


Остановите войну!
for scientists:


default search action
BMC Bioinformatics, Volume 23
Volume 23, Number 1, December 2022
- Brandon Reyes, Irene Otero-Muras, Vladislav A. Petyuk:
A numerical approach for detecting switch-like bistability in mass action chemical reaction networks with conservation laws. 1 - Shaoheng Liang, Jason Willis, Jinzhuang Dou, Vakul Mohanty, Yuefan Huang, Eduardo Vilar, Ken Chen:
Sensei: how many samples to tell a change in cell type abundance? 2 - Laurent S. V. Thomas
, Jochen Gehrig:
Correction to: Multi-template matching: a versatile tool for object-localization in microscopy images. 3 - Aparna Elangovan
, Yuan Li, Douglas E. V. Pires, Melissa J. Davis
, Karin Verspoor
:
Large-scale protein-protein post-translational modification extraction with distant supervision and confidence calibrated BioBERT. 4 - Liugen Wang, Min Shang, Qi Dai, Pingan He:
Prediction of lncRNA-disease association based on a Laplace normalized random walk with restart algorithm on heterogeneous networks. 5 - M. A. Hakim Newton
, Fereshteh Mataeimoghadam, Rianon Zaman, Abdul Sattar
:
Secondary structure specific simpler prediction models for protein backbone angles. 6 - Shiming Wang, Jie Li, Yadong Wang:
M2PP: a novel computational model for predicting drug-targeted pathogenic proteins. 7 - Zhaoying Chai, Han Jin, Shenghui Shi, Siyan Zhan, Lin Zhuo, Yu Yang:
Hierarchical shared transfer learning for biomedical named entity recognition. 8 - Han-Jing Jiang, Yabing Huang:
An effective drug-disease associations prediction model based on graphic representation learning over multi-biomolecular network. 9 - Gustavo Daniel Vega Magdaleno, Vladislav Bespalov, Yalin Zheng, Alex Alves Freitas, João Pedro de Magalhães:
Machine learning-based predictions of dietary restriction associations across ageing-related genes. 10 - Li Wang, Cheng Zhong:
gGATLDA: lncRNA-disease association prediction based on graph-level graph attention network. 11 - Nathan P. Gill, Raji Balasubramanian, James R. Bain
, Michael J. Muehlbauer, William L. Lowe Jr., Denise M. Scholtens:
Path-level interpretation of Gaussian graphical models using the pair-path subscore. 12 - Johannes Hettich, J. Christof M. Gebhardt
:
Periodic synchronization of isolated network elements facilitates simulating and inferring gene regulatory networks including stochastic molecular kinetics. 13 - Yuliya Shapovalova, Tom Heskes, Tjeerd Dijkstra
:
Non-parametric synergy modeling of chemical compounds with Gaussian processes. 14 - Albert E. Zhou
, Zalak V. Shah, Katie R. Bradwell
, James B. Munro
, Andrea A. Berry, David Serre, Shannon Takala-Harrison, Timothy D. O'Connor, Joana C. Silva, Mark A. Travassos
:
STRIDE: a command-line HMM-based identifier and sub-classifier of Plasmodium falciparum RIFIN and STEVOR variant surface antigen families. 15 - Huijian Feng
, Lihui Lin, Jiekai Chen
:
scDIOR: single cell RNA-seq data IO software. 16 - Tulika Kakati, Dhruba K. Bhattacharyya, Jugal K. Kalita, Trina M. Norden-Krichmar
:
DEGnext: classification of differentially expressed genes from RNA-seq data using a convolutional neural network with transfer learning. 17 - Jörg Winkler
, Gianvito Urgese, Elisa Ficarra, Knut Reinert
:
LaRA 2: parallel and vectorized program for sequence-structure alignment of RNA sequences. 18 - Junhui Qiu, Qi Zhou, Weicai Ye, Qianjun Chen
, Yun-Juan Bao
:
