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ORCIDBioinformatics, Volume 40
Volume 40, Number 1, January 2024
- Zongquan Li, Pengxuan Ren, Hao Yang
, Jie Zheng, Fang Bai:
TEFDTA: a transformer encoder and fingerprint representation combined prediction method for bonded and non-bonded drug-target affinities. - Ting Liu, K. Anton Feenstra, Zhisheng Huang, Jaap Heringa:
Mining literature and pathway data to explore the relations of ketamine with neurotransmitters and gut microbiota using a knowledge-graph. - Jeffrey K. Ng, Tychele Turner:
HAT: de novo variant calling for highly accurate short-read and long-read sequencing data. - Chunyue Feng, Kok Haur Ong, David M. Young, Bingxian Chen, Longjie Li, Xinmi Huo, Haoda Lu, Weizhong Gu, Fei Liu, Hongfeng Tang, Manli Zhao, Min Yang, Kun Zhu, Limin Huang, Qiang Wang, Gabriel Pik Liang Marini, Kun Gui, Hao Han, Stephan J. Sanders, Lin Li, Weimiao Yu, Jianhua Mao:
Artificial intelligence-assisted quantification and assessment of whole slide images for pediatric kidney disease diagnosis. - Pinglu Zhang, Huan Liu, Yanming Wei, Yixiao Zhai, Qinzhong Tian, Quan Zou:
FMAlign2: a novel fast multiple nucleotide sequence alignment method for ultralong datasets. - T. J. Sego:
SimService: a lightweight library for building simulation services in Python. - Aditi Shenoy, Yogesh Kalakoti, Durai Sundar, Arne Elofsson:
M-Ionic: prediction of metal-ion-binding sites from sequence using residue embeddings. - Xuejiao Wang, Tingfang Wu, Yelu Jiang, Taoning Chen, Deng Pan, Zhi Jin, Jingxin Xie, Lijun Quan, Qiang Lyu:
RPEMHC: improved prediction of MHC-peptide binding affinity by a deep learning approach based on residue-residue pair encoding. - Zsolt Balázs, Todor Gitchev, Ivna Ivankovic, Michael Krauthammer:
Fragmentstein - facilitating data reuse for cell-free DNA fragment analysis. - Timothy G. Vaughan:
ReMASTER: improved phylodynamic simulation for BEAST 2.7. - Seyedmohsen Hosseini, Geoffrey Brian Golding, Lucian Ilie:
Seq-InSite: sequence supersedes structure for protein interaction site prediction. - Parsa Ghadermazi, Siu Hung Joshua Chan:
Microbial interactions from a new perspective: reinforcement learning reveals new insights into microbiome evolution. - Felix M. Weidner, Nensi Ikonomi, Silke D. Werle, Julian D. Schwab, Hans A. Kestler:
GatekeepR: an R Shiny application for the identification of nodes with high dynamic impact in Boolean networks. - Tareian A. Cazares, Richard E. Higgs, Jibo Wang, Hatice Gulcin Ozer:
SeedMatchR: identify off-target effects mediated by siRNA seed regions in RNA-seq experiments. - Seungjun Ahn, Somnath Datta:
SOHPIE: statistical approach via pseudo-value information and estimation for differential network analysis of microbiome data. - Alexander Peltzer, Christopher Mohr, Kai Bernd Stadermann, Matthias Zwick, Ramona Schmid:
nf-core/nanostring: a pipeline for reproducible NanoString nCounter analysis. - Rui Cao, Evan Olawsky, Edward McFowland, Erin Marcotte, Logan Spector, Tianzhong Yang:
Subset scanning for multi-trait analysis using GWAS summary statistics. - Lorenzo Pantolini, Gabriel Studer, Joana Pereira, Janani Durairaj, Gerardo Tauriello, Torsten Schwede:
Embedding-based alignment: combining protein language models with dynamic programming alignment to detect structural similarities in the twilight-zone. - Daniel Ji, Robert Aboukhalil, Niema Moshiri:
ViralWasm: a client-side user-friendly web application suite for viral genomics.
