{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,9]],"date-time":"2026-01-09T02:40:54Z","timestamp":1767926454544,"version":"3.49.0"},"reference-count":145,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2022,10,6]],"date-time":"2022-10-06T00:00:00Z","timestamp":1665014400000},"content-version":"vor","delay-in-days":1,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31900473"],"award-info":[{"award-number":["31900473"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31871322"],"award-info":[{"award-number":["31871322"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"State Key Laboratory of Space Medicine Fundamentals and Application","award":["SMFA19B01"],"award-info":[{"award-number":["SMFA19B01"]}]},{"name":"State Key Laboratory of Space Medicine Fundamentals and Application","award":["SMFA19C01"],"award-info":[{"award-number":["SMFA19C01"]}]},{"name":"State Key Laboratory of Space Medicine Fundamentals and Application","award":["SMFA19A03"],"award-info":[{"award-number":["SMFA19A03"]}]},{"name":"Space Medical Experiment Project of China Manned Space Program","award":["HYZHXM01004"],"award-info":[{"award-number":["HYZHXM01004"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,11,19]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>As space exploration programs progress, manned space missions will become more frequent and farther away from Earth, putting a greater emphasis on astronaut health. Through the collaborative efforts of researchers from various countries, the effect of the space environment factors on living systems is gradually being uncovered. Although a large number of interconnected research findings have been produced, their connection seems to be confused, and many unknown effects are left to be discovered. Simultaneously, several valuable data resources have emerged, accumulating data measuring biological effects in space that can be used to further investigate the unknown biological adaptations. In this review, the previous findings and their correlations are sorted out to facilitate the understanding of biological adaptations to space and the design of countermeasures. The biological effect measurement methods\/data types are also organized to provide references for experimental design and data analysis. To aid deeper exploration of the data resources, we summarized common characteristics of the data generated from longitudinal experiments, outlined challenges or caveats in data analysis and provided corresponding solutions by recommending bioinformatics strategies and available models\/tools.<\/jats:p>","DOI":"10.1093\/bib\/bbac415","type":"journal-article","created":{"date-parts":[[2022,10,6]],"date-time":"2022-10-06T11:42:50Z","timestamp":1665056570000},"source":"Crossref","is-referenced-by-count":3,"title":["Integrating bioinformatic strategies in spatial life science research"],"prefix":"10.1093","volume":"23","author":[{"given":"Yangyang","family":"Hao","sequence":"first","affiliation":[{"name":"Key Laboratory of DGHD, MOE, School of Life Science and Technology, Southeast University , Nanjing, China"}]},{"given":"Liang","family":"Lu","sequence":"additional","affiliation":[{"name":"The State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center , No. 26 Beiqing Road, Haidian District, Beijing, 100094, China"}]},{"given":"Anna","family":"Liu","sequence":"additional","affiliation":[{"name":"Key Laboratory of DGHD, MOE, School of Life Science and Technology, Southeast University , Nanjing, China"}]},{"given":"Xue","family":"Lin","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics, School of Biomedical Engineering and Informatics, Nanjing Medical University , Nanjing, China"}]},{"given":"Li","family":"Xiao","sequence":"additional","affiliation":[{"name":"The State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center , No. 26 Beiqing Road, Haidian District, Beijing, 100094, China"}]},{"given":"Xiaoyue","family":"Kong","sequence":"additional","affiliation":[{"name":"Key Laboratory of DGHD, MOE, School of Life Science and Technology, Southeast University , Nanjing, China"}]},{"given":"Kai","family":"Li","sequence":"additional","affiliation":[{"name":"The State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center , No. 26 Beiqing Road, Haidian