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Bioinformatics, Volume 39
Volume 39, Number 1, January 2023
- Hong Zhang
, Devan V. Mehrotra, Judong Shen
:
AWOT and CWOT for genotype and genotype-by-treatment interaction joint analysis in pharmacogenetics GWAS. - Xuezhi Xie, Pedro A. Valiente
, Philip M. Kim:
HelixGAN a deep-learning methodology for conditional de novo design of α-helix structures. - Xiaokun Hong, Ningshan Li, Jiyang Lv, Yan Zhang
, Jing Li
, Jian Zhang
, Hai-Feng Chen
:
PTMint database of experimentally verified PTM regulation on protein-protein interaction. - Alessandro Vinceti, Lucia Trastulla, Umberto Perron, Andrea Raiconi
, Francesco Iorio
:
A heuristic algorithm solving the mutual-exclusivity-sorting problem. - Nelle Varoquaux
, William S. Noble
, Jean-Philippe Vert:
Inference of 3D genome architecture by modeling overdispersion of Hi-C data. - Teresa De Jesus Martinez
, Elliot A. Hershberg
, Emma Guo, Garrett Stevens
, Colin M. Diesh
, Peter Xie, Caroline Bridge, Scott Cain, Robin Haw, Robert M. Buels, Lincoln D. Stein, Ian H. Holmes:
JBrowse Jupyter: a Python interface to JBrowse 2. - Neda Shokraneh, Mariam Arab, Maxwell W. Libbrecht
:
Integrative chromatin domain annotation through graph embedding of Hi-C data. - Shivam Kumar, Dipanka Sarmah, Shailendra Asthana, Samrat Chatterjee
:
konnect2prot: a web application to explore the protein properties in a functional protein-protein interaction network. - Ngoc-Quang Nguyen
, Gwanghoon Jang, Hajung Kim, Jaewoo Kang
:
Perceiver CPI: a nested cross-attention network for compound-protein interaction prediction. - Manuel Glöckler
, Andreas Dräger
, Reihaneh Mostolizadeh
:
Hierarchical modelling of microbial communities. - José Camacho
, Raffaele Vitale, David Morales-Jiménez
, Carolina Gómez-Llorente:
Variable-selection ANOVA Simultaneous Component Analysis (VASCA). - Filippo Grazioli
, Pierre Machart
, Anja Mösch
, Kai Li, Leonardo V. Castorina, Nico Pfeifer, Martin Renqiang Min:
Attentive Variational Information Bottleneck for TCR-peptide interaction prediction. - Marcus T. Moen, Iain G. Johnston
:
HyperHMM: efficient inference of evolutionary and progressive dynamics on hypercubic transition graphs. - Xingqi Wu
, Yi Shi
, Minghui Wang, Ao Li:
CAMR: cross-aligned multimodal representation learning for cancer survival prediction. - Jinding Liu
, Yaru Zhang, Yapin Shi, Yiqing Zheng, Yali Zhu, Zhuoran Guan, Danyu Shen
, Daolong Dou
:
FungiExp: a user-friendly database and analysis platform for exploring fungal gene expression and alternative splicing. - Marija Stanojevic
, Jovan Andjelkovic, Adrienne Kasprowicz, Louise A. Huuki, Jennifer Chao, S. Blair Hedges, Sudhir Kumar
, Zoran Obradovic:
Discovering research articles containing evolutionary timetrees by machine learning. - Correction to: FASTRAL: improving scalability of phylogenomic analysis.
- Jonathan K. Vis
, Mark A. Santcroos
, Walter A. Kosters
, Jeroen F. J. Laros
:
A Boolean algebra for genetic variants. - Vamsi Nallapareddy
, Nicola Bordin
, Ian Sillitoe
, Michael Heinzinger
, Maria Littmann
, Vaishali P. Waman, Neeladri Sen
, Burkhard Rost
, Christine A. Orengo:
CATHe: detection of remote homologues for CATH superfamilies using embeddings from protein language models. - Chenxi Zhou
, Shane A. McCarthy
, Richard Durbin
:
YaHS: yet another Hi-C scaffolding tool. - Correction to: Automated classification of cytogenetic abnormalities in hematolymphoid neoplasms.
