| 1 | -- | 0 | Yauheniya Zhdanovich, Jörg Ackermann 0001, Peter J. Wild, Jens Köllermann, Katrin Bankov, Claudia Döring 0002, Nadine Flinner, Henning Reis, Mike Wenzel, Benedikt Höh, Philipp Mandel, Thomas J. Vogl, Patrick Harter, Katharina Filipski, Ina Koch, Simon Bernatz. Evaluation of automatic discrimination between benign and malignant prostate tissue in the era of high precision digital pathology |
| 2 | -- | 0 | Jianjun Zhang, Xiaoyu Liang, Samantha Gonzales, Jianguo Liu, Xiaoyi Raymond Gao, Xuexia Wang. A gene based combination test using GWAS summary data |
| 3 | -- | 0 | Zicheng Zhang, Xinyue Lin, Shanshan Wu. A hybrid algorithm for clinical decision support in precision medicine based on machine learning |
| 4 | -- | 0 | Chunhua Liu, Simin Wu, Liying Lai, Jinyu Liu, Zhaofu Guo, Zegen Ye, Xiang Chen. Comprehensive analysis of cuproptosis-related lncRNAs in immune infiltration and prognosis in hepatocellular carcinoma |
| 5 | -- | 0 | Chaozhong Liu, Linhua Wang, Zhandong Liu. Single-cell multi-omics integration for unpaired data by a siamese network with graph-based contrastive loss |
| 6 | -- | 0 | Maria Prager, Daniel Lundin, Fredrik Ronquist, Anders F. Andersson. ASV portal: an interface to DNA-based biodiversity data in the Living Atlas |
| 7 | -- | 0 | Xuehan Liu, Md Rakibul Hasan, Khandaker Asif Ahmed, Md. Zakir Hossain. Machine learning to analyse omic-data for COVID-19 diagnosis and prognosis |
| 8 | -- | 0 | Seungjun Ahn, Tyler Grimes, Somnath Datta. A pseudo-value regression approach for differential network analysis of co-expression data |
| 9 | -- | 0 | Annette Spooner, Gelareh Mohammadi, Perminder S. Sachdev, Henry Brodaty, Arcot Sowmya. Ensemble feature selection with data-driven thresholding for Alzheimer's disease biomarker discovery |
| 10 | -- | 0 | Bram van Es, Leon C. Reteig, Sander C. Tan, Marijn Schraagen, Myrthe M. Hemker, Sebastiaan R. S. Arends, Miguel A. R. Rios, Saskia Haitjema. Negation detection in Dutch clinical texts: an evaluation of rule-based and machine learning methods |
| 11 | -- | 0 | Emmanuel P. Mwanga, Doreen J. Siria, Joshua Mitton, Issa H. Mshani, Mario González-Jiménez, Prashanth Selvaraj, Klaas Wynne, Francesco Baldini, Fredros O. Okumu, Simon A. Babayan. Using transfer learning and dimensionality reduction techniques to improve generalisability of machine-learning predictions of mosquito ages from mid-infrared spectra |
| 12 | -- | 0 | Li Guo, Yangyang Xiang, Yuyang Dou, Zibo Yin, Xinru Xu, Lihua Tang, Jiafeng Yu, Jun Wang, Tingming Liang. GBCdb: RNA expression landscapes and ncRNA-mRNA interactions in gallbladder carcinoma |
| 13 | -- | 0 | Junliang Shang, Xuhui Zhu, Yan Sun, Feng Li 0033, Xiangzhen Kong, Jin-Xing Liu. DM-MOGA: a multi-objective optimization genetic algorithm for identifying disease modules of non-small cell lung cancer |
| 16 | -- | 0 | Wei Peng 0004, Rong Wu, Wei Dai, Ning Yu. Identifying cancer driver genes based on multi-view heterogeneous graph convolutional network and self-attention mechanism |
| 17 | -- | 0 | Carolina Peixoto, Marta B. Lopes, Marta Martins, Sandra Casimiro, Daniel Sobral, Ana Rita Grosso, Catarina Abreu, Daniela Macedo, Ana Lúcia Costa, Helena Pais, Cecília Alvim, André Mansinho, Pedro Filipe, Pedro Marques da Costa, Afonso Fernandes, Paula Borralho, Cristina Ferreira, João Malaquias, António Quintela, Shannon Kaplan, Mahdi Golkaram, Michael Salmans, Nafeesa Khan, Raakhee Vijayaraghavan, Shile Zhang, Traci Pawlowski, Jim Godsey, Alex So, Li Liu, Luís Costa, Susana Vinga. Identification of biomarkers predictive of metastasis development in early-stage colorectal cancer using network-based regularization |
| 18 | -- | 0 | Ping Zhang, Weicheng Sun, Dengguo Wei, Guodong Li, Jinsheng Xu, Zhuhong You, Bowei Zhao, Li Li. PDA-PRGCN: identification of Piwi-interacting RNA-disease associations through subgraph projection and residual scaling-based feature augmentation |
| 19 | -- | 0 | Hai-Ming Feng, Ye Zhao, Wei-Jian Yan, Bin Li. Genomic and immunogenomic analysis of three prognostic signature genes in LUAD |
| 20 | -- | 0 | Zhong-Hua Chen, Wen-Yuan Zhang, Hui Ye, Yu-Qian Guo, Kai Zhang, Xiang-Ming Fang. A signature of immune-related genes correlating with clinical prognosis and immune microenvironment in sepsis |
| 21 | -- | 0 | Peijie Zheng, Guiyang Zhang, Yuewu Liu, Guohua Huang. MultiScale-CNN-4mCPred: a multi-scale CNN and adaptive embedding-based method for mouse genome DNA N4-methylcytosine prediction |
| 22 | -- | 0 | Hoseung Song, Wodan Ling, Ni Zhao, Anna M. Plantinga, Courtney A. Broedlow, Nichole R. Klatt, Tiffany Hensley-McBain, Michael C. Wu. Accommodating multiple potential normalizations in microbiome associations studies |
| 23 | -- | 0 | Luis F. Paulin, Muthuswamy Raveendran, R. Alan Harris, Jeffrey Rogers, Arndt von Haeseler, Fritz J. Sedlazeck. SVhound: detection of regions that harbor yet undetected structural variation |
| 24 | -- | 0 | Sávio S. Costa, Gislenne da Silva Moia, Artur Silva, Rafael A. Baraúna, Adonney Allan de Oliveira Veras. BADASS: BActeriocin-Diversity ASsessment Software |
| 25 | -- | 0 | Wencan Zhu, Céline Lévy-Leduc, Nils Ternès. Identification of prognostic and predictive biomarkers in high-dimensional data with PPLasso |
| 31 | -- | 0 | Anjana Senanayake, Hasindu Gamaarachchi, Damayanthi Herath, Roshan G. Ragel. DeepSelectNet: deep neural network based selective sequencing for oxford nanopore sequencing |
| 32 | -- | 0 | Dhiego Souto Andrade, Patrick Terrematte, César Rennó-Costa, Alona Zilberberg, Sol Efroni. GENTLE: a novel bioinformatics tool for generating features and building classifiers from T cell repertoire cancer data |
| 33 | -- | 0 | Qun-Ting Lin, Wei Yang, Xin Zhang, Qi-gang Li, Yong-Feng Liu, Qin Yan, Lei Sun. Systematic and benchmarking studies of pipelines for mammal WGBS data in the novel NGS platform |
| 34 | -- | 0 | Jingwen Suo, Lize Gu, Xingyu Yan, Sijia Yang, Xiaoya Hu, Licheng Wang. PP-DDP: a privacy-preserving outsourcing framework for solving the double digest problem |
| 35 | -- | 0 | Qing Ma, Yaqin Tan, Lei Wang. GACNNMDA: a computational model for predicting potential human microbe-drug associations based on graph attention network and CNN-based classifier |
| 36 | -- | 0 | Renaud L. M. Tissier, Janne J. M. van Schie, Rob M. F. Wolthuis, Job de Lange, Renée X. de Menezes. ShrinkCRISPR: a flexible method for differential fitness analysis of CRISPR-Cas9 screen data |
| 37 | -- | 0 | Yidong Zhu, Jun He, Zihua Li, Wenzhong Yang. Cuproptosis-related lncRNA signature for prognostic prediction in patients with acute myeloid leukemia |
| 38 | -- | 0 | Lingzhi Hu, Chengzhou Fu, Zhonglu Ren, Yongming Cai, Jin Yang 0004, Siwen Xu, Wenhua Xu, Deyu Tang. SSELM-neg: spherical search-based extreme learning machine for drug-target interaction prediction |
| 39 | -- | 0 | Seungwon Oh, Sae-Ryung Kang, In-Jae Oh, Min-Soo Kim. Deep learning model integrating positron emission tomography and clinical data for prognosis prediction in non-small cell lung cancer patients |
| 40 | -- | 0 | Jiaxing Chen, Yen Kaow Ng, Lu Lin, Xianglilan Zhang, Shuaicheng Li. On triangle inequalities of correlation-based distances for gene expression profiles |
| 41 | -- | 0 | Pawel Pratyush, Suresh Pokharel, Hiroto Saigo, Dukka B. Kc. pLMSNOSite: an ensemble-based approach for predicting protein S-nitrosylation sites by integrating supervised word embedding and embedding from pre-trained protein language model |
| 42 | -- | 0 | Zhengyi Guan, Xiaobing Zhou. A prefix and attention map discrimination fusion guided attention for biomedical named entity recognition |
| 43 | -- | 0 | Zilin Ren, Quan Li, Kajia Cao, Marilyn M. Li, Yunyun Zhou, Kai Wang. Model performance and interpretability of semi-supervised generative adversarial networks to predict oncogenic variants with unlabeled data |
| 43 | -- | 0 | Zilin Ren, Quan Li, Kajia Cao, Marilyn M. Li, Yunyun Zhou, Kai Wang. Model performance and interpretability of semi-supervised generative adversarial networks to predict oncogenic variants with unlabeled data |
| 44 | -- | 0 | Yang Yu, Yanyan Sun, Zhaoxian Li, Jiang Li, Dazhi Tian. Systematic analysis identifies XRCC4 as a potential immunological and prognostic biomarker associated with pan-cancer |
| 44 | -- | 0 | Yang Yu, Yanyan Sun, Zhaoxian Li, Jiang Li, Dazhi Tian. Systematic analysis identifies XRCC4 as a potential immunological and prognostic biomarker associated with pan-cancer |
| 45 | -- | 0 | Tony Hauptmann, Stefan Kramer. A fair experimental comparison of neural network architectures for latent representations of multi-omics for drug response prediction |
| 46 | -- | 0 | Nand Sharma, Joshua Millstein. CausNet: generational orderings based search for optimal Bayesian networks via dynamic programming with parent set constraints |
| 47 | -- | 0 | Shiva Afshar, Patricia R. Braun, Shizhong Han, Ying Lin. A multimodal deep learning model to infer cell-type-specific functional gene networks |
| 48 | -- | 0 | Daniyal Rajput, Wei-Jen Wang, Chun-Chuan Chen. Evaluation of a decided sample size in machine learning applications |
| 49 | -- | 0 | Mikhail Gudkov, Loïc Thibaut, Matloob Khushi, Gillian M. Blue, David S. Winlaw, Sally L. Dunwoodie, Eleni Giannoulatou. ConanVarvar: a versatile tool for the detection of large syndromic copy number variation from whole-genome sequencing data |
| 50 | -- | 0 | Christopher J. Nunn, Eugene Klyshko, Sidhartha Goyal. petiteFinder: an automated computer vision tool to compute Petite colony frequencies in baker's yeast |
