Jiahong Sun

Bioinformatics · Omics · Scientific Computing

Build knowledge, not just notes.

I am a bioinformatics postdoctoral researcher studying genetic variation, cancer evolution, and computational methods. This site is my structured, evolving map of what I have learned—and what I am still curious about.

Explore the knowledge map About me

Knowledge areas

Bioinformatics

Classical tools, algorithms, workflow languages, and databases.

Omics data analysis

Genomics, transcriptomics, epigenomics, multiomics, and spatial data.

Machine learning

Core methods, deep learning, and biological applications.

Statistics

Distributions, mixture models, inference, and statistical modelling.

Linux

Commands, systems, environments, networking, and reproducibility.

Python & R

Programming foundations, advanced patterns, and visualization.

Recent writing

Bioinformatics Algorithms

Bioinformatics

Algorithms

Algorithms and mathematical ideas behind biological data analysis.

4 min

Bioinformatics Databases

Bioinformatics

Databases

A curated index of reliable biological databases and reference resources.

1 min

Bioinformatics

Tools and computational ideas that underpin modern biological data analysis.

1 min

Classic Bioinformatics Software

Bioinformatics

Software

How foundational command-line tools work, when to use them, and how they fit together.

1 min

Workflow Languages

Bioinformatics

Workflows

Reproducible, portable, and scalable computational workflows.

1 min

Biology

Biological knowledge that improves the interpretation of bioinformatics discoveries

1 min

Experimental Techniques

Biology

Technique

Principles underlying important experimental techniques

1 min

Knowledge Map

A structured map of bioinformatics, omics, computation, and statistics.

1 min

Linux Basic Commands

Linux

Shell

Files, text streams, processes, permissions, and shell composition.

1 min

Environments & Networking

Linux

Reproducibility

Networking

Git, Conda/Mamba, containers, web servers, and network fundamentals.

1 min

Linux

Practical Linux for scientific computing and reproducible research.

1 min

Linux System Management

Linux

Systems

Processes, storage, services, users, logging, and performance.

1 min

Machine Learning Foundations

Machine Learning

Data, objectives, validation, regularization, and classical models.

1 min

Deep Learning

Machine Learning

Deep Learning

Neural-network foundations, architectures, training, and biological applications.

1 min

Machine Learning

Machine-learning foundations and models for biological data.

1 min

Epigenomics

Omics

Epigenomics

Chromatin accessibility, protein–DNA binding, and histone modifications.

1 min

Genomics

Omics

Genomics

Whole-genome, whole-exome, and single-cell DNA sequencing.

1 min

Omics Data Analysis

From experimental design and raw data to biological interpretation.

1 min

Multiomics

Omics

Multiomics

Joint profiling and integration across molecular modalities.

1 min

Spatial, Proteomics & Metabolomics

Omics

Spatial

Proteomics

Metabolomics

Spatially resolved expression and molecular phenotyping beyond nucleic acids.

1 min

Transcriptomics

Omics

Transcriptomics

Bulk and single-cell RNA sequencing workflows and interpretation.

1 min

Python & R

Programming foundations and scientific data analysis.

1 min

Python Advanced

Python

Programming

Python internals, metaprogramming, systems, web, and debugging.

1 min

Python Basics

Python

Programming

Core Python for reliable scientific programs.

1 min

R Basics

Programming

R language foundations and data analysis.

1 min

R Visualization

Visualization

Principles and tools for clear statistical graphics.

1 min

Advanced Modeling

Statistics

Advanced Modeling

Regularization, hierarchical models, mixtures, survival analysis, and multivariate methods.

1 min

Mixture Models

Statistics

Mixture Models

Latent populations, identifiability, and estimation.

1 min

Asymptotic Thinking

Statistics

Asymptotics

Convergence, laws of large numbers, central limit theory, and approximation.

1 min

Real Bioinformatics Problems

Statistics

Bioinformatics

Statistical reasoning for experimental design and high-throughput biological data.

1 min

Statistics

Probability, inference, and models for biological variation.

1 min

Probability Distributions

Statistics

Probability

Discrete and continuous probability distributions and their biological uses.

1 min

Probability & Randomness

Statistics

Probability

Probability foundations, random variables, distributions, and moments.

1 min

Regression & Statistical Models

Statistics

Modelling

Regression, generalized linear models, diagnostics, and model selection.

1 min

Statistical Modelling

Statistics

Modelling

From regression to hierarchical and Bayesian models.

1 min

Statistical Inference

Statistics

Inference

Estimation, uncertainty, testing, power, resampling, and multiplicity.

1 min

Book Notes

Ideas and reflections from books.

1 min

English Learning

English vocabulary, writing, speaking, and academic communication.

1 min

Blog

Dated notes, reading, language learning, and other observations.

1 min

Others

Daily notes, weekly reviews, life, recipes, and uncategorized explorations.

1 min

Logistic Regression

Statistics

Regression

Logistic Regression

Binary Outcomes

Logistic regression from the binary data-generating model through likelihood estimation, coefficient interpretation, uncertainty, diagnostics, separation, and bioinformatics design.

Oct 16, 2026

7 min

Odds Ratios, Probabilities, and Calibration

Statistics

Regression

Odds Ratios

Calibration

Prediction

Odds ratios, absolute probabilities, non-collapsibility, standardization, calibration, discrimination, proper scores, validation, and biological interpretation.

Oct 16, 2026

9 min

ANCOVA and Regression-based ANOVA

Statistics

Regression

ANCOVA

Experimental Design

Analysis of covariance and regression-based ANOVA, including adjusted contrasts, covariate interactions, baseline adjustment, assumptions, diagnostics, and bioinformatics design.

Oct 15, 2026

8 min

One-way and Factorial ANOVA

Statistics

Regression

ANOVA

Experimental Design

One-way and factorial analysis of variance as linear models, with sums of squares, interactions, assumptions, contrasts, diagnostics, and bioinformatics design guidance.

Oct 15, 2026

7 min

Categorical Predictors and Contrasts

Statistics

Regression

Categorical Predictors

Contrasts

Indicator coding, planned contrasts, marginal means, uncertainty, and interpretation for categorical predictors in regression models.

