Evidence map›Paper›PMID 42680988›Full record

ArticleMethods in molecular biology (Clifton, N.J.)2026

Using Biological Networks to Guide Biomedical Prediction.

Xiaoyu Zhao, JungHo Kong, Karen Pu, Christopher Churas, Jillian A Parker, Trey Ideker

Abstract read
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In one paragraph

Article in Methods in molecular biology (Clifton, N.J.), 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

6 authors.

Xiaoyu Zhao *Department of Medicine, University of California San Diego, La Jolla, USA.
JungHo Kong *Department of Medicine, University of California San Diego, La Jolla, USA.
Karen Pu *Department of Medicine, University of California San Diego, La Jolla, USA.
Christopher ChurasDepartment of Medicine, University of California San Diego, La Jolla, USA.
Jillian A ParkerDepartment of Medicine, University of California San Diego, La Jolla, USA. jillianparker@ucsd.edu.
Trey IdekerDepartment of Medicine, University of California San Diego, La Jolla, USA. tideker@ucsd.edu.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Predictive modeling is a transformative tool for understanding complex biological systems and advancing biomedical discovery. A central challenge is ensuring that predictive models are not only accurate but also biologically interpretable. One way to address this challenge is through network-guided approaches, which integrate prior biological knowledge into bioinformatic algorithms and model architectures. By aligning predictive models with biological networks at various scales, these approaches can improve biological interpretability while maintaining strong predictive performance. In this chapter, we introduce the fundamentals of biological networks and describe strategies for incorporating networks into modeling frameworks for predicting biomedically relevant phenotypes. These concepts are explored via a case study of network-guided drug response prediction, in which hierarchical knowledge of cell biology is instrumental to achieving interpretable predictions and biological insights into chemoresistance.

Indexed as

Computational BiologyModels, BiologicalAlgorithmsGene Regulatory NetworksHumansPrediction AlgorithmsBiological networksDrug responseInterpretabilityPredictive modeling

Identifiers

What Socratic holds

Textmetadata
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.