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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. - Bogeum Seo, Dohee Lee, Heungjin Jeon, Junhyoung Ha, SeungBeum Suh:
MotGen: a closed-loop bacterial motility control framework using generative adversarial networks. - Edo Dotan, Gal Jaschek, Tal Pupko, Yonatan Belinkov:
Effect of tokenization on transformers for biological sequences.
Volume 40, Number 5, 2024
- Wenmin Zhang, Tianyuan Lu, Robert Sladek, Yue Li, Hamed S. Najafabadi, Josée Dupuis:
SharePro: an accurate and efficient genetic colocalization method accounting for multiple causal signals.
Volume 40, Number 6, 2024
- Xingjian Chen, Jiecong Lin, Yuchen Wang, Weitong Zhang, Weidun Xie, Zetian Zheng, Ka-Chun Wong:
HE2Gene: image-to-RNA translation via multi-task learning for spatial transcriptomics data. - Aditya K. Mishra, Iqbal Mahmud, Philip L. Lorenzi, Robert R. Jenq, Jennifer A Wargo, Nadim J. Ajami, Christine B. Peterson:
TARO: tree-aggregated factor regression for microbiome data integration. - Yueyu Jiang, Daniel McDonald, Daniela Perry, Rob Knight, Siavash Mirarab:
Scaling DEPP phylogenetic placement to ultra-large reference trees: a tree-aware ensemble approach. - Xiying Chen, Jinsha Huang, Tianqiao Shen, Houjin Zhang, Li Xu, Min Yang, Xiaoman Xie, Yunjun Yan, Jinyong Yan:
DEAttentionDTA: protein-ligand binding affinity prediction based on dynamic embedding and self-attention. - Delaney K. Sullivan, Lior Pachter:
Flexible parsing, interpretation, and editing of technical sequences with splitcode. - Jiangmei Xiong, Harsimran Kaur, Cody N. Heiser, Eliot T. McKinley, Joseph T. Roland, Robert J. Coffey, Martha J. Shrubsole, Julia Wrobel, Siyuan Ma, Ken S. Lau, Simon N. Vandekar:
GammaGateR: semi-automated marker gating for single-cell multiplexed imaging. - Xiaopeng Xu, Chencheng Xu, Wenjia He, Lesong Wei, Haoyang Li, Juexiao Zhou, Ruochi Zhang, Yu Wang, Yuanpeng Xiong, Xin Gao:
HELM-GPT: de novo macrocyclic peptide design using generative pre-trained transformer. - Jonathan Chacko, Hakan Özadam, Can Cenik:
RiboGraph: an interactive visualization system for ribosome profiling data at read length resolution.
Volume 40, Number 7, 2024
- Yichi Zhang, Chenghui Hu, Xiaohui Wu, Jian Song:
Calib-RT: an open source python package for peptide retention time calibration in DIA mass spectrometry data. - Cedric Landerer, Maxim Scheremetjew, HongKee Moon, Lena Hersemann, Ágnes Tóth-Petróczy:
deTELpy: Python package for high-throughput detection of amino acid substitutions in mass spectrometry datasets. - Guangzhi Xiong, Nathan Leroy, Stefan Bekiranov, Nathan C. Sheffield, Aidong Zhang:
DeepGSEA: explainable deep gene set enrichment analysis for single-cell transcriptomic data. - Thang V. Pham, Alex A. Henneman, Nam X. Truong, Connie R. Jimenez:
msproteomics sitereport: reporting DIA-MS phosphoproteomics experiments at site level with ease. - Gohta Aihara, Kalen Clifton, Mayling Chen, Zhuoyan Li, Lyla Atta, Brendan F. Miller, Rahul Satija, John W. Hickey, Jean Fan:
SEraster: a rasterization preprocessing framework for scalable spatial omics data analysis. - Sebastian Deorowicz, Adam Gudys:
Efficient protein structure archiving using ProteStAr. - Kyle Swanson, Parker Walther, Jeremy Leitz, Souhrid Mukherjee, Joseph C. Wu, Rabindra V. Shivnaraine, James Zou:
ADMET-AI: a machine learning ADMET platform for evaluation of large-scale chemical libraries. - Hamed Vasei, Mohammad-Hadi Foroughmand-Araabi, Amir Daneshgar:
Weighted centroid trees: a general approach to summarize phylogenies in single-labeled tumor mutation tree inference. - Mo Li, Xing Hua, Shuai Li, Michael C. Wu, Ni Zhao:
A multi-bin rarefying method for evaluating alpha diversities in TCR sequencing data. - Zilin Ren, Lili Jiang, Yaxin Di, Dufei Zhang, Jianli Gong, Jianting Gong, Qiwei Jiang, Zhiguo Fu, Pingping Sun, Bo Zhou, Ming Ni:
CodonBERT: a BERT-based architecture tailored for codon optimization using the cross-attention mechanism.