Oct 14, 2026

7 min

Interaction Terms and Effect Modification

Statistics

Regression

Interaction

Effect Modification

Regression interactions, conditional effects, scale dependence, causal effect modification, uncertainty, diagnostics, and interpretation.

Oct 14, 2026

8 min

Linear-model Assumptions and Diagnostics

Statistics

Regression

Linear Models

Diagnostics

A practical guide to linear-model assumptions, residual and influence diagnostics, sensitivity analysis, and defensible interpretation.

Oct 13, 2026

8 min

Robust Standard Errors and Robust Regression

Statistics

Regression

Robust Statistics

Heteroskedasticity-consistent covariance estimation, cluster-aware uncertainty, M-estimation, influence, and robust interpretation in linear models.

Oct 13, 2026

8 min

Least Squares and the Geometry of Regression

Statistics

Regression

Linear Models

A geometric account of ordinary least squares, including projection matrices, partial regression, rank, leverage, and weighted least squares.

Oct 11, 2026

7 min

Regression Uncertainty and Coefficient Interpretation

Statistics

Regression

Statistical Inference

How regression coefficients, standard errors, confidence intervals, and prediction intervals depend on the target, design, and error assumptions.

Oct 11, 2026

8 min

Multiple Linear Regression

Statistics

Regression

Linear Models

Multiple linear regression, coefficient interpretation, least squares geometry, assumptions, diagnostics, and sensitivity in biological studies.

Oct 9, 2026

7 min

Simple Linear Regression

Statistics

Regression

Linear Models

Simple linear regression as a data-generating model, an estimation problem, and a framework for prediction and scientific interpretation.

Oct 9, 2026

6 min

Reproducibility and Effect-size Inflation

Statistics

Inference

Reproducibility

Effect Size

A statistical guide to reproducibility, replication, Type M errors, selective reporting, heterogeneity, and effect-size calibration.

Oct 8, 2026

10 min

Selection Bias and Winner’s Curse

Statistics

Inference

Selection Bias

Winner's Curse

Selection mechanisms, collider bias, post-selection effect inflation, winner’s-curse derivations, diagnostics, and design-aware remedies.

Oct 8, 2026

9 min

Monte Carlo Estimation and Uncertainty

Statistics

Inference

Monte Carlo

Simulation

Monte Carlo estimators, standard errors, effective sample size, variance reduction, stopping rules, and reproducible simulation practice.

Oct 7, 2026

8 min

Sensitivity Analysis and Robustness

Statistics

Inference

Sensitivity Analysis

Robustness

A structured guide to robustness, quantitative sensitivity analysis, tipping points, multiverse analyses, and design-aware interpretation.

Oct 7, 2026

10 min

Benjamini–Hochberg and Storey q-values

Statistics

Inference

Multiple Testing

Bioinformatics

The Benjamini–Hochberg step-up procedure, Storey’s adaptive q-values, their assumptions, and responsible use in high-dimensional studies.

Oct 6, 2026

7 min

Bonferroni, Holm, and Hochberg Procedures

Statistics

Inference

Multiple Testing

How Bonferroni, Holm, and Hochberg procedures control family-wise error, how their algorithms differ, and when their guarantees apply.

Oct 6, 2026

6 min

Permutation and Randomization Tests

Statistics

Inference

Resampling

Experimental Design

Exact and Monte Carlo randomization inference, permutation tests, exchangeability, restricted shuffles, and design-aware interpretation.

Oct 6, 2026

8 min

Rank-based Nonparametric Tests

Statistics

Inference

Nonparametric Methods

Wilcoxon, Mann–Whitney, Kruskal–Wallis, and Friedman tests, their estimands, assumptions, ties, and design-aware interpretation.

Oct 6, 2026

8 min

False Discovery Rate

Statistics

Inference

Multiple Testing

FDR

Definitions, Benjamini-Hochberg control, adjusted p-values, dependence, q-values, and interpretation for high-dimensional studies.

Oct 5, 2026

8 min

Family-wise Error Rate

Statistics

Inference

Multiple Testing

FWER

Definitions, strong and weak control, Bonferroni and Holm procedures, simultaneous inference, and design choices for family-wise error control.

Oct 5, 2026

7 min

Likelihood-ratio, Wald, and Score Tests

Statistics

Inference

Hypothesis Testing

Likelihood

Construction, asymptotic equivalence, finite-sample differences, diagnostics, and interpretation of likelihood-ratio, Wald, and score tests.

Oct 4, 2026

7 min

One-sided, Two-sided, and Equivalence Tests

Statistics

Inference

Hypothesis Testing

Equivalence

Directional, two-sided, and equivalence hypotheses; confidence-interval duality; margin choice; design; and interpretation.

Oct 4, 2026

8 min

Statistical Power and Sample-size Calculation

Statistics

Inference

Study Design

Prospective power, sample-size equations, effect assumptions, multiplicity, simulation, and bioinformatics study design.

Oct 1, 2026

9 min

Type I and Type II Errors

Statistics

Inference

Hypothesis Testing

Type I and Type II errors, size, power, trade-offs, interpretation, and design-aware use in bioinformatics.

Oct 1, 2026

7 min

Hypothesis Tests and Test Statistics

Statistics

Inference

Hypothesis Testing

Hypotheses, test statistics, rejection regions, size, power, calibration, and design-aware interpretation.

Sep 30, 2026

8 min

Null Distributions and P-values

Statistics

Inference

P-values

Null reference distributions, valid p-values, discreteness, composite hypotheses, interpretation, and multiplicity.

Sep 30, 2026

9 min

Daily Translation: An Early Night Ruined by Urgent Work

English Learning

Daily Translation

你这周一直很忙，打算今晚早点休息。下班回家后，你简单煮了晚饭，洗完碗，准备上床。刚关灯躺下，突然收到领导发来的消息，有一份紧急文件需要你今晚修改并且发送。你只好重新打开电脑，坐在书桌前处理。等全部弄完，已经很晚，原本早睡的计划泡汤了

Sep 30, 2026

1 min

Effect Sizes

Statistics

Inference

Effect Size

Effect-size estimands, estimates, standardized measures, uncertainty, scale choice, and design-aware interpretation in bioinformatics.

