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29th International Conference on Research in Computational Molecular Biology, RECOMB 2025

作者： Liu, Tianyu De Brouwer, Edward Kuo, Tony Diamant, Nathaniel Missarova, Alsu Wang, Hanchen Hao, Minsheng Bravo, Hector Corrada Scalia, Gabriele Regev, Aviv Heimberg, Graham Research and Early Development Genentech South San FranciscoCA94080 United States Interdepartmental Program in Computational Biology and Bioinformatics Yale University New HavenCT06511 United States Roche Informatics F. Hoffmann-La Roche Ltd. Mississauga Canada Department of Computer Science Stanford University Palo AltoCA94035 United States

ISBN: (纸本)9783031902512

Single-cell RNA-seq (scRNA-seq) has become a prominent tool for studying human biology and disease. The availability of massive scRNA-seq datasets and advanced machine learning techniques has recently driven the development of single-cell foundation models that provide informative and versatile cell representations based on expression profiles. However, to understand disease states, we need to consider entire tissue ecosystems, simultaneously considering many different interacting cells. Here, we tackle this challenge by generating patient-level representations derived from multi-cellular expression context measured with scRNA-seq of tissues. We develop PaSCient, a novel model that employs a multi-level representation learning paradigm and provides importance scores at the individual cell and gene levels for fine-grained analysis across multiple cell types and gene programs characteristic of a given disease. We apply PaSCient to learn a disease model across a large-scale scRNA-seq atlas of 12.5 million cells from over 2,700 patients. Comprehensive and rigorous benchmarking demonstrates the superiority of PaSCient in disease classification and its multiple downstream applications, including dimensionality reduction, gene/cell type prioritization, and patient subgroup discovery. © The Author(s), under exclusive license to Springer Nature Switzerland AG 2025.

关键词： Biomolecules

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GranatumX:A Community-engaging, Modularized, and Flexible Webtool for Single-cell Data Analysis

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Genomics, Proteomics & bioinformatics 2021年第3期19卷 452-460页

作者： David G.Garmire Xun Zhu Aravind Mantravadi Qianhui Huang Breck Yunits Yu Liu Thomas Wolfgruber Olivier Poirion Tianying Zhao Cédric Arisdakessian Stefan Stanojevic Lana X.Garmire Department of Electrical Engineering&Computer Science University of MichiganAnn ArborMI 48109USA Epidemiology Program University of Hawaii Cancer CenterHonoluluHI 96813USA Department of Biostatistics University of MichiganAnn ArborMI 48109USA Department of Computational Medicine and Bioinformatics University of MichiganAnn ArborMI 48105USA Molecular Biosciences and Bioengineering Graduate Program University of Hawaii at ManoaHonoluluHI 96822USA

We present GranatumX,a next-generation software environment for single-cell RNA sequencing(scRNA-seq)data *** is inspired by the interactive webtool *** enables biologists to access the latest scRNA-seq bioinformatics methods in a web-based graphical *** also offers software developers the opportunity to rapidly promote their own tools with others in customizable *** architecture of GranatumX allows for easy inclusion of plugin modules,named Gboxes,which wrap around bioinformatics tools written in various programming languages and on various *** can be run on the cloud or private servers and generate reproducible *** is a community-engaging,flexible,and evolving software ecosystem for scRNA-seq analysis,connecting developers with bench *** is freely accessible at http://***/granatumx/app.

关键词： Single-cell RNA sequencing Analysis Pipeline Webtool Module

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PepTune: De Novo Generation of Therapeutic Peptides with Multi-Objective-Guided Discrete Diffusion

arXiv

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arXiv 2024年

作者： Tang, Sophia Zhang, Yinuo Chatterjee, Pranam Department of Biomedical Engineering Duke University United States Management and Technology Program University of Pennsylvania United States Center of Computational Biology Duke-NUS Medical School Singapore Department of Computer Science Duke University United States Department of Biostatistics and Bioinformatics Duke University United States

Peptide therapeutics, a major class of medicines, have achieved remarkable success across diseases such as diabetes and cancer, with landmark examples such as GLP-1 receptor agonists revolutionizing the treatment of type-2 diabetes and obesity. Despite their success, designing peptides that satisfy multiple conflicting objectives, such as target binding affinity, solubility, and membrane permeability, remains a major challenge. Classical drug development and target structure-based design are ineffective for such tasks, as they fail to optimize global functional properties critical for therapeutic efficacy. Existing generative frameworks are largely limited to continuous spaces, unconditioned outputs, or single-objective guidance, making them unsuitable for discrete sequence optimization across multiple properties. To address this, we present PepTune, a multi-objective discrete diffusion model for the simultaneous generation and optimization of therapeutic peptide SMILES. Built on the Masked Discrete Language Model (MDLM) framework, PepTune ensures valid peptide structures with bond-dependent masking schedules and penalty-based objectives. To guide the diffusion process, we propose a Monte Carlo Tree Search (MCTS)-based strategy that balances exploration and exploitation to iteratively refine Pareto-optimal sequences. MCTS integrates classifier-based rewards with search-tree expansion, overcoming gradient estimation challenges and data sparsity. Using PepTune, we generate diverse, chemically modified peptides optimized for multiple therapeutic properties, including target binding affinity, membrane permeability, solubility, hemolysis, and non-fouling for various disease-relevant targets. In total, our results demonstrate that MCTS-guided masked discrete diffusion is a powerful and modular approach for multi-objective sequence design in discrete state spaces. © 2024, CC BY-NC-ND.

