{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,4,12]],"date-time":"2026-04-12T08:43:28Z","timestamp":1775983408784,"version":"3.50.1"},"posted":{"date-parts":[[2025,6,3]]},"group-title":"Bioinformatics","reference-count":47,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2025,6,3]],"date-time":"2025-06-03T00:00:00Z","timestamp":1748908800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"NIH","award":["R01AI171984"],"award-info":[{"award-number":["R01AI171984"]}]},{"name":"NIH","award":["R03CA290259"],"award-info":[{"award-number":["R03CA290259"]}]},{"name":"NIH","award":["R01CA251066"],"award-info":[{"award-number":["R01CA251066"]}]},{"name":"NIH","award":["R01GM12130"],"award-info":[{"award-number":["R01GM12130"]}]},{"name":"NIH","award":["R01HG012444"],"award-info":[{"award-number":["R01HG012444"]}]},{"name":"Michelle Lunn Hope Foundation"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2025,6,3]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                <jats:sec>\n                  <jats:title>Background<\/jats:title>\n                  <jats:p>Disease heterogeneity is a persistent challenge in medicine, complicating both research and treatment. Standard analytical pipelines often assume patient populations are homogeneous, overlooking variance patterns that may signal biologically distinct subgroups. Variance heterogeneity (VH)\u2014including skewness, outliers, and multimodal distributions\u2014offers a powerful but underused lens for detecting latent etiological structures relevant to prognosis and therapeutic response.<\/jats:p>\n                <\/jats:sec>\n                <jats:sec>\n                  <jats:title>Methods<\/jats:title>\n                  <jats:p>A major barrier to VH analysis is the fragmented landscape of available methods, many of which rely on normality assumptions that biological data frequently violate. In addition, existing tools often require programming expertise, and clear guidance on study design considerations\u2014such as sample size and method selection\u2014is lacking. To address these issues, we developed BifurcatoR, an open-source software platform that simplifies the detection, modeling, and interpretation of VH. BifurcatoR integrates simulation-based method evaluation, study design recommendations, and a user-friendly web interface to support VH analysis across a range of data distributions. We benchmarked VH methods through simulation and applied BifurcatoR to two clinical datasets: acute myeloid leukemia (AML) and obesity.<\/jats:p>\n                <\/jats:sec>\n                <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Simulation studies revealed that VH method performance is highly context-specific, varying with distribution shape, mean-variance coupling, and underlying subgroup structure. In AML, BifurcatoR identified two molecularly distinct subgroups with different treatment responses, including an EVI1-high group with significantly poorer prognosis (p &lt; 0.005) among KMT2A-rearranged cases. In a separate study, VH analysis uncovered immunophenotypic subgroups in obesity based on gene-level discordance across monozygotic twin pairs, highlighting latent variation in adipose immune cell composition.<\/jats:p>\n                <\/jats:sec>\n                <jats:sec>\n                  <jats:title>Conclusions<\/jats:title>\n                  <jats:p>VH is not \u201cnoise\u201d, biological variation without clinical relevance. Instead, VH is a structured signal that can reveal latent and clinically meaningful subtypes. BifurcatoR offers a practical, accessible framework for incorporating VH into biomedical research, with implications for biomarker discovery, patient stratification, and precision medicine.