Sep 29, 2026

8 min

Nonparametric Bootstrap

Statistics

Inference

Resampling

The empirical-distribution bootstrap, design-aware resampling, uncertainty estimation, failure cases, and bioinformatics interpretation.

Sep 29, 2026

8 min

Parametric Bootstrap

Statistics

Inference

Resampling

Parametric bootstrap simulation, uncertainty estimation, interval construction, diagnostics, and design-aware interpretation.

Sep 29, 2026

7 min

Statistical versus Practical Significance

Statistics

Inference

Scientific Interpretation

Statistical significance, practical importance, minimum effects of interest, interval-based decisions, and bioinformatics interpretation.

Sep 29, 2026

9 min

Daily Translation: Leaving an Umbrella in the Pantry

English Learning

Daily Translation

早上出门的时候我记得带了雨伞。上班到下午，窗外下起大雨。下班时我翻遍背包，却找不到伞。我回忆了半天，才想起把它靠在公司茶水间的窗边了。茶水间已经关灯锁门。我只好在大楼门口等雨变小，顺便刷手机打发时间，足足等了四十分钟雨才小一些，然后冒雨快步赶去地铁站。

Sep 29, 2026

2 min

Daily Translation: Getting Distracted by Old Photos

English Learning

Daily Translation

昨天下午，我打算整理电脑里的照片文件夹。里面存了很多旅行、和朋友聚会的照片。本来只想分类归档，结果看着旧照片，忍不住一张一张仔细翻看。不知不觉花了两个多小时。等回过神来，我才发现原本计划要完成的工作一点都没动，只好晚上加班。

Sep 28, 2026

1 min

Bayesian Credible Intervals

Statistics

Bayesian

Uncertainty

Equal-tailed, highest-density, and decision-focused Bayesian intervals, with computation, diagnostics, prior sensitivity, and interpretation.

Sep 27, 2026

8 min

Confidence Intervals

Statistics

Inference

Uncertainty

Confidence intervals, coverage, exact and approximate constructions, interpretation, diagnostics, and design-aware use in bioinformatics.

Sep 27, 2026

8 min

Daily Translation: Forgetting a Wallet at the Supermarket

English Learning

Daily Translation

今天下班之后，你想去超市买食材准备做晚餐。你推了购物车，挑好了蔬菜、鸡蛋和一块牛排。排队结账的时候，你才想起忘记带钱包。手机里的支付软件也因为网络太差打不开。没办法，只能把挑好的东西放回货架，空手离开超市

Sep 27, 2026

1 min

Sampling Distributions

Statistics

Inference

Sampling

Sampling distributions, exact and approximate derivations, design dependence, simulation, and interpretation for statistical inference.

Sep 26, 2026

8 min

Standard Errors

Statistics

Inference

Uncertainty

Standard errors as estimated sampling standard deviations, with plug-in, information, delta-method, bootstrap, robust, and cluster-aware calculations.

Sep 26, 2026

8 min

Daily Translation: Jogging in Wind and Rain

English Learning

Daily Translation

周末早上，你打算出门去公园慢跑。你换上运动服，带上水杯和耳机。出门之后才发现外面风特别大，还很冷。你犹豫了一会儿，不想白跑一趟，还是继续往公园走。跑到一半，天开始下起小雨。你只能提前结束跑步，快步往家走

Sep 26, 2026

1 min

Fisher Information and the Cramér–Rao Bound

Statistics

Inference

Estimation

Scores, expected and observed Fisher information, the Cramér–Rao inequality, efficiency, nuisance parameters, and nonregular failure cases.

Sep 25, 2026

6 min

Sufficient Statistics

Statistics

Inference

Estimation

Sufficiency, factorization, minimal and complete statistics, Rao–Blackwell improvement, and limits of model-based data reduction.

Sep 25, 2026

7 min

Daily Translation: A Power Cut during Movie Night

English Learning

Daily Translation

本来打算今晚在家好好看一部存了很久的电影。我提前准备好零食和饮料，关掉房间大灯，打开电脑。电影才放了二十分钟，突然家里停电了。屏幕一下子变黑，房间里一片暗。我摸出手机打开手电筒，检查电闸，试了好几次都没用，只好放弃看电影。

Sep 25, 2026

1 min

Daily Translation: An Interrupted Coffee Break

English Learning

Daily Translation

今天午休的时候，我打算下楼去咖啡店买一杯热饮。排队的人有点多，等了大概十分钟。拿到咖啡之后，我坐在窗边的位置，拿出手机想简单回几条消息。刚喝两口，就看到同事发来消息，说有个紧急小任务需要我马上处理。我只好快速喝完咖啡，收拾东西赶回办公室。

Sep 24, 2026

2 min

Bayesian Priors, Likelihoods, and Posteriors

Statistics

Inference

Bayesian

A practical foundation for Bayesian inference: priors, likelihoods, posterior distributions, prediction, computation, checking, and sensitivity.

Sep 23, 2026

9 min

Maximum a Posteriori Estimation

Statistics

Inference

Bayesian

Estimation

Maximum a posteriori estimation, its relationship to likelihood and regularization, exact examples, optimization, interpretation, and failure modes.

Sep 23, 2026

7 min

Daily Translation: Stopping at a Bakery after Work

English Learning

Daily Translation

今天下班路上，我路过一家面包店。橱窗里的面包闻起来很香，于是进去挑了几个。回家之后，我尝了一个，味道很不错，打算之后有空再来买。

Sep 23, 2026

1 min

Likelihood and Log-likelihood

Statistics

Inference

Likelihood

Likelihood, log-likelihood, likelihood ratios, score, curvature, and the assumptions behind likelihood-based evidence.

Sep 22, 2026

6 min

Maximum-likelihood Estimation

Statistics

Inference

Estimation

Maximum-likelihood estimators, derivations, invariance, uncertainty, computation, diagnostics, and nonregular failure cases.

Sep 22, 2026

6 min

Daily Translation: Rushing to Finish a Work Document

English Learning

Daily Translation

下午你打算完成一份工作文档。刚写了一半，同事过来找你讨论项目问题。你们聊了挺久。等同事走后，你发现留给写文档的时间不多了，只好加快速度赶进度

Sep 22, 2026

1 min

Point Estimators: Bias, Variance, and Mean Squared Error

Statistics

Inference

Estimation

Point estimation through estimands, sampling distributions, bias, variance, standard error, and mean squared error.