SweepCluster: A SNP clustering tool for detecting gene-specific sweeps in prokaryotes. 19 - Jing Chen, Baotian Hu, Weihua Peng, Qingcai Chen
, Buzhou Tang:
Biomedical relation extraction via knowledge-enhanced reading comprehension. 20 - Julia Vetter
, Susanne Schaller, Andreas Heinzel, Constantin Aschauer
, Roman Reindl-Schwaighofer, Kira Jelencsics, Karin Hu, Rainer Oberbauer, Stephan M. Winkler:
ImmunoDataAnalyzer: a bioinformatics pipeline for processing barcoded and UMI tagged immunological NGS data. 21 - Vi Ngoc-Nha Tran
, Alireza Shams
, Sinan Ascioglu, Antal Martinecz, Jingyi Liang, Fabrizio Clarelli
, Rafal Mostowy, Ted Cohen, Pia Abel zur Wiesch:
vCOMBAT: a novel tool to create and visualize a computational model of bacterial antibiotic target-binding. 22 - Juan J. Lastra-Díaz
, Alicia Lara-Clares, Ana García-Serrano:
HESML: a real-time semantic measures library for the biomedical domain with a reproducible survey. 23 - Yang Yu, Dezhou Kong:
Protein complexes detection based on node local properties and gene expression in PPI weighted networks. 24 - Atul Sharma, Pranjal Jain, Ashraf Mahgoub, Zihan Zhou, Kanak Mahadik, Somali Chaterji
:
Lerna: transformer architectures for configuring error correction tools for short- and long-read genome sequencing. 25 - Xuemin Dong, Shanshan Dong, Shengkai Pan, Xiangjiang Zhan:
RNA-combine: a toolkit for comprehensive analyses on transcriptome data from different sequencing platforms. 26 - Renmao Tian, Behzad Imanian
:
ASAP 2: a pipeline and web server to analyze marker gene amplicon sequencing data automatically and consistently. 27 - James J. Yang, Xi Luo, Elisa M. Trucco, Anne Buu:
Polygenic risk prediction based on singular value decomposition with applications to alcohol use disorder. 28 - Xifang Sun, Donglin Wang, Jiaqiang Zhu
, Shiquan Sun:
A novel nonparametric computational strategy for identifying differential methylation regions. 29 - Xiong Yuan, Zirong Li, Liwen Xiong, Sufeng Song, Xingfei Zheng, Zhonghai Tang, Zheming Yuan, Lanzhi Li:
Effective identification of varieties by nucleotide polymorphisms and its application for essentially derived variety identification in rice. 30 - Lu Li, Huub C. J. Hoefsloot, Albert A. de Graaf, Evrim Acar, Age K. Smilde
:
Exploring dynamic metabolomics data with multiway data analysis: a simulation study. 31 - Katrin Madjar
, Manuela Zucknick, Katja Ickstadt, Jörg Rahnenführer:
Correction to: Combining heterogeneous subgroups with graph-structured variable selection priors for Cox regression. 32 - Lakshay Anand
, Carlos M. Rodriguez Lopez:
ChromoMap: an R package for interactive visualization of multi-omics data and annotation of chromosomes. 33 - Fei Song, Shiyin Tan, Zengfa Dou, Xiaogang Liu, Xiaoke Ma:
Predicting combinations of drugs by exploiting graph embedding of heterogeneous networks. 34 - Miaoshan Lu, Shaowei An, Ruimin Wang, Jinyin Wang, Changbin Yu
:
Aird: a computation-oriented mass spectrometry data format enables a higher compression ratio and less decoding time. 35 - Lucille Lopez-Delisle
, Jean-Baptiste Delisle
:
baredSC: Bayesian approach to retrieve expression distribution of single-cell data. 36 - Jeremy J. Yang, Christopher Gessner, Joel Duerksen, Daniel Biber, Jessica L. Binder, Murat Ozturk, Brian Foote, Robin McEntire, Kyle Stirling, Ying Ding, David J. Wild:
Knowledge graph analytics platform with LINCS and IDG for Parkinson's disease target illumination. 37 - Emily Kaczmarek, Jina Nanayakkara, Alireza Sedghi, Mehran Pesteie, Thomas Tuschl, Neil Renwick, Parvin Mousavi:
Topology preserving stratification of tissue neoplasticity using Deep Neural Maps and microRNA signatures. 38 - Andrea Hita, Gilles Brocart, Ana Fernandez, Marc Rehmsmeier, Anna Alemany, Sol Schvartzman
:
MGcount: a total RNA-seq quantification tool to address multi-mapping and multi-overlapping alignments ambiguity in non-coding transcripts. 39 - Ludwig Mann
, Kathrin M. Seibt
, Beatrice Weber
, Tony Heitkam
:
ECCsplorer: a pipeline to detect extrachromosomal circular DNA (eccDNA) from next-generation sequencing data. 40 - Maia H. Malonzo
, Viivi Halla-aho, Mikko Konki, Riikka J. Lund
, Harri Lähdesmäki:
LuxRep: a technical replicate-aware method for bisulfite sequencing data analysis. 41 - Mehrdad Mansouri, Sahand Khakabimamaghani, Leonid Chindelevitch
, Martin Ester:
Aristotle: stratified causal discovery for omics data. 42 - Elena Rojano, Fernando Moreno Jabato
, James Richard Perkins
, José Córdoba-Caballero
, Federico García-Criado, Ian Sillitoe, Christine A. Orengo, Juan A. G. Ranea, Pedro Seoane-Zonjic:
Assigning protein function from domain-function associations using DomFun. 43 - Vy Nguyen
, Johannes Griss
:
scAnnotatR: framework to accurately classify cell types in single-cell RNA-sequencing data. 44 - Xiaopu Zhang, Musa A. Hassan, James G. D. Prendergast
:
Using machine learning to detect the differential usage of novel gene isoforms. 45 - Michael Y. Lee, Jacob S. Bedia
, Salil S. Bhate
, Graham L. Barlow
, Darci Phillips
, Wendy J. Fantl
, Garry P. Nolan
, Christian M. Schürch
:
CellSeg: a robust, pre-trained nucleus segmentation and pixel quantification software for highly multiplexed fluorescence images. 46 - Il-Hyung Lee
, Sam Passaro, Selin Ozturk, Juan Ureña, Weitian Wang:
Intelligent fluorescence image analysis of giant unilamellar vesicles using convolutional neural network. 48 - Brandon Signal
, Tim Kahlke:
how_are_we_stranded_here: quick determination of RNA-Seq strandedness. 49 - Albert Rosenberger
, Viola Tozzi, Heike Bickeböller, Rayjean J. Hung, David C. Christiani, Neil E. Caporaso, Geoffrey Liu, Stig E. Bojesen
, Loic Le Marchand, Demetrios Albanes, Melinda C. Aldrich, Adonina Tardon, Guillermo Fernández-Tardón
, Gad Rennert
, John K. Field, Mike Davies, Triantafillos Liloglou, Lambertus A. Kiemeney, Philip Lazarus, Aage Haugen, Shanbeh Zienolddiny, Stephen Lam, Matthew B. Schabath, Angeline S. Andrew, Eric J. Duell, Susanne M. Arnold
, Hans Brunnström, Olle Melander, Gary E. Goodman, Chu Chen, Jennifer A. Doherty, Marion Dawn Teare
, Angela Cox
, Penella J. Woll, Angela Risch
, Thomas R. Muley, Mikael Johansson, Paul Brennan, Maria Teresa Landi, Sanjay Shete, Christopher I. Amos:
Iam hiQ - a novel pair of accuracy indices for imputed genotypes. 50 - Zhaonan Zou
, Michio Iwata
, Yoshihiro Yamanishi
, Shinya Oki
:
Epigenetic landscape of drug responses revealed through large-scale ChIP-seq data analyses. 51 - Gavin Mackenzie, Rasmus W. Jensen
, Thomas Lavstsen, Thomas D. Otto
:
Varia: a tool for prediction, analysis and visualisation of variable genes. 52 - Niloofar Borhani, Jafar Ghaisari, Maryam Abedi, Marzieh Kamali, Yousof Gheisari:
A deep learning approach to predict inter-omics interactions in multi-layer networks. 53 - Himangi Srivastava
, Drew Ferrell, George V. Popescu
:
NetSeekR: a network analysis pipeline for RNA-Seq time series data. 54 - Sonja Mathias