| 51 | -- | 0 | Zequn Zheng, Yongfei Song. Integrated analysis of the voltage-gated potassium channel-associated gene KCNH2 across cancers |
| 52 | -- | 0 | S. Morteza Hashemi, Arash Zabihian, Mohsen Hooshmand, Sajjad Gharaghani. DRaW: prediction of COVID-19 antivirals by deep learning - an objection on using matrix factorization |
| 53 | -- | 0 | Anna-Maria Liebhoff, Kevin Menden, Alena Laschtowitz, Andre Franke, Christoph Schramm, Stefan Bonn. Pathogen detection in RNA-seq data with Pathonoia |
| 54 | -- | 0 | Yang Ma, Wan-liang Sun, Shuo Shuo Ma, Guanru Zhao, Zhong Liu, Zheng Lu, Dengyong Zhang. LincRNA ZNF529-AS1 inhibits hepatocellular carcinoma via FBXO31 and predicts the prognosis of hepatocellular carcinoma patients |
| 55 | -- | 0 | Yifan Zhang, Duc Tran, Tin Nguyen 0001, Sergiu M. Dascalu, Frederick C. Harris. A robust and accurate single-cell data trajectory inference method using ensemble pseudotime |
| 56 | -- | 0 | Xiao Liu, Li Teng, Wenqi Zuo, Shixun Zhong, Yuqiao Xu, Jing Sun. Deafness gene screening based on a multilevel cascaded BPNN model |
| 57 | -- | 0 | Brian Kwan, Tobias Fuhrer, Daniel Montemayor, Jeffery C. Fink, Jiang He, Chi-Yuan Hsu, Karen Messer, Robert G. Nelson, Minya Pu, Ana C. Ricardo, Hernan Rincon-Choles, Vallabh O. Shah, Hongping Ye, Jing Zhang, Kumar Sharma, Loki Natarajan. A generalized covariate-adjusted top-scoring pair algorithm with applications to diabetic kidney disease stage classification in the Chronic Renal Insufficiency Cohort (CRIC) Study |
| 58 | -- | 0 | Maia H. Malonzo, Harri Lähdesmäki. LuxHMM: DNA methylation analysis with genome segmentation via hidden Markov model |
| 59 | -- | 0 | Ho Yin Yuen, Jesper Jansson 0001. Normalized L3-based link prediction in protein-protein interaction networks |
| 60 | -- | 0 | Malik Yousef, Fatma Ozdemir, Amhar Jaber, Jens Allmer, Burcu Bakir-Gungor. PriPath: identifying dysregulated pathways from differential gene expression via grouping, scoring, and modeling with an embedded feature selection approach |
| 61 | -- | 0 | Elie-Julien El Hachem, Nataliya Sokolovska, Hédi Soula. Latent dirichlet allocation for double clustering (LDA-DC): discovering patients phenotypes and cell populations within a single Bayesian framework |
| 62 | -- | 0 | Sungyoung Lee, Choong-Hyun Sun, Heejun Jang, Daeyoon Kim, Sung-Soo Yoon, Youngil Koh, Seung Chan Na, Sung Im Cho, Man Jin Kim, Moon-Woo Seong, Ja Min Byun, Hongseok Yun. ITDetect: a method to detect internal tandem duplication of FMS-like tyrosine kinase (FLT3) from next-generation sequencing data with high sensitivity and clinical application |
| 63 | -- | 0 | Babak Beikzadeh. Immunoinformatics design of multi-epitope vaccine using OmpA, OmpD and enterotoxin against non-typhoidal salmonellosis |
| 64 | -- | 0 | Adam B. Olshen, Mark R. Segal. Does multi-way, long-range chromatin contact data advance 3D genome reconstruction? |
| 65 | -- | 0 | Hamid Motamedi, Marzie Mahdizade Ari, Mohsen Shahlaei, Sajad Moradi, Parisa Farhadikia, Amirhoushang Alvandi, Ramin Abiri. Designing multi-epitope vaccine against important colorectal cancer (CRC) associated pathogens based on immunoinformatics approach |
| 66 | -- | 0 | Jae Yong Ryu, Woo Dae Jang, Jidon Jang, Kwang-Seok Oh. PredAOT: a computational framework for prediction of acute oral toxicity based on multiple random forest models |
| 67 | -- | 0 | Mona Shafaghi, Zohreh Bahadori, Hamid Madanchi, Mohammad Mehdi Ranjbar, Ali Akbar Shabani, Seyed Fazlollah Mousavi. Immunoinformatics-aided design of a new multi-epitope vaccine adjuvanted with domain 4 of pneumolysin against Streptococcus pneumoniae strains |
| 68 | -- | 0 | Kai Chen, Xiaodong Zhu, Jiahao Wang, Lei Hao, Zhen Liu, Yuanning Liu. ncDENSE: a novel computational method based on a deep learning framework for non-coding RNAs family prediction |
| 69 | -- | 0 | Antonio Benítez-Hidalgo, José Francisco Aldana Montes, Ismael Navas Delgado, María del Mar Roldán García. SALON ontology for the formal description of sequence alignments |
| 70 | -- | 0 | Nika Abdollahi, Lucile Jeusset, Anne Langlois De Septenville, Frédéric Davi, Juliana S. Bernardes. Reconstructing B cell lineage trees with minimum spanning tree and genotype abundances |
| 71 | -- | 0 | Jonathan Tellechea-Luzardo, Hèctor Martín Lázaro, Raúl Moreno López, Pablo Carbonell. Sensbio: an online server for biosensor design |
| 72 | -- | 0 | Xiangjun Ji, Junwei Cai, Lixin Liang, Tieliu Shi, Jinghua Liu. Gene expression variability across cells and species shapes the relationship between renal resident macrophages and infiltrated macrophages |
| 73 | -- | 0 | Koen Swaerts, Franceska Dedeurwaerdere, Dieter De Smet, Peter De Jaeger, Geert A. Martens. DeltaMSI: artificial intelligence-based modeling of microsatellite instability scoring on next-generation sequencing data |
| 74 | -- | 0 | Arianna I. Krinos, Natalie R. Cohen, Michael J. Follows, Harriet Alexander. Reverse engineering environmental metatranscriptomes clarifies best practices for eukaryotic assembly |
| 75 | -- | 0 | Yusra A. Ameen, Dalia M. Badary, Ahmad Elbadry I. Abonnoor, Khaled F. Hussain, Adel A. Sewisy. Which data subset should be augmented for deep learning? a simulation study using urothelial cell carcinoma histopathology images |
| 76 | -- | 0 | Rui Chen, Jun-Min Wei. Integrated analysis identifies oxidative stress-related lncRNAs associated with progression and prognosis in colorectal cancer |
| 77 | -- | 0 | Lacey W. Heinsberg, Daniel E. Weeks. dbGaPCheckup: pre-submission checks of dbGaP-formatted subject phenotype files |
| 78 | -- | 0 | Erik Huckvale, Hunter N. B. Moseley. kegg_pull: a software package for the RESTful access and pulling from the Kyoto Encyclopedia of Gene and Genomes |
| 79 | -- | 0 | Zhijian Li, Chao-Chung Kuo, Fabio Ticconi, Mina Shaigan, Julia Gehrmann, Eduardo G. Gusmão, Manuel Allhoff, Martin Manolov, Martin Zenke, Ivan G. Costa. RGT: a toolbox for the integrative analysis of high throughput regulatory genomics data |
| 80 | -- | 0 | Runtian Gao, Junwei Luo, Hongyu Ding, Haixia Zhai. INSnet: a method for detecting insertions based on deep learning network |
| 81 | -- | 0 | Saiyidan Yalimaimaiti, Xiaoqiao Liang, Haili Zhao, Hong Dou, Wei Liu, Ying Yang, Li Ning. Establishment of a prognostic signature for lung adenocarcinoma using cuproptosis-related lncRNAs |
| 82 | -- | 0 | Malu Luz Calle, Meritxell Pujolassos, Antonio Susín. coda4microbiome: compositional data analysis for microbiome cross-sectional and longitudinal studies |
| 83 | -- | 0 | Aleksandr Kotov, Andrei Zinovyev, Anne-Helene Monsoro-Burq. scEvoNet: a gradient boosting-based method for prediction of cell state evolution |
| 84 | -- | 0 | Lior I. Shachaf, Elijah Roberts, Patrick Cahan, Jie Xiao. Gene regulation network inference using k-nearest neighbor-based mutual information estimation: revisiting an old DREAM |
| 85 | -- | 0 | ShaoMing Pan, Xin Liu, Ningdi Xie, Yanwen Chong. EG-TransUNet: a transformer-based U-Net with enhanced and guided models for biomedical image segmentation |
| 86 | -- | 0 | Patrick M. Carry, Tim Vigers, Lauren A. Vanderlinden, Carson Keeter, Fran Dong, Teresa Buckner, Elizabeth Litkowski, Ivana Yang, Jill M. Norris, Katherina J. Kechris. Propensity scores as a novel method to guide sample allocation and minimize batch effects during the design of high throughput experiments |
| 87 | -- | 0 | Katherine F. Steward, Mohammed Refai, William E. Dyer, Valérie Copié, Jennifer Lachowiec, Brian Bothner. Acute stress reduces population-level metabolic and proteomic variation |
| 88 | -- | 0 | Mirjam Figaschewski, Bilge Sürün, Thorsten Tiede, Oliver Kohlbacher. The personalized cancer network explorer (PeCaX) as a visual analytics tool to support molecular tumor boards |
| 89 | -- | 0 | Wan-Xia Yang, Hong-Wei Gao, Jia-Bo Cui, An-An Zhang, Fang-Fang Wang, Jian-Qin Xie, Ming-hua Lu, Chong-Ge You. Development and validation of a coagulation-related genes prognostic model for hepatocellular carcinoma |
| 90 | -- | 0 | Petter Mostad, Andreas Tillmar, Daniel Kling. Improved computations for relationship inference using low-coverage sequencing data |
| 91 | -- | 0 | Fan Chang, Jiang-hui Zhang, Wen-Song Wu, Shuai Tang, Zheng Lv, Fang-min Chen. FDC-SP as a diagnostic and prognostic biomarker and modulates immune infiltrates in renal cell carcinoma |
| 92 | -- | 0 | Luísa C. de Souza, Karolayne S. Azevedo, Jackson Gomes de Souza, Raquel de M. Barbosa, Marcelo A. C. Fernandes. New proposal of viral genome representation applied in the classification of SARS-CoV-2 with deep learning |
| 93 | -- | 0 | Jing Wang 0080, Shuo Zhang, Runzhi Li, Gang Chen, Siyu Yan, Lihong Ma 0004. Multi-view feature representation and fusion for drug-drug interactions prediction |
| 94 | -- | 0 | Yoonsung Joh, Kangbae Lee, Hyunwoo Kim, Heejin Park. Progressive search in tandem mass spectrometry |
| 95 | -- | 0 | Nahla AlKurabi, Ahad AlGahtani, Turki M. Sobahy. CACSV: a computational web-sever that provides classification for cancer somatic genetic variants from different tissues |
| 96 | -- | 0 | Shaima Belhechmi, Gwénaël Le Teuff, Riccardo De Bin, Federico Rotolo, Stefan Michiels. Favoring the hierarchical constraint in penalized survival models for randomized trials in precision medicine |
| 97 | -- | 0 | Siyu Yang, Peiliang Zhang, Chao Che, Zhaoqian Zhong. B-LBConA: a medical entity disambiguation model based on Bio-LinkBERT and context-aware mechanism |
| 98 | -- | 0 | Timothy Dunn, David T. Blaauw, Reetuparna Das, Satish Narayanasamy. nPoRe: n-polymer realigner for improved pileup-based variant calling |