- Marek S. Wiewiórka, Agnieszka Szmurlo, Pawel Stankiewicz, Tomasz Gambin
:
Cloud-native distributed genomic pileup operations. - Fernando Zhapa-Camacho
, Maxat Kulmanov
, Robert Hoehndorf
:
mOWL: Python library for machine learning with biomedical ontologies. - Dailin Gan
, Jun Li
:
SCIBER: a simple method for removing batch effects from single-cell RNA-sequencing data. - Parnal Joshi
, Sagnik Banerjee
, Xiao Hu
, Pranav M. Khade
, Iddo Friedberg
:
GOThresher: a program to remove annotation biases from protein function annotation datasets. - Yufeng Liu
, Ye Zhong, Xuan Zhao, Lijuan Liu, Liya Ding
, Hanchuan Peng:
Tracing weak neuron fibers. - Yuwei Wang, Bin Lian, Haohui Zhang, Yuanke Zhong, Jie He, Fashuai Wu, Knut Reinert, Xuequn Shang, Hui Yang, Jialu Hu
:
A multi-view latent variable model reveals cellular heterogeneity in complex tissues for paired multimodal single-cell data. - Abin Abraham
, Abigail L. Labella, Mary Lauren Benton, Antonis Rokas
, John A. Capra
:
GSEL: a fast, flexible python package for detecting signatures of diverse evolutionary forces on genomic regions. - Licai Huang, James P. Long, Ehsan Irajizad, James D. Doecke, Kim-Anh Do, Min Jin Ha
:
A unified mediation analysis framework for integrative cancer proteogenomics with clinical outcomes. - Jialun Wu
, Yuxin Dong, Zeyu Gao
, Tieliang Gong, Chen Li:
Dual Attention and Patient Similarity Network for drug recommendation. - Wei Chen
, Zhiwei Li, Hongyi Fang, Qianyuan Yao, Cheng Zhong, Jianye Hao, Qi Zhang, Xuanjing Huang, Jiajie Peng
, Zhongyu Wei:
A benchmark for automatic medical consultation system: frameworks, tasks and datasets. - Afif Elghraoui
, Siavash Mirarab, Krister M. Swenson
, Faramarz Valafar
:
Evaluating impacts of syntenic block detection strategies on rearrangement phylogeny using Mycobacterium tuberculosis isolates.
Volume 39, Number 2, February 2023
- Andy Lin, Brooke L. Deatherage Kaiser, Janine R. Hutchison, Jeffrey A. Bilmes, William Stafford Noble
:
MS1Connect: a mass spectrometry run similarity measure. - Xiang Cheng, Md Amanullah, Weigang Liu, Yi Liu, Xiaoqing Pan, Honghe Zhang, Haiming Xu, Peng-Yuan Liu
, Yan Lu
:
WMDS.net: a network control framework for identifying key players in transcriptome programs. - Kun Zhu, Hong Su, Zhenling Peng
, Jianyi Yang
:
A unified approach to protein domain parsing with inter-residue distance matrix. - Piotr Klukowski, Roland Riek, Peter Güntert
:
NMRtist: an online platform for automated biomolecular NMR spectra analysis. - Xabier Rey-Barreiro
, Alejandro F. Villaverde
:
Benchmarking tools for a priori identifiability analysis. - Yunhe Wang, Zhuohan Yu, Shaochuan Li, Chuang Bian, Yanchun Liang, Ka-Chun Wong
, Xiangtao Li
:
scBGEDA: deep single-cell clustering analysis via a dual denoising autoencoder with bipartite graph ensemble clustering.
Volume 39, Number 3, March 2023
- Adam Streck
, Tom L. Kaufmann, Roland F. Schwarz:
SMITH: spatially constrained stochastic model for simulation of intra-tumour heterogeneity. - Elisabet Munté
, Lidia Feliubadaló
, Marta Pineda, Eva Tornero, Maribel González, José Marcos Moreno-Cabrera
, Carla Roca, Joan Bales Rubio, Laura Arnaldo, Gabriel Capellá, Jose Luis Mosquera
, Conxi Lázaro:
vaRHC: an R package for semi-automation of variant classification in hereditary cancer genes according to ACMG/AMP and gene-specific ClinGen guidelines. - Zhourun Wu, Mingyue Guo, Xiaopeng Jin, Junjie Chen
, Bin Liu
:
CFAGO: cross-fusion of network and attributes based on attention mechanism for protein function prediction.