Volume 40, Number 2, February 2024
- Diogo A. C. Narciso, Ana Pereira, Nuno O. Dias, Manuel Monteiro, Luis F. Melo, Fernando Gomes Martins:
3D Optical Coherence Tomography image processing in BISCAP: characterization of biofilm structure and properties. - Elya Wygoda, Gil Loewenthal, Asher Moshe, Michael Alburquerque, Itay Mayrose, Tal Pupko:
Statistical framework to determine indel-length distribution. - Jinyu Yu, Junxi Mu, Ting Wei, Hai-Feng Chen:
Multi-indicator comparative evaluation for deep learning-based protein sequence design methods. - Arnaud Chol, Roman Sarrazin-Gendron, Eric Lécuyer, Mathieu Blanchette, Jérôme Waldispühl:
PERFUMES: pipeline to extract RNA functional motifs and exposed structures. - David Koslicki, Stephen White, Chunyu Ma, Alexei Novikov:
YACHT: an ANI-based statistical test to detect microbial presence/absence in a metagenomic sample. - Karthik Gangavarapu, Xiang Ji, Guy Baele, Mathieu Fourment, Philippe Lemey, Frederick A. Matsen IV, Marc A. Suchard:
Many-core algorithms for high-dimensional gradients on phylogenetic trees. - Gabriel Loyer, Vladimir Reinharz:
Concurrent prediction of RNA secondary structures with pseudoknots and local 3D motifs in an integer programming framework. - Loïc Lannelongue, Michael Inouye:
Pitfalls of machine learning models for protein-protein interaction networks. - Ping Xuan, Jing Gu, Hui Cui, Shuai Wang, Toshiya Nakaguchi, Cheng Liu, Tiangang Zhang:
Multi-scale topology and position feature learning and relationship-aware graph reasoning for prediction of drug-related microbes. - Yue Zhuo, Heng Du, Chenguang Diao, Weining Li, Lei Zhou, Li Jiang, Jicai Jiang, Jianfeng Liu:
MAGE: metafounders-assisted genomic estimation of breeding value, a novel additive-dominance single-step model in crossbreeding systems. - Xin Liu, Jieni Hu, Jie Zheng:
SL-Miner: a web server for mining evidence and prioritization of cancer-specific synthetic lethality. - Bjarne Daenekas, Eilís Pérez, Fabio Boniolo, Sabina Stefan, Salvatore Benfatto, Martin Sill, Dominik Sturm, David T. W. Jones, David Capper, Marc Zapatka, Volker Hovestadt:
Conumee 2.0: enhanced copy-number variation analysis from DNA methylation arrays for humans and mice. - Kuan Xie, Yuying Hou, Xionghui Zhou:
Deep centroid: a general deep cascade classifier for biomedical omics data classification. - Haohui Zhang, Yuwei Wang, Bin Lian, Yiran Wang, Xingyi Li, Tao Wang, Xuequn Shang, Hui Yang, Ahmad Aziz, Jialu Hu:
Scbean: a python library for single-cell multi-omics data analysis. - Peiying Cai, Mark D. Robinson, Simone Tiberi:
DESpace: spatially variable gene detection via differential expression testing of spatial clusters. - Zeyu Chen, Yuxin Miao, Zhiyuan Tan, Qifan Hu, Yanhong Wu, Xinqi Li, Wenbo Guo, Jin Gu:
scCancer2: data-driven in-depth annotations of the tumor microenvironment at single-level resolution. - Huangqingbo Sun, Jiayi Li, Robert F. Murphy:
Expanding the coverage of spatial proteomics: a machine learning approach. - Xiao Wang, Ziyi Chai, Shaohua Li, Yan Liu, Chen Li, Yu Jiang, Quanzhong Liu:
CTISL: a dynamic stacking multi-class classification approach for identifying cell types from single-cell RNA-seq data. - Juanru Guo, Wenjin Zhang, Xuhua Chen, Allen Yen, Lucy Chen, Christian A Shively, Daofeng Li, Ting Wang, Joseph D. Dougherty, Robi D. Mitra:
Pycallingcards: an integrated environment for visualizing, analyzing, and interpreting Calling Cards data. - Yash Patel, Chenghao Zhu, Takafumi N. Yamaguchi, Yuan Zhe Bugh, Mao Tian, Aaron Holmes, Sorel T. Fitz-Gibbon, Paul C. Boutros:
NFTest: automated testing of Nextflow pipelines. - Fabrizio Pucci, Mehari B. Zerihun, Marianne Rooman, Alexander Schug:
pycofitness - Evaluating the fitness landscape of RNA and protein sequences. - Correction to: GTExVisualizer: a web platform for supporting ageing studies.