| 99 | -- | 0 | Gianluca Ascolani, Fabrizio Angaroni, Davide Maspero, Francesco Craighero, Narra Lakshmi Sai Bhavesh, Rocco Piazza, Chiara Damiani, Daniele Ramazzotti, Marco Antoniotti, Alex Graudenzi. LACE 2.0: an interactive R tool for the inference and visualization of longitudinal cancer evolution |
| 100 | -- | 0 | Bin Zhao, Fang Fang, Yiqun Liao, Yuji Chen, Fei Wang, Yichao Ma, Chen Wei, Jiahao Zhao, Hao Ji, Daorong Wang, Dong Tang. Novel m7G-related lncRNA signature for predicting overall survival in patients with gastric cancer |
| 101 | -- | 0 | Yannis Schumann, Julia E. Neumann, Philipp Neumann. Robust classification using average correlations as features (ACF) |
| 102 | -- | 0 | Guanjue Xiang, Belinda Giardine, Lin An, Chen Sun, Cheryl A. Keller, Elisabeth F. Heuston, Stacie M. Anderson, Martha Kirby, David M. Bodine, Yu Zhang 0002, Ross C. Hardison. Snapshot: a package for clustering and visualizing epigenetic history during cell differentiation |
| 103 | -- | 0 | Zuming Xiong, Wenxin Li, Xiangrong Luo, Yirong Lin, Wei Huang, Sen Zhang. Seven bacterial response-related genes are biomarkers for colon cancer |
| 104 | -- | 0 | Puyu Liu, Jihang Luo, Na Tan, Chengfang Li, Jieyu Xu, Xiaorong Yang. Establishing a prognostic model of chromatin modulators and identifying potential drug candidates in renal clear cell patients |
| 105 | -- | 0 | Seokjin Han, Jinhee Hong, So Jeong Yun, Hee Jung Koo, Tae-Yong Kim. PWN: enhanced random walk on a warped network for disease target prioritization |
| 106 | -- | 0 | Kevin M. Shebek, Jonathan Strutz, Linda J. Broadbelt, Keith E. J. Tyo. Pickaxe: a Python library for the prediction of novel metabolic reactions |
| 107 | -- | 0 | Ivo Henrique Provensi Vieira, Eduardo Buganemi Botelho, Thales Junior de Souza Gomes, Roger Kist, Rafael A. Caceres, Fernando Berton Zanchi. Visual dynamics: a WEB application for molecular dynamics simulation using GROMACS |
| 108 | -- | 0 | Xu Zhang, Ya Su, Andrew N. Lane, Arnold J. Stromberg, Teresa W.-M. Fan, Chi Wang 0003. Bayesian kinetic modeling for tracer-based metabolomic data |
| 109 | -- | 0 | Saleh Musleh, Mohammad Tariqul Islam 0002, Rizwan Qureshi, Nihad Alajez, Tanvir Alam. MSLP: mRNA subcellular localization predictor based on machine learning techniques |
| 110 | -- | 0 | Zihao Yang, Kuiyuan Tong, Shiyu Jin, Shiyan Wang, Chao Yang, Feng Jiang. CNN-Siam: multimodal siamese CNN-based deep learning approach for drug‒drug interaction prediction |
| 111 | -- | 0 | Ranze Xie, Xiangzhen Zan, Ling Chu, Yanqing Su, Peng Xu, Wenbin Liu. Study of the error correction capability of multiple sequence alignment algorithm (MAFFT) in DNA storage |
| 112 | -- | 0 | Mpho Mokoatle, Vukosi Marivate, Darlington S. Mapiye, Riana Bornman, Vanessa M. Hayes. A review and comparative study of cancer detection using machine learning: SBERT and SimCSE application |
| 113 | -- | 0 | Xuping Xie, Yan Wang 0028, Kai He, Nan Sheng. Predicting miRNA-disease associations based on PPMI and attention network |
| 114 | -- | 0 | Bingran Shen, Gloria M. Coruzzi, Dennis E. Shasha. EnsInfer: a simple ensemble approach to network inference outperforms any single method |
| 115 | -- | 0 | Dario Tommasini, Brent L. Fogel. multiWGCNA: an R package for deep mining gene co-expression networks in multi-trait expression data |
| 116 | -- | 0 | Scott D. Brown, Lisa Dreolini, Jessica F. Wilson, Miruna Balasundaram, Robert A. Holt. Complete sequence verification of plasmid DNA using the Oxford Nanopore Technologies' MinION device |
| 117 | -- | 0 | Christiam Camacho, Grzegorz M. Boratyn, Victor Joukov, Roberto Vera Alvarez, Thomas L. Madden. ElasticBLAST: accelerating sequence search via cloud computing |
| 118 | -- | 0 | Canxuan Li, Weibin Xie. Identification and validation of tumor-infiltrating lymphocyte-related prognosis signature for predicting prognosis and immunotherapeutic response in bladder cancer |
| 119 | -- | 0 | Huidong Ma, Cheng Zhong, Danyang Chen, Haofa He, Feng Yang. cnnLSV: detecting structural variants by encoding long-read alignment information and convolutional neural network |
| 120 | -- | 0 | Léo Bürgy, Martin Weigert, Georgios Hatzopoulos, Matthias Minder, Adrien Journé, Sahand Jamal Rahi, Pierre Gonczy. CenFind: a deep-learning pipeline for efficient centriole detection in microscopy datasets |
| 121 | -- | 0 | Yeremia Gunawan Adhisantoso, Jan Voges, Christian Rohlfing, Viktor Tunev, Jens-Rainer Ohm, Jörn Ostermann. GVC: efficient random access compression for gene sequence variations |
| 122 | -- | 0 | Chun-Chi Chen, Yi-Ming Chan. REDfold: accurate RNA secondary structure prediction using residual encoder-decoder network |
| 123 | -- | 0 | Chaozhong Liu, Linhua Wang, Zhandong Liu. Correction: Single-cell multi-omics integration for unpaired data by a siamese network with graph-based contrastive loss |
| 124 | -- | 0 | Changbeom Shim, Wooil Kim, Tran Thien Dat Nguyen, Du Yong Kim, Yu Suk Choi, Yon Dohn Chung. CellTrackVis: interactive browser-based visualization for analyzing cell trajectories and lineages |
| 125 | -- | 0 | Jose Laborde, Paul A. Stewart, Zhihua Chen, Yian A. Chen, Naomi C. Brownstein. Sparse clusterability: testing for cluster structure in high dimensions |
| 126 | -- | 0 | K. Syama, J. Angel Arul Jothi, Namita Khanna. Automatic disease prediction from human gut metagenomic data using boosting GraphSAGE |
| 127 | -- | 0 | Abdullah Karaaslanli, Satabdi Saha, Tapabrata Maiti, Selin Aviyente. Kernelized multiview signed graph learning for single-cell RNA sequencing data |
| 128 | -- | 0 | Cong Ji, Junbin Shao. Shine: A novel strategy to extract specific, sensitive and well-conserved biomarkers from massive microbial genomic datasets |
| 129 | -- | 0 | Yu Sun, Hongwei Wu, Zhengrong Xu, Zhenyu Yue, Ke Li. Prediction of hot spots in protein-DNA binding interfaces based on discrete wavelet transform and wavelet packet transform |
| 130 | -- | 0 | Wei Li 0117, Yuhuan Chi, Kun Yu, Weidong Xie. A two-stage hybrid biomarker selection method based on ensemble filter and binary differential evolution incorporating binary African vultures optimization |
| 131 | -- | 0 | Christoffer Trier Maansson, Emma Roger Andersen, Maiken Parm Ulhoi, Peter Meldgaard, Boe Sandahl Sorensen. DNAfusion: an R/Bioconductor package for increased sensitivity of detecting gene fusions in liquid biopsies |
| 132 | -- | 0 | Rishab Jain, Aditya Jain, Elizabeth Mauro, Kevin LeShane, Douglas Densmore. ICOR: improving codon optimization with recurrent neural networks |
| 133 | -- | 0 | Timothy R. Fallon, Tereza Calounová, Martin Mokrejs, Jing-Ke Weng, Tomás Pluskal. transXpress: a Snakemake pipeline for streamlined de novo transcriptome assembly and annotation |
| 134 | -- | 0 | Maija Utriainen, John H. Morris. clusterMaker2: a major update to clusterMaker, a multi-algorithm clustering app for Cytoscape |
| 135 | -- | 0 | Elena Solovieva, Hiroaki Sakai. PSReliP: an integrated pipeline for analysis and visualization of population structure and relatedness based on genome-wide genetic variant data |
| 136 | -- | 0 | Vandana Sreedharan, Upinder S. Bhalla, Naren Ramakrishnan. Using sensitivity analyses to understand bistable system behavior |
| 137 | -- | 0 | Yu Chen, Lixin Gao, Tianjiao Zhang. Stack-VTP: prediction of vesicle transport proteins based on stacked ensemble classifier and evolutionary information |
| 138 | -- | 0 | Jin Du, Chaojie Wang 0008, Lijun Wang, Shanjun Mao, Bencong Zhu, Zheng Li, Xiaodan Fan. Automatic block-wise genotype-phenotype association detection based on hidden Markov model |
| 139 | -- | 0 | Zixuan Wang, Yi Zhou, Tatsuya Takagi, Jiangning Song, Yu-Shi Tian, Tetsuo Shibuya. Genetic algorithm-based feature selection with manifold learning for cancer classification using microarray data |
| 140 | -- | 0 | Negar Hossein-Nezhad Daneshvar, Yosef Masoudi-Sobhanzadeh, Yadollah Omidi. A voting-based machine learning approach for classifying biological and clinical datasets |
| 141 | -- | 0 | Pooja Arora, Neha Periwal, Yash Goyal, Vikas Sood, Baljeet Kaur. iIL13Pred: improved prediction of IL-13 inducing peptides using popular machine learning classifiers |
| 142 | -- | 0 | Junjie Zhang, Guoli Ji, Xilin Gao, Jinting Guan. Single-nucleus gene and gene set expression-based similarity network fusion identifies autism molecular subtypes |
| 143 | -- | 0 | Pasquale Claudio Africa, Roberto Piersanti, Marco Fedele, Luca Dede', Alfio Quarteroni. lifex-fiber: an open tool for myofibers generation in cardiac computational models |
| 144 | -- | 0 | Behrouz Bokharaeian, Mohammad Dehghani, Alberto Díaz 0001. Automatic extraction of ranked SNP-phenotype associations from text using a BERT-LSTM-based method |
| 145 | -- | 0 | James F. Fleming, Torsten H. Struck. nRCFV: a new, dataset-size-independent metric to quantify compositional heterogeneity in nucleotide and amino acid datasets |
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| 156 | -- | 0 | Saleh Musleh, Mohammad Tariqul Islam 0002, Rizwan Qureshi, Nihad Alajez, Tanvir Alam. Correction: MSLP: mRNA subcellular localization predictor based on machine learning techniques |
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| 162 | -- | 0 | Linlin Zhang, Dianrong Lu, Xuehua Bi, Kai Zhao, Guanglei Yu, Na Quan. Predicting disease genes based on multi-head attention fusion |
| 163 | -- | 0 | Qian Wang, Maozu Guo, Jian Chen, Ran Duan. A gene regulatory network inference model based on pseudo-siamese network |
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| 165 | -- | 0 | William Breslin, Doan Pham. Machine learning and drug discovery for neglected tropical diseases |