District, Beijing, 100094, China"}]},{"given":"Fengji","family":"Liang","sequence":"additional","affiliation":[{"name":"The State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center , No. 26 Beiqing Road, Haidian District, Beijing, 100094, China"}]},{"given":"Jianghui","family":"Xiong","sequence":"additional","affiliation":[{"name":"The State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center , No. 26 Beiqing Road, Haidian District, Beijing, 100094, China"}]},{"given":"Lina","family":"Qu","sequence":"additional","affiliation":[{"name":"The State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center , No. 26 Beiqing Road, Haidian District, Beijing, 100094, China"}]},{"given":"Yinghui","family":"Li","sequence":"additional","affiliation":[{"name":"The State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center , No. 26 Beiqing Road, Haidian District, Beijing, 100094, China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8706-6421","authenticated-orcid":false,"given":"Jian","family":"Li","sequence":"additional","affiliation":[{"name":"Key Laboratory of DGHD, MOE, School of Life Science and Technology, Southeast University , Nanjing, China"}]}],"member":"286","published-online":{"date-parts":[[2022,10,5]]},"reference":[{"key":"2022112111121037100_ref1","doi-asserted-by":"crossref","first-page":"100172","DOI":"10.1016\/j.patter.2020.100172","article-title":"International Space Station open-source data","volume":"1","author":"Warren","year":"2020","journal-title":"Patterns"},{"key":"2022112111121037100_ref2","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.lssr.2019.05.001","article-title":"Current status of space radiobiological studies in China","volume":"22","author":"Pei","year":"2019","journal-title":"Life Sci Space Res"},{"key":"2022112111121037100_ref3","doi-asserted-by":"crossref","first-page":"8","DOI":"10.1038\/d41586-020-01620-1","article-title":"SpaceX's astronaut launch is a boost for the International Space Station","volume":"582","year":"2020","journal-title":"Nature"},{"key":"2022112111121037100_ref4","article-title":"Towards a unified eulerian modeling framework for two-phase flows: geometrical small scale phenomena and associated flexible computing strategies","author":"Di Battista","year":"2021","journal-title":"Institut Polytechnique de Paris"},{"key":"2022112111121037100_ref5","doi-asserted-by":"crossref","first-page":"1244797","DOI":"10.1126\/science.1244797","article-title":"Mars' surface radiation environment measured with the Mars Science Laboratory's Curiosity rover","volume":"343","author":"Hassler","year":"2014","journal-title":"Science"},{"key":"2022112111121037100_ref6","doi-asserted-by":"crossref","first-page":"1162","DOI":"10.1016\/j.cell.2020.10.050","article-title":"Fundamental biological features of spaceflight: advancing the field to enable deep-space exploration","volume":"183","author":"Afshinnekoo","year":"2020","journal-title":"Cell"},{"key":"2022112111121037100_ref7","doi-asserted-by":"crossref","first-page":"S176","DOI":"10.4103\/0028-3886.259123","article-title":"Human health during space travel: an overview","volume":"67","author":"Kandarpa","year":"2019","journal-title":"Neurol India"},{"key":"2022112111121037100_ref8","first-page":"354","article-title":"Space stress injury and related protective measures","volume-title":"Sheng Li Ke Xue Jin Zhan","author":"Li","year":"2013"},{"key":"2022112111121037100_ref9","doi-asserted-by":"crossref","first-page":"720","DOI":"10.1093\/jrr\/rru014","article-title":"The combined effects of X-ray radiation and hindlimb suspension on bone loss","volume":"55","author":"Xu","year":"2014","journal-title":"J Radiat Res"},{"key":"2022112111121037100_ref10","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1007\/978-3-030-74022-1_3","article-title":"Success stories: incremental progress and scientific breakthroughs in life science research","author":"Ruyters","year":"2021","journal-title":"Breakthroughs in Space Life Science Research Springer"},{"key":"2022112111121037100_ref11","first-page":"eaau8650","article-title":"The NASA Twins Study: a multidimensional analysis of a year-long human spaceflight","volume-title":"Science","author":"Garrett-Bakelman","year":"2019"},{"key":"2022112111121037100_ref12","doi-asserted-by":"crossref","first-page":"D1515","DOI":"10.1093\/nar\/gkaa887","article-title":"NASA