Sep 21, 2026

7 min

Populations, Samples, Parameters, and Estimands

Statistics

Inference

Study Design

A design-first guide to populations, samples, parameters, estimands, experimental units, and the scope of statistical inference.

Sep 21, 2026

8 min

Daily Translation: Missing a Lunchtime Nap

English Learning

Daily Translation

午休的时候，你坐在工位，本来打算小睡一会儿。结果刷手机翻看以前的聊天记录，看得入了神。等反应过来，午休时间已经结束，你根本没来得及休息

Sep 21, 2026

1 min

Asymptotic Bias, Consistency, and Efficiency

Statistics

Asymptotics

Inference

Finite-sample and asymptotic bias, consistency, asymptotic variance, and efficiency under explicit regularity conditions.

Sep 20, 2026

5 min

When Asymptotic Approximations Fail

Statistics

Asymptotics

Diagnostics

Mechanisms that invalidate or delay large-sample approximations, with diagnostics and design-faithful remedies.

Sep 20, 2026

7 min

Daily Translation: Finding Old Notes and Photos

English Learning

Daily Translation

你周末在家整理书桌。翻出很多旧笔记和旧照片。翻看的时候回忆起以前上学的日子。不知不觉过去了一个多小时，书桌还没有完全收拾完。

Sep 20, 2026

1 min

Delta Method

Statistics

Asymptotics

Inference

The univariate and multivariate delta method, its Taylor expansion, standard-error propagation, and important failure cases.

Sep 19, 2026

4 min

Slutsky’s Theorem and Continuous Mapping

Statistics

Asymptotics

Inference

Continuous mapping and Slutsky’s theorem, with conditions, proof intuition, studentization, and failure cases.

Sep 19, 2026

5 min

Daily Translation: Choosing What to Order for Dinner

English Learning

Daily Translation

你下班回家感觉很累。打算点一份外卖当晚饭。浏览外卖软件看了很久，纠结不知道吃什么，花了二十多分钟才最终选好下单

Sep 19, 2026

1 min

Central Limit Theorem

Statistics

Asymptotics

Probability

The iid central limit theorem, its characteristic-function intuition, finite-sample checks, and failures.

Sep 18, 2026

4 min

Convergence in Distribution

Statistics

Asymptotics

Probability

Weak convergence through CDFs, continuity sets, and expectations, with its implications and limits.

Sep 18, 2026

4 min

Daily Translation: Making It to Work Just in Time

English Learning

Daily Translation

早上你起床比平时晚，来不及在家吃早饭。路上买了个面包，一边走路一边吃。赶到公司的时候刚好踩点打卡，坐下来之后心跳还有点快。

Sep 18, 2026

1 min

Convergence in Probability and Almost-Sure Convergence

Statistics

Asymptotics

Probability

Definitions, implications, counterexamples, and conditions for two fundamental modes of stochastic convergence.

Sep 17, 2026

4 min

Law of Large Numbers

Statistics

Asymptotics

Probability

Weak and strong laws, a Chebyshev derivation, finite-sample bounds, and failure cases relevant to biological sampling.

Sep 17, 2026

5 min

Daily Translation: Carrying Groceries Home

English Learning

Daily Translation

周末你去超市采购。货架上很多商品在打折，你拿了不少东西。排队结账的时候队伍特别长，等结完账拎着大包小包走回家，胳膊都有点酸。

Sep 17, 2026

1 min

Order Statistics and Extreme Values

Statistics

Probability

Extreme Values

Exact order-statistic laws, beta quantile transform, extreme-value limits, and practical cautions for biological data.

Sep 16, 2026

5 min

Probability-generating and Moment-generating Functions

Statistics

Probability

Distributions

Definitions, derivatives, sum rules, examples, and existence limits for probability- and moment-generating functions.

Sep 16, 2026

4 min

Daily Translation: Work Interrupting an Evening Show

English Learning

Daily Translation

晚上在家，你本来想看一集剧集放松。刚点开视频，突然收到好几条工作消息。你只好停下看剧，花了不少时间处理工作，等忙完之后已经没有精力看剧了

Sep 16, 2026

1 min

Dirichlet–Multinomial Distribution

Statistics

Probability

Distributions

Compositional Data

The Dirichlet–multinomial distribution, including its mixture derivation, moments, covariance, overdispersion, assumptions, and interpretation for compositional count data.

Sep 15, 2026

7 min

Zero-inflated and Hurdle Distributions

Statistics

Probability

Distributions

Count Data

Zero-inflated and hurdle count distributions, including their probability laws, moments, generative interpretations, identifiability, diagnostics, and bioinformatics cautions.

Sep 15, 2026

8 min

Daily Translation: A Late Takeout Delivery

English Learning

Daily Translation

你午休点了外卖，外卖比预计时间晚了很久送到。饭拿到手已经有点凉了，简单吃完之后，你只剩下很短的休息时间，很快就要回去继续工作

Sep 15, 2026

1 min

Beta-binomial Distribution

Statistics

Probability

Distributions

Proportion Data

The beta-binomial distribution, including its mixture derivation, moments, intracluster correlation, overdispersion, and biological interpretation.

Sep 14, 2026

8 min

Negative Binomial Distribution and Overdispersion

Statistics

Probability

Distributions

Count Data

Negative binomial parameterizations, moments, Poisson–gamma mixing, overdispersion, assumptions, and interpretation in sequencing count data.

Sep 14, 2026

7 min

Daily Translation: Finding a Seat at the Library

English Learning

Daily Translation

周末你想去图书馆复习备考。出门前你确认带上笔记本、笔还有复习资料。到了才发现图书馆座位几乎全满。你四处逛了一圈，好不容易才找到一个靠窗的空位。坐下之后你拿出东西，静下心开始学习

Sep 14, 2026

1 min

Dirichlet Distribution

Statistics

Probability

Distributions

Compositional Data

The Dirichlet distribution on the simplex, including normalization, moments, gamma construction, aggregation, conjugacy, and compositional interpretation.

Sep 13, 2026

7 min

Gamma and Beta Distributions

Statistics

Probability

Distributions

Gamma and beta distributions, their parameterizations, moments, transformations, conjugate roles, and biological interpretation.