| 166 | -- | 0 | Ksenia Zlobina, Eric Malekos, Han Chen, Marcella Gomez. Robust classification of wound healing stages in both mice and humans for acute and burn wounds based on transcriptomic data |
| 167 | -- | 0 | Ho-min Park, Jongbum Won, Yunseol Park, Esla Timothy Anzaku, Joris Vankerschaver, Arnout Van Messem, Wesley De Neve, Hyunjin Shim. CRISPR-Cas-Docker: web-based in silico docking and machine learning-based classification of crRNAs with Cas proteins |
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| 169 | -- | 0 | Joungmin Choi, Heejoon Chae. moBRCA-net: a breast cancer subtype classification framework based on multi-omics attention neural networks |
| 170 | -- | 0 | Jitong Cai, Jianan Zhan, Dan E. Arking, Joel S. Bader. Priors, population sizes, and power in genome-wide hypothesis tests |
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| 175 | -- | 0 | Hui Zhang, Weiyang Chen. Automated recognition and analysis of body bending behavior in C. elegans |
| 176 | -- | 0 | Tong Wu 0004, Na Li, Fengyuan Luo, Zhihong Chen, Liyuan Ma, Tao Hu, Guini Hong, Hongdong Li. Screening prognostic markers for hepatocellular carcinoma based on pyroptosis-related lncRNA pairs |
| 177 | -- | 0 | Changlong Gu, Xiaoying Li. Prediction of disease-related miRNAs by voting with multiple classifiers |
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| 183 | -- | 0 | Youjin Kim, Junseok Kwon. AttSec: protein secondary structure prediction by capturing local patterns from attention map |
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| 190 | -- | 0 | Seung Min Baik, Kyung Sook Hong, Dong Jin Park. Deep learning approach for early prediction of COVID-19 mortality using chest X-ray and electronic health records |
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| 192 | -- | 0 | Chunxun Liu, Zhaowei Qu, Haoran Zhao, Peng Wang, Chao Zhan, Yubao Zhang. Pan-cancer analysis of SYNGR2 with a focus on clinical implications and immune landscape in liver hepatocellular carcinoma |
| 193 | -- | 0 | Jing Huang, Yuting Zhou, Haoran Zhang, Yiming Wu. A neural network model to screen feature genes for pancreatic cancer |
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| 196 | -- | 0 | Li Rao, Bo Peng, Tao Li. Nonnegative matrix factorization analysis and multiple machine learning methods identified IL17C and ACOXL as novel diagnostic biomarkers for atherosclerosis |
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| 198 | -- | 0 | Magdalena Wysocka, Oskar Wysocki, Marie Zufferey, Dónal Landers, André Freitas. A systematic review of biologically-informed deep learning models for cancer: fundamental trends for encoding and interpreting oncology data |
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| 203 | -- | 0 | Peiqiang Liu, Chang Liu, Yanyan Mao, Junhong Guo, Fanshu Liu, Wangmin Cai, Feng Zhao. Identification of essential proteins based on edge features and the fusion of multiple-source biological information |
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| 206 | -- | 0 | Yuya Hatano, Tomohiko Ishihara, Osamu Onodera. Accuracy of a machine learning method based on structural and locational information from AlphaFold2 for predicting the pathogenicity of TARDBP and FUS gene variants in ALS |
| 207 | -- | 0 | Chloe Engler Hart, Daniel Ence, David Healey, Daniel Domingo-Fernández. On the correspondence between the transcriptomic response of a compound and its effects on its targets |
| 208 | -- | 0 | Damian J. Magill, Timofey A. Skvortsov. DePolymerase Predictor (DePP): a machine learning tool for the targeted identification of phage depolymerases |
| 209 | -- | 0 | Budi Permana, Scott A. Beatson, Brian M. Forde. GraphSNP: an interactive distance viewer for investigating outbreaks and transmission networks using a graph approach |
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| 211 | -- | 0 | Jingli Wu, Qinghua Nie, Gaoshi Li, Kai Zhu. Identifying driver pathways based on a parameter-free model and a partheno-genetic algorithm |
| 212 | -- | 0 | Georgios Argyris, Alberto Lluch-Lafuente, Mirco Tribastone, Max Tschaikowski, Andrea Vandin. Reducing Boolean networks with backward equivalence |
| 213 | -- | 0 | Yan Zheng, Xuequn Shang. SVcnn: an accurate deep learning-based method for detecting structural variation based on long-read data |
| 214 | -- | 0 | Yunze Liu, Gang Li. Empowering biologists to decode omics data: the Genekitr R package and web server |
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| 224 | -- | 0 | Hongfang Zhou, Yinbo Xin, Suli Li. A diabetes prediction model based on Boruta feature selection and ensemble learning |
| 225 | -- | 0 | Guihua Tang, Jianqiao Peng, Longwei Huo, Wen Yin. An N6-methyladenosine regulation- and mRNAsi-related prognostic index reveals the distinct immune microenvironment and immunotherapy responses in lower-grade glioma |
| 226 | -- | 0 | Qiaonan Duan, Weiyi Wang, Feiling Feng, Xiaoqing Jiang, Hao Chen, Dadong Zhang, Tongyi Zhang. Comut-viz: efficiently creating and browsing comutation plots online |
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| 235 | -- | 0 | Lisa Fiedler, Matthias Bernt, Martin Middendorf, Peter F. Stadler. Detecting gene breakpoints in noisy genome sequences using position-annotated colored de-Bruijn graphs |
| 236 | -- | 0 | Patrick Kunzmann, Tom David Müller, Maximilian Greil, Jan Hendrik Krumbach, Jacob Marcel Anter, Daniel Bauer, Faisal Islam, Kay Hamacher. Biotite: new tools for a versatile Python bioinformatics library |
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| 238 | -- | 0 | Liang Chen, Yiming Weng, Xue Cui, Qian Li, Min Peng, Qibin Song. + T cell infiltration related gene signature with regard to the prediction of prognosis and immunotherapy response in lung squamous cell carcinoma |
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| 243 | -- | 0 | Rohan S. Mehta, Robert Petit, Timothy D. Read, Daniel B. Weissman. Detecting patterns of accessory genome coevolution in Staphylococcus aureus using data from thousands of genomes |
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| 245 | -- | 0 | Huangchao Xu, Baohua Zhang, Qian Liu. Deep learning-based classification model for GPR151 activator activity prediction |
| 246 | -- | 0 | Willow Carretero Chavez, Marcus Krantz, Edda Klipp, Irina Kufareva. kboolnet: a toolkit for the verification, validation, and visualization of reaction-contingency (rxncon) models |
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| 256 | -- | 0 | Yue Pan, T. Landis Justin, Razia Moorad, Di Wu, J. S. Marron, Dirk P. Dittmer. The Poisson distribution model fits UMI-based single-cell RNA-sequencing data |
| 257 | -- | 0 | Weiwei Qian, Jian Zhou, Songtao Shou. 6A methylation regulators as epigenetic targets for immunotherapy in advanced sepsis |
| 258 | -- | 0 | Cansu Alakus, Denis Larocque, Aurélie Labbe. Covariance regression with random forests |
| 259 | -- | 0 | Ashna Dhingra, Zayla Schaeffer, Natalia I. Majewska Nepomuceno, Jennifer Au, Joomi Ahn. A MATLAB-based app to improve LC-MS/MS data analysis for N-linked glycan peak identification |
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| 261 | -- | 0 | Yongxian Fan, Hui Xiong, Guicong Sun. DeepASDPred: a CNN-LSTM-based deep learning method for Autism spectrum disorders risk RNA identification |
| 263 | -- | 0 | Aysam Guerler, Dannon Baker, Marius van den Beek, Björn A. Grüning, Dave Bouvier, Nate Coraor, Stephen D. Shank, Jordan D. Zehr, Michael C. Schatz, Anton Nekrutenko. Fast and accurate genome-wide predictions and structural modeling of protein-protein interactions using Galaxy |
| 264 | -- | 0 | Jiayao Zhang, Chunling Hu, Qianqian Zhang. Gene regulatory network inference based on a nonhomogeneous dynamic Bayesian network model with an improved Markov Monte Carlo sampling |
| 265 | -- | 0 | Iakes Goenaga, Edgar Andrés, Koldo Gojenola, Aitziber Atutxa. Advances in monolingual and crosslingual automatic disability annotation in Spanish |
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| 269 | -- | 0 | Yunbin Shi, Juntao Huang, Yi Hu, Yi Shen. Multiomics data analyses to identify SLC25A17 as a novel biomarker to predict the prognosis and immune microenvironment in head and neck squamous cell carcinoma |
| 270 | -- | 0 | Xue-Qin Chen, Jie Ma, Di Xu, Zuo-Lin Xiang. Comprehensive analysis of KLF2 as a prognostic biomarker associated with fibrosis and immune infiltration in advanced hepatocellular carcinoma |
| 271 | -- | 0 | Cédric Beaulac, Sidi Wu, Erin Gibson, Michelle F. Miranda, Jiguo Cao, Leno Rocha, Mirza Faisal Beg, Farouk S. Nathoo. Neuroimaging feature extraction using a neural network classifier for imaging genetics |
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| 273 | -- | 0 | Fareed Ahmad, Muhammad Usman Ghani Khan, Ahsen Tahir, Farhan Masud. Deep ensemble approach for pathogen classification in large-scale images using patch-based training and hyper-parameter optimization |
| 274 | -- | 0 | Ran Li, Haiyan Chen, Chaoxi Li, Yiwei Qi, Kai Zhao, Junwen Wang, Chao You, Haohao Huang. The prognostic value and immune landscaps of m6A/m5C-related lncRNAs signature in the low grade glioma |
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| 277 | -- | 0 | Samuel Boyd, Chad Slawson, Jeffrey A. Thompson. AMEND: active module identification using experimental data and network diffusion |
| 278 | -- | 0 | Yuanyuan Zhang, Yinfei Feng, Mengjie Wu, Zengqian Deng, Shudong Wang. VGAEDTI: drug-target interaction prediction based on variational inference and graph autoencoder |