GeneLab: interfaces for the exploration of space omics data","volume":"49","author":"Berrios","year":"2021","journal-title":"Nucleic Acids Res"},{"key":"2022112111121037100_ref13","doi-asserted-by":"crossref","first-page":"40","DOI":"10.1186\/s40798-017-0107-y","article-title":"The effect of long-term confinement and the efficacy of exercise countermeasures on muscle strength during a simulated mission to Mars: data from the Mars500 study","volume":"3","author":"Gaffney","year":"2017","journal-title":"Sports Med Open"},{"key":"2022112111121037100_ref14","first-page":"575","article-title":"Multi-system adaptation to confinement during the 180-day controlled ecological life support system (CELSS) experiment","volume-title":"Front Physiol","author":"Yuan","year":"2019"},{"key":"2022112111121037100_ref15","doi-asserted-by":"crossref","DOI":"10.3390\/ijms19124106","article-title":"Effects of space flight on mouse liver versus kidney: gene pathway analyses","volume":"19","author":"Hammond","year":"2018","journal-title":"Int J Mol Sci"},{"issue":"Suppl","key":"2022112111121037100_ref16","first-page":"S3","article-title":"How cells (might) sense microgravity","volume":"13","author":"Ingber","year":"1999","journal-title":"FASEB J"},{"key":"2022112111121037100_ref17","first-page":"423","article-title":"Genetic and apoptotic changes in lungs of mice flown on the STS-135 mission in space","volume":"29","author":"Gridley","year":"2015","journal-title":"In Vivo"},{"key":"2022112111121037100_ref18","doi-asserted-by":"crossref","DOI":"10.3390\/ijms21249373","article-title":"Influence of microgravity on apoptosis in cells, tissues, and other systems in vivo and in vitro","volume":"21","author":"Prasad","year":"2020","journal-title":"Int J Mol Sci"},{"key":"2022112111121037100_ref19","doi-asserted-by":"crossref","DOI":"10.1155\/2021\/5566872","article-title":"Microgravity, stem cells, and cancer: a new hope for cancer treatment","volume-title":"Stem Cells Int","author":"Topal","year":"2021"},{"key":"2022112111121037100_ref20","first-page":"7345","article-title":"Breast cancer cells in microgravity: new aspects for cancer research","volume-title":"Int J Mol Sci","author":"Nassef","year":"2020"},{"key":"2022112111121037100_ref21","doi-asserted-by":"crossref","first-page":"917","DOI":"10.1038\/nm0897-917","article-title":"A novel anti-apoptosis gene, survivin, expressed in cancer and lymphoma","volume":"3","author":"Ambrosini","year":"1997","journal-title":"Nat Med"},{"key":"2022112111121037100_ref22","doi-asserted-by":"crossref","first-page":"652434","DOI":"10.1155\/2014\/652434","article-title":"Phenotypic switch induced by simulated microgravity on MDA-MB-231 breast cancer cells","volume":"2014","author":"Masiello","year":"2014","journal-title":"Biomed Res Int"},{"key":"2022112111121037100_ref23","doi-asserted-by":"crossref","first-page":"813","DOI":"10.1096\/fj.13-243287","article-title":"Differential gene expression profile and altered cytokine secretion of thyroid cancer cells in space","volume":"28","author":"Ma","year":"2014","journal-title":"FASEB J"},{"key":"2022112111121037100_ref24","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1016\/j.bone.2015.12.057","article-title":"The impact of microgravity on bone in humans","volume":"87","author":"Grimm","year":"2016","journal-title":"Bone"},{"key":"2022112111121037100_ref25","doi-asserted-by":"crossref","first-page":"122","DOI":"10.1097\/CRD.0000000000000236","article-title":"Effects of spaceflight on cardiovascular physiology and health","volume":"27","author":"Shen","year":"2019","journal-title":"Cardiol Rev"},{"key":"2022112111121037100_ref26","doi-asserted-by":"crossref","first-page":"463","DOI":"10.1089\/ast.2009.0415","article-title":"Bioastronautics: the influence of microgravity on astronaut health","volume":"10","author":"Blaber","year":"2010","journal-title":"Astrobiology"},{"key":"2022112111121037100_ref27","doi-asserted-by":"crossref","first-page":"74","DOI":"10.1016\/j.lssr.2020.07.009","article-title":"The effects of microgravity on the digestive system and the new insights it brings to the life sciences","volume":"27","author":"Yang","year":"2020","journal-title":"Life Sci