Content-Type: text/html; Oxford Academic
 
 
 
Oxford Academic
 
 
 
 
New issue alert
 
 
 
 
Bioinformatics  
Volume 40 Issue Supplement_1
 
July 2024
 
button-issue.png
 
 
Editorial
 
 
 
 
ISMB 2024 Proceedings border= 
 
Tijana Milenković, Yann Ponty
 
 
 
Awards Papers
 
 
 
 
The 2024 ISCB Overton Prize Award'Dr Martin Steinegger border= 
 
Mallory L Wiper
 
 
 
The 2024 ISCB Innovator Award'Dr Sui-In Lee border= 
 
Mallory L Wiper
 
 
 
The 2024 ISCB Accomplishments by a Senior Scientist Award'Dr Tandy Warnow border=  
 
Mallory L Wiper
 
 
 
The 2024 Outstanding Contributions to ISCB Award'Dr Scott Markel border= 
 
Mallory L Wiper
 
 
 
 
 
Bioinformatics Education and Citizen Science
 
 
 
 
Closing the computational biology knowledge gap': Spanish Wikipedia as a case study border= 
 
Nelly Sélem-Mojica, Tülay Karakulak, Audra Anjum, Antón Pashkov, Rafael Pérez-Estrada ...
 
 
 
Teaching bioinformatics through the analysis of SARS-CoV-2: project-based training for computer science students border= 
 
Pavlin G Poličar, Martin Špendl, Tomaž Curk, Blaž Zupan
 
 
 
Bioinformatics of Microbes and Microbiomes
 
 
 
 
Floria: fast and accurate strain haplotyping in metagenomes border= 
 
Jim Shaw, Jean-Sebastien Gounot, Hanrong Chen, Niranjan Nagarajan, Yun William Yu
 
 
 
Scalable de novo classification of antibiotic resistance of Mycobacterium tuberculosis border= 
 
Mohammadali Serajian, Simone Marini, Jarno N Alanko, Noelle R Noyes, Mattia Prosperi ...
 
 
 
Conway'Bromage'Lyndon (CBL): an exact, dynamic representation of k -mer sets border= 
 
Igor Martayan, Bastien Cazaux, Antoine Limasset, Camille Marchet
 
 
 
 
Reference-free structural variant detection in microbiomes via long-read co-assembly graphs border= 
 
Kristen D Curry, Feiqiao Brian Yu, Summer E Vance, Santiago Segarra, Devaki Bhaya ...
 
 
 
Towards more accurate microbial source tracking via non-negative matrix factorization (NMF) border= 
 
Ziyi Huang, Dehan Cai, Yanni Sun
 
 
 
Biomedical Informatics
 
 
 
 
PhiHER2: phenotype-informed weakly supervised model for HER2 status prediction from pathological images border= 
 
Chaoyang Yan, Jialiang Sun, Yiming Guan, Jiuxin Feng, Hong Liu ...
 
 
 
CODEX: COunterfactual Deep learning for the in silico EXploration of cancer cell line perturbations border= 
 
Stefan Schrod, Helena U Zacharias, Tim Beißbarth, Anne-Christin Hauschild, Michael Altenbuchinger
 
 
 
Adaptive digital tissue deconvolution border=  
 
Franziska Görtler, Malte Mensching-Buhr, Ørjan Skaar, Stefan Schrod, Thomas Sterr ...
 
 
 
Approximating facial expression effects on diagnostic accuracy via generative AI in medical genetics border= 
 
Tanviben Patel, Amna A Othman, Ömer Sümer, Fabio Hellman, Peter Krawitz ...
 
 
 
Improving medical reasoning through retrieval and self-reflection with retrieval-augmented large language models border= 
 
Minbyul Jeong, Jiwoong Sohn, Mujeen Sung, Jaewoo Kang
 
 
 
Transfer learning of condition-specific perturbation in gene interactions improves drug response prediction border= 
 
Dongmin Bang, Bonil Koo, Sun Kim
 
 
 
Modeling metastatic progression from cross-sectional cancer genomics data border=  
 
Kevin Rupp, Andreas Lösch, Yanren Linda Hu, Chenxi Nie, Rudolf Schill ...
 