| 279 | -- | 0 | Gideon Klaila, Vladimir Vutov, Anastasios Stefanou. Supervised topological data analysis for MALDI mass spectrometry imaging applications |
| 280 | -- | 0 | Li Fu, Qun Huang, Yongfeng Wu, Diang Chen. Prognostic analysis of uveal melanoma based on the characteristic genes of M2-type macrophages in the tumor microenvironment |
| 281 | -- | 0 | Junyao Kuang, Kristin Michel, Caterina M. Scoglio. GeCoNet-Tool: a software package for gene co-expression network construction and analysis |
| 282 | -- | 0 | Mitja Briscik, Marie-Agnès Dillies, Sébastien Déjean. Improvement of variables interpretability in kernel PCA |
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| 285 | -- | 0 | Yanwen Chong, Ningdi Xie, Xin Liu, ShaoMing Pan. P-TransUNet: an improved parallel network for medical image segmentation |
| 286 | -- | 0 | Aimin Yan, Cristina Baricordi, Quoc Nguyen, Luigi Barbarossa, Mariana Loperfido, Luca Biasco. IS-Seq: a bioinformatics pipeline for integration sites analysis with comprehensive abundance quantification methods |
| 287 | -- | 0 | Kobe Janssen, Ramon Duran-Romaña, Guy Bottu, Mainak Guharoy, Alexander Botzki, Frederic Rousseau 0001, Joost Schymkowitz. SNPeffect 5.0: large-scale structural phenotyping of protein coding variants extracted from next-generation sequencing data using AlphaFold models |
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| 290 | -- | 0 | Nikitha Karkera, Sathwik Acharya, Sucheendra K. Palaniappan. Leveraging pre-trained language models for mining microbiome-disease relationships |
| 291 | -- | 0 | Irene Ortega-Sanz, José Antonio Barbero-Aparicio, Antonio Canepa-Oneto, Jordi Rovira, Beatriz Melero. CamPype: an open-source workflow for automated bacterial whole-genome sequencing analysis focused on Campylobacter |
| 292 | -- | 0 | Adam J. H. Newton, David Chartash, Steven H. Kleinstein, Robert A. McDougal. A pipeline for the retrieval and extraction of domain-specific information with application to COVID-19 immune signatures |
| 293 | -- | 0 | Yue Wu, Xinran Ni, ZhiHao Wang, Weike Feng. Enhancing drug property prediction with dual-channel transfer learning based on molecular fragment |
| 294 | -- | 0 | Senay Kafkas, Marwa Abdelhakim, Mahmut Uludag, Azza Althagafi, Malak Alghamdi, Robert Hoehndorf. Starvar: symptom-based tool for automatic ranking of variants using evidence from literature and genomes |
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| 296 | -- | 0 | Xiu-e Gao, Jian-Gang Hu, Bo Chen, Yun-Ming Wang, Shengbin Zhou. Causal discovery approach with reinforcement learning for risk factors of type II diabetes mellitus |
| 297 | -- | 0 | Yan Li, Yinying Yao, Yu Xia, Mingjing Tang. Searching for protein variants with desired properties using deep generative models |
| 298 | -- | 0 | Misung Yi, Tingting Zhan, Amy R. Peck, Jeffrey Hooke, Albert J. Kovatich, Craig D. Shriver, Hai Hu, Yunguang Sun, Hallgeir Rui, Inna Chervoneva. Selection of optimal quantile protein biomarkers based on cell-level immunohistochemistry data |
| 299 | -- | 0 | Christian D. Powell, Hunter N. B. Moseley. The metabolomics workbench file status website: a metadata repository promoting FAIR principles of metabolomics data |
| 300 | -- | 0 | Sven Berres, Jörg Gromoll, Marius Wöste, Sarah Sandmann, Sandra Laurentino. OGRE: calculate, visualize, and analyze overlap between genomic input regions and public annotations |
| 301 | -- | 0 | Phasit Charoenkwan, Nalini Schaduangrat, Watshara Shoombuatong. StackTTCA: a stacking ensemble learning-based framework for accurate and high-throughput identification of tumor T cell antigens |
| 302 | -- | 0 | Yi Cheng, Xiuli Ma, Lang Yuan, Zhaoguo Sun, Pingzhang Wang. Evaluating imputation methods for single-cell RNA-seq data |
| 303 | -- | 0 | Alvin Farrel, Peng Li, Sharon Veenbergen, Khushbu Patel, John M. Maris, Warren J. Leonard. ROGUE: an R Shiny app for RNA sequencing analysis and biomarker discovery |
| 304 | -- | 0 | Ali Al-Fatlawi, Eka Rusadze, Alexander Shmelkin, Negin Malekian, Cigdem Ozen, Christian Pilarsky, Michael Schroeder 0001. Netrank: network-based approach for biomarker discovery |
| 305 | -- | 0 | Fréderique Boeykens, Sofie F. M. Bhatti, Luc Peelman, Bart J. G. Broeckx. VariantscanR: an R-package as a clinical tool for variant filtering of known phenotype-associated variants in domestic animals |
| 306 | -- | 0 | Meghana V. Palukuri, Ridhi S. Patil, Edward M. Marcotte. Molecular complex detection in protein interaction networks through reinforcement learning |
| 307 | -- | 0 | K. Syama, J. Angel Arul Jothi, Namita Khanna. Correction: Automatic disease prediction from human gut metagenomic data using boosting GraphSAGE |
| 308 | -- | 0 | Huijing Yu, Zhenxian Zheng, Junhao Su, Tak Wah Lam, Ruibang Luo. Boosting variant-calling performance with multi-platform sequencing data using Clair3-MP |
| 309 | -- | 0 | Yabing Song, Jianbin Wang. ggcoverage: an R package to visualize and annotate genome coverage for various NGS data |
| 310 | -- | 0 | Jérémie Scire, Jana S. Huisman, Ana Grosu, Daniel C. Angst, Adrian Lison, Jinzhou Li, Marloes H. Maathuis, Sebastian Bonhoeffer, Tanja Stadler. estimateR: an R package to estimate and monitor the effective reproductive number |
| 311 | -- | 0 | Michael J. Casey, Jörg Fliege, Rubén J. Sánchez-García, Ben D. MacArthur. An information-theoretic approach to single cell sequencing analysis |
| 312 | -- | 0 | Maria V. Meneses, Alberto Riva, Marco Salemi, Carla Mavian. ARCA: the interactive database for arbovirus reported cases in the Americas |
| 313 | -- | 0 | Suraiya Akhter, John H. Miller. BaPreS: a software tool for predicting bacteriocins using an optimal set of features |
| 314 | -- | 0 | Richard Border, Osman Asif Malik. rBahadur: efficient simulation of structured high-dimensional genotype data with applications to assortative mating |
| 315 | -- | 0 | Na Zhang, Juan Liu 0007, Yu Jin, Wensi Duan, Ziling Wu, Zhaohui Cai, Meng Wu. An adaptive multi-modal hybrid model for classifying thyroid nodules by combining ultrasound and infrared thermal images |
| 316 | -- | 0 | Graham Alvare, Abiel Roche-Lima, Brian Fristensky. BioLegato: a programmable, object-oriented graphic user interface |
| 317 | -- | 0 | Shelvasha Burkes-Patton, Elizabeth A. Cooper, Jessica Schlueter. RepBox: a toolbox for the identification of repetitive elements |
| 318 | -- | 0 | Yunqing Liu, Jiayi Zhao, Taylor Sterling Adams, Ningya Wang, Jonas Schupp, Weimiao Wu, John E. McDonough, Geoffrey Lowell Chupp, Naftali Kaminski, Zuoheng Wang, Xiting Yan. iDESC: identifying differential expression in single-cell RNA sequencing data with multiple subjects |
| 319 | -- | 0 | Pinar Karadayi Atas. A novel hybrid model to predict concomitant diseases for Hashimoto's thyroiditis |
| 320 | -- | 0 | Joseph T. Vecchi, Sean Mullan, Josue A. Lopez, Madeline Rhomberg, Annamarie Yamamoto, Annabelle Hallam, Amy Lee, Milan Sonka, Marlan R. Hansen. Sensitivity of CNN image analysis to multifaceted measurements of neurite growth |
| 321 | -- | 0 | Sophie Le Bars, Mathieu Bolteau, Jérémie Bourdon, Carito Guziolowski. Predicting weighted unobserved nodes in a regulatory network using answer set programming |
| 322 | -- | 0 | Haoyu Chen, Marta Pelizzola, Andreas Futschik. Haplotype based testing for a better understanding of the selective architecture |
| 323 | -- | 0 | Ying Qian, Xinyi Li, Jian Wu, Qian Zhang. MCL-DTI: using drug multimodal information and bi-directional cross-attention learning method for predicting drug-target interaction |
| 324 | -- | 0 | Alexandre Renaux, Chloé Terwagne, Michael Cochez, Ilaria Tiddi, Ann Nowé, Tom Lenaerts. A knowledge graph approach to predict and interpret disease-causing gene interactions |
| 325 | -- | 0 | Jing Chen, Lianlian Wu, KunHong Liu 0001, Yong Xu, Song He, Xiaochen Bo. EDST: a decision stump based ensemble algorithm for synergistic drug combination prediction |
| 326 | -- | 0 | John K. L. Wong, Lena Jassowicz, Christel Herold-Mende, Martina Seiffert, Jan-Phillip Mallm, Peter Lichter, Marc Zapatka. scSNPdemux: a sensitive demultiplexing pipeline using single nucleotide polymorphisms for improved pooled single-cell RNA sequencing analysis |
| 327 | -- | 0 | Tomás Bruna, Heng Li, Joseph Guhlin, Daniel Honsel, Steffen Herbold, Mario Stanke, Natalia Nenasheva, Matthis Ebel, Lars Gabriel, Katharina Jasmin Hoff. Galba: genome annotation with miniprot and AUGUSTUS |
| 328 | -- | 0 | Haitham Elmarakeby, Pavel S. Trukhanov, Vidal M. Arroyo, Irbaz Bin Riaz, Deborah Schrag, Eliezer M. Van Allen, Kenneth L. Kehl. Empirical evaluation of language modeling to ascertain cancer outcomes from clinical text reports |
| 329 | -- | 0 | Ali Ebrahimi, Uffe Kock Wiil, Ruben Baskaran, Abdolrahman Peimankar, Kjeld Andersen, Anette Søgaard Nielsen. AUD-DSS: a decision support system for early detection of patients with alcohol use disorder |
| 330 | -- | 0 | Tychele Turner. Acorn: an R package for de novo variant analysis |
| 331 | -- | 0 | Evgueni Jacob, Angélique Perrillat-Mercerot, Jean-Louis Palgen, Adèle L'Hostis, Nicoletta Ceres, Jean-Pierre Boissel, Jim Bosley, Cláudio Monteiro, Riad Kahoul. Empirical methods for the validation of time-to-event mathematical models taking into account uncertainty and variability: application to EGFR + lung adenocarcinoma |
| 332 | -- | 0 | Peng Du, Xiaofeng Niu, Xukun Li, Chiqing Ying, Yukun Zhou, Chang-He, Shuangzhi Lv, Xiaoli Liu, Weibo Du, Wei Wu. Automatically transferring supervised targets method for segmenting lung lesion regions with CT imaging |