关键词： Trees (mathematics)

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Lockdown strategy worth lives: The SEIRD modelling in COVID-19 outbreak in Indonesia 2

Lockdown strategy worth lives: The SEIRD modelling in COVID-...

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2nd International Conference on Biospheric Harmony Advanced Research, ICOBAR 2020

作者： Nurlaila, I. Hidayat, A.A. Pardamean, B. Information Systems Department BINUS Online Learning Bina Nusantara University Jakarta11480 Indonesia Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta11480 Indonesia Computer Science Department BINUS Graduate Program-Master of Computer Science Bina Nusantara University Jakarta11480 Indonesia

Lockdowns, despite their conflicting restrictions and consequences they might offer when enforced as a national strategy, are deemed to be suggestive for a prompt conquer to the Coronavirus Disease-19 (COVID-19) outbreak. There have been some success stories such as in China, South Korea and our ASEAN member fellow, Vietnam, which exhibited extremely fallen numbers of COVID-19 cases post the enforcement of lockdown. Indonesia, however, remains in the crux of dispute whether or not the lockdown is opted to force COVID-19 transmission down under control. We, in this respect, employ the most popular model which has been broadly applied in the field of epidemiology, referred to as SEIRD (Susceptible, Exposed, Infectious, Recovered, and Death), the extension form of an age-structured SEIR, where the Death (D) is included to provide more factual situation. We modify the I (Infectious) fraction as symp-tomatic (Is) and asymptomatic (Ia) infectives. There are three lockdown scenarios simulated in our modified SEIRD with the starting date are 26 April 2020 when the immediate lockdown was enacted-and a-week and two-week-gaps, respectively. We figured out that by stipulating the lockdown without delay (26 April 2020), the new cases could be kept below 10,000. A week delay escalates case number to 5,000 and delay for one more week results in beyond 20,000 new cases. Furthermore, when the intervention is delayed following the delayed lockdown, normalization would demand a longer period within which dealing with more critical and dying patients is unavoidable and should be more anticipated. © Published under licence by IOP Publishing Ltd.

关键词： Coronavirus

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South jakarta's air quality using PM 2.5 data at the beginning of COVID-19 Restriction 6

South jakarta's air quality using PM 2.5 data at the beginni...

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6th International Conference on Information Management and Technology, ICIMTech 2021

作者： Rahutomo, Reza Purwandari, Kartika Hidayat, Alam Ahmad Pardamean, Bens Bina Nusantara University School of Information Systems Information System Department Jakarta11480 Indonesia Bina Nusantara University Bioinformatics and Data Science Research Center Jakarta11480 Indonesia Bina Nusantara University BINUS Graduate Program - Master of Computer Science Computer Science Department Jakarta11480 Indonesia

ISBN: (纸本)9781665449373

As soon as the lockdown was established in Jakarta, Indonesia, people experienced a change in Jakarta's air quality. This research was conducted to answer several challenges such as: where to find Indonesia's air quality open data platforms, how to handle the acquired data with SQL technology, and how to validate whether the air quality of Jakarta was significantly changed from a period to another or not. With particulate matter 2.5 (PM 2.5) data acquired by The United States Diplomatic Post in South Jakarta, a data visualization was generated to describe the fluctuation of PM 2.5 from February 29th to June 29th. By conducting a two-sample t-test, a significant change in South Jakarta's air quality was revealed. The test concluded that South Jakarta's air quality got worse even after a lockdown was established. © 2021 IEEE.