 
 
Integrating patients in time series clinical transcriptomics data border=  
 
Euxhen Hasanaj, Sachin Mathur, Ziv Bar-Joseph
 
 
 
Representing mutations for predicting cancer drug response border=  
 
Patrick Wall, Trey Ideker
 
 
 
TA-RNN: an attention-based time-aware recurrent neural network architecture for electronic health records border= 
 
Mohammad Al Olaimat, Serdar Bozdag
 
 
 
Oncotree2vec ' a method for embedding and clustering of tumor mutation trees border=  
 
Monica-Andreea Baciu-Drăgan, Niko Beerenwinkel
 
 
 
Probabilistic pathway-based multimodal factor analysis border=  
 
Alexander Immer, Stefan G Stark, Francis Jacob, Ximena Bonilla, Tinu Thomas ...
 
 
 
Equity and Diversity
 
 
 
 
Epidemiological topology data analysis links severe COVID-19 to RAAS and hyperlipidemia associated metabolic syndrome conditions border= 
 
Daniel Platt, Aritra Bose, Kahn Rhrissorrakrai, Chaya Levovitz, Laxmi Parida
 
 
 
Evolutionary, Comparative and Population Genomics
 
 
 
 
A machine-learning-based alternative to phylogenetic bootstrap border= 
 
Noa Ecker, Dorothée Huchon, Yishay Mansour, Itay Mayrose, Tal Pupko
 
 
 
Joint inference of cell lineage and mitochondrial evolution from single-cell sequencing data border= 
 
Palash Sashittal, Viola Chen, Amey Pasarkar, Benjamin J Raphael
 
 
 
Maximum likelihood phylogeographic inference of cell motility and cell division from spatial lineage tracing data border= 
 
Uyen Mai, Gary Hu, Benjamin J Raphael
 
 
 
Median and small parsimony problems on RNA trees border=  
 
Bertrand Marchand, Yoann Anselmetti, Manuel Lafond, Aïda Ouangraoua
 
 
 
General Computational Biology
 
 
 
 
An empirical study on KDIGO-defined acute kidney injury prediction in the intensive care unit border= 
 
Xinrui Lyu, Bowen Fan, Matthias Hüser, Philip Hartout, Thomas Gumbsch ...
 
 
 
SpecEncoder: deep metric learning for accurate peptide identification in proteomics border= 
 
Kaiyuan Liu, Chenghua Tao, Yuzhen Ye, Haixu Tang
 
 
 
BioCoder: a benchmark for bioinformatics code generation with large language models border= 
 
Xiangru Tang, Bill Qian, Rick Gao, Jiakang Chen, Xinyun Chen ...
 
 
 
Genome Sequence Analysis
 
 
 
 
Optimal phylogenetic reconstruction of insertion and deletion events border= 
 
Sanjana Tule, Gabriel Foley, Chongting Zhao, Michael Forbes, Mikael Bodén
 
 
 
Sigmoni: classification of nanopore signal with a compressed pangenome index border=  
 
Vikram S Shivakumar, Omar Y Ahmed, Sam Kovaka, Mohsen Zakeri, Ben Langmead
 
 
 
Forseti : a mechanistic and predictive model of the splicing status of scRNA-seq reads border= 
 
Dongze He, Yuan Gao, Spencer Skylar Chan, Natalia Quintana-Parrilla, Rob Patro
 
 
 
Accurate assembly of multiple RNA-seq samples with Aletsch border=  
 
Qian Shi, Qimin Zhang, Mingfu Shao
 
 
 
Learning locality-sensitive bucketing functions border=  
 
Xin Yuan, Ke Chen, Xiang Li, Qian Shi, Mingfu Shao
 
 
 
Fast multiple sequence alignment via multi-armed bandits border=  
 
Kayvon Mazooji, Ilan Shomorony
 
 
 
Label-guided seed-chain-extend alignment on annotated De Bruijn graphs border=  
 
Harun Mustafa, Mikhail Karasikov, Nika Mansouri Ghiasi, Gunnar Rätsch, André Kahles
 
 
 
Macromolecular Sequence, Structure, and Function
 
 
 
 
RiboDiffusion: tertiary structure-based RNA inverse folding with generative diffusion models border= 
 
Han Huang, Ziqian Lin, Dongchen He, Liang Hong, Yu Li
 
 
 
MolLM : a unified language model for integrating biomedical text with 2D and 3D molecular representations border= 
 
Xiangru Tang, Andrew Tran, Jeffrey Tan, Mark B Gerstein
 
 
 
MolPLA: a molecular pretraining framework for learning cores, R-groups and their linker joints border= 
 
Mogan Gim, Jueon Park, Soyon Park, Sanghoon Lee, Seungheun Baek ...
 