| 333 | -- | 0 | Yongxian Fan, Xiqian Lu, Guicong Sun. IHCP: interpretable hepatitis C prediction system based on black-box machine learning models |
| 334 | -- | 0 | Shourun Pan, Leiming Xia, Lei Xu, Zhen Li. SubMDTA: drug target affinity prediction based on substructure extraction and multi-scale features |
| 335 | -- | 0 | Shiyang Liang, Siwei Liu 0001, Junliang Song, Qiang Lin, Shihong Zhao, Shuaixin Li, Jiahui Li, Shangsong Liang, Jingjie Wang. HMCDA: a novel method based on the heterogeneous graph neural network and metapath for circRNA-disease associations prediction |
| 336 | -- | 0 | Alvise Spanò, Lorenzo Fanton, Davide Pizzolato, Jacopo Moi, Francesco Vinci, Alberto Pesce, Cedrix Jurgal Dongmo Foumthuim, Achille Giacometti, Marta Simeoni. Rinmaker: a fast, versatile and reliable tool to determine residue interaction networks in proteins |
| 336 | -- | 0 | Alvise Spanò, Lorenzo Fanton, Davide Pizzolato, Jacopo Moi, Francesco Vinci, Alberto Pesce, Cedrix Jurgal Dongmo Foumthuim, Achille Giacometti, Marta Simeoni. Rinmaker: a fast, versatile and reliable tool to determine residue interaction networks in proteins |
| 337 | -- | 0 | Karlo Abnoosian, Rahman Farnoosh, Mohammad Hassan Behzadi. Prediction of diabetes disease using an ensemble of machine learning multi-classifier models |
| 338 | -- | 0 | Binyou Wang, Jianmin Guo, Xiaofeng Liu, Yang Yu, Jianming Wu, Yiwei Wang. Prediction of the effects of small molecules on the gut microbiome using machine learning method integrating with optimal molecular features |
| 339 | -- | 0 | Xiaohong Wang, Xiaoli Jing, Fangkun Dou, Haowei Cao. An approach for proteins and their encoding genes synonyms integration based on protein ontology |
| 340 | -- | 0 | Nicholas J. Eagles, Richard Wilton, Andrew E. Jaffe, Leonardo Collado-Torres. BiocMAP: a Bioconductor-friendly, GPU-accelerated pipeline for bisulfite-sequencing data |
| 341 | -- | 0 | Nirmal Singh Mahar, Rohit Satyam, Durai Sundar, Ishaan Gupta. A systematic comparison of human mitochondrial genome assembly tools |
| 342 | -- | 0 | Juan Domingo, Teresa León, Esther Durá. Scellpam: an R package/C++ library to perform parallel partitioning around medoids on scRNAseq data sets |
| 343 | -- | 0 | Shuangshuang Xu, Jacob Williams, Marco A. R. Ferreira. BG2: Bayesian variable selection in generalized linear mixed models with nonlocal priors for non-Gaussian GWAS data |
| 344 | -- | 0 | Layla Hosseini-Gerami, Rosa D. Hernansaiz-Ballesteros, Anika Liu, Howard Broughton, David A. Collier, Andreas Bender. MAVEN: compound mechanism of action analysis and visualisation using transcriptomics and compound structure data in R/Shiny |
| 345 | -- | 0 | Jidong Zhang, Bo Liu, Jiahui Wu, Zhihan Wang, JianQiang Li. DeepCAC: a deep learning approach on DNA transcription factors classification based on multi-head self-attention and concatenate convolutional neural network |
| 346 | -- | 0 | Nouman Ahmad, Robin Strand, Björn Sparresäter, Sambit Tarai, Elin Lundström, Göran Bergström, Håkan Ahlström, Joel Kullberg. Automatic segmentation of large-scale CT image datasets for detailed body composition analysis |
| 347 | -- | 0 | Troy M. LaPolice, Yi-Fei Huang. An unsupervised deep learning framework for predicting human essential genes from population and functional genomic data |
| 348 | -- | 0 | Han Bao 0019, Jinhui Zhao, XinJie Zhao, Chunxia Zhao, Xin Lu, Guowang Xu. Prediction of plant secondary metabolic pathways using deep transfer learning |
| 349 | -- | 0 | Nicholas K. O'Neill, Thor D. Stein, Junming Hu, Habbiburr Rehman, Joshua D. Campbell, Masanao Yajima, Xiaoling Zhang, Lindsay A. Farrer. Bulk brain tissue cell-type deconvolution with bias correction for single-nuclei RNA sequencing data using DeTREM |
| 350 | -- | 0 | Cheng Yong Tham, Touati Benoukraf. Correspondence on NanoVar's performance outlined by Jiang T. et al. in "Long-read sequencing settings for efficient structural variation detection based on comprehensive evaluation" |
| 351 | -- | 0 | Chen Zhou, Shuaijian Dai, Shengzhi Lai, Yuanqiao Lin, Xuechen Zhang, Ning Li, Weichuan Yu. ECL 3.0: a sensitive peptide identification tool for cross-linking mass spectrometry data analysis |
| 352 | -- | 0 | Tao Jiang 0021, Shiqi Liu, Hongzhe Guo. Reply: Correspondence on NanoVar's performance outlined by Jiang T. et al. in 'Long-read sequencing settings for efficient structural variation detection based on comprehensive evaluation' |
| 353 | -- | 0 | Jiahao Wang, Xiaodong Zhu 0001, Kai Chen, Lei Hao, Yuanning Liu. HAHNet: a convolutional neural network for HER2 status classification of breast cancer |
| 354 | -- | 0 | Amira Al-Aamri, Syafiq Kamarul Azman, Gihan Dawelbait, Habiba AlSafar, Andreas Henschel. Critical assessment of on-premise approaches to scalable genome analysis |
| 355 | -- | 0 | Kira J. Stanzick, Klaus J. Stark, Mathias Gorski, Johannes Schödel, René Krüger, Florian Kronenberg, Richard Warth, Iris M. Heid, Thomas W. Winkler. KidneyGPS: a user-friendly web application to help prioritize kidney function genes and variants based on evidence from genome-wide association studies |
| 356 | -- | 0 | Phasit Charoenkwan, Sasikarn Kongsompong, Nalini Schaduangrat, Pramote Chumnanpuen, Watshara Shoombuatong. TIPred: a novel stacked ensemble approach for the accelerated discovery of tyrosinase inhibitory peptides |
| 357 | -- | 0 | Jianan Sui, Jiazi Chen, Yuehui Chen, Naoki Iwamori, Jin Sun. Identification of plant vacuole proteins by using graph neural network and contact maps |
| 358 | -- | 0 | Anand K. Keshri, Rimanpreet Kaur, Suraj S. Rawat, Naina Arora, Rajan K. Pandey, Bajarang V. Kumbhar, Amit Mishra, Shweta Tripathi, Amit Prasad. Designing and development of multi-epitope chimeric vaccine against Helicobacter pylori by exploring its entire immunogenic epitopes: an immunoinformatic approach |
| 359 | -- | 0 | Völundur Hafstað, Jari Häkkinen, Helena Persson. Fast and sensitive validation of fusion transcripts in whole-genome sequencing data |
| 360 | -- | 0 | Lina Ma, Sitao Zhang, Qi Liang, Wenting Huang, Hui Wang, Emily Pan, Ping Xu, Shuguang Zhang, Fei Tao, Jin Tang, Rui Qing. CrMP-Sol database: classification, bioinformatic analyses and comparison of cancer-related membrane proteins and their water-soluble variant designs |
| 362 | -- | 0 | Shuwen Hu, Yi Jing, Tao Li, You-Gan Wang, Zhenyu Liu, Jing Gao 0006, Yu-Chu Tian. Inferring circadian gene regulatory relationships from gene expression data with a hybrid framework |
| 363 | -- | 0 | Lizhen Shao, Cong Fu, Xunying Chen. A heterogeneous graph convolutional attention network method for classification of autism spectrum disorder |
| 364 | -- | 0 | Sz-Wei Chu, Feng-Sheng Wang. Fuzzy optimization for identifying antiviral targets for treating SARS-CoV-2 infection in the heart |
| 365 | -- | 0 | Siti Nurmaini, Ade Iriani Sapitri, Bambang Tutuko, Muhammad Naufal Rachmatullah, Dian Palupi Rini, Annisa Darmawahyuni, Firdaus, Satria Mandala, Ria Nova, Nuswil Bernolian. Automatic echocardiographic anomalies interpretation using a stacked residual-dense network model |
| 366 | -- | 0 | Jiaxiang Jiang, Michael Goebel, Cezar Borba, William Smith 0001, B. S. Manjunath. A robust approach to 3D neuron shape representation for quantification and classification |
| 367 | -- | 0 | Haixia Zhai, Hongli Hou, Junwei Luo, Xiaoyan Liu, Zhengjiang Wu, Junfeng Wang. DGDTA: dynamic graph attention network for predicting drug-target binding affinity |
| 368 | -- | 0 | Mathias Cardner, Francesco Marass, Erika Gedvilaite, Julie L. Yang, Dana W. Y. Tsui, Niko Beerenwinkel. Predicting tumour content of liquid biopsies from cell-free DNA |
| 369 | -- | 0 | Zhiwen Lu, Lu Guo, Jianhua Chen, Rongshu Wang. Reference-based genome compression using the longest matched substrings with parallelization consideration |
| 370 | -- | 0 | Eric Kofman, Brian Yee, Hugo C. Medina-Munoz, Gene W. Yeo. FLARE: a fast and flexible workflow for identifying RNA editing foci |
| 371 | -- | 0 | Ignas Rumbavicius, Trine Rounge, Torbjørn Rognes. HoCoRT: host contamination removal tool |
| 372 | -- | 0 | Kiran Kumar Patro, Allam Jaya Prakash, Umamaheswararao Sanapala, Chaitanya Kumar Marpu, Nagwan M. Abdel Samee, Maali Alabdulhafith, Pawel Plawiak. An effective correlation-based data modeling framework for automatic diabetes prediction using machine and deep learning techniques |
| 373 | -- | 0 | F. Adriaan Lategan, Caroline Schreiber, Hugh-George Patterton. SeqPredNN: a neural network that generates protein sequences that fold into specified tertiary structures |
| 374 | -- | 0 | Zahra Ghorbanali, Fatemeh Zare-Mirakabad, Najmeh Salehi, Mohammad Akbari, Ali Masoudi-Nejad. DrugRep-HeSiaGraph: when heterogenous siamese neural network meets knowledge graphs for drug repurposing |
| 375 | -- | 0 | Junjun Zhang, Minzhu Xie. 2,1 norm regularization terms for drug-target interactions prediction |
| 376 | -- | 0 | Monika Khandelwal, Ranjeet Kumar Rout. PRMxAI: protein arginine methylation sites prediction based on amino acid spatial distribution using explainable artificial intelligence |
| 377 | -- | 0 | Mikhail I. Schelkunov. Mabs, a suite of tools for gene-informed genome assembly |
| 378 | -- | 0 | Jianqiu Wu, Hongyang Chen, Minhao Cheng, Haoyi Xiong. CurvAGN: Curvature-based Adaptive Graph Neural Networks for Predicting Protein-Ligand Binding Affinity |
| 379 | -- | 0 | Eman Ismail, Walaa K. Gad, Mohamed Hashem. A hybrid Stacking-SMOTE model for optimizing the prediction of autistic genes |