关键词： COVID-19

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Graph Fourier MMD for Signals on Graphs

Graph Fourier MMD for Signals on Graphs

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2023 International Conference on Sampling Theory and Applications, SampTA 2023

作者： Leone, Samuel Venkat, Aarthi Huguet, Guillaume Tong, Alexander Wolf, Guy Krishnaswamy, Smita Applied Math Program New HavenCT United States Yale University Computational Biology & Bioinformatics Program New HavenCT United States Université de Montréal Mila - Quebec Ai Institute Dept. of Math. & Stat Montreal Canada Université de Montréal Mila-Quebec Ai Institute Dept. of Comp. Sci. & Oper. Res. Montreal Canada Yale University Department of Computer Science Department of Genetics New HavenCT United States

ISBN: (纸本)9798350328851

While numerous methods have been proposed for computing distances between probability distributions in Euclidean space, relatively little attention has been given to computing such distances for distributions on graphs. However, there has been a marked increase in data that either lies on graph (such as protein interaction networks) or can be modeled as a graph (single cell data), particularly in the biomedical sciences. Thus, it becomes important to find ways to compare signals defined on such graphs. Here, we propose Graph Fourier MMD (GFMMD), a novel distance between distributions and signals on graphs. GFMMD is defined via an optimal witness function that is both smooth on the graph and maximizes the difference in expectation between the pair of distributions on the graph. We find an analytical solution to this optimization problem as well as an embedding of distributions that results from this method. We also prove several properties of this method including scale invariance and applicability to disconnected graphs. We showcase it on graph benchmark datasets as well on single cell RNA-sequencing data analysis. In the latter, we use the GFMMD-based gene embeddings to find meaningful gene clusters. We also propose a novel type of score for gene selection called gene localization score which helps select genes for cellular state space characterization. © 2023 IEEE.

关键词： Genes

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Decomposition of dynamic transcriptomic responses during effector-triggered immunity reveals conserved responses in two distinct plant cell populations

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Plant Communications 2024年第8期5卷 1-17页

作者： Xiaotong Liu Daisuke Igarashi Rachel A.Hillmer Thomas Stoddard You Lu Kenichi Tsuda Chad L.Myers Fumiaki Katagiri Department of Plant and Microbial Biology University of Minnesota-Twin CitiesSt PaulMN 55108USA Department of Computer Science and Engineering University of Minnesota-Twin CitiesMinneapolisMN 55455USA Bioinformatics and Computational Biology Graduate Program University of Minnesota-Twin CitiesMinneapolisMN 55455USA Institute for Innovation Ajinomoto Co.Inc.KawasakiJapan State Key Laboratory of Agricultural Microbiology Hubei Hongshan LaboratoryHubei Key Lab of Plant PathologyCollege of Plant Science and TechnologyHuazhong Agricultural UniversityWuhan 430070China Present address:225 S 6th St MinneapolisMN 55402USA Present address:Biotalys Inc.2520 Meridian Parkway Suite 480DurhamNC 27713USA Present address:Life Sciences Institute and Department of Cell and Developmental Biology University of Michigan Medical SchoolAnn ArborMI 48109USA

Rapid plant immune responses in the appropriate cells are needed for effective defense against *** transcriptome analysis is often used to describe overall immune responses,collection of transcriptome data with sufficient resolution in both space and time is *** reanalyzed public Arabidopsis time-course transcriptome data obtained after low-dose inoculation with a Pseudomonas syringae strain expressing the effector AvrRpt2,which induces effector-triggered immunity in ***-peak time-course patterns are prevalent among thousands of upregulated *** implemented a multicompartment modeling approach to decompose the double-peak pattern into two single-peak patterns for each *** decomposed peaks reveal an“echoing”pattern:the peak times of the first and second peaks correlate well across most upregulated *** demonstrated that the two peaks likely represent responses of two distinct cell populations that respond either cell autonomously or indirectly to ***,the peak decomposition has extracted spatial information from the time-course *** echoing pattern also indicates a conserved transcriptome response with different initiation times between the two cell populations despite different elicitor types.A gene set highly overlapping with the conserved gene set is also upregulated with similar kinetics during pattern-triggered *** of a WRKY network via different entry-point WRKYs can explain the similar but not identical transcriptome responses elicited by different elicitor *** discuss potential benefits of the properties of the WRKY activation network as an immune signaling network in light of pressure from rapidly evolving pathogens.

关键词： Arabidopsis Pseudomonas syringae plant immune response multi-compartment model WRKY transcription factors resilient immune signaling network

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Web Development of Direct-to-consumer Genetics Testing

Web Development of Direct-to-consumer Genetics Testing

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International Conference on Cybernetics and Intelligent System (ICORIS)

作者： Kians Azizatikarna Deby Erina Parung Dian Amirullah Alam Ahmad Hidayat Tjeng Wawan Cenggoro Arif Budiarto Simon Bens Pardamean Genetics Indonesia Jakarta Indonesia Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta Indonesia Computer Science Department School of Computer Science Bina Nusantara University Jakarta Indonesia Computer Science Department BINUS Graduate Program - Master of Computer Science Bina Nusantara University Jakarta Indonesia