<\/jats:p>\n                <\/jats:sec>","DOI":"10.1101\/2025.06.01.657083","type":"posted-content","created":{"date-parts":[[2025,6,4]],"date-time":"2025-06-04T05:25:16Z","timestamp":1749014716000},"source":"Crossref","is-referenced-by-count":0,"title":["BifurcatoR: A Framework for Revealing Clinically Actionable Signal in Variance Masquerading as Noise"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2330-0500","authenticated-orcid":false,"given":"Zachary","family":"Madaj","sequence":"first","affiliation":[{"name":"Bioinformatics and Biostatistics Core, Van Andel Institute, Grand Rapids, MI 49503, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mao","family":"Ding","sequence":"additional","affiliation":[{"name":"MaineHealth Institute for Research, Scarborough, ME"},{"name":"Roux Institute at Northeastern University, Portland, ME"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Carmen","family":"Khoo","sequence":"additional","affiliation":[{"name":"Roux Institute at Northeastern University, Portland, ME"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ember","family":"Tokarski","sequence":"additional","affiliation":[{"name":"Van Andel Research Institute, Grand Rapids, MI 49503, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9551-5474","authenticated-orcid":false,"given":"Luca","family":"Fagnocchi","sequence":"additional","affiliation":[{"name":"Van Andel Research Institute, Grand Rapids, MI 49503, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"name":"PERMUTE","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2755-9299","authenticated-orcid":false,"given":"Ziru","family":"Li","sequence":"additional","affiliation":[{"name":"MaineHealth Institute for Research, Scarborough, ME"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6734-3954","authenticated-orcid":false,"given":"Jesse","family":"Riordan","sequence":"additional","affiliation":[{"name":"Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9745-0977","authenticated-orcid":false,"given":"John Andrew","family":"Pospisilik","sequence":"additional","affiliation":[{"name":"Van Andel Research Institute, Grand Rapids, MI 49503, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9570-7361","authenticated-orcid":false,"given":"Joseph H.","family":"Nadeau","sequence":"additional","affiliation":[{"name":"MaineHealth Institute for Research, Scarborough, ME"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5399-9602","authenticated-orcid":false,"given":"Christine W.","family":"Lary","sequence":"additional","affiliation":[{"name":"MaineHealth Institute for Research, Scarborough, ME"},{"name":"Roux Institute at Northeastern University, Portland, ME"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5665-946X","authenticated-orcid":false,"given":"Timothy J.","family":"Triche","sequence":"additional","affiliation":[{"name":"Van Andel Research Institute, Grand Rapids, MI 49503, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"54368","reference":[{"key":"2026041200521616000_2025.06.01.657083v1.1","doi-asserted-by":"publisher","DOI":"10.1146\/annurev-statistics-030718-105251"},{"key":"2026041200521616000_2025.06.01.657083v1.2","doi-asserted-by":"publisher","DOI":"10.4137\/BII.S31559"},{"key":"2026041200521616000_2025.06.01.657083v1.3","doi-asserted-by":"publisher","DOI":"10.1177\/2050312120934839"},{"key":"2026041200521616000_2025.06.01.657083v1.4","doi-asserted-by":"publisher","DOI":"10.1016\/j.crbiot.2022.02.004"},{"key":"2026041200521616000_2025.06.01.657083v1.5","doi-asserted-by":"publisher","DOI":"10.1016\/j.mjafi.2021.06.020"},{"key":"2026041200521616000_2025.06.01.657083v1.6","doi-asserted-by":"publisher","DOI":"10.1016\/j.wneu.2024.06.142"},{"key":"2026041200521616000_2025.06.01.657083v1.7","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0081699"},{"key":"2026041200521616000_2025.06.01.657083v1.8","unstructured":"Senn S. Dichotomania: an obsessive compulsive disorder that is badly affecting the quality of analysis of pharmaceutical trials 2014."},{"key":"2026041200521616000_2025.06.01.657083v1.9","doi-asserted-by":"publisher","DOI":"10.1177\/0962280215588569"},{"key":"2026041200521616000_2025.06.01.657083v1.10","doi-asserted-by":"publisher","DOI":"10.1016\/j.conctc.2023.101119"},{"key":"2026041200521616000_2025.06.01.657083v1.11","doi-asserted-by":"publisher","DOI":"10.21105\/joss.04031"},{"key":"2026041200521616000_2025.06.01.657083v1.12","doi-asserted-by":"publisher","DOI":"10.32614\/RJ-2016-021"},{"key":"2026041200521616000_2025.06.01.657083v1.13","doi-asserted-by":"publisher","DOI":"10.18637\/jss.v097.i09"},{"key":"2026041200521616000_2025.06.01.657083v1.14","doi-asserted-by":"publisher","DOI":"10.1038\/nm.4439"},{"key":"2026041200521616000_2025.06.01.657083v1.15","doi-asserted-by":"publisher","DOI":"10.3324\/haematol.2022.281653"},{"key":"2026041200521616000_2025.06.01.657083v1.16","unstructured":"Therneau TM . survival: Survival Analysis."},{"key":"2026041200521616000_2025.06.01.657083v1.17","unstructured":"Kassambara A , Kosinski M , Biecek P. survminer: Drawing Survival Curves using ggplot2."