Space Res"},{"key":"2022112111121037100_ref28","doi-asserted-by":"crossref","first-page":"317","DOI":"10.1093\/neuros\/nyy531","article-title":"Neurosurgery and manned spaceflight","volume":"86","author":"Panesar","year":"2020","journal-title":"Neurosurgery"},{"key":"2022112111121037100_ref29","doi-asserted-by":"crossref","first-page":"444","DOI":"10.1016\/j.wneu.2017.10.062","article-title":"Spaceflight and neurosurgery: a comprehensive review of the relevant literature","volume":"109","author":"Swinney","year":"2018","journal-title":"World Neurosurg"},{"key":"2022112111121037100_ref30","doi-asserted-by":"crossref","first-page":"2058","DOI":"10.1016\/j.ophtha.2011.06.021","article-title":"Optic disc edema, globe flattening, choroidal folds, and hyperopic shifts observed in astronauts after long-duration space flight","volume":"118","author":"Mader","year":"2011","journal-title":"Ophthalmology"},{"key":"2022112111121037100_ref31","first-page":"19","article-title":"Cosmic ray effects on the eyes of rats flown on Cosmos No. 782, experimental K-007","volume":"49","author":"Philpott","year":"1978","journal-title":"Aviat Space Environ Med"},{"key":"2022112111121037100_ref32","doi-asserted-by":"crossref","first-page":"4703286","DOI":"10.1155\/2020\/4703286","article-title":"Space radiation biology for \"living in space\"","volume":"2020","author":"Furukawa","year":"2020","journal-title":"Biomed Res Int"},{"key":"2022112111121037100_ref33","volume-title":"Radiobiology for the Radiologist","author":"Hall","edition":"6th"},{"key":"2022112111121037100_ref34","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1667\/RR13804.1","article-title":"Understanding cancer development processes after HZE-particle exposure: roles of ROS, DNA damage repair and inflammation","volume":"183","author":"Sridharan","year":"2015","journal-title":"Radiat Res"},{"key":"2022112111121037100_ref35","doi-asserted-by":"crossref","first-page":"78","DOI":"10.1016\/j.mrrev.2009.12.006","article-title":"Spatiotemporal characterization of ionizing radiation induced DNA damage foci and their relation to chromatin organization","volume":"704","author":"Costes","year":"2010","journal-title":"Mutat Res"},{"key":"2022112111121037100_ref36","first-page":"129","article-title":"The individual and combined effects of spaceflight radiation and microgravity on biologic systems and functional outcomes","volume":"39","author":"Willey","year":"2021","journal-title":"J Environ Sci Health C Toxicol Carcinog"},{"key":"2022112111121037100_ref37","first-page":"180","article-title":"Consequences of space radiation on the brain and cardiovascular system","volume":"39","author":"Davis","year":"2021","journal-title":"J Environ Sci Health C Toxicol Carcinog"},{"key":"2022112111121037100_ref38","doi-asserted-by":"crossref","first-page":"211","DOI":"10.1016\/S0027-5107(99)00132-3","article-title":"Combined effects of space flight factors and radiation on humans","volume":"430","author":"Todd","year":"1999","journal-title":"Mutat Res"},{"key":"2022112111121037100_ref39","doi-asserted-by":"crossref","first-page":"2107","DOI":"10.1016\/S0273-1177(99)01062-5","article-title":"Genomic instability induced by high and low LET ionizing radiation","volume":"25","author":"Limoli","year":"2000","journal-title":"Adv Space Res"},{"key":"2022112111121037100_ref40","doi-asserted-by":"crossref","first-page":"1431","DOI":"10.1080\/09553002.2018.1547848","article-title":"Risk of second cancer after ion beam radiotherapy: insights from animal carcinogenesis studies","volume":"95","author":"Imaoka","year":"2019","journal-title":"Int J Radiat Biol"},{"key":"2022112111121037100_ref41","doi-asserted-by":"crossref","first-page":"123","DOI":"10.1016\/j.lfs.2013.12.008","article-title":"Simulated microgravity increases heavy ion radiation-induced apoptosis in human B lymphoblasts","volume":"97","author":"Dang","year":"2014","journal-title":"Life Sci"},{"key":"2022112111121037100_ref42","doi-asserted-by":"crossref","first-page":"559","DOI":"10.1089\/ars.2012.4938","article-title":"New insights into the link between DNA damage and apoptosis","volume":"19","author":"De Zio","year":"2013","journal-title":"Antioxid Redox Signal"},{"key":"2022112111121037100_ref43","doi-asserted-by":"crossref","first-page":"9911","DOI":"10.1038\/s41598-019-46303-8","article-title":"Study