| 380 | -- | 0 | Molly G. Hayes, Morgan G. I. Langille, Hong Gu. Cross-study analyses of microbial abundance using generalized common factor methods |
| 381 | -- | 0 | Kipoong Kim, Tae-Hwan Jun, Bo-Keun Ha, Shuang Wang, Hokeun Sun. New statistical selection method for pleiotropic variants associated with both quantitative and qualitative traits |
| 382 | -- | 0 | A. Rohini, Carol Praveen, Sandeep Kumar Mathivanan 0001, V. Muthukumaran, Saurav Mallik, Mohammed S. Alqahtani, Amal Al-Rasheed, Ben Othman Soufiene. Multimodal hybrid convolutional neural network based brain tumor grade classification |
| 383 | -- | 0 | Narumi Hatano, Mayumi Kamada, Ryosuke Kojima, Yasushi Okuno. Network-based prediction approach for cancer-specific driver missense mutations using a graph neural network |
| 384 | -- | 0 | Ganghui Zhou, Jing Gao, Dongshi Zuo, Jin Li, Rui Li. MSXFGP: combining improved sparrow search algorithm with XGBoost for enhanced genomic prediction |
| 385 | -- | 0 | Chris C. R. Smith, Andrew D. Kern. disperseNN2: a neural network for estimating dispersal distance from georeferenced polymorphism data |
| 386 | -- | 0 | Luigi Di Biasi, Fabiola De Marco, Alessia Auriemma Citarella, Modesto Castrillón Santana, Paola Barra, Genoveffa Tortora. Refactoring and performance analysis of the main CNN architectures: using false negative rate minimization to solve the clinical images melanoma detection problem |
| 387 | -- | 0 | Xu Zhu, Lili Zhao, Lihong Huang, Wenxian Yang, Liansheng Wang, Rongshan Yu. cgMSI: pathogen detection within species from nanopore metagenomic sequencing data |
| 388 | -- | 0 | Vishakha Goyal, Nicholas J. Schaub, Ty C. Voss, Nathan Hotaling. Unbiased image segmentation assessment toolkit for quantitative differentiation of state-of-the-art algorithms and pipelines |
| 389 | -- | 0 | Pasquale Claudio Africa, Roberto Piersanti, Francesco Regazzoni 0002, Michele Bucelli, Matteo Salvador, Marco Fedele, Stefano Pagani, Luca Dede', Alfio Quarteroni. lifex-ep: a robust and efficient software for cardiac electrophysiology simulations |
| 390 | -- | 0 | Dao-Feng Zhang, Wei He, Zongze Shao, Iftikhar Ahmed, Yuqin Zhang, Wen-jun Li, Zhe Zhao. EasyCGTree: a pipeline for prokaryotic phylogenomic analysis based on core gene sets |
| 391 | -- | 0 | Élise Maigné, Céline Noirot, Julien Henry, Yaa Adu Kesewaah, Ludovic Badin, Sébastien Déjean, Camille Guilmineau, Arielle Krebs, Fanny Mathevet, Audrey Segalini, Laurent Thomassin, David Colongo, Christine Gaspin, Laurence Liaubet, Nathalie Vialaneix. Asterics: a simple tool for the ExploRation and Integration of omiCS data |
| 392 | -- | 0 | Rahi Jain, Wei Xu 0030. Artificial Intelligence based wrapper for high dimensional feature selection |
| 393 | -- | 0 | Leonie Schürmeyer, Kirsten Schorning, Jörg Rahnenführer. Designs for the simultaneous inference of concentration-response curves |
| 394 | -- | 0 | Yunqing Liu, Jiayi Zhao, Taylor Sterling Adams, Ningya Wang, Jonas Schupp, Weimiao Wu, John E. McDonough, Geoffrey Lowell Chupp, Naftali Kaminski, Zuoheng Wang, Xiting Yan. Correction: iDESC: identifying differential expression in single-cell RNA sequencing data with multiple subjects |
| 395 | -- | 0 | Silvia Cascianelli, Gaia Ceddia, Alberto Marchesi, Marco Masseroli. Identification of transcription factor high accumulation DNA zones |
| 396 | -- | 0 | Valeriy Titarenko, Sofya Titarenko. PerFSeeB: designing long high-weight single spaced seeds for full sensitivity alignment with a given number of mismatches |
| 397 | -- | 0 | Jianhua Jia, Zhangying Wei, Mingwei Sun. EMDL_m6Am: identifying N6,2′-O-dimethyladenosine sites based on stacking ensemble deep learning |
| 398 | -- | 0 | Charlie M. Carpenter, Lucas A. Gillenwater, Russell Bowler, Katerina J. Kechris, Debashis Ghosh. TreeKernel: interpretable kernel machine tests for interactions between -omics and clinical predictors with applications to metabolomics and COPD phenotypes |
| 399 | -- | 0 | Aurélie C. Lozano, Hantian Ding, Naoki Abe, Alexander E. Lipka. Regularized multi-trait multi-locus linear mixed models for genome-wide association studies and genomic selection in crops |
| 400 | -- | 0 | Lore Depuydt, Luca Renders, Thomas Abeel, Jan Fostier. Pan-genome de Bruijn graph using the bidirectional FM-index |
| 401 | -- | 0 | Sadam Hussain, Yareth Lafarga-Osuna, Mansoor Ali, Usman Naseem, Masroor Ahmed, José Gerardo Tamez-Peña. Deep learning, radiomics and radiogenomics applications in the digital breast tomosynthesis: a systematic review |
| 402 | -- | 0 | Alexis Germán Murillo Carrasco, Tatiane Katsue Furuya, Miyuki Uno, Tharcisio Citrangulo Tortelli, Roger Chammas. deltaXpress (ΔXpress): a tool for mapping differentially correlated genes using single-cell qPCR data |
| 403 | -- | 0 | Óscar Castellanos-Rodríguez, Roberto R. Expósito, Juan Touriño. SeQual-Stream: approaching stream processing to quality control of NGS datasets |
| 404 | -- | 0 | William Kumler, Bryna J. Hazelton, Anitra E. Ingalls. Picky with peakpicking: assessing chromatographic peak quality with simple metrics in metabolomics |
| 405 | -- | 0 | Maryam Gholipour, Reza Khajouei, Parastoo Amiri, Sadrieh Hajesmaeel Gohari, Leila Ahmadian. Extracting cancer concepts from clinical notes using natural language processing: a systematic review |
| 406 | -- | 0 | Awwab Mohammad, Farheen Siddiqui, M. Afshar Alam, Sheikh Mohammad Idrees. Tri-model classifiers for EEG based mental task classification: hybrid optimization assisted framework |
| 407 | -- | 0 | Hatice Yagmur Zengin, Erdem Karabulut. Biomarker detection using corrected degree of domesticity in hybrid social network feature selection for improving classifier performance |
| 408 | -- | 0 | Adrià Caballé-Mestres, Antoni Berenguer-Llergo, Camille Stephan-Otto Attolini. Roastgsa: a comparison of rotation-based scores for gene set enrichment analysis |
| 409 | -- | 0 | Chenyu Ma, Yuanbo Shi, Yueyang Huang, Gongwei Dai. Raman spectroscopy-based prediction of ofloxacin concentration in solution using a novel loss function and an improved GA-CNN model |
| 410 | -- | 0 | Guohao Lv, Yingchun Xia, Zhao Qi, Zihao Zhao, Lianggui Tang, Cheng Chen, Shuai Yang, Qingyong Wang, Lichuan Gu. LncRNA-protein interaction prediction with reweighted feature selection |
| 411 | -- | 0 | Aritra Bose, Myson C. Burch, Agniva Chowdhury, Peristera Paschou, Petros Drineas. Structure-informed clustering for population stratification in association studies |
| 412 | -- | 0 | Robert J. Millikin, Kalpana Raja, John W. Steill, Cannon Lock, Xuancheng Tu, Ian Ross, Lam C. Tsoi, Finn Kuusisto, Zijian Ni, Miron Livny, Brian Bockelman, James A. Thomson, Ron M. Stewart. Serial KinderMiner (SKiM) discovers and annotates biomedical knowledge using co-occurrence and transformer models |
| 413 | -- | 0 | Joel Zirkle, Xiaomei Han, Rebecca Racz, Mohammadreza Samieegohar, Anik Chaturbedi, John Mann, Shilpa Chakravartula, Zhihua Li. Deep learning-enabled natural language processing to identify directional pharmacokinetic drug-drug interactions |
| 414 | -- | 0 | Ximei Luo, Qun Li, Yifan Tang, Yan Liu, Quan Zou 0001, Jie Zheng, Ying Zhang, Lei Xu. Predicting active enhancers with DNA methylation and histone modification |
| 415 | -- | 0 | Thomas A. Delomas, Stuart C. Willis. Estimating microhaplotype allele frequencies from low-coverage or pooled sequencing data |
| 416 | -- | 0 | Pietro Cinaglia, Marianna Milano, Mario Cannataro. Multilayer network alignment based on topological assessment via embeddings |
| 417 | -- | 0 | Hanjing Jiang, Yabing Huang, Qianpeng Li, Boyuan Feng. ScLSTM: single-cell type detection by siamese recurrent network and hierarchical clustering |
| 418 | -- | 0 | Irena Roterman, Katarzyna Stapor, Leszek Konieczny. Ab initio protein structure prediction: the necessary presence of external force field as it is delivered by Hsp40 chaperone |
| 419 | -- | 0 | Pegah Mavaie, Lawrence Holder, Michael K. Skinner. Hybrid deep learning approach to improve classification of low-volume high-dimensional data |
| 420 | -- | 0 | Koki Tsuyuzaki, Manabu Ishii, Itoshi Nikaido. Sctensor detects many-to-many cell-cell interactions from single cell RNA-sequencing data |
| 421 | -- | 0 | Grégoire Prunier, Mehdi Cherkaoui, Albane Lysiak, Olivier Langella, Mélisande Blein-Nicolas, Virginie Lollier, Emile Benoist, Géraldine Jean, Guillaume Fertin, Hélène Rogniaux, Dominique Tessier. Fast alignment of mass spectra in large proteomics datasets, capturing dissimilarities arising from multiple complex modifications of peptides |
| 422 | -- | 0 | Thomas Binet, Séverine Padiolleau-Lefèvre, Stéphane Octave, Bérangère Avalle, Irene Maffucci. Comparative Study of Single-stranded Oligonucleotides Secondary Structure Prediction Tools |
| 423 | -- | 0 | Yixin Zhang, Wei Liu, Weiliang Qiu. A model-based clustering via mixture of hierarchical models with covariate adjustment for detecting differentially expressed genes from paired design |
| 424 | -- | 0 | Noah Herrick, Susan Walsh. ILIAD: a suite of automated Snakemake workflows for processing genomic data for downstream applications |
| 425 | -- | 0 | Irena Roterman, Katarzyna Stapor, Leszek Konieczny. Role of environmental specificity in CASP results |
| 426 | -- | 0 | Yesol Sapozhnikov, Jagdish Suresh Patel, F. Marty Ytreberg, Craig R. Miller. Statistical modeling to quantify the uncertainty of FoldX-predicted protein folding and binding stability |
| 427 | -- | 0 | Rongyuan Li, Jingli Wu, Gaoshi Li, Jiafei Liu, Junbo Xuan, Qi Zhu. Mdwgan-gp: data augmentation for gene expression data based on multiple discriminator WGAN-GP |