ISBN: (纸本)9781665453967

As the cost of genetic testing becomes more affordable each year, direct-to-customer (DTC) genetic testing services witness rapid market growth. This has encouraged the development of an easy-to-use website application to optimize potential customers to obtain informed choice regarding the offered DTC genetic testing as well as purchasing information. We present a wireframing process as a part of the agile software development process to build a web portal prototype for an Indonesia-based genetic testing service called DNAku. The approach in building the prototype used in this case is a part of the Agile Software Development Method. In brief, the wireframing stage resulted in this work consists of three main important outcomes. The first one is the use case diagram as a blueprint of this web-based system. A site map is then proposed as an extended version of the use case diagram which visualizes the whole pages with the links. Finally, based on this site map a series of page mock-ups are designed using Hyper Text Marking Language (HTML) and Cascading Style Sheets (CSS). The result of the prototype can be used as the basis for the next development stage, which is the coding stage based on the collected feedback from users. Considering the continuous application development via the wireframing method by taking into account the cycle of feedbacks from involved parties, this approach can strengthen the infrastructure to sustain DTC genetic business model, which has a niche market in Indonesia.

关键词： Visualization Costs Buildings Prototypes Agile software development Genetics Encoding

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Mobile Application Implementation as Agriculture 4.0 Strategy for Sugarcane Yield Prediction

Mobile Application Implementation as Agriculture 4.0 Strateg...

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HCI and UX Conference in Indonesia (CHIuXiD), International

作者： Hangger Gahara Mawandha Reza Rahutomo Teddy Suparyanto Bens Pardamean Faculty of Agricultural Technology Institut Pertanian Stiper Yogyakarta Indonesia Information Systems Department School of Information Systems Bina Nusantara University Jakarta Indonesia Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta Indonesia Computer Science Department BINUS Graduate Program - Master of Computer Science Bina Nusantara University Jakarta Indonesia

ISBN: (数字)9798350304084

ISBN: (纸本)9798350304091

Information engineering strategies play a significant and transformative role in shaping the landscape of digital agriculture. It drives innovation and efficiency in modern farming practices, with a specific focus on enhancing the value of agricultural commodities, such as sugarcane. The application of mobile technology plays a crucial part in achieving increased sugarcane productivity. Mobile applications, equipped with advanced developer features, offer rapid and user-friendly access to vital information. Traditional methods of estimating sugarcane production relied on manual data recording on paper, followed by data transfer to computer systems, typically managed by sugar factory junior plant officers. This conventional approach presents several inherent weaknesses, including time and effort intensiveness during data recording and entry. Additionally, the potential for errors in calculation and data input is a concern. The storage capacity for paper-based documents is finite, and farmers are often unable to autonomously assess their production potential. The objective of this research is to confront these obstacles by creating a sugarcane production application for Android. This application functions as an information engineering approach focused on forecasting sugarcane yields for plantation owners and their assistants. The development procedure adhered to the systematic waterfall method, following the principles of the Software Development Life Cycle (SDLC) model. Data collection was carried out through observations, while interviews with junior plant officers provided valuable insights into sugarcane estimation techniques. Analysis involved the synthesis of observational and interview data to inform the design of the application’s interface and algorithmic system. The resulting application significantly simplifies the process of estimating production potential for farmers, enabling them to access sugarcane productivity data during harvest. Consequently, sugar

关键词： Productivity Operating systems Estimation Production facilities Raw materials Mobile applications Recording

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Evolution Of SARS-CoV-2 In The Presence Of Vaccines.

Evolution Of SARS-CoV-2 In The Presence Of Vaccines.

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IEEE International Conference on bioinformatics and Biomedicine (BIBM)

作者： Vishwajeet Marathe Changhui Yan Department of Computer Scienceline North Dakota State University Fargo ND USA Department of Computer Science Genomics Phenomics and Bioinformatics Graduate Program North Dakota State University Fargo ND USA

ISBN: (数字)9781665468190

ISBN: (纸本)9781665468206

The COVID pandemic has caused tremendous loss worldwide. Now vaccines are the primary weapon to combat the pandemic. Understanding how SARS-CoV-2, the virus that causes the COVID, may mutate in the presence of the vaccines is critical for designing drugs and vaccines for future variants of the virus. In this study, we investigated the numbers of mutations that SARS-CoV-2 accumulated on each protein over time. We found that different proteins of the virus accumulated different levels of mutations and their mutation rates changed over time following different patterns. We also presented evidence that the mutation of the Spike protein might have been suppressed by the vaccines. This is the first time that such a relation was reported based on real world data. Although the discovery was not meant to be conclusive, this study sheds light onto how the virus may response to the vaccines. If confirmed by further studies, the discovery will have significant impacts on many fields, including drug and vaccine designs.

关键词： Proteins Drugs COVID-19 Protein engineering Pandemics Weapons Vaccines

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