Volume 39, Number 4, April 2023
- Mingqian Zhang, Wenke Zhang, Yuzhu Chen, Jin Zhao, Shunyao Wu, Xiaoquan Su
:
Flex Meta-Storms elucidates the microbiome local beta-diversity under specific phenotypes. - Charles Tapley Hoyt
, Amelia L. Hoyt
, Benjamin M. Gyori
:
Prediction and curation of missing biomedical identifier mappings with Biomappings. - Bansho Masutani
, Riki Kawahara, Shinichi Morishita
:
Decomposing mosaic tandem repeats accurately from long reads. - Nikola Benes
, Lubos Brim, Ondrej Huvar, Samuel Pastva, David Safránek:
Boolean network sketches: a unifying framework for logical model inference.
Volume 39, Number 5, May 2023
- Yongxin Ji
, Jiayu Shang
, Xubo Tang
, Yanni Sun
:
HOTSPOT: hierarchical host prediction for assembled plasmid contigs with transformer. - Ran Wang, Xubin Zheng, Fangda Song, Man Hon Wong, Kwong-Sak Leung, Lixin Cheng
:
Deciphering associations between gut microbiota and clinical factors using microbial modules. - Tianqi Wu, Zhiye Guo, Jianlin Cheng
:
Atomic protein structure refinement using all-atom graph representations and SE(3)-equivariant graph transformer. - Kijin Kim
, Kyungmin Park, Seonghyeon Lee, Seung-Hwan Baek, Tae-Hun Lim, Jongwoo Kim, Balachandran Manavalan
, Jin-Won Song
, Won-Keun Kim
:
VirPipe: an easy-to-use and customizable pipeline for detecting viral genomes from Nanopore sequencing. - Correction to: wpLogicNet: logic gate and structure inference in gene regulatory networks.
- Zixuan Wang, Shuwen Xiong, Yun Yu, Jiliu Zhou, Yongqing Zhang
:
HAMPLE: deciphering TF-DNA binding mechanism in different cellular environments by characterizing higher-order nucleotide dependency. - Joël Lindegger
, Damla Senol Cali, Mohammed Alser, Juan Gómez-Luna, Nika Mansouri-Ghiasi, Onur Mutlu:
Scrooge: a fast and memory-frugal genomic sequence aligner for CPUs, GPUs, and ASICs.
Volume 39, Number 8, August 2023
- Tong Xin
, Yanan Lv, Haoran Chen, Linlin Li, Lijun Shen, Guangcun Shan, Xi Chen, Hua Han
:
A novel registration method for long-serial section images of EM with a serial split technique based on unsupervised optical flow network. - Russell B. Davidson
, Mark Coletti, Mu Gao
, Bryan Piatkowski
, Avinash Sreedasyam
, Farhan Quadir, David J. Weston, Jeremy Schmutz
, Jianlin Cheng
, Jeffrey Skolnick, Jerry M. Parks
, Ada Sedova
:
Predicted structural proteome of Sphagnum divinum and proteome-scale annotation. - Abbi Abdel-Rehim
, Oghenejokpeme I. Orhobor, Hang Lou, Hao Ni, Ross D. King
:
Protein-ligand binding affinity prediction exploiting sequence constituent homology.
Volume 39, Number 9, September 2023
- Hui Yu, Limin Jiang, Chung-I Li, Scott Ness, Sara G. M. Piccirillo, Yan Guo
:
Somatic mutation effects diffused over microRNA dysregulation. - Lechuan Li
, Ruth Dannenfelser, Yu Zhu, Nathaniel Hejduk, Santiago Segarra, Vicky Yao:
Joint embedding of biological networks for cross-species functional alignment. - Matthew D. Smith, Marshall A Case, Emily K. Makowski, Peter M. Tessier
:
Position-Specific Enrichment Ratio Matrix scores predict antibody variant properties from deep sequencing data. - Pin Lyu
, Yijie Zhai, Taibo Li
, Jiang Qian
:
CellAnn: a comprehensive, super-fast, and user-friendly single-cell annotation web server.

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