Sep 13, 2026

6 min

Daily Translation: Saving a Dish from Burning

English Learning

Daily Translation

下班之后你打算在家做饭。你去菜市场买好了蔬菜和肉。回到厨房开始处理食材。炒菜的时候手机弹出几条工作消息，你分心看了一会儿。结果锅里的菜差点烧焦。你赶紧调小炉火，不停翻炒，总算挽救回来。

Sep 13, 2026

1 min

Chi-squared, Student’s t, and F Distributions

Statistics

Probability

Distributions

Sampling Distributions

Chi-squared, Student’s t, and F distributions, their constructions, moments, relationships, assumptions, and roles in finite-sample inference.

Sep 12, 2026

7 min

Normal and Multivariate Normal Distributions

Statistics

Probability

Distributions

Multivariate Analysis

Univariate and multivariate normal distributions, linear transformations, conditional laws, Mahalanobis distance, assumptions, and biological interpretation.

Sep 12, 2026

7 min

Daily Translation: Meeting a Friend at a Café

English Learning

Daily Translation

你周末约了朋友线下见面。你提前出门，搭乘公交前往约定的咖啡馆。路上交通拥堵，比预想花费了更久。等你赶到的时候，朋友已经到了。你们点了两杯饮品，坐下来聊天，分享最近各自工作生活里发生的趣事。

Sep 12, 2026

1 min

Exponential and Geometric Distributions

Statistics

Probability

Distributions

Waiting Times

Exponential and geometric waiting-time distributions, memorylessness, hazards, parameterizations, process relationships, assumptions, and biological interpretation.

Sep 11, 2026

7 min

Poisson Distribution and Poisson Processes

Statistics

Probability

Distributions

Stochastic Processes

The Poisson distribution and homogeneous Poisson process, including derivations, waiting-time relationships, assumptions, and biological interpretation.

Sep 11, 2026

6 min

Daily Translation: Losing Time on Social Media

English Learning

Daily Translation

早上你本来打算早点出门去图书馆学习。收拾好背包，吃完简单的早餐之后，你打开电脑想查一点学习资料。结果刷社交软件不知不觉耗掉了不少时间。等你反应过来，已经快中午了。你有点懊恼，只好改变计划，决定下午再去图书馆。

Sep 11, 2026

1 min

Bernoulli and Binomial Distributions

Statistics

Probability

Distributions

Bernoulli and binomial probability models, moments, derivations, assumptions, likelihood, and biological interpretation.

Sep 10, 2026

6 min

Categorical and Multinomial Distributions

Statistics

Probability

Distributions

Categorical and multinomial probability models, moments, covariance, aggregation, assumptions, and biological interpretation.

Sep 10, 2026

7 min

Daily Translation: Leaving the Keys at a Store

English Learning

Daily Translation

你下班去便利店买了晚饭，回到家掏出钥匙，才发现把家门钥匙落在便利店柜台了，只好折回去拿。

Sep 10, 2026

1 min

Covariance and Correlation

Statistics

Probability

Association

Population and sample covariance, Pearson and rank correlation, covariance matrices, interpretation, and limitations in biological data.

Sep 9, 2026

7 min

Transformations of Random Variables

Statistics

Probability

Transformations

CDF, change-of-variables, Jacobian, convolution, expectation, and uncertainty propagation methods for transformed random variables.

Sep 9, 2026

7 min

Daily Translation: A Grocery Bag Tearing Open

English Learning

Daily Translation

你在超市采购，拎着满满两大袋东西回家。走到半路袋子破了，水果和零食掉了一地，你手忙脚乱地蹲下来捡。

Sep 9, 2026

1 min

Bayes’ Theorem and Bayesian Updating

Statistics

Probability

Bayesian

Bayes’ theorem for events and parameters, likelihood ratios, sequential updating, posterior prediction, and sensitivity to prior information.

Sep 8, 2026

7 min

Conditional Probability and the Law of Total Probability

Statistics

Probability

Conditional probability, multiplication and chain rules, partitions, total probability, and the role of base rates in biological examples.

Sep 8, 2026

6 min

Expectation, Variance, and Moments

Statistics

Probability

Expectation as probability-weighted integration, variance, covariance identities, higher moments, and their limitations.

Sep 7, 2026

6 min

Independence and Conditional Independence

Statistics

Probability

Event and random-variable independence, factorization, conditional independence, common causes, colliders, and implications for biological data.

Sep 7, 2026

6 min

Joint, Marginal, and Conditional Distributions

Statistics

Probability

Joint laws, marginalization, conditional distributions, support, and the multiplication rule for discrete and continuous random variables.

Sep 7, 2026

6 min

Random Variables and Probability Distributions

Statistics

Probability

Random variables, distribution functions, discrete and continuous laws, quantiles, and mixed distributions.

Sep 7, 2026

5 min

Daily Translation: Losing Track of Time at the Library

English Learning

Daily Translation

下午你在图书馆看书，看得太投入忘记时间。等你合上书，才发现图书馆快要闭馆。收拾好随身物品出门，才发现外面刮起大风，你赶紧快步走向地铁站。

Sep 7, 2026

1 min

Counting Rules and Combinatorial Probability

Statistics

Probability

Product and sum rules, permutations, combinations, and hypergeometric sampling for finite probability models.

Sep 6, 2026

5 min

Probability Spaces, Events, and Probability Axioms

Statistics

Probability

Sample spaces, events, sigma-algebras, and the axioms that make probability calculus consistent.

Sep 6, 2026

4 min

Daily Translation: Boiling the Kettle Dry

English Learning

Daily Translation

早上你打算煮咖啡，烧水的时候收到同事消息，处理工作消息分心。等你反应过来，水已经完全烧干，水壶还冒出白烟。

Sep 6, 2026

1 min

Daily Translation: Getting Caught in Heavy Rain

English Learning

Daily Translation

早上你出门的时候天还好好的，不料下午突然下起大雨。你没有带雨伞，下班之后只能在公司大楼门口等候。等了很久雨也没有变小，最后只好叫网约车回家。

Sep 5, 2026

1 min

Bipartite Matching Algorithms in Bioinformatics

Bioinformatics

Algorithms

Graphs

Optimization

A guide to bipartite graphs, maximum and weighted matching, assignment algorithms, and validation of biological pairings.

