Bioinform.

Keyphrases

Publications

volume 39, number 1, 2023

Chenxi Zhou, Shane A. McCarthy, Richard Durbin
YaHS: yet another Hi-C scaffolding tool. Bioinform. 39 (1) (2023)
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. Bioinform. 39 (1) (2023)
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. Bioinform. 39 (1) (2023)
Xingqi Wu, Yi Shi, Minghui Wang, Ao Li
CAMR: cross-aligned multimodal representation learning for cancer survival prediction. Bioinform. 39 (1) (2023)
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. Bioinform. 39 (1) (2023)
Marcus T. Moen, Iain G. Johnston
HyperHMM: efficient inference of evolutionary and progressive dynamics on hypercubic transition graphs. Bioinform. 39 (1) (2023)
Neda Shokraneh, Mariam Arab, Maxwell W. Libbrecht
Integrative chromatin domain annotation through graph embedding of Hi-C data. Bioinform. 39 (1) (2023)
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. Bioinform. 39 (1) (2023)
Xuezhi Xie, Pedro A. Valiente, Philip M. Kim
design of α-helix structures. Bioinform. 39 (1) (2023)
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. Bioinform. 39 (1) (2023)
Manuel Glöckler, Andreas Dräger, Reihaneh Mostolizadeh
Hierarchical modelling of microbial communities. Bioinform. 39 (1) (2023)
Ngoc-Quang Nguyen, Gwanghoon Jang, Hajung Kim, Jaewoo Kang
Perceiver CPI: a nested cross-attention network for compound-protein interaction prediction. Bioinform. 39 (1) (2023)
Alessandro Vinceti, Lucia Trastulla, Umberto Perron, Andrea Raiconi, Francesco Iorio
A heuristic algorithm solving the mutual-exclusivity-sorting problem. Bioinform. 39 (1) (2023)
Yufeng Liu, Ye Zhong, Xuan Zhao, Lijuan Liu, Liya Ding, Hanchuan Peng
Tracing weak neuron fibers. Bioinform. 39 (1) (2023)
Jonathan K. Vis, Mark A. Santcroos, Walter A. Kosters, Jeroen F. J. Laros
A Boolean algebra for genetic variants. Bioinform. 39 (1) (2023)
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. Bioinform. 39 (1) (2023)
Hong Zhang, Devan V. Mehrotra, Judong Shen
AWOT and CWOT for genotype and genotype-by-treatment interaction joint analysis in pharmacogenetics GWAS. Bioinform. 39 (1) (2023)
José Camacho, Raffaele Vitale, David Morales-Jiménez, Carolina Gómez-Llorente
Variable-selection ANOVA Simultaneous Component Analysis (VASCA). Bioinform. 39 (1) (2023)
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. Bioinform. 39 (1) (2023)
Dailin Gan, Jun Li
SCIBER: a simple method for removing batch effects from single-cell RNA-sequencing data. Bioinform. 39 (1) (2023)
Parnal Joshi, Sagnik Banerjee, Xiao Hu, Pranav M. Khade, Iddo Friedberg
GOThresher: a program to remove annotation biases from protein function annotation datasets. Bioinform. 39 (1) (2023)
Shivam Kumar, Dipanka Sarmah, Shailendra Asthana, Samrat Chatterjee
konnect2prot: a web application to explore the protein properties in a functional protein-protein interaction network. Bioinform. 39 (1) (2023)
Marek S. Wiewiórka, Agnieszka Szmurlo, Pawel Stankiewicz, Tomasz Gambin
Cloud-native distributed genomic pileup operations. Bioinform. 39 (1) (2023)
Afif Elghraoui, Siavash Mirarab, Krister M. Swenson, Faramarz Valafar
isolates. Bioinform. 39 (1) (2023)
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. Bioinform. 39 (1) (2023)
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. Bioinform. 39 (1) (2023)
Jialun Wu, Yuxin Dong, Zeyu Gao, Tieliang Gong, Chen Li
Dual Attention and Patient Similarity Network for drug recommendation. Bioinform. 39 (1) (2023)
Nelle Varoquaux, William S. Noble, Jean-Philippe Vert
Inference of 3D genome architecture by modeling overdispersion of Hi-C data. Bioinform. 39 (1) (2023)
Fernando Zhapa-Camacho, Maxat Kulmanov, Robert Hoehndorf
mOWL: Python library for machine learning with biomedical ontologies. Bioinform. 39 (1) (2023)

volume 39, number 2, 2023

volume 39, number 3, 2023

volume 39, number 4, 2023

volume 39, number 5, 2023

volume 39, number 8, 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. Bioinform. 39 (8) (2023)