-causal network. 469 - Lei Zhang, Bailong Liu, Zhengwei Li, Xiaoyan Zhu, Zhizhen Liang, Ji-Yong An:
Predicting MiRNA-disease associations by multiple meta-paths fusion graph embedding model. 470 - Alexander Eng, Adrian J. Verster, Elhanan Borenstein:
MetaLAFFA: a flexible, end-to-end, distributed computing-compatible metagenomic functional annotation pipeline. 471 - Nikolaos Tsiantis, Julio R. Banga:
Using optimal control to understand complex metabolic pathways. 472 - Mikhail G. Dozmorov, Kellen Garrison Cresswell, Silviu-Alin Bacanu, Carl F. Craver, Mark Reimers, Kenneth S. Kendler:
A method for estimating coherence of molecular mechanisms in major human disease and traits. 473 - Jing Zhang, Jason Liu, Patrick D. McGillivray, Caroline Yi, Lucas Lochovsky, Donghoon Lee, Mark Gerstein:
NIMBus: a negative binomial regression based Integrative Method for mutation Burden Analysis. 474 - Fatemeh Zamani, Mohammad Hossein Olyaee, Ali Reza Khanteymoori:
NCMHap: a novel method for haplotype reconstruction based on Neutrosophic c-means clustering. 475 - Viola Fanfani, Fabio Cassano, Giovanni Stracquadanio:
PyGNA: a unified framework for geneset network analysis. 476 - Alexander H. S. Vargo, Anna C. Gilbert:
A rank-based marker selection method for high throughput scRNA-seq data. 477 - Meng Li:
Calculating the most likely intron splicing orders in S. pombe, fruit fly, Arabidopsis thaliana, and humans. 478 - Eustasio del Barrio, Hristo Inouzhe, Jean-Michel Loubes, Carlos Matrán, Agustín Mayo-Íscar:
optimalFlow: optimal transport approach to flow cytometry gating and population matching. 479 - Jian Zhang, Lixin Lv, Donglei Lu, Denan Kong, Mohammed Abdoh Ali Al-Alashaari, Xudong Zhao:
Variable selection from a feature representing protein sequences: a case of classification on bacterial type IV secreted effectors. 480 - Miha Moskon:
CosinorPy: a python package for cosinor-based rhythmometry. 485 - Hyein Seo, Dong-Ho Cho:
Feature selection algorithm based on dual correlation filters for cancer-associated somatic variants. 486 - Zhilong Mi, Bing-Hui Guo, Xiaobo Yang, Ziqiao Yin, Zhiming Zheng:
LAMP: disease classification derived from layered assessment on modules and pathways in the human gene network. 487 - Xinyan Zhang, Nengjun Yi:
NBZIMM: negative binomial and zero-inflated mixed models, with application to microbiome/metagenomics data analysis. 488 - Xiao Chen, Yi Xiong, Yinbo Liu, Yuqing Chen, Shoudong Bi, Xiaolei Zhu:
m5CPred-SVM: a novel method for predicting m5C sites of RNA. 489 - Marten Moore, Corinna Wesemann, Nikolaj Gossmann, Arne Sahm, Jan Krüger, Alexander Sczyrba, Karl-Josef Dietz:
ConCysFind: a pipeline tool to predict conserved amino acids of protein sequences across the plant kingdom. 490 - Samuel B. Fernandes, Alexander E. Lipka:
simplePHENOTYPES: SIMulation of pleiotropic, linked and epistatic phenotypes. 491 - Christophe Djemiel, Samuel Dequiedt, Battle Karimi, Aurélien Cottin, Thibault Girier, Yassin El Djoudi, Patrick Wincker, Mélanie Lelièvre, Samuel Mondy, Nicolas Chemidlin Prévost-Bouré, Pierre-Alain Maron, Lionel Ranjard, Sébastien Terrat:
BIOCOM-PIPE: a new user-friendly metabarcoding pipeline for the characterization of microbial diversity from 16S, 18S and 23S rRNA gene amplicons. 492 - Abhigyan Nath, André Leier:
Improved cytokine-receptor interaction prediction by exploiting the negative sample space. 493 - Ichcha Manipur, Ilaria Granata, Lucia Maddalena, Mario R. Guarracino:
Correction to: Clustering analysis of tumor metabolic networks. 494 - Samir Rachid Zaim, Colleen Kenost, Joanne Berghout, Wesley Chiu, Liam Wilson, Hao Helen Zhang, Yves A. Lussier:
Correction to: binomialRF: interpretable combinatoric efficiency of random forests to identify biomarker interactions. 495 - Umair Ayub, Imran Haider, Hammad Naveed:
SAlign-a structure aware method for global PPI network alignment. 500 - Blaise Hanczar, Farida Zehraoui, Tina Issa, Mathieu Arles:
Biological interpretation of deep neural network for phenotype prediction based on gene expression. 501 - Qi Zhang, Jianwei Zhu, Fusong Ju, Lupeng Kong, Shiwei Sun, Wei-Mou Zheng, Dongbo Bu:
ISSEC: inferring contacts among protein secondary structure elements using deep object detection. 503 - Jun Wang, Liangjiang Wang:
Prediction and prioritization of autism-associated long non-coding RNAs using gene expression and sequence features. 505 - Ahmed Ibrahim S. Khalil, Siti Rawaidah Binte Mohammad Muzaki, Anupam Chattopadhyay, Amartya Sanyal:
Identification and utilization of copy number information for correcting Hi-C contact map of cancer cell lines. 506 - Fang Jing, Shao-Wu Zhang, Shihua Zhang:
Prediction of enhancer-promoter interactions using the cross-cell type information and domain adversarial neural network. 507 - Adil Al-Azzawi, Anes Ouadou, Highsmith Max, Ye Duan, John J. Tanner, Jianlin Cheng:
DeepCryoPicker: fully automated deep neural network for single protein particle picking in cryo-EM. 509 - Steffen Klamt, Radhakrishnan Mahadevan, Axel von Kamp:
Speeding up the core algorithm for the dual calculation of minimal cut sets in large metabolic networks. 510 - Priyojit Das, Tongye Shen, Rachel Patton McCord:
Inferring chromosome radial organization from Hi-C data. 511 - Xiangjun Li, Zhixin Dou, Yuqing Sun, Lushan Wang, Bin Gong, Lin Wan:
A sequence embedding method for enzyme optimal condition analysis. 512 - Corentin Meyer, Nicolas Scalzitti, Anne Jeannin-Girardon, Pierre Collet, Olivier Poch, Julie Dawn Thompson:
Understanding the causes of errors in eukaryotic protein-coding gene prediction: a case study of primate proteomes. 513 - Ralf C. Mueller, Nicolai Mallig, Jacqueline Smith, Lél Eöery, Richard I. Kuo, Robert H. S. Kraus:
Avian Immunome DB: an example of a user-friendly interface for extracting genetic information. 502 - Rahul Kosarwal, Don Kulasiri, Sandhya Samarasinghe:
Novel domain expansion methods to improve the computational efficiency of the Chemical Master Equation solution for large biological networks. 515 - Zhaojuan Zhang, Wanliang Wang, Ruofan Xia, Gaofeng Pan, Jiandong Wang, Jijun Tang:
Achieving large and distant ancestral genome inference by using an improved discrete quantum-behaved particle swarm optimization algorithm. 516 - Nick Vereecke, Jade Bokma, Freddy Haesebrouck, Hans Nauwynck, Filip Boyen, Bart Pardon, Sebastiaan Theuns:
High quality genome assemblies of Mycoplasma bovis using a taxon-specific Bonito basecaller for MinION and Flongle long-read nanopore sequencing. 517 - Junhua Rao, Lihua Peng, Xinming Liang, Hui Jiang, Chunyu Geng, Xia Zhao, Xin Liu, Guangyi Fan, Fang Chen, Feng Mu:
Performance of copy number variants detection based on whole-genome sequencing by DNBSEQ platforms. 518 - Lei Deng, Wei Lin, Jiacheng Wang, Jingpu Zhang:
DeepciRGO: functional prediction of circular RNAs through hierarchical deep neural networks using heterogeneous network features. 519 - Liang-Chin Huang, Wayland Yeung, Ye Wang, Huimin Cheng, Aarya Venkat, Sheng Li, Ping Ma, Khaled Rasheed, Natarajan Kannan:
Quantitative Structure-Mutation-Activity Relationship Tests (QSMART) model for protein kinase inhibitor response prediction. 520 - Vivekananda Sarangi, Alexandre Jourdon, Taejeong Bae, Arijit Panda, Flora Vaccarino, Alexej Abyzov:
SCELLECTOR: ranking amplification bias in single cells using shallow sequencing. 521 - Yu Zhang, Yahui Long, Chee Keong Kwoh:
Deep learning based DNA: RNA triplex forming potential prediction. 522 - Tobias Hepp, Jakob Zierk, Manfred Rauh, Markus Metzler, Andreas Mayr:
Latent class distributional regression for the estimation of non-linear reference limits from contaminated data sources. 524 - Mahmood Parsamanesh, Majid Erfanian, Saeed Mehrshad:
Stability and bifurcations in a discrete-time epidemic model with vaccination and vital dynamics. 525 - Marius Welzel, Anja Lange, Dominik Heider, Michael Schwarz, Bernd Freisleben, Manfred Jensen, Jens Boenigk, Daniela Beisser:
Natrix: a Snakemake-based workflow for processing, clustering, and taxonomically assigning amplicon sequencing reads. 526 - Ming-Feng Hsieh, Chin Lung Lu, Chuan Yi Tang:
Clover: a clustering-oriented de novo assembler for Illumina sequences. 528 - Ana Luísa Cartaxo, Jaime Almeida, Emilio J. Gualda, Maria Marsal, Pablo Loza-Alvarez, Catarina Brito, Inês A. Isidro:
A computational diffusion model to study antibody transport within reconstructed tumor microenvironments. 529 - Xiangnan Xu, Samantha Solon-Biet, Alistair M. Senior, David Raubenheimer, Stephen J. Simpson, Luigi Fontana, Samuel Müller, Jean Yee Hwa Yang:
LC-N2G: a local consistency approach for nutrigenomics data analysis. 530 - Giulio Caravagna, Guido Sanguinetti, Trevor A. Graham, Andrea Sottoriva:
The MOBSTER R package for tumour subclonal deconvolution from bulk DNA whole-genome sequencing data. 531 - Yunxia Tang, Yu Wang, Jiaqian Wang, Miao Li, Linmin Peng, Guochao Wei, Yixing Zhang, Jin Li, Zhibo Gao:
TruNeo: an integrated pipeline improves personalized true tumor neoantigen identification. 532 - Juan R. González, Marcos López-Sánchez, Alejandro Cáceres, Pere Puig, Tõnu Esko, Luis A. Pérez-Jurado:
MADloy: robust detection of mosaic loss of chromosome Y from genotype-array-intensity data. 533 - Jacqueline Milet, David Courtin, André Garcia, Hervé Perdry:
Mixed logistic regression in genome-wide association studies. 536 - Yuanhe Tian, Wang Shen, Yan Song, Fei Xia, Min He, Kenli Li:
Improving biomedical named entity recognition with syntactic information. 539 - Wei Wang, Xi Yang, Chengkun Wu, Canqun Yang:
CGINet: graph convolutional network-based model for identifying chemical-gene interaction in an integrated multi-relational graph. 544 - Valeriia Sherina, Helene R. McMurray, Winslow Powers, Hartmut Land, Tanzy M. T. Love, Matthew N. McCall:
Multiple imputation and direct estimation for qPCR data with non-detects. 545 - Yusuf Khan, Daniel Hammarström, Bent R. Rønnestad, Stian Ellefsen, Rafi Ahmad:
Increased biological relevance of transcriptome analyses in human skeletal muscle using a model-specific pipeline. 548 - Juan S. Medina-Martínez, Juan E. Arango-Ossa, Max F. Levine, Yangyu Zhou, Gunes Gundem, Andrew L. Kung, Elli Papaemmanuil:
Isabl Platform, a digital biobank for processing multimodal patient data. 549 - Fangtang Yu, Chao Xu, Hong-Wen Deng, Hui Shen:
A novel computational strategy for DNA methylation imputation using mixture regression model (MRM). 552 - Anna Quaglieri, Christoffer Flensburg, Terence P. Speed, Ian J. Majewski:
Finding a suitable library size to call variants in RNA-Seq. 553 - Yubin Xiao, Zheng Xiao, Xiang Feng, Zhiping Chen, Linai Kuang, Lei Wang:
A novel computational model for predicting potential LncRNA-disease associations based on both direct and indirect features of LncRNA-disease pairs. 555 - Bo Zhao, Luke Bryant, Rebecca Cordell, Michael Wilde, Dahlia Salman, Dorota Ruszkiewicz, Wadah Ibrahim, Amisha Singapuri, Tim Coats, Erol Gaillard, Caroline Beardsmore, Toru Suzuki, Leong Ng, Neil Greening, C. L. Paul Thomas, Paul S. Monks, Christopher Brightling, Salman Siddiqui, Robert C. Free:
LabPipe: an extensible bioinformatics toolkit to manage experimental data and metadata. 556 - Mahsa Paknezhad, Sheng Yang Michael Loh, Yukti Choudhury, Valerie Koh Cui Koh, Timothy Tay Kwang Yong, Hui Shan Tan, Ravindran Kanesvaran, Puay Hoon Tan, John Yuen Shyi Peng, Weimiao Yu, Yongcheng Benjamin Tan, Yong Zhen Loy, Min-Han Tan, Hwee Kuan Lee:
Regional registration of whole slide image stacks containing major histological artifacts. 558 - Sebastian Canzler, Jörg Hackermüller:
multiGSEA: a GSEA-based pathway enrichment analysis for multi-omics data. 561 - Sierra Gillis, Andrew Roth:
PyClone-VI: scalable inference of clonal population structures using whole genome data. 571 - David Boho, Michael Rzanny, Jana Wäldchen, Fabian Nitsche, Alice Deggelmann, Hans Christian Wittich, Marco Seeland, Patrick Mäder:
Flora Capture: a citizen science application for collecting structured plant observations. 576 - Krutika S. Gaonkar, Federico Marini, Komal S. Rathi, Payal Jain, Yuankun Zhu, Nicholas A. Chimicles, Miguel A. Brown, Ammar S. Naqvi, Bo Zhang, Phillip B. Storm, John M. Maris, Pichai Raman, Adam C. Resnick, Konstantin Strauch, Jaclyn N. Taroni, Jo Lynne Rokita:
annoFuse: an R Package to annotate, prioritize, and interactively explore putative oncogenic RNA fusions. 577 - Markus Suhr, Christoph Lehmann, Christian R. Bauer, Theresa Bender, Cornelius Knopp, Luca Freckmann, Björn Öst Hansen, Christian Henke, Georg Aschenbrandt, Lea Kühlborn, Sophia Rheinländer, Linus Weber, Bartlomiej Marzec, Marcel Hellkamp, Philipp Wieder, Ulrich Sax, Harald Kusch, Sara Y. Nussbeck:
Menoci: lightweight extensible web portal enhancing data management for biomedical research projects. 582 - H. Jonathan G. Lindström, Ran Friedman:
Inferring time-dependent population growth rates in cell cultures undergoing adaptation. 583 - Sara Salmanian, Hamid Pezeshk, Mehdi Sadeghi:
Inter-protein residue covariation information unravels physically interacting protein dimers. 584 - Matthew D. Koslovsky, Marina Vannucci:
Correction to: MicroBVS: Dirichlet-tree multinomial regression models with Bayesian variable selection - an R package. 585 - Rodrigo Ochoa, Mikhail D. Magnitov, Roman A. Laskowski, Pilar Cossio, Janet M. Thornton:
An automated protocol for modelling peptide substrates to proteases. 586 - Meng Zhou, Dan Shan, Chunhui Zhang, Jianhua Nie, Guangyu Wang, Yanqiao Zhang, Yang Zhou, Tongsen Zheng:
Value of gadoxetic acid-enhanced MRI for microvascular invasion of small hepatocellular carcinoma: a retrospective study. 40 - Firas Souleiman, Martin Heilemann, Robert Hennings, Mareike Hennings, Alexis Klengel, Pierre Hepp, Georg Osterhoff, Annette B. Ahrberg:
A standardized approach for exact CT-based three-dimensional position analysis in the distal tibiofibular joint. 41 - Zhehao Lyu, Lili Liu, Huimin Li, Haibo Wang, Qi Liu, Tingting Chen, Meiling Xu, Lin Tian, Peng Fu:
Imaging analysis of 13 rare cases of renal collecting (Bellini) duct carcinoma in northern China: a case series and literature review. 42 - Jin Hyun Nam, Daniel Couch, Willian A. da Silveira, Zhenning Yu, Dongjun Chung:
PALMER: improving pathway annotation based on the biomedical literature mining with a constrained latent block model. 432 - Zhengfeng Wang, Xiujuan Lei:
Matrix factorization with neural network for predicting circRNA-RBP interactions. 229 - Bingbo Wang, Jie Hu, Yajun Wang, Chenxing Zhang, Yuanjun Zhou, Liang Yu, Xingli Guo, Lin Gao, Yunru Chen:
C3: connect separate connected components to form a succinct disease module. 433 - Gong-Hua Li, Shaoxing Dai, Feifei Han, Wenxin Li, Jingfei Huang, Wenzhong Xiao:
Correction to: FastMM: an efficient toolbox for personalized constraint-based metabolic modeling. 409 - Mark D. Temple:
Real-time audio and visual display of the Coronavirus genome. 431 - Nathaniel P. Delos Santos, Lorane Texari, Christopher Benner:
MEIRLOP: improving score-based motif enrichment by incorporating sequence bias covariates. 410
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