Sep 4, 2026

6 min

Network-Flow Algorithms in Bioinformatics

Bioinformatics

Algorithms

Graphs

Optimization

A guide to max-flow, min-cost flow, residual graphs, and biological interpretations of flow models.

Sep 4, 2026

6 min

Minimum Spanning Trees in Bioinformatics

Bioinformatics

Algorithms

Graphs

Optimization

How minimum spanning trees summarize weighted biological graphs, and how to use them without mistaking a sparse graph for a unique evolutionary history.

Sep 3, 2026

6 min

Shortest-Path Algorithms in Biological Graphs

Bioinformatics

Algorithms

Graphs

Optimization

How shortest-path algorithms turn weighted biological graphs into auditable routes, and how to distinguish path cost from biological mechanism.

Sep 3, 2026

7 min

Daily Translation: Tidying Up the Room

English Learning

Daily Translation

下班回家之后，你打算简单收拾下房间。先把散落的衣服收好，擦拭桌面，再把垃圾扔掉。做完这些家务，房间看着整洁不少，你感觉心情也舒畅了。

Sep 3, 2026

1 min

Dynamic Programming in Bioinformatics

Bioinformatics

Algorithms

Dynamic Programming

How dynamic programming turns recursively structured bioinformatics problems into exact, auditable algorithms.

Sep 2, 2026

6 min

Integer Linear Programming in Bioinformatics

Bioinformatics

Algorithms

Optimization

Integer Programming

A practical guide to integer linear programming formulations, solvers, certificates, and pitfalls in bioinformatics.

Sep 2, 2026

6 min

Daily Translation: A Coffee Break with a Colleague

English Learning

Daily Translation

午休的时候，同事约你下楼喝咖啡。咖啡店人有点多，排队等了一小会儿。你们边喝边闲聊工作和生活，短暂休息之后，你们回到工位继续下午的工作。

Sep 2, 2026

1 min

Gene-Set Enrichment Algorithms

Bioinformatics

Algorithms

Statistics

Functional Genomics

How over-representation analysis and ranked-list gene-set enrichment test whether predefined biological programs show coordinated signal, with appropriate null models and multiple-testing control.

Sep 1, 2026

7 min

Multiple-Testing Correction

Bioinformatics

Algorithms

Statistics

Multiple Testing

How family-wise error rate and false-discovery-rate procedures turn many biological p-values into calibrated, interpretable decisions.

Sep 1, 2026

7 min

Daily Translation: Oversleeping and Forgetting a Wallet

English Learning

Daily Translation

早上闹钟响了好几次，你起晚了。来不及做早餐，抓了面包就出门赶地铁。地铁里人非常拥挤，你好不容易挤上去，结果发现自己忘记带钱包。

Sep 1, 2026

1 min

Leiden Community Detection

Bioinformatics

Algorithms

Graphs

Clustering

Single-Cell

How the Leiden algorithm improves multilevel graph community detection through local moves, within-community refinement, and aggregation, with practical guidance for omics graphs.

Aug 31, 2026

6 min

Louvain Community Detection

Bioinformatics

Algorithms

Graphs

Clustering

Single-Cell

How the Louvain algorithm finds graph communities by locally optimizing modularity, aggregates them into coarser graphs, and should be diagnosed in bioinformatics workflows.

Aug 31, 2026

5 min

Daily Translation: A Tiring Friday Evening

English Learning

Daily Translation

周五下班之后，你感觉很累。回到家，你简单煮了一碗面条当晚饭。吃完之后，你不想做任何家务，就躺在沙发上刷手机，看短视频放松自己。不知不觉时间过得很快，等你反应过来，已经快半夜了。

Aug 31, 2026

1 min

Diffusion Maps

Bioinformatics

Algorithms

Dimensionality Reduction

Graphs

Omics

Single-Cell

How diffusion maps use a Markov random walk on local similarities to reveal continuous geometry, denoise omics data, and support trajectory exploration.

Aug 30, 2026

6 min

UMAP Dimensionality Reduction

Bioinformatics

Algorithms

Dimensionality Reduction

Graphs

Omics

Single-Cell

How UMAP builds a weighted neighbor graph and optimizes a low-dimensional layout, with practical guidance for single-cell and other omics data.

Aug 30, 2026

6 min

k-Nearest-Neighbor Graphs for Omics Data

Bioinformatics

Algorithms

Graphs

Omics

Single-Cell

How k-nearest-neighbor graphs turn an omics embedding into local neighborhoods for visualization, clustering, trajectory analysis, and batch-aware diagnostics.

Aug 29, 2026

7 min

t-SNE Dimensionality Reduction

Bioinformatics

Algorithms

Dimensionality Reduction

Omics

Single-Cell

How t-distributed stochastic neighbor embedding constructs a two-dimensional view of local similarities, how to interpret it, and why it should not be used as evidence for cluster size or global distance.

Aug 29, 2026

6 min

Hierarchical Clustering

Bioinformatics

Algorithms

Clustering

Omics

A practical guide to agglomerative and divisive hierarchical clustering, linkage choices, dendrogram interpretation, and validation for omics and sequence-derived data.

Aug 28, 2026

7 min

k-means and k-medoids Clustering

Bioinformatics

Algorithms

Clustering

Omics

How k-means and k-medoids partition omics profiles, what their objectives assume, and how to validate clusters without mistaking an algorithmic partition for biology.

Aug 28, 2026

7 min

Daily Translation: Making a Simple Dinner

English Learning

Daily Translation

傍晚在家做简单晚餐。走进厨房，从冰箱拿出蔬菜和鸡蛋。冲洗蔬菜，切好食材。开火，倒油，炒了一盘青菜再煎两个鸡蛋。饭菜做好，端到餐桌上，一边吃饭一边看会儿短视频，吃完之后洗碗收拾厨房。

Aug 28, 2026

1 min

Non-negative Matrix Factorization

Bioinformatics

Algorithms

Omics

Matrix Factorization

How non-negative matrix factorization decomposes a nonnegative omics matrix into additive feature programs and sample exposures, with practical interpretation and validation guidance.