- Xiaoshu Zhu, Shuang Meng, Gaoshi Li, Jian-Xin Wang, Xiaoqing Peng:
AGImpute: imputation of scRNA-seq data based on a hybrid GAN with dropouts identification. - Anna Sintsova, Hans-Joachim Ruscheweyh, Christopher M. Field, Lilith Feer, Bidong D. Nguyen, Benjamin Daniel, Wolf-Dietrich Hardt, Julia A. Vorholt, Shinichi Sunagawa:
mBARq: a versatile and user-friendly framework for the analysis of DNA barcodes from transposon insertion libraries, knockout mutants, and isogenic strain populations. - Lap Sum Chan, Gen Li:
Zero is not absence: censoring-based differential abundance analysis for microbiome data. - Lu Yang, Pei Wang, Jun Chen:
2dGBH: Two-dimensional group Benjamini-Hochberg procedure for false discovery rate control in two-way multiple testing of genomic data. - Haixiang Zhang, Xiumei Hong, Yinan Zheng, Lifang Hou, Cheng Zheng, Xiaobin Wang, Lei Liu:
High-dimensional quantile mediation analysis with application to a birth cohort study of mother-newborn pairs. - Kexin Shi, Yuanpeng Xiong, Yu Wang, Yifan Deng, Wenjia Wang, Bingyi Jing, Xin Gao:
PractiCPP: a deep learning approach tailored for extremely imbalanced datasets in cell-penetrating peptide prediction. - Zongyang Du, Zhenling Peng, Jianyi Yang:
RNA threading with secondary structure and sequence profile. - Niek van Hilten, Nino Verwei, Jeroen Methorst, Carsten Nase, Andrius Bernatavicius, Herre Jelger Risselada:
PMIpred: a physics-informed web server for quantitative protein-membrane interaction prediction. - Diego Mañanes, Inés Rivero-García, Carlos Relaño, Miguel Torres, David Sancho, Daniel Jimenez-Carretero, Carlos Torroja Fungairino, Fátima Sánchez-Cabo:
SpatialDDLS: an R package to deconvolute spatial transcriptomics data using neural networks. - Jun Wang, Marc Horlacher, Lixin Cheng, Ole Winther:
DeepLocRNA: an interpretable deep learning model for predicting RNA subcellular localization with domain-specific transfer-learning. - Yash Patel, Arpi Beshlikyan, Madison Jordan, Gina Kim, Aaron Holmes, Takafumi N. Yamaguchi, Paul C. Boutros:
PipeVal: light-weight extensible tool for file validation. - Xinyuan Huang, Xiujuan Gao, Ling Fu:
BINGO: a blind unmixing algorithm for ultra-multiplexing fluorescence images. - Chenglin Yin, Ruheng Wang, Jianbo Qiao, Hua Shi, Hongliang Duan, Xinbo Jiang, Saisai Teng, Leyi Wei:
NanoCon: contrastive learning-based deep hybrid network for nanopore methylation detection. - Ioan Ieremie, Rob M. Ewing, Mahesan Niranjan:
Protein language models meet reduced amino acid alphabets. - Junchi Ma, Xiaoyu Zhao, Enfeng Qi, Renmin Han, Ting Yu, Guojun Li:
Highly efficient clustering of long-read transcriptomic data with GeLuster. - Carson M. Andorf, Olivia C. Haley, Rita K. Hayford, John L. Portwood II, Stephen Harding, Shatabdi Sen, Ethalinda K. S. Cannon, Jack M. Gardiner, Hye-Seon Kim, Margaret Woodhouse:
PanEffect: a pan-genome visualization tool for variant effects in maize. - Nezar Abdennur, Geoffrey Fudenberg, Ilya M. Flyamer, Aleksandra A. Galitsyna, Anton Goloborodko, Maxim Imakaev, Sergey Venev:
Bioframe: operations on genomic intervals in Pandas dataframes. - Jue Yang, Weiwen Wang, Xiwen Zhang:
scSemiGCN: boosting cell-type annotation from noise-resistant graph neural networks with extremely limited supervision. - Nicole Pradas, Federico Jurado-Ruiz, Carles Onielfa, Pere Arús, Maria José Aranzana:
PERSEUS: an interactive and intuitive web-based tool for pedigree visualization. - Mikaela Koutrouli, Katerina C. Nastou, Pau Piera Líndez, Robbin Bouwmeester, Simon Rasmussen, Lennart Martens, Lars Juhl Jensen:
FAVA: high-quality functional association networks inferred from scRNA-seq and proteomics data. - Alex Morehead, Jianlin Cheng:
Geometry-complete perceptron networks for 3D molecular graphs. - Ding Wang, Junru Jin, Zhongshen Li, Yu Wang, Mushuang Fan, Sirui Liang, Ran Su, Leyi Wei:
StructuralDPPIV: a novel deep learning model based on atom structure for predicting dipeptidyl peptidase-IV inhibitory peptides. - Yuzhen Mao, Yen-Yi Lin, Nelson K. Y. Wong, Stanislav Volik, Funda Sar, Colin C. Collins, Martin Ester:
Phenotype prediction from single-cell RNA-seq data using attention-based neural networks. - Yongtao Guan, Daniel Levy:
Estimation of inbreeding and kinship coefficients via latent identity-by-descent states. - Xiaoyu Guan, Wei Shao, Daoqiang Zhang:
T-S2Inet: Transformer-based sequence-to-image network for accurate nanopore sequence recognition. - Qiao Jin, Yifan Yang, Qingyu Chen, Zhiyong Lu:
GeneGPT: augmenting large language models with domain tools for improved access to biomedical information. - Philippe Charron, Mingsong Kang:
VariantDetective: an accurate all-in-one pipeline for detecting consensus bacterial SNPs and SVs. - Kemal Demirtas, Burak Erman, Türkan Haliloglu:
Dynamic correlations: exact and approximate methods for mutual information.
Volume 40, Number 3, March 2024
- David Ferreiro, Catarina Branco, Miguel Arenas:
Selection among site-dependent structurally constrained substitution models of protein evolution by approximate Bayesian computation. - Zuher Jahshan, Leonid Yavits:
ViTAL: Vision TrAnsformer based Low coverage SARS-CoV-2 lineage assignment. - Jiqing Wu, Viktor H. Koelzer:
SST-editing: in silico spatial transcriptomic editing at single-cell resolution. - Oliver Cheng, Min Hao Ling, Changqing Wang, Shuyi Wu, Matthew E. Ritchie, Jonathan Göke, Noorul Amin, Nadia M. Davidson:
Flexiplex: a versatile demultiplexer and search tool for omics data. - Correction to: OncoThreads: visualization of large-scale longitudinal cancer molecular data.