, Adrien Coulier, Andreas Hellander:
CBMOS: a GPU-enabled Python framework for the numerical study of center-based models. 55 - Xianwei Pan, Peng Huang, Shan Li, Lei Cui:
MCRWR: a new method to measure the similarity of documents based on semantic network. 56 - Andrew Walakira
, Junior Ocira, Diane Duroux, Ramouna Fouladi, Miha Moskon, Damjana Rozman, Kristel Van Steen:
Detecting gene-gene interactions from GWAS using diffusion kernel principal components. 57 - Mehdi Saman Booy, Alexander Ilin, Pekka Orponen
:
RNA secondary structure prediction with convolutional neural networks. 58 - Sanna Abrahamsson
, Frida Eiengård, Anna Rohlin, Marcela Dávila López
:
PΨFinder: a practical tool for the identification and visualization of novel pseudogenes in DNA sequencing data. 59 - Cinzia Klemm, Rowan S. M. Howell
, Peter H. Thorpe
:
ScreenGarden: a shinyR application for fast and easy analysis of plate-based high-throughput screens. 60 - Luis Kuhn Cuellar
, Andreas Friedrich, Gisela Gabernet, Luis de la Garza, Sven Fillinger, Adrian Seyboldt, Tobias Koch, Sven zur Oven-Krockhaus, Friederike Wanke, Sandra Richter, Wolfgang Maximilian Thaiss, Marius Horger, Nisar Malek, Klaus Harter, Michael Bitzer
, Sven Nahnsen
:
A data management infrastructure for the integration of imaging and omics data in life sciences. 61 - Walker Gussler, David S. Campo
, Zoya Dimitrova, Pavel Skums, Yury Khudyakov:
Primary case inference in viral outbreaks through analysis of intra-host variant population. 62 - Liyu Liu, Meng Si, Hecheng Ma, Menglin Cong, Quanzheng Xu, Qinghua Sun, Weiming Wu, Cong Wang, Michael J. Fagan, Luis A. J. Mur, Qing Yang, Bing Ji:
A hierarchical opportunistic screening model for osteoporosis using machine learning applied to clinical data and CT images. 63 - Jia-Ming Chang
, Yi-Fu Weng, Wei-Ting Chang, Fu-An Lin, Giacomo Cavalli
:
HiCmapTools: a tool to access HiC contact maps. 64 - Juliane Pfeil, Alina S. Nechyporenko, Marcus Frohme, Frank T. Hufert, Katja Schulze:
Examination of blood samples using deep learning and mobile microscopy. 65 - Yuan Jin, Yang Yang:
ProtPlat: an efficient pre-training platform for protein classification based on FastText. 66 - Min Xie
, Linfeng Yang, Chenglin Jiang, Shenshen Wu, Cheng Luo, Xin Yang, Lijuan He, Shixuan Chen, Tianquan Deng, Mingzhi Ye, Jianbing Yan, Ning Yang
:
gcaPDA: a haplotype-resolved diploid assembler. 68 - Ziyin Xin, Yujun Cai, Louis T. Dang, Hannah M. S. Burke
, Jerico Revote, Natalie Charitakis, Denis Bienroth, Hieu T. Nim, Yuan-Fang Li, Mirana Ramialison
:
MonaGO: a novel gene ontology enrichment analysis visualisation system. 69 - Cheng Peng, Xinben Zhang, Zhijian Xu, Zhaoqiang Chen, Yanqing Yang, Tingting Cai, Weiliang Zhu
:
D3PM: a comprehensive database for protein motions ranging from residue to domain. 70 - Basak Kocaoglu, William H. Alexander:
Degeneracy measures in biologically plausible random Boolean networks. 71 - Xiaoquan Chu
, Tanlin Sun, Qian Li, Youjun Xu, Zhuqing Zhang, Luhua Lai, Jianfeng Pei
:
Prediction of liquid-liquid phase separating proteins using machine learning. 72 - Umberto Ferraro Petrillo, Francesco Palini, Giuseppe Cattaneo, Raffaele Giancarlo:
Correction to: FASTA/Q data compressors for MapReduce-Hadoop genomics: space and time savings made easy. 73 - Hans Müller Paul, Dave D. Istanto, Jacob R Heldenbrand, Matthew E. Hudson:
CROPSR: an automated platform for complex genome-wide CRISPR gRNA design and validation. 74 - Zun Liu, Xing-Nan Wang, Hui Yu, Jian-Yu Shi