Aug 27, 2026

6 min

Principal Component Analysis for Omics Data

Bioinformatics

Algorithms

Omics

Dimensionality Reduction

How principal component analysis projects high-dimensional omics measurements into variance-maximizing components for exploration, quality control, and covariate discovery.

Aug 27, 2026

6 min

Daily Translation: Tidying the Desk

English Learning

Daily Translation

周末下午你打算整理书桌。先把桌面上散乱的书本、笔记和杂物全部挪开，擦掉桌面上的灰尘。把书本分类摆到书架，没用的废纸扔进垃圾桶。整理完之后桌面变得干干净净，你倒了一杯水，坐在桌前休息，看着整洁的桌面感觉很舒服。

Aug 27, 2026

1 min

Bayesian Phylogenetic Inference

Bioinformatics

Algorithms

Phylogenetics

Evolution

How Bayesian phylogenetics combines an alignment likelihood with prior assumptions and MCMC sampling to report posterior uncertainty over trees and evolutionary parameters.

Aug 26, 2026

7 min

Maximum-Likelihood Phylogenetics

Bioinformatics

Algorithms

Phylogenetics

Evolution

How maximum-likelihood phylogenetics evaluates tree topologies, branch lengths, and substitution models using the probability of observed alignment columns.

Aug 26, 2026

7 min

Daily Translation: Working Late at the Office

English Learning

Daily Translation

工作日晚上公司有紧急工作需要处理，你不得不留下来加班。办公室其他人陆续下班走了，只剩下你。你对着电脑处理报表，中间泡了一杯速溶咖啡提神。一直忙到快九点才做完手上的活，收拾好东西关灯锁门，拖着疲惫的身体坐地铁回家。

Aug 26, 2026

1 min

Neighbor-Joining Trees

Bioinformatics

Algorithms

Phylogenetics

Evolution

How the neighbor-joining algorithm repeatedly joins taxa that are close after accounting for their average distance to all other taxa.

Aug 25, 2026

5 min

Phylogenetic Distance Models

Bioinformatics

Algorithms

Phylogenetics

Evolution

How substitution models turn an alignment’s observed mismatches into evolutionary distance estimates for phylogenetic inference.

Aug 25, 2026

6 min

Copy-Number Segmentation Algorithms

Bioinformatics

Algorithms

Genomics

Copy Number Variation

How segmentation detects change-points in ordered copy-number measurements and reports coherent genomic gains, losses, and copy-neutral regions.

Aug 24, 2026

6 min

Structural-Variant Discovery Algorithms

Bioinformatics

Algorithms

Genomics

Structural Variation

How structural-variant callers combine anomalous read pairs, split reads, depth shifts, and assemblies to locate and genotype genomic rearrangements.

Aug 24, 2026

6 min

Haplotype Assembly and Phasing

Bioinformatics

Algorithms

Genomics

Haplotype Phasing

How read-backed haplotype assembly and statistical phasing recover which heterozygous alleles occur together on the same chromosome.

Aug 23, 2026

7 min

Variant-Calling Likelihood Models

Bioinformatics

Algorithms

Variant Calling

Statistical Inference

How variant callers turn aligned bases and their uncertainty into genotype likelihoods, posterior calls, and calibrated quality scores.

Aug 23, 2026

7 min

Bayesian Inference in Bioinformatics

Bioinformatics

Algorithms

Statistical Inference

Bayesian Methods

How Bayesian inference turns prior assumptions and data likelihoods into posterior distributions for biological parameters, hypotheses, and latent states.

Aug 22, 2026

6 min

Markov Chain Monte Carlo

Bioinformatics

Algorithms

Statistical Inference

Bayesian Methods

How Markov chain Monte Carlo approximates posterior distributions with dependent samples, and how to diagnose whether biological inferences are reliable.

Aug 22, 2026

6 min

Expectation–Maximization

Bioinformatics

Algorithms

Statistical Inference

Hidden Markov Models

How expectation–maximization alternates between soft latent-variable assignments and parameter updates, with applications to hidden Markov models and mixture models in bioinformatics.

Aug 21, 2026

5 min

Viterbi and Forward–Backward Algorithms

Bioinformatics

Algorithms

Hidden Markov Models

Dynamic Programming

How the Viterbi, Forward, and Backward recurrences extract best paths, total likelihoods, and posterior state probabilities from hidden Markov models.

Aug 21, 2026

5 min

Pairwise Hidden Markov Models

Bioinformatics

Algorithms

Sequence Alignment

Hidden Markov Models

How pairwise HMMs turn substitution and indel assumptions into probabilities for alignments and alignment uncertainty.

Aug 20, 2026

5 min

Profile HMMs for Protein Families

Bioinformatics

Algorithms

Protein Families

Hidden Markov Models

How profile hidden Markov models represent conserved protein-family positions, insertions, and deletions for sensitive sequence annotation.

Aug 20, 2026

6 min

Mapping Quality Estimation

Bioinformatics

Algorithms

Read Mapping

Statistical Inference

How aligners summarize uncertainty that a reported read alignment is at the correct reference location.

Aug 19, 2026

5 min

Read Mapping and Seed Chaining

Bioinformatics

Algorithms

Read Mapping

Sequence Alignment

How modern read mappers use seeds, collinear chaining, and local alignment to place sequencing reads on a reference.

Aug 19, 2026

5 min

Hash-Based Sequence Indexing

Bioinformatics

Algorithms

Sequence Search

Data Structures

How hash tables index k-mer seeds and their reference positions for fast candidate generation in sequence search and read mapping.

Aug 18, 2026

5 min

Suffix Trees and Suffix Arrays

Bioinformatics

Algorithms

Sequence Search

Data Structures

How suffix trees and suffix arrays index every suffix of a biological sequence to support exact substring search and related sequence analyses.

Aug 18, 2026

4 min

Burrows–Wheeler Transform

Bioinformatics

Algorithms

Sequence Analysis

Data Structures

How the Burrows–Wheeler transform permutes a sequence reversibly, clustering similar characters to support compact genomic indexes.

Aug 17, 2026

4 min

FM-index for Sequence Search

Bioinformatics

Algorithms

Sequence Search

Data Structures

How an FM-index combines the Burrows–Wheeler transform with rank queries to find exact sequence matches in compressed reference indexes.