 
 
Unveil cis -acting combinatorial mRNA motifs by interpreting deep neural network border= 
 
Xiaocheng Zeng, Zheng Wei, Qixiu Du, Jiaqi Li, Zhen Xie ...
 
 
 
Integration of background knowledge for automatic detection of inconsistencies in gene ontology annotation border= 
 
Jiyu Chen, Benjamin Goudey, Nicholas Geard, Karin Verspoor
 
 
 
Predicting protein functions using positive-unlabeled ranking with ontology-based priors border= 
 
Fernando Zhapa-Camacho, Zhenwei Tang, Maxat Kulmanov, Robert Hoehndorf
 
 
 
A learned score function improves the power of mass spectrometry database search border= 
 
Varun Ananth, Justin Sanders, Melih Yilmaz, Bo Wen, Sewoong Oh ...
 
 
 
DDAffinity: predicting the changes in binding affinity of multiple point mutations using protein 3D structure border= 
 
Guanglei Yu, Qichang Zhao, Xuehua Bi, Jianxin Wang
 
 
 
An algorithm for decoy-free false discovery rate estimation in XL-MS/MS proteomics border= 
 
Yisu Peng, Shantanu Jain, Predrag Radivojac
 
 
 
Partial RNA design border= 
 
Frederic Runge, Jörg Franke, Daniel Fertmann, Rolf Backofen, Frank Hutter
 
 
 
Regulatory and Functional Genomics
 
 
 
 
Optimal sequencing budget allocation for trajectory reconstruction of single cells border= 
 
Noa Moriel, Edvin Memet, Mor Nitzan
 
 
 
AttentionPert: accurately modeling multiplexed genetic perturbations with multi-scale effects border= 
 
Ding Bai, Caleb N Ellington, Shentong Mo, Le Song, Eric P Xing
 
 
 
Predicting single-cell cellular responses to perturbations using cycle consistency learning border= 
 
Wei Huang, Hui Liu
 
 
 
Enhancing Hi-C contact matrices for loop detection with Capricorn: a multiview diffusion model border= 
 
Tangqi Fang, Yifeng Liu, Addie Woicik, Minsi Lu, Anupama Jha ...
 
 
 
A count-based model for delineating cell'cell interactions in spatial transcriptomics data border= 
 
Hirak Sarkar, Uthsav Chitra, Julian Gold, Benjamin J Raphael
 
 
 
scGrapHiC: deep learning-based graph deconvolution for Hi-C using single cell gene expression border= 
 
Ghulam Murtaza, Byron Butaney, Justin Wagner, Ritambhara Singh
 
 
 
Systems Biology and Networks
 
 
 
 
Biomarker identification by interpretable maximum mean discrepancy border= 
 
Michael F Adamer, Sarah C Brüningk, Dexiong Chen, Karsten Borgwardt
 
 
 
Identifying new cancer genes based on the integration of annotated gene sets via hypergraph neural networks border= 
 
Chao Deng, Hong-Dong Li, Li-Shen Zhang, Yiwei Liu, Yaohang Li ...
 
 
 
SPRITE: improving spatial gene expression imputation with gene and cell networks border= 
 
Eric D Sun, Rong Ma, James Zou
 
 
 
Deciphering high-order structures in spatial transcriptomes with graph-guided Tucker decomposition border= 
 
Charles Broadbent, Tianci Song, Rui Kuang
 
 
 
Enhancing generalizability and performance in drug'target interaction identification by integrating pharmacophore and pre-trained models border= 
 
Zuolong Zhang, Xin He, Dazhi Long, Gang Luo, Shengbo Chen
 
 
 
GraphCompass: spatial metrics for differential analyses of cell organization across conditions border= 
 
Mayar Ali, Merel Kuijs, Soroor Hediyeh-zadeh, Tim Treis, Karin Hrovatin ...
 
 
 
Efficient parameter estimation for ODE models of cellular processes using semi-quantitative data border= 
 
Domagoj Dorešić, Stephan Grein, Jan Hasenauer
 
 
 
REUNION: transcription factor binding prediction and regulatory association inference from single-cell multi-omics data border= 
 
Yang Yang, Dana Pe'er
 
 
Unsubscribe       Manage email alerts
 
Written requests to unsubscribe can be sent to: Journals Marketing, Oxford University Press, Great Clarendon Street, Oxford, OX2 6DP, UK.

Our Privacy Policy sets out how Oxford University Press handles your personal information.

The content of this email is protected by copyright.
 
Oxford University Press
 
 
                                 



This email is intended for bionet@evol.biology.mcmaster.ca. ------=_Part_695777593.1721586893143--