Volume 40, Number 8, 2024
- Andrew Dickson, Mohammad R. K. Mofrad:
Fine-tuning protein embeddings for functional similarity evaluation. - Samson Weiner, Bingjun Li, Sheida Nabavi:
Improved allele-specific single-cell copy number estimation in low-coverage DNA-sequencing. - Yuelei Hao, Xuyang Liu, Haohao Fu, Xueguang Shao, Wensheng Cai:
PGAT-ABPp: harnessing protein language models and graph attention networks for antibacterial peptide identification with remarkable accuracy. - Aditya J. Sethi, Pablo Acera Mateos, Rippei Hayashi, Nikolay E. Shirokikh, Eduardo Eyras:
R2Dtool: integration and visualization of isoform-resolved RNA features. - Nuwan Goonasekera, Alexandru Mahmoud, Keith Suderman, Enis Afgan:
Galaxy Helm chart: a standardized method for deploying production Galaxy servers.
Volume 40, Number 9, 2024
- Yue Lyu, Steven H. Lin, Hao Wu, Ziyi Li:
SCIntRuler: guiding the integration of multiple single-cell RNA-seq datasets with a novel statistical metric.
Volume 40, Number 10, 2024
- Oliver Pain, Ammar Al-Chalabi, Cathryn M. Lewis:
The GenoPred pipeline: a comprehensive and scalable pipeline for polygenic scoring.
Volume 40, Number Supplement_1, 2024
ISMB 2024: Montreal, QC, Canada
- Tijana Milenkovic, Yann Ponty:
ISMB 2024 Proceedings. i1-i2 - Mallory L. Wiper:
The 2024 ISCB Overton Prize Award - Dr Martin Steinegger. i3-i4 - Mallory L. Wiper:
The 2024 ISCB Innovator Award - Dr Su-In Lee. i5-i6 - Mallory L. Wiper:
The 2024 ISCB Accomplishments by a Senior Scientist Award - Dr Tandy Warnow. i7-i8 - Mallory L. Wiper:
The 2024 Outstanding Contributions to ISCB Award - Dr Scott Markel. i9-i10 - Nelly Sélem-Mojica, Tülay Karakulak, Audra Anjum, Anton Pashkov, Rafael Pérez-Estrada, Karina Enriquez-Guillén, Dan F. DeBlasio, Sofia Ferreira-Gonzalez, Alejandra Medina-Rivera, Daniel Rodrigo-Torres, Alastair M. Kilpatrick, Lonnie R. Welch, Farzana Rahman:
Closing the computational biology 'knowledge gap': Spanish Wikipedia as a case study. i11-i19 - Pavlin G. Policar, Martin Spendl, Tomaz Curk, Blaz Zupan:
Teaching bioinformatics through the analysis of SARS-CoV-2: project-based training for computer science students. i20-i29 - Jim Shaw, Jean-Sébastien Gounot, Hanrong Chen, Niranjan Nagarajan, Yun William Yu:
Floria: fast and accurate strain haplotyping in metagenomes. i30-i38 - Mohammadali Serajian, Simone Marini, Jarno N. Alanko, Noelle R. Noyes, Mattia Prosperi, Christina Boucher:
Scalable de novo classification of antibiotic resistance of Mycobacterium tuberculosis. i39-i47 - Igor Martayan, Bastien Cazaux, Antoine Limasset, Camille Marchet:
Conway-Bromage-Lyndon (CBL): an exact, dynamic representation of k-mer sets. i48-i57 - Kristen D. Curry, Feiqiao Brian Yu, Summer E. Vance, Santiago Segarra, Devaki Bhaya, Rayan Chikhi, Eduardo P. C. Rocha, Todd J. Treangen:
Reference-free structural variant detection in microbiomes via long-read co-assembly graphs. i58-i67 - Ziyi Huang, Dehan Cai, Yanni Sun:
Towards more accurate microbial source tracking via non-negative matrix factorization (NMF). i68-i78 - Chaoyang Yan, Jialiang Sun, Yiming Guan, Jiuxin Feng, Hong Liu, Jian Liu:
PhiHER2: phenotype-informed weakly supervised model for HER2 status prediction from pathological images. i79-i90 - Stefan Schrod, Helena U. Zacharias, Tim Beißbarth, Anne-Christin Hauschild, Michael Altenbuchinger:
CODEX: COunterfactual Deep learning for the in silico EXploration of cancer cell line perturbations. i91-i99 - Franziska Görtler, Malte Mensching-Buhr, Ørjan Skaar, Stefan Schrod, Thomas Sterr, Andreas Schäfer, Tim Beißbarth, Anagha Joshi, Helena U. Zacharias, Sushma Nagaraja Grellscheid, Michael Altenbuchinger:
Adaptive digital tissue deconvolution. i100-i109 - Tanviben Patel, Amna A. Othman, Ömer Sümer, Fabio Hellmann, Peter M. Krawitz, Elisabeth André, Molly E. Ripper, Chris Fortney, Susan Persky, Ping Hu, Cedrik Tekendo-Ngongang, Suzanna E. Ledgister Hanchard, Kendall A. Flaharty, Rebekah L. Waikel, Dat Duong, Benjamin D. Solomon:
Approximating facial expression effects on diagnostic accuracy via generative AI in medical genetics. i110-i118 - Minbyul Jeong, Jiwoong Sohn, Mujeen Sung, Jaewoo Kang:
Improving medical reasoning through retrieval and self-reflection with retrieval-augmented large language models. i119-i129 - Dongmin Bang, Bonil Koo, Sun Kim:
Transfer learning of condition-specific perturbation in gene interactions improves drug response prediction. i130-i139 - Kevin Rupp, Andreas Lösch, Y. Linda Hu, Chenxi Nie, Rudolf Schill, Maren Klever, Simon Pfahler, Lars Grasedyck, Tilo Wettig, Niko Beerenwinkel, Rainer Spang:
Modeling metastatic progression from cross-sectional cancer genomics data. i140-i150 - Euxhen Hasanaj, Sachin Mathur, Ziv Bar-Joseph:
Integrating patients in time series clinical transcriptomics data. i151-i159 - Patrick Wall, Trey Ideker:
Representing mutations for predicting cancer drug response. i160-i168 - Mohammad Al Olaimat, Serdar Bozdag:
TA-RNN: an attention-based time-aware recurrent neural network architecture for electronic health records. i169-i179 - Monica-Andreea Baciu-Dragan, Niko Beerenwinkel:
Oncotree2vec - a method for embedding and clustering of tumor mutation trees. i180-i188 - Alexander Immer, Stefan G. Stark, Francis Jacob, Ximena Bonilla, Tinu Thomas, André Kahles, Sandra Götze, Emanuela S. Milani, Bernd Wollscheid, Tumor Profiler Consortium, Gunnar Rätsch, Kjong-Van Lehmann:
Probabilistic pathway-based multimodal factor analysis. i189-i198 - Daniel E. Platt, Aritra Bose, Kahn Rhrissorrakrai, Chaya Levovitz, Laxmi Parida:
Epidemiological topology data analysis links severe COVID-19 to RAAS and hyperlipidemia associated metabolic syndrome conditions. i199-i207 - Noa Ecker, Dorothée Huchon, Yishay Mansour, Itay Mayrose, Tal Pupko:
A machine-learning-based alternative to phylogenetic bootstrap. i208-i217 - Palash Sashittal, Viola Chen, Amey Pasarkar, Benjamin J. Raphael:
Joint inference of cell lineage and mitochondrial evolution from single-cell sequencing data. i218-i227 - Uyen Mai, Gary Hu, Benjamin J. Raphael:
Maximum likelihood phylogeographic inference of cell motility and cell division from spatial lineage tracing data. i228-i236 - Bertrand Marchand, Yoann Anselmetti, Manuel Lafond, Aïda Ouangraoua:
Median and small parsimony problems on RNA trees. i237-i246 - Xinrui Lyu, Bowen Fan, Matthias Hüser, Philip Hartout, Thomas Gumbsch, Martin Faltys, Tobias M. Merz, Gunnar Rätsch, Karsten M. Borgwardt:
An empirical study on KDIGO-defined acute kidney injury prediction in the intensive care unit. i247-i256 - Kaiyuan Liu, Chenghua Tao, Yuzhen Ye, Haixu Tang:
SpecEncoder: deep metric learning for accurate peptide identification in proteomics. i257-i265 - Xiangru Tang, Bill Qian, Rick Gao, Jiakang Chen, Xinyun Chen, Mark B. Gerstein:
BioCoder: a benchmark for bioinformatics code generation with large language models. i266-i276 - Sanjana Tule, Gabriel Foley, Chongting Zhao, Michael Forbes, Mikael Bodén:
Optimal phylogenetic reconstruction of insertion and deletion events. i277-i286 - Vikram S. Shivakumar, Omar Y. Ahmed, Sam Kovaka, Mohsen Zakeri, Ben Langmead:
Sigmoni: classification of nanopore signal with a compressed pangenome index. i287-i296 - Dongze He, Yuan Gao, Spencer Skylar Chan, Natalia Quintana-Parrilla, Rob Patro:
Forseti: a mechanistic and predictive model of the splicing status of scRNA-seq reads. i297-i306 - Qian Shi, Qimin Zhang, Mingfu Shao:
Accurate assembly of multiple RNA-seq samples with Aletsch. i307-i317 - Xin Yuan, Ke Chen, Xiang Li, Qian Shi, Mingfu Shao:
Learning locality-sensitive bucketing functions. i318-i327 - Kayvon Mazooji, Ilan Shomorony:
Fast multiple sequence alignment via multi-armed bandits. i328-i336 - Harun Mustafa, Mikhail Karasikov, Nika Mansouri-Ghiasi, Gunnar Rätsch, André Kahles:
Label-guided seed-chain-extend alignment on annotated De Bruijn graphs. i337-i346 - Han Huang, Ziqian Lin, Dongchen He, Liang Hong, Yu Li:
RiboDiffusion: tertiary structure-based RNA inverse folding with generative diffusion models. i347-i356 - Xiangru Tang, Andrew Tran, Jeffrey Tan, Mark B. Gerstein:
MolLM: a unified language model for integrating biomedical text with 2D and 3D molecular representations. i357-i368 - Mogan Gim, Jueon Park, Soyon Park, Sanghoon Lee, Seungheun Baek, Junhyun Lee, Ngoc-Quang Nguyen, Jaewoo Kang:
MolPLA: a molecular pretraining framework for learning cores, R-groups and their linker joints. i369-i380 - Xiaocheng Zeng, Zheng Wei, Qixiu Du, Jiaqi Li, Zhen Xie, Xiaowo Wang:
Unveil cis-acting combinatorial mRNA motifs by interpreting deep neural network. i381-i389 - Jiyu Chen, Benjamin Goudey, Nicholas Geard, Karin Verspoor:
Integration of background knowledge for automatic detection of inconsistencies in gene ontology annotation. i390-i400 - Fernando Zhapa-Camacho, Zhenwei Tang, Maxat Kulmanov, Robert Hoehndorf:
Predicting protein functions using positive-unlabeled ranking with ontology-based priors. i401-i409 - Varun Ananth, Justin Sanders, Melih Yilmaz, Bo Wen, Sewoong Oh, William Stafford Noble:
A learned score function improves the power of mass spectrometry database search. i410-i417 - Guanglei Yu, Qichang Zhao, Xuehua Bi, Jianxin Wang:
DDAffinity: predicting the changes in binding affinity of multiple point mutations using protein 3D structure. i418-i427 - Yisu Peng, Shantanu Jain, Predrag Radivojac:
An algorithm for decoy-free false discovery rate estimation in XL-MS/MS proteomics. i428-i436 - Frederic Runge, Jörg K. H. Franke, Daniel Fertmann, Rolf Backofen, Frank Hutter:
Partial RNA design. i437-i445 - Noa Moriel, Edvin Memet, Mor Nitzan:
Optimal sequencing budget allocation for trajectory reconstruction of single cells. i446-i452 - Ding Bai, Caleb N. Ellington, Shentong Mo, Le Song, Eric P. Xing:
AttentionPert: accurately modeling multiplexed genetic perturbations with multi-scale effects. i453-i461 - Wei Huang, Hui Liu:
Predicting single-cell cellular responses to perturbations using cycle consistency learning. i462-i470 - Tangqi Fang, Yifeng Liu, Addie Woicik, Minsi Lu, Anupama Jha, Xiao Wang, Gang Li, Borislav H. Hristov, Zixuan Liu, Hanwen Xu, William S. Noble, Sheng Wang:
Enhancing Hi-C contact matrices for loop detection with Capricorn: a multiview diffusion model. i471-i480 - Hirak Sarkar, Uthsav Chitra, Julian Gold, Benjamin J. Raphael:
A count-based model for delineating cell-cell interactions in spatial transcriptomics data. i481-i489 - Ghulam Murtaza, Byron Butaney, Justin Wagner, Ritambhara Singh:
scGrapHiC: deep learning-based graph deconvolution for Hi-C using single cell gene expression. i490-i500 - Michael F. Adamer, Sarah C. Brüningk, Dexiong Chen, Karsten M. Borgwardt:
Biomarker identification by interpretable maximum mean discrepancy. i501-i510 - Chao Deng, Hong-Dong Li, Li-Shen Zhang, Yiwei Liu, Yaohang Li, Jianxin Wang:
Identifying new cancer genes based on the integration of annotated gene sets via hypergraph neural networks. i511-i520 - Eric D. Sun, Rong Ma, James Zou:
SPRITE: improving spatial gene expression imputation with gene and cell networks. i521-i528 - Charles Broadbent, Tianci Song, Rui Kuang:
Deciphering high-order structures in spatial transcriptomes with graph-guided Tucker decomposition. i529-i538 - Zuolong Zhang, Xin He, Dazhi Long, Gang Luo, Shengbo Chen:
Enhancing generalizability and performance in drug-target interaction identification by integrating pharmacophore and pre-trained models. i539-i547 - Mayar Ali, Merel Kuijs, Soroor Hediyeh-Zadeh, Tim Treis, Karin Hrovatin, Giovanni Palla, Anna C. Schaar, Fabian J. Theis:
GraphCompass: spatial metrics for differential analyses of cell organization across conditions. i548-i557 - Domagoj Doresic, Stephan Grein, Jan Hasenauer:
Efficient parameter estimation for ODE models of cellular processes using semi-quantitative data. i558-i566 - Yang Yang, Dana Pe'er:
REUNION: transcription factor binding prediction and regulatory association inference from single-cell multi-omics data. i567-i575
Volume 40, Number Supplement_2, 2024
ECCB 2024: Turku, Finland
- Anu Kukkonen-Macchi, Sampsa Hautaniemi, Katharina F. Heil, Merja Heinäniemi, Lars Juhl Jensen, Sini Junttila, Lukas Käll, Asta Laiho, Peter Maccallum, Matti Nykter, Bengt Persson, Tomi Suomi, Tim Van Den Bossche, Tommi H. Nyrönen, Laura L. Elo:
ECCB2024: The 23rd European Conference on Computational Biology. ii1-ii3 - Alexander Rakowski, Remo Monti, Viktoriia Huryn, Marta Lemanczyk, Uwe Ohler, Christoph Lippert:
Metadata-guided feature disentanglement for functional genomics. ii4-ii10 - Tim Mirus, Robert Lohmayer, Clementine Döhring, Bjarni V. Halldórsson, Birte Kehr:
GGTyper: genotyping complex structural variants using short-read sequencing data. ii11-ii19 - Zhi Yan, Zhen Cao, Luay Nakhleh:
Polyphest: fast polyploid phylogeny estimation. ii20-ii28 - Sjoerd van den Belt, Hanqing Zhao, Nikolaos Alachiotis:
Scalable CNN-based classification of selective sweeps using derived allele frequencies. ii29-ii36 - Soufyan Lakbir, Caterina Buranelli, Gerrit A. Meijer, Jaap Heringa, Remond J. A. Fijneman, Sanne Abeln:
CIBRA identifies genomic alterations with a system-wide impact on tumor biology. ii37-ii44 - Katerina C. Nastou, Mikaela Koutrouli, Sampo Pyysalo, Lars Juhl Jensen:
Improving dictionary-based named entity recognition with deep learning. ii45-ii52 - Huiying Yan, Shaojun Wang, Hancheng Liu, Hiroshi Mamitsuka, Shanfeng Zhu:
GORetriever: reranking protein-description-based GO candidates by literature-driven deep information retrieval for protein function annotation. ii53-ii61 - Yutong Li, Pedro Henrique da Costa Avelar, Xinyue Chen, Li Zhang, Min Wu, Sophia Tsoka:
CLigOpt: controllable ligand design through target-specific optimization. ii62-ii69 - Tobias Pietz, Sukrit Gupta, Christoph N. Schlaffner, Saima Ahmed, Hanno Steen, Bernhard Y. Renard, Katharina Baum:
PEPerMINT: peptide abundance imputation in mass spectrometry-based proteomics using graph neural networks. ii70-ii78 - Felix Becker, Mario Stanke:
learnMSA2: deep protein multiple alignments with large language and hidden Markov models. ii79-ii86 - Yuehua Zhu, Panayiotis V. Benos, Maria Chikina:
A hybrid constrained continuous optimization approach for optimal causal discovery from biological data. ii87-ii97 - Piotr Stomma, Witold R. Rudnicki:
HCS - hierarchical algorithm for simulation of omics datasets. ii98-ii104 - Rami Nasser, Leah V. Schaffer, Trey Ideker, Roded Sharan:
Multi-modal contrastive learning of subcellular organization using DICE. ii105-ii110 - Tianci Song, Eric Cosatto, Gaoyuan Wang, Rui Kuang, Mark Gerstein, Martin Renqiang Min, Jonathan Warrell:
Predicting spatially resolved gene expression via tissue morphology using adaptive spatial GNNs. ii111-ii119 - Qi Jiang, Lin Wan:
A physics-informed neural SDE network for learning cellular dynamics from time-series scRNA-seq data. ii120-ii127 - Yimin Fan, Yaxuan Li, Yunhua Zhong, Liang Hong, Lei Li, Yu Li:
Learning meaningful representation of single-neuron morphology via large-scale pre-training. ii128-ii136 - Zizhan Gao, Kai Cao, Lin Wan:
Graspot: a graph attention network for spatial transcriptomics data integration with optimal transport. ii137-ii145 - Jiaqi Zhang, Erica Larschan, Jeremy Bigness, Ritambhara Singh:
scNODE : generative model for temporal single cell transcriptomic data prediction. ii146-ii154 - Xiaolei Brian Zhang, Grace Oualline, Jim Shaw, Yun William Yu:
skandiver: a divergence-based analysis tool for identifying intercellular mobile genetic elements. ii155-ii164 - Mahmudur Rahman Hera, Shaopeng Liu, Wei Wei, Judith S. Rodríguez, Chunyu Ma, David Koslicki:
Metagenomic functional profiling: to sketch or not to sketch? ii165-ii173 - Srijay Deshpande, Sokratia Georgaka, Michael Haley, Robert Sellers, James Minshull, Jayakrupakar Nallala, Martin Fergie, Nicholas Stone, Nasir M. Rajpoot, Syed Murtuza Baker, Mudassar Iqbal, Kevin Couper, Federico Roncaroli, Fayyaz Minhas:
Ouroboros: cross-linking protein expression perturbations and cancer histology imaging with generative-predictive modeling. ii174-ii181 - Teemu J. Rintala, Francesco Napolitano, Vittorio Fortino:
Multi-task deep latent spaces for cancer survival and drug sensitivity prediction. ii182-ii189 - Zhijian Huang, Ziyu Fan, Siyuan Shen, Min Wu, Lei Deng:
MolMVC: Enhancing molecular representations for drug-related tasks through multi-view contrastive learning. ii190-ii197 - Bastian Pfeifer, Christel Sirocchi, Marcus D. Bloice, Markus Kreuzthaler, Martin Urschler:
Federated unsupervised random forest for privacy-preserving patient stratification. ii198-ii207
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