| 428 | -- | 0 | Xin Feng, Yihuai Cai, Ruihao Xin. Optimizing diabetes classification with a machine learning-based framework |
| 429 | -- | 0 | Linjun Chen, Xiao-Yuan Jing, Yaru Hao, Wei Liu, Xiaoke Zhu, Wei Han. A novel two-way rebalancing strategy for identifying carbonylation sites |
| 430 | -- | 0 | Ye Yuan, Qushuo Chen, Jun Mao, Guipeng Li, Xiaoyong Pan. DG-Affinity: predicting antigen-antibody affinity with language models from sequences |
| 431 | -- | 0 | Ruimin Wang, Miaoshan Lu, Shaowei An, Jinyin Wang, Changbin Yu. G-Aligner: a graph-based feature alignment method for untargeted LC-MS-based metabolomics |
| 432 | -- | 0 | Gwangwoo Kim, Hyonho Chun. Similarity-assisted variational autoencoder for nonlinear dimension reduction with application to single-cell RNA sequencing data |
| 433 | -- | 0 | Orly Avraham, Tomer Tsaban, Ziv Ben-Aharon, Linoy Tsaban, Ora Schueler-Furman. Protein language models can capture protein quaternary state |
| 434 | -- | 0 | Zhichao Hou, Jiacheng Leng, Jiating Yu, Zheng Xia, Ling-Yun Wu. PathExpSurv: pathway expansion for explainable survival analysis and disease gene discovery |
| 435 | -- | 0 | Brijesh Kumar Sriwastava, Anup Kumar Halder, Subhadip Basu, Tapabrata Chakraborti. RUBic: rapid unsupervised biclustering |
| 437 | -- | 0 | Luke Staniscia, Yun William Yu. Image-centric compression of protein structures improves space savings |
| 438 | -- | 0 | Jakob P. Pettersen, Sandra Castillo, Paula Jouhten, Eivind Almaas. Genome-scale metabolic models reveal determinants of phenotypic differences in non-Saccharomyces yeasts |
| 442 | -- | 0 | Ramin Amiri, Jafar Razmara, Sepideh Parvizpour, Habib Izadkhah. A novel efficient drug repurposing framework through drug-disease association data integration using convolutional neural networks |
| 443 | -- | 0 | Elena Pianfetti, Marta Lovino, Elisa Ficarra, Loredana Martignetti. MiREx: mRNA levels prediction from gene sequence and miRNA target knowledge |
| 444 | -- | 0 | Mingwei Pang, Wangqiu He, Xufeng Lu, Yuting She, Liangxu Xie, Ren Kong, Shan Chang. CoDock-Ligand: combined template-based docking and CNN-based scoring in ligand binding prediction |
| 445 | -- | 0 | Valentina Nale, Alice Chiodi, Noemi Di Nanni, Ingrid Cifola, Marco Moscatelli, Cinzia Cocola, Matteo Gnocchi, Eleonora Piscitelli, Ada Sula, Ileana Zucchi, Rolland A. Reinbold, Luciano Milanesi, Alessandra Mezzelani, Paride Pelucchi, Ettore Mosca. scMuffin: an R package to disentangle solid tumor heterogeneity by single-cell gene expression analysis |
| 446 | -- | 0 | Anup Kumar, Björn A. Grüning, Rolf Backofen. Transformer-based tool recommendation system in Galaxy |
| 447 | -- | 0 | Incheol Shin, Keumseok Kang, Juseong Kim, Sanghun Sel, Jeonghoon Choi, Jae-Wook Lee, Ho-Young Kang, Giltae Song. AptaTrans: a deep neural network for predicting aptamer-protein interaction using pretrained encoders |
| 448 | -- | 0 | DanYi Chen, Xiaowen Wang, Hongming Zhu, Yizhi Jiang, Yulong Li, Qi Liu, Qin Liu. Predicting anticancer synergistic drug combinations based on multi-task learning |
| 449 | -- | 0 | Mahdi Pourmirzaei, Shahin Ramazi, Farzaneh Esmaili, Seyedehsamaneh Shojaeilangari, Abdollah Allahvardi. Machine learning-based approaches for ubiquitination site prediction in human proteins |
| 450 | -- | 0 | Nan Shao, Chenshuo Ren, Tianyuan Hu, Dianbing Wang, Xiaofan Zhu, Min Li, Tao Cheng, Yingchi Zhang, Xian-En Zhang. Detection of continuous hierarchical heterogeneity by single-cell surface antigen analysis in the prognosis evaluation of acute myeloid leukaemia |
| 451 | -- | 0 | Dong-Xu Li, Peng Zhou, Bo-Wei Zhao, Xiao-Rui Su, Guo-Dong Li, Jun Zhang, Peng-Wei Hu, Lun Hu. Biocaiv: an integrative webserver for motif-based clustering analysis and interactive visualization of biological networks |
| 452 | -- | 0 | He Zhao, Guixia Liu, Xintian Cao. A seed expansion-based method to identify essential proteins by integrating protein-protein interaction sub-networks and multiple biological characteristics |
| 453 | -- | 0 | Joel Nulsen, Nosheen Hussain, Aws Al-Deka, Jason Yap, Khalil Uddin, Christopher Yau, Ahmed Ashour Ahmed. Completing a genomic characterisation of microscopic tumour samples with copy number |
| 454 | -- | 0 | Hui Sun, Yingfeng Zheng, Haonan Xie, Huidong Ma, Xiaoguang Liu, Gang Wang. PMFFRC: a large-scale genomic short reads compression optimizer via memory modeling and redundant clustering |
| 455 | -- | 0 | Zhaoyan Ming, XiangJun Chen, Shunlong Wang, Hong Liu, Zhiming Yuan, Minghui Wu, Han-xia. HostNet: improved sequence representation in deep neural networks for virus-host prediction |
| 456 | -- | 0 | Hanhan Cong, Hong Liu 0013, Yi Cao, Cheng Liang, Yuehui Chen. Protein-protein interaction site prediction by model ensembling with hybrid feature and self-attention |
| 457 | -- | 0 | Eduardo N. Castanho, João Lobo, Rui Henriques, Sara C. Madeira. G-bic: generating synthetic benchmarks for biclustering |
| 458 | -- | 0 | P. Kavitha, G. Ayyappan, Prabhu Jayagopal, Sandeep Kumar Mathivanan 0001, Saurav Mallik, Amal Al-Rasheed, Mohammed S. Alqahtani, Ben Othman Soufiene. Detection for melanoma skin cancer through ACCF, BPPF, and CLF techniques with machine learning approach |
| 459 | -- | 0 | Abdelkader Behdenna, Maximilien Colange, Julien Haziza, Aryo Gema, Guillaume Appé, Chloé-Agathe Azencott, Akpéli Nordor. pyComBat, a Python tool for batch effects correction in high-throughput molecular data using empirical Bayes methods |
| 460 | -- | 0 | Baptiste Turpin, Eline Y. Bijman, Hans-Michael Kaltenbach, Jörg Stelling. Efficient design of synthetic gene circuits under cell-to-cell variability |
| 461 | -- | 0 | Xuechun Xu, Nayanika Bhalla, Patrik Stahl, Joakim Jaldén. Lokatt: a hybrid DNA nanopore basecaller with an explicit duration hidden Markov model and a residual LSTM network |
| 462 | -- | 0 | Yiyun Rao, Nabeel Ahmed, Justin Pritchard, Edward P. O'Brien. Incorporating mutational heterogeneity to identify genes that are enriched for synonymous mutations in cancer |
| 463 | -- | 0 | Kun Wang, Xiao Zhang, Hansen Cheng, Wenhao Ma, Guangchao Bao, Liting Dong, Yixiong Gou, Jian Yang, Haoyang Cai. SingleScan: a comprehensive resource for single-cell sequencing data processing and mining |
| 477 | -- | 0 | Meng Zhang, Madhuri Sankaranarayanapillai, Jingcheng Du, Yang Xiang 0003, Frank J. Manion, Marcelline R. Harris, Cooper Stansbury, Huy Anh Pham, Cui Tao. Machine learning-based donor permission extraction from informed consent documents |
| 478 | -- | 0 | Diana Zarei, Amene Saghazadeh, Nima Rezaei. Subtyping irritable bowel syndrome using cluster analysis: a systematic review |
| 479 | -- | 0 | Rajul Mahto, Saboor Uddin Ahmed, Rizwan Ur Rahman, Rabia Musheer Aziz, Priyanka Roy, Saurav Mallik, Aimin Li, Mohd Asif Shah. A novel and innovative cancer classification framework through a consecutive utilization of hybrid feature selection |
| 480 | -- | 0 | Yining Liu, Yinuo Jin, Elham Azizi, Andrew J. Blumberg. Cellstitch: 3D cellular anisotropic image segmentation via optimal transport |
| 481 | -- | 0 | Zhen-Hao Guo, Yan Wu, Siguo Wang, Qinhu Zhang, Jin-Ming Shi, Yan-Bin Wang, Zhan-Heng Chen. scInterpreter: a knowledge-regularized generative model for interpretably integrating scRNA-seq data |
| 482 | -- | 0 | Michael J. Kane, Casey King, Denise Esserman, Nancy K. Latham, Erich J. Greene, David A. Ganz. A compressed large language model embedding dataset of ICD 10 CM descriptions |
| 483 | -- | 0 | Chenqi Liao, Xiong Wang. TCGAplot: an R package for integrative pan-cancer analysis and visualization of TCGA multi-omics data |
| 484 | -- | 0 | Yingke Yang, Peiluan Li. GPDRP: a multimodal framework for drug response prediction with graph transformer |
| 485 | -- | 0 | Daniel Marrama, William D. Chronister, Luise Westernberg, Randi Vita, Zeynep Kosaloglu-Yalçin, Alessandro Sette, Morten Nielsen 0001, Jason A. Greenbaum, Bjoern Peters. PEPMatch: a tool to identify short peptide sequence matches in large sets of proteins |
| 486 | -- | 0 | Xiangwen Zheng, Xuanze Wang, Xiaowei Luo, Fan Tong, Dongsheng Zhao. BioEGRE: a linguistic topology enhanced method for biomedical relation extraction based on BioELECTRA and graph pointer neural network |
| 487 | -- | 0 | Katerina Faltejsková, Jirí Vondrásek. PAPerFly: Partial Assembly-based Peak Finder for ab initio binding site reconstruction |
| 488 | -- | 0 | Warith Eddine Djeddi, Khalil Hermi, Sadok Ben Yahia, Gayo Diallo. Advancing drug-target interaction prediction: a comprehensive graph-based approach integrating knowledge graph embedding and ProtBert pretraining |
| 489 | -- | 0 | Miaoshan Lu, Hengxuan Jiang, Ruimin Wang, Shaowei An, Jiawei Wang, Changbin Yu. Injectiondesign: web service of plate design with optimized stratified block randomization for modern GC/LC-MS-based sample preparation |
| 490 | -- | 0 | Xiaomeng Zhang, Hongtao Zhang, ZhiHao Wang, Xiaofei Ma, Jiancheng Luo, Yingying Zhu. PWSC: a novel clustering method based on polynomial weight-adjusted sparse clustering for sparse biomedical data and its application in cancer subtyping |
| 491 | -- | 0 | Daniel Dorey-Robinson, Giuseppe Maccari, John A. Hammond. IgMAT: immunoglobulin sequence multi-species annotation tool for any species including those with incomplete antibody annotation or unusual characteristics |
| 492 | -- | 0 | Thummarat Paklao, Apichat Suratanee, Kitiporn Plaimas. ICON-GEMs: integration of co-expression network in genome-scale metabolic models, shedding light through systems biology |