, Wenmin Dong:
Predict multi-type drug-drug interactions in cold start scenario. 75 - Eryk Kropiwnicki, Alexander Lachmann, Daniel J. B. Clarke
, Zhuorui Xie, Kathleen M. Jagodnik, Avi Ma'ayan
:
DrugShot: querying biomedical search terms to retrieve prioritized lists of small molecules. 76 - Olivér M. Balogh
, Bettina Benczik, András Horváth, Mátyás Pétervári, Péter Csermely, Péter Ferdinandy, Bence Ágg
:
Efficient link prediction in the protein-protein interaction network using topological information in a generative adversarial network machine learning model. 78 - Jakob P. Pettersen, Eivind Almaas
:
csdR, an R package for differential co-expression analysis. 79 - Leonardo R. Souza, Juan Gabriel Colonna, Joseana Macêdo Fechine, Felipe G. Naveca:
Using amino acids co-occurrence matrices and explainability model to investigate patterns in dengue virus proteins. 80 - Modupeore O. Adetunji
, Brian J. Abraham
:
SEAseq: a portable and cloud-based chromatin occupancy analysis suite. 77 - Jie Hou
, Xiufen Ye
, Weixing Feng, Qiaosheng Zhang, Yatong Han, Yusong Liu
, Yu Li, Yufen Wei:
Distance correlation application to gene co-expression network analysis. 81 - Raphaël Mourad:
TADreg: a versatile regression framework for TAD identification, differential analysis and rearranged 3D genome prediction. 82 - Omer Ali, Amna Farooq, Mingyi Yang
, Victor X. Jin, Magnar Bjørås, Junbai Wang
:
abc4pwm: affinity based clustering for position weight matrices in applications of DNA sequence analysis. 83 - Florin Ratajczak
, Mitchell Joblin, Martin Ringsquandl, Marcel Hildebrandt:
Task-driven knowledge graph filtering improves prioritizing drugs for repurposing. 84 - Wiktor Kusmirek
, Robert M. Nowak:
CNVind: an open source cloud-based pipeline for rare CNVs detection in whole exome sequencing data based on the depth of coverage. 85 - Quang-Huy Nguyen
, Tin Nguyen
, Duc-Hau Le
:
DrGA: cancer driver gene analysis in a simpler manner. 86 - Hui Zhang, Shan Gao, Weiyang Chen:
Automated recognition and analysis of head thrashes behavior in C. elegans. 87 - Chengcheng Zhang, Yao Lu, Tianyi Zang
:
CNN-DDI: a learning-based method for predicting drug-drug interactions using convolution neural networks. 88 - Ningyi Zhang, Tianyi Zang
:
A multi-network integration approach for measuring disease similarity based on ncRNA regulation and heterogeneous information. 89 - Mohammad Neamul Kabir, Limsoon Wong:
EnsembleFam: towards more accurate protein family prediction in the twilight zone. 90 - Shang Liu, Hailiang Cheng, Javaria Ashraf, Youping Zhang, Qiaolian Wang, Limin Lv, Man He, Guoli Song, Dongyun Zuo:
Interpretation of convolutional neural networks reveals crucial sequence features involving in transcription during fiber development. 91 - Adil Al-Azzawi, Anes Ouadou, Ye Duan, Jianlin Cheng
:
Correction to: Auto3DCryoMap: an automated particle alignment approach for 3D cryo-EM density map reconstruction. 92 - Yiyu Hong, Juyong Lee
, Junsu Ko:
A-Prot: protein structure modeling using MSA transformer. 93 - Francis C. Motta, Robert C. Moseley, Bree Cummins, Anastasia Deckard
, Steven B. Haase:
Conservation of dynamic characteristics of transcriptional regulatory elements in periodic biological processes. 94 - Robert Logan, Zoe Fleischmann, Sofia Annis
, Amy Wangsness Wehe, Jonathan L. Tilly, Dori C. Woods, Konstantin Khrapko:
3GOLD: optimized Levenshtein distance for clustering third-generation sequencing data. 95 - Michela Quadrini, Sebastian Daberdaku
, Carlo Ferrari:
Hierarchical representation for PPI sites prediction. 96 - Michael Lau
, Claudia Wigmann, Sara Kress, Tamara Schikowski, Holger Schwender:
Evaluation of tree-based statistical learning methods for constructing genetic risk scores. 97 - Malcolm E. Fisher
, Erik Segerdell
, Nicolas Matentzoglu
, Mardi J. Nenni, Joshua D. Fortriede, Stanley Chu, Troy J. Pells, David Osumi-Sutherland
, Praneet Chaturvedi, Christina James-Zorn, Nivitha Sundararaj, Vaneet S. Lotay, Virgilio Ponferrada, Dong Zhuo Wang, Eugene Kim, Sergei Agalakov, Bradley I. Arshinoff, Kamran Karimi
, Peter D. Vize, Aaron M. Zorn:
The Xenopus phenotype ontology: bridging model organism phenotype data to human health and development. 99 - Katarzyna Stapor
, Krzysztof Kotowski, Tomasz Smolarczyk, Irena Roterman:
Lightweight ProteinUnet2 network for protein secondary structure prediction: a step towards proper evaluation. 100 - Lindsay V. Clark, Wittney Mays, Alexander E. Lipka, Erik J. Sacks:
A population-level statistic for assessing Mendelian behavior of genotyping-by-sequencing data from highly duplicated genomes. 101 - Xinyue Qi, Shouhao Zhou, Martyn Plummer:
On Bayesian modeling of censored data in JAGS. 102 - Wuming Gong
, Hyunwoo J. Kim, Daniel J. Garry, Il-Youp Kwak
:
Single cell lineage reconstruction using distance-based algorithms and the R package, DCLEAR. 103 - Yun Chao Lin, Ansaf Salleb-Aouissi, Thomas Hooven:
Interpretable prediction of necrotizing enterocolitis from machine learning analysis of premature infant stool microbiota. 104 - Mathisca C. M. de Gunst, Michel Mandjes, Birgit Sollie:
Statistical inference for a quasi birth-death model of RNA transcription. 105 - Elliott Swanson
, Julian Reading
, Lucas T. Graybuck
, Peter J. Skene
:
BarWare: efficient software tools for barcoded single-cell genomics. 106 - David Chisanga, Yang Liao, Wei Shi:
Impact of gene annotation choice on the quantification of RNA-seq data. 107 - Jimmy Ka Ho Chiu, Rick Twee-Hee Ong:
Clustering biological sequences with dynamic sequence similarity threshold. 108 - Honglan Li, Seungjin Na, Kyu-Baek Hwang, Eunok Paek:
TIDD: tool-independent and data-dependent machine learning for peptide identification. 109 - Josip Rudar
, Teresita M. Porter, Michael Wright, Geoffrey Brian Golding, Mehrdad Hajibabaei:
LANDMark: an ensemble approach to the supervised selection of biomarkers in high-throughput sequencing data. 110 - Stefano Marchesin
, Gianmaria Silvello:
TBGA: a large-scale Gene-Disease Association dataset for Biomedical Relation Extraction. 111 - Xu Yang, Masahiro Kasahara
:
LPMX: a pure rootless composable container system. 112 - Ana B. Romero-Losada, Christina Arvanitidou, Pedro de los Reyes, Mercedes García-González, Francisco José Romero-Campero
:
ALGAEFUN with MARACAS, microALGAE FUNctional enrichment tool for MicroAlgae RnA-seq and Chip-seq AnalysiS. 113 - Gerard P. Quinn, Tamas Sessler, Baharak Ahmaderaghi, Shauna Lambe, Harper VanSteenhouse, Mark Lawler, Mark Wappett, Bruce Seligmann, Daniel B. Longley, Simon S. McDade
:
classifieR a flexible interactive cloud-application for functional annotation of cancer transcriptomes. 114 - Bolin Wang, Yuanyuan Sun, Yonghe Chu, Di Zhao, Zhihao Yang, Jian Wang:
Refining electronic medical records representation in manifold subspace. 115