},{"key":"2026041200521616000_2025.06.01.657083v1.18","doi-asserted-by":"publisher","DOI":"10.1038\/s42255-022-00629-2"},{"key":"2026041200521616000_2025.06.01.657083v1.19","doi-asserted-by":"publisher","DOI":"10.1016\/j.xinn.2021.100141"},{"key":"2026041200521616000_2025.06.01.657083v1.20","unstructured":"Yu G. enrichplot: Visualization of Functional Enrichment Result."},{"key":"2026041200521616000_2025.06.01.657083v1.21","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.3192"},{"key":"2026041200521616000_2025.06.01.657083v1.22","doi-asserted-by":"publisher","DOI":"10.3324\/haematol.2019.220962"},{"key":"2026041200521616000_2025.06.01.657083v1.23","doi-asserted-by":"publisher","DOI":"10.1182\/blood.2024026598"},{"key":"2026041200521616000_2025.06.01.657083v1.24","doi-asserted-by":"publisher","DOI":"10.1200\/JCO.22.01114"},{"key":"2026041200521616000_2025.06.01.657083v1.25","doi-asserted-by":"publisher","DOI":"10.1056\/NEJMoa021423"},{"key":"2026041200521616000_2025.06.01.657083v1.26","doi-asserted-by":"publisher","DOI":"10.1038\/s41574-019-0176-8"},{"key":"2026041200521616000_2025.06.01.657083v1.27","doi-asserted-by":"publisher","DOI":"10.1016\/j.cmet.2017.02.016"},{"key":"2026041200521616000_2025.06.01.657083v1.28","doi-asserted-by":"publisher","DOI":"10.1016\/j.cmet.2019.03.009"},{"key":"2026041200521616000_2025.06.01.657083v1.29","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2015.12.025"},{"key":"2026041200521616000_2025.06.01.657083v1.30","doi-asserted-by":"publisher","DOI":"10.1016\/j.cmet.2017.02.013"},{"key":"2026041200521616000_2025.06.01.657083v1.31","doi-asserted-by":"publisher","DOI":"10.1038\/s42255-022-00731-5"},{"key":"2026041200521616000_2025.06.01.657083v1.32","doi-asserted-by":"publisher","DOI":"10.1016\/j.cmet.2018.09.022"},{"key":"2026041200521616000_2025.06.01.657083v1.33","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2458-14-233"},{"key":"2026041200521616000_2025.06.01.657083v1.34","doi-asserted-by":"publisher","DOI":"10.1016\/j.mcna.2017.08.011"},{"key":"2026041200521616000_2025.06.01.657083v1.35","doi-asserted-by":"publisher","DOI":"10.1007\/s11695-020-05160-5"},{"key":"2026041200521616000_2025.06.01.657083v1.36","doi-asserted-by":"publisher","DOI":"10.1016\/j.soard.2016.02.021"},{"key":"2026041200521616000_2025.06.01.657083v1.37","doi-asserted-by":"publisher","DOI":"10.1001\/jama.2018.14433"},{"key":"2026041200521616000_2025.06.01.657083v1.38","doi-asserted-by":"publisher","DOI":"10.1177\/19322968241245680"},{"key":"2026041200521616000_2025.06.01.657083v1.39","doi-asserted-by":"publisher","DOI":"10.1136\/bmjopen-2024-089477"},{"key":"2026041200521616000_2025.06.01.657083v1.40","doi-asserted-by":"publisher","DOI":"10.1080\/17512433.2018.1501271"},{"key":"2026041200521616000_2025.06.01.657083v1.41","doi-asserted-by":"publisher","DOI":"10.3324\/haematol.2014.107128"},{"key":"2026041200521616000_2025.06.01.657083v1.42","doi-asserted-by":"publisher","DOI":"10.18637\/jss.v061.i08"},{"key":"2026041200521616000_2025.06.01.657083v1.43","doi-asserted-by":"publisher","DOI":"10.1097\/MOP.0000000000000226"},{"key":"2026041200521616000_2025.06.01.657083v1.44","doi-asserted-by":"publisher","DOI":"10.1212\/WNL.0000000000007957"},{"key":"2026041200521616000_2025.06.01.657083v1.45","doi-asserted-by":"publisher","DOI":"10.1214\/13-ejs781"},{"key":"2026041200521616000_2025.06.01.657083v1.46","unstructured":"Ester M , Kriegel H-P , Sander J , Xu X. A Density-Based Algorithm for Discovering Clusters in Large Spatial Da tabases with Noise. In: Simoudis E , Han J , Fayyad UM , eds.: AAAI Press:226\u2013231."},{"key":"2026041200521616000_2025.06.01.657083v1.47","doi-asserted-by":"publisher","DOI":"10.1111\/j.2517-6161.1977.tb01600.x"}],"container-title":[],"original-title":[],"link":[{"URL":"https:\/\/syndication.highwire.org\/content\/doi\/10.1101\/2025.06.01.657083","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,4,12]],"date-time":"2026-04-12T07:52:24Z","timestamp":1775980344000},"score":1,"resource":{"primary":{"URL":"http:\/\/biorxiv.org\/lookup\/doi\/10.1101\/2025.06.01.657083"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,6,3]]},"references-count":47,"URL":"https:\/\/doi.org\/10.1101\/2025.06.01.657083","relation":{},"subject":[],"published":{"date-parts":[[2025,6,3]]},"subtype":"preprint"}}