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BMC 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