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Bioinformatics  
Volume 38 Issue Supplement_1
 
July 2022
 
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ISCB/ISMB 2022
 
 
 
2022 ISCB Accomplishments by a Senior Scientist Award: Ron Shamir border= 
 
Christina Fogg; Diane Kovats; Martin Vingron
 
 
2022 ISCB Overton Prize: Po-Ru Loh border= 
 
Christina Fogg; Diane Kovats; Martin Vingron
 
 
2022 ISCB Innovator Award: Núria López-Bigas border= 
 
Christina Fogg; Diane Kovats; Martin Vingron
 
 
2022 Outstanding Contributions to ISCB Award: Reinhard Schneider border= 
 
Christina Fogg; Diane Kovats; Martin Vingron
 
 
ISMB 2022 proceedings border= 
 
Christophe Dessimoz; Sushmita Roy
 
 
 
 
 
Bioinformatics education
 
 
 
An approachable, flexible and practical machine learning workshop for biologists border= 
 
Chris S Magnano; Fangzhou Mu; Rosemary S Russ; Milica Cvetkovic ; Debora Treu ...
 
 
Characterizing domain-specific open educational resources by linking ISCB Communities of Special Interest to Wikipedia border= 
 
Alastair M Kilpatrick; Farzana Rahman; Audra Anjum ; Sayane Shome; K M Salim Andalib ...
 
 
 
Bioinformatics of microbes and microbiomes
 
 
 
CMash: fast, multi-resolution estimation of k-mer-based Jaccard and containment indices border= 
 
Shaopeng Liu; David Koslicki
 
 
CALDERA: finding all significant de Bruijn subgraphs for bacterial GWAS border= 
 
Hector Roux de Bézieux; Leandro Lima; Fanny Perraudeau; Arnaud Mary ; Sandrine Dudoit ...
 
 
Phage'bacterial contig association prediction with a convolutional neural network border= 
 
Tianqi Tang; Shengwei Hou; Jed A Fuhrman ; Fengzhu Sun
 
 
 
 
 
Biomedical informatics
 
 
 
Synthetic-to-real: instance segmentation of clinical cluster cells with unlabeled synthetic training border= 
 
Meng Zhao; Siyu Wang; Fan Shi ; Chen Jia; Xuguo Sun ...
 
 
BITES: balanced individual treatment effect for survival data border= 
 
S Schrod; A Schäfer; S Solbrig; R Lohmayer ; W Gronwald ...
 
 
From drug repositioning to target repositioning: prediction of therapeutic targets using genetically perturbed transcriptomic signatures border= 
 
Satoko Namba; Michio Iwata; Yoshihiro Yamanishi
 
 
Fast and interpretable genomic data analysis using multiple approximate kernel learning border= 
 
Ayyüce Begüm Bekta┼č; Çi─čdem Ak; Mehmet Gönen
 
 
A graph neural network approach for molecule carcinogenicity prediction border= 
 
Philip Fradkin; Adamo Young; Lazar Atanackovic; Brendan Frey ; Leo J Lee ...
 
 
Scaling multi-instance support vector machine to breast cancer detection on the BreaKHis dataset border= 
 
Hoon Seo; Lodewijk Brand; Lucia Saldana Barco ; Hua Wang
 
 
Prediction of recovery from multiple organ dysfunction syndrome in pediatric sepsis patients border= 
 
Bowen Fan; Juliane Klatt; Michael M Moor ; Latasha A Daniels; Philipp K A Agyeman ...
 
 
 
Evolutionary, comparative and population genomics
 
 
 
Quintet Rooting: rooting species trees under the multi-species coalescent model border= 
 
Yasamin Tabatabaee; Kowshika Sarker; Tandy Warnow
 
 
A LASSO-based approach to sample sites for phylogenetic tree search border= 
 
Noa Ecker; Dana Azouri; Ben Bettisworth; Alexandros Stamatakis ; Yishay Mansour ...
 
 
Reconstructing tumor clonal lineage trees incorporating single-nucleotide variants, copy number alterations and structural variations border= 
 
Xuecong Fu; Haoyun Lei; Yifeng Tao ; Russell Schwartz
 
 
Simulating domain architecture evolution border= 
 
Xiaoyue Cui; Yifan Xue; Collin McCormack; Alejandro Garces ; Thomas W Rachman ...
 
 
 
Genome privacy and security
 
 
 
Robust fingerprinting of genomic databases border= 
 
Tianxi Ji; Erman Ayday; Emre Yilmaz; Pan Li
 
 
 
Genome sequence analysis
 
 
 
ReadBouncer: precise and scalable adaptive sampling for nanopore sequencing border= 
 
Jens-Uwe Ulrich; Ahmad Lutfi; Kilian Rutzen; Bernhard Y Renard
 
 
DeepCRISTL: deep transfer learning to predict CRISPR/Cas9 functional and endogenous on-target editing efficiency border= 
 
Shai Elkayam; Yaron Orenstein
 
 
The minimizer Jaccard estimator is biased and inconsistent border= 
 
Mahdi Belbasi; Antonio Blanca; Robert S Harris; David Koslicki ; Paul Medvedev
 
 
Syotti: scalable bait design for DNA enrichment border= 
 
Jarno N Alanko; Ilya B Slizovskiy; Daniel Lokshtanov; Travis Gagie ; Noelle R Noyes ...
 