- Jun Xue, Bingyi Wang, Hongchao Ji, Weihua Li:
RT-Transformer: retention time prediction for metabolite annotation to assist in metabolite identification. - Yiyang Yu, Shivani Muthukumar, Peter K. Koo:
EvoAug-TF: extending evolution-inspired data augmentations for genomic deep learning to TensorFlow. - Hamza Biyuzan, Mohamed-Akram Masrour, Lucas Grandmougin, Frédéric Payan, Dominique Douguet:
SENSAAS-Flex: a joint optimization approach for aligning 3D shapes and exploring the molecular conformation space. - Hannah-Marie Martiny, Nikiforos Pyrounakis, Thomas Nordahl Petersen, Oksana Lukjancenko, Frank Aarestrup, Philip T. L. C. Clausen, Patrick Munk:
ARGprofiler - a pipeline for large-scale analysis of antimicrobial resistance genes and their flanking regions in metagenomic datasets. - J. Harry Caufield, Harshad Hegde, Vincent Emonet, Nomi L. Harris, Marcin P. Joachimiak, Nicolas Matentzoglu, Hyeongsik Kim, Sierra A. T. Moxon, Justin T. Reese, Melissa A. Haendel, Peter N. Robinson, Christopher J. Mungall:
Structured Prompt Interrogation and Recursive Extraction of Semantics (SPIRES): a method for populating knowledge bases using zero-shot learning. - Chiung-Ting Wu, Dongping Du, Lulu Chen, Rujia Dai, Chunyu Liu, Guoqiang Yu, Saurabh Bhardwaj, Sarah J. Parker, Zhen Zhang, Robert Clarke, David M. Herrington, Yue Wang:
CAM3.0: determining cell type composition and expression from bulk tissues with fully unsupervised deconvolution. - Arik Ermshaus, Michael Piechotta, Gina Rüter, Ulrich Keilholz, Ulf Leser, Manuela Benary:
preon: Fast and accurate entity normalization for drug names and cancer types in precision oncology. - Emese I Végh, Katerina Douka:
SpecieScan: semi-automated taxonomic identification of bone collagen peptides from MALDI-ToF-MS. - Guillermo Dufort y Álvarez, Martí Xargay-Ferrer, Alba Pagès-Zamora, Idoia Ochoa:
EMVC-2: an efficient single-nucleotide variant caller based on expectation maximization. - Kristofer Sandås, Jacob Lewerentz, Edvin Karlsson, Linda Karlsson, David Sundell, Kotryna Simonyté-Sjödin, Andreas Sjödin:
Nanometa Live: a user-friendly application for real-time metagenomic data analysis and pathogen identification. - Xiangxin Zhan, Yanbin Yin, Han Zhang:
BERMAD: batch effect removal for single-cell RNA-seq data using a multi-layer adaptation autoencoder with dual-channel framework. - Florian J. Gisdon, Mariella Zunker, Jan Niclas Wolf, Kai Prüfer, Jörg Ackermann, Christoph Welsch, Ina Koch:
Graph-theoretical prediction of biological modules in quaternary structures of large protein complexes. - Jaroslaw Chilimoniuk, Krystyna Grzesiak, Jakub Kala, Dominik Nowakowski, Adam Kretowski, Rafal Kolenda, Michal Ciborowski, Michal Burdukiewicz:
imputomics: web server and R package for missing values imputation in metabolomics data. - Shreyas Arvindekar, Aditi S. Pathak, Kartik Majila, Shruthi Viswanath:
Optimizing representations for integrative structural modeling using Bayesian model selection. - Zhengyang Guo, Yang Wang, Guangshuo Ou:
Utilizing the scale-invariant feature transform algorithm to align distance matrices facilitates systematic protein structure comparison. - Melpomeni Kasapi, Kexin Xu, Timothy M. D. Ebbels, Declan P. O'Regan, James S. Ware, Joram M. Posma:
LAVASET: Latent Variable Stochastic Ensemble of Trees. An ensemble method for correlated datasets with spatial, spectral, and temporal dependencies. - Haoliang Xue, Mélina Gallopin, Camille Marchet, Ha N. Nguyen, Yunfeng Wang, Antoine Lainé, Chloé Bessiere, Daniel Gautheret:
KaMRaT: a C++ toolkit for k-mer count matrix dimension reduction. - Milind Misra, Jeffy Jeffy, Charis Liao, Stephanie Pickthorn, Kshitij Wagh, Alon Herschhorn:
HIResist: a database of HIV-1 resistance to broadly neutralizing antibodies. - Woosung Jeon, Dongsup Kim:
AbFlex: designing antibody complementarity determining regions with flexible CDR definition. - Jose L. Figueroa III, Eliza Dhungel, Madeline Bellanger, Cory R. Brouwer, Richard Allen White III:
MetaCerberus: distributed highly parallelized HMM-based processing for robust functional annotation across the tree of life.
Volume 40, Number 4, 2024
- Ruochi Zhang, Chao Wu, Qian Yang, Chang Liu, Yan Wang, Kewei Li, Lan Huang, Fengfeng Zhou:
MolFeSCue: enhancing molecular property prediction in data-limited and imbalanced contexts using few-shot and contrastive learning.
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