Aug 17, 2026

5 min

de Bruijn Graphs for Genome Assembly

Bioinformatics

Algorithms

Genome Assembly

Graphs

How de Bruijn graphs turn sequencing reads into k-mer connectivity, enabling scalable genome assembly while exposing repeats and errors.

Aug 16, 2026

5 min

Overlap–Layout–Consensus Assembly

Bioinformatics

Algorithms

Genome Assembly

Graphs

How overlap–layout–consensus assembly finds reliable read overlaps, resolves their layout, and derives a consensus sequence.

Aug 16, 2026

5 min

k-mers and Sequence Composition

Bioinformatics

Algorithms

Sequence Analysis

Genomics

How k-mers represent sequence content, enable fast counting and comparison, and introduce statistical and practical trade-offs.

Aug 15, 2026

5 min

Minimizers and Sequence Sketching

Bioinformatics

Algorithms

Sequence Analysis

Genome Assembly

How minimizers subsample k-mers while preserving shared local sequence context for indexing, mapping, and assembly.

Aug 15, 2026

5 min

BLAST Seed-and-Extend Search

Bioinformatics

Algorithms

Sequence Search

Database Indexing

How BLAST finds statistically interpretable local sequence matches quickly through word hits and extension.

Aug 14, 2026

5 min

FASTA Sequence-Search Algorithm

Bioinformatics

Algorithms

Sequence Search

Local Alignment

How the FASTA algorithm identifies likely local sequence similarities before calculating detailed alignments.

Aug 14, 2026

5 min

Global Sequence Alignment: Needleman–Wunsch

Bioinformatics

Algorithms

Sequence Alignment

Dynamic Programming

A practical and mathematical guide to Needleman–Wunsch global alignment.

Aug 13, 2026

9 min

Local Sequence Alignment: Smith–Waterman

Bioinformatics

Algorithms

Sequence Alignment

Dynamic Programming

A practical and mathematical guide to Smith–Waterman local alignment.

Aug 13, 2026

8 min

CNV Detection by FISH, Microarray/SNP Array, and Whole-Genome Sequencing

Biology

Summarize the principles of FISH, SNP-array and NGS for CNV detection

Aug 12, 2026

33 min

Daily Translation: A Weekend at the Mall

English Learning

Daily Translation

你周末和朋友一起去商场逛街，先在几家服装店随便逛了逛，试了几件衣服但没买。之后你们去电影院看了一部刚上映的喜剧片，电影很搞笑，看得很轻松。看完电影在商场楼下买了两杯奶茶，边喝边聊，然后一起回家了。

Apr 4, 2026

1 min

Daily Translation: Hotpot with a Friend

English Learning

Daily Translation

你下午和朋友发消息，约好晚上一起去家附近的火锅店吃饭。你提前几分钟到了餐厅门口等他，朋友到了之后你们一起进去，找了个靠窗的位置坐下，点了肥牛、毛肚和一些蔬菜，边吃边聊最近的工作和生活，吃得很开心，最后一起结账离开。

Apr 2, 2026

1 min

Daily Translation: Putting Away the Laundry

English Learning

Daily Translation

你洗完澡出来，觉得房间有点闷，就把窗户打开透透气。然后去阳台把晾干的衣服收下来，一件件叠好，分别放进衣柜和抽屉。弄完之后觉得有点累，就坐在椅子上喝了杯温水，歇了一会儿。

Mar 25, 2026

1 min

Daily Translation: Scrambled Eggs with Tomatoes

English Learning

Daily Translation

你晚上打算做番茄炒蛋。先从冰箱拿出番茄和鸡蛋，把番茄洗干净切成块，打了两个鸡蛋搅匀。锅里倒油烧热，先把鸡蛋炒好盛出来，再炒番茄，等番茄出汁后把鸡蛋倒回去一起翻炒，加点盐和糖调味，简单的家常菜就做好了。

Mar 24, 2026

1 min

Daily Translation: Picking Up a Parcel

English Learning

Daily Translation

你下午出门去小区门口取快递，顺便在楼下便利店买了一瓶冰饮料。回家路上碰到邻居带着小狗散步，你停下来摸了摸小狗，跟邻居简单聊了几句天气，然后就上楼回家了。

Mar 23, 2026

1 min

Daily Translation: A Slow Weekend Morning

English Learning

Daily Translation

你周末早上醒得不算早，躺在床上刷了会儿短视频，磨蹭半天才起床。简单洗漱完，给自己泡了杯咖啡，烤了两片面包当早餐。吃完后收拾了一下桌子，把脏衣服扔进洗衣机，打算下午再出门逛逛。

Mar 22, 2026

1 min

Daily Translation: An Evening at Home

English Learning

Daily Translation

你下班回家，路上顺便去超市买了点水果和牛奶，回到家发现冰箱里还有昨天没吃完的外卖，于是先把新买的东西放进冰箱，然后简单热了点东西当晚饭，吃完后坐在沙发上刷了会儿手机，准备等会儿去洗澡睡觉。

Mar 21, 2026

1 min

Daily Translation: A Rushed Morning

English Learning

Daily Translation

你早上起晚了，匆匆忙忙洗漱、换衣服，出门发现没带钥匙和手机，又跑回去拿，结果赶到地铁站时刚好错过一班地铁，只能在站台等下一班，心里有点着急，怕上班迟到。

Mar 20, 2026

1 min

20251218-Linux skills

daily

Linux

# print a file and show only two decimal digits for floating-point numbers
awk 'BEGIN{FS=OFS="\t"} {
    for(i=1; i<=NF; i++) {
        if ($i ~ /^[-+]?[0-9]*\.?[0-9]+$…

Dec 18, 2025

1 min

20251217-Linux skills

daily

Linux

# 从metadata里取cell id，然后在matrix里提取有这个cell id的行
awk 'NR==FNR {words["\"" $1 "\""] = 1; next} $1 in words' normal/PC1_clusterA_normal_metadata.tsv PC1_clusterA_matrix.txt > no…

Dec 17, 2025

1 min

20251216-Efficient-MST

daily

Python

MST

"""
Constructs a Minimum Spanning Tree (MST) from single-cell copy number profiles
based on the Euclidean distance.

Optimized version using pandas, scipy.spatial, and…