 
Sparse and skew hashing of K-mers border= 
 
Giulio Ermanno Pibiri
 
 
Phylovar: toward scalable phylogeny-aware inference of single-nucleotide variations from single-cell DNA sequencing data border= 
 
Mohammadamin Edrisi; Monica V Valecha; Sunkara B V Chowdary ; Sergio Robledo; Huw A Ogilvie ...
 
 
Markov chains improve the significance computation of overlapping genome annotations border= 
 
Askar Gafurov; Bro┼ła Brejová; Paul Medvedev
 
 
PolarMorphism enables discovery of shared genetic variants across multiple traits from GWAS summary statistics border= 
 
Joanna von Berg; Michelle ten Dam; Sander W van der Laan ; Jeroen de Ridder
 
 
 
Macromolecular sequence, structure, and function
 
 
 
DeepMHCII: a novel binding core-aware deep interaction model for accurate MHC-II peptide binding affinity prediction border= 
 
Ronghui You; Wei Qu; Hiroshi Mamitsuka ; Shanfeng Zhu
 
 
Bridging the gaps in statistical models of protein alignment border= 
 
Dinithi Sumanaweera; Lloyd Allison; Arun S Konagurthu
 
 
DeepGOZero: improving protein function prediction from sequence and zero-shot learning based on ontology axioms border= 
 
Maxat Kulmanov; Robert Hoehndorf
 
 
DECODE: a computational pipeline to discover T cell receptor binding rules border= 
 
Iliana Papadopoulou; An-Phi Nguyen; Anna Weber; María Rodríguez Martínez
 
 
On the reliability and the limits of inference of amino acid sequence alignments border= 
 
Sandun Rajapaksa; Dinithi Sumanaweera; Arthur M Lesk; Lloyd Allison ; Peter J Stuckey ...
 
 
Topsy-Turvy: integrating a global view into sequence-based PPI prediction border= 
 
Rohit Singh; Kapil Devkota; Samuel Sledzieski; Bonnie Berger ; Lenore Cowen
 
 
Exploring automatic inconsistency detection for literature-based gene ontology annotation border= 
 
Jiyu Chen; Benjamin Goudey; Justin Zobel ; Nicholas Geard; Karin Verspoor
 
 
 
Regulatory and functional genomics
 
 
 
MOJITOO: a fast and universal method for integration of multimodal single-cell data border= 
 
Mingbo Cheng; Zhijian Li; Ivan G Costa
 
 
psupertime: supervised pseudotime analysis for time-series single-cell RNA-seq data border= 
 
Will Macnair; Revant Gupta; Manfred Claassen
 
 
PhyloPGM: boosting regulatory function prediction accuracy using evolutionary information border= 
 
Faizy Ahsan; Zichao Yan; Doina Precup ; Mathieu Blanchette
 
 
MeConcord: a new metric to quantitatively characterize DNA methylation heterogeneity across reads and CpG sites border= 
 
Xianglin Zhang; Xiaowo Wang
 
 
Visualizing hierarchies in scRNA-seq data using a density tree-biased autoencoder border= 
 
Quentin Garrido; Sebastian Damrich; Alexander Jäger ; Dario Cerletti; Manfred Claassen ...
 
 
 
Systems biology and networks
 
 
 
MLGL-MP: a Multi-Label Graph Learning framework enhanced by pathway interdependence for Metabolic Pathway prediction border= 
 
Bing-Xue Du; Peng-Cheng Zhao; Bei Zhu ; Siu-Ming Yiu; Arnold K Nyamabo ...
 
 
SPARSE: a sparse hypergraph neural network for learning multiple types of latent combinations to accurately predict drug'drug interactions border= 
 
Duc Anh Nguyen; Canh Hao Nguyen; Peter Petschner ; Hiroshi Mamitsuka
 
 
Deep kernel learning improves molecular fingerprint prediction from tandem mass spectra border= 
 
Kai Dührkop
 
 
Do-calculus enables estimation of causal effects in partially observed biomolecular pathways border= 
 
Sara Mohammad-Taheri; Jeremy Zucker; Charles Tapley Hoyt ; Karen Sachs; Vartika Tewari ...
 
 
DEMA: a distance-bounded energy-field minimization algorithm to model and layout biomolecular networks with quantitative features border= 
 
Zhenyu Weng; Zongliang Yue; Yuesheng Zhu ; Jake Yue Chen
 
 
Computing optimal factories in metabolic networks with negative regulation border= 
 
Spencer Krieger; John Kececioglu
 
 
 
General computational biology
 
 
 
High-sensitivity pattern discovery in large, paired multiomic datasets border= 
 
Andrew R Ghazi; Kathleen Sucipto; Ali Rahnavard; Eric A Franzosa ; Lauren J McIver ...
 
 
Semi-deconvolution of bulk and single-cell RNA-seq data with application to metastatic progression in breast cancer border= 
 
Haoyun Lei; Xiaoyan A Guo; Yifeng Tao ; Kai Ding; Xuecong Fu ...
 
 
Self-supervised learning of cell type specificity from immunohistochemical images border= 
 
Michael Murphy; Stefanie Jegelka; Ernest Fraenkel
 
 
The effect of genome graph expressiveness on the discrepancy between genome graph distance and string set distance border= 
 
Yutong Qiu; Carl Kingsford
 
 
QuCo: quartet-based co-estimation of species trees and gene trees border= 
 
Maryam Rabiee; Siavash Mirarab
 
 
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