of the impact of long-duration space missions at the International Space Station on the astronaut microbiome","volume":"9","author":"Voorhies","year":"2019","journal-title":"Sci Rep"},{"key":"2022112111121037100_ref44","doi-asserted-by":"crossref","first-page":"1409","DOI":"10.1136\/gutjnl-2020-320666","article-title":"Time series analysis of microbiome and metabolome at multiple body sites in steady long-term isolation confinement","volume":"70","author":"Feng","year":"2021","journal-title":"Gut"},{"key":"2022112111121037100_ref45","doi-asserted-by":"crossref","first-page":"14","DOI":"10.1111\/jam.14789","article-title":"Gut microbiome and human health under the space environment","volume":"130","author":"Siddiqui","year":"2021","journal-title":"J Appl Microbiol"},{"key":"2022112111121037100_ref46","first-page":"215","article-title":"The gut microbiome and digestive health\u2013a new frontier","volume-title":"Clin Gastroenterol Hepatol","author":"Ananthakrishnan","year":"2019"},{"key":"2022112111121037100_ref47","article-title":"Transcriptomics, NF-kappaB pathway, and their potential spaceflight-related health consequences","volume":"18","author":"Zhang","year":"2017","journal-title":"Int J Mol Sci"},{"key":"2022112111121037100_ref48","doi-asserted-by":"crossref","DOI":"10.3389\/fphys.2019.00932","article-title":"Personalized epigenome remodeling under biochemical and psychological changes during long-term isolation environment","author":"Liang","year":"2019"},{"key":"2022112111121037100_ref49","doi-asserted-by":"crossref","first-page":"e87087","DOI":"10.1371\/journal.pone.0087087","article-title":"During the long way to Mars: effects of 520 days of confinement (Mars500) on the assessment of affective stimuli and stage alteration in mood and plasma hormone levels","volume":"9","author":"Wang","year":"2014","journal-title":"PLoS One"},{"key":"2022112111121037100_ref50","doi-asserted-by":"crossref","first-page":"208","DOI":"10.1016\/j.bbr.2010.03.034","article-title":"Exercise as a countermeasure to psycho-physiological deconditioning during long-term confinement","volume":"211","author":"Schneider","year":"2010","journal-title":"Behav Brain Res"},{"key":"2022112111121037100_ref51","doi-asserted-by":"crossref","first-page":"203","DOI":"10.1016\/j.bbi.2014.03.018","article-title":"520-d Isolation and confinement simulating a flight to Mars reveals heightened immune responses and alterations of leukocyte phenotype","volume":"40","author":"Yi","year":"2014","journal-title":"Brain Behav Immun"},{"key":"2022112111121037100_ref52","doi-asserted-by":"crossref","first-page":"39","DOI":"10.1186\/s40168-017-0256-8","article-title":"Temporal dynamics of the gut microbiota in people sharing a confined environment, a 520-day ground-based space simulation, MARS500","volume":"5","author":"Turroni","year":"2017","journal-title":"Microbiome"},{"key":"2022112111121037100_ref53","doi-asserted-by":"crossref","first-page":"6539","DOI":"10.1172\/JCI136105","article-title":"A GABAergic neural circuit in the ventromedial hypothalamus mediates chronic stress-induced bone loss","volume":"130","author":"Yang","year":"2020","journal-title":"J Clin Invest"},{"key":"2022112111121037100_ref54","doi-asserted-by":"crossref","first-page":"2635","DOI":"10.1073\/pnas.1212646110","article-title":"Mars 520-d mission simulation reveals protracted crew hypokinesis and alterations of sleep duration and timing","volume":"110","author":"Basner","year":"2013","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2022112111121037100_ref55","first-page":"23","article-title":"Keeping the right time in space: importance of circadian clock and sleep for physiology and performance of astronauts","volume":"1","author":"Guo","year":"2014","journal-title":"Mil Med Res"},{"key":"2022112111121037100_ref56","doi-asserted-by":"crossref","first-page":"413","DOI":"10.1016\/j.neubiorev.2021.03.032","article-title":"Psychosocial issues in isolated and confined extreme environments","volume":"126","author":"Palinkas","year":"2021","journal-title":"Neurosci Biobehav Rev"},{"key":"2022112111121037100_ref57","doi-asserted-by":"crossref","first-page":"1185, e1120","DOI":"10.1016\/j.cell.2020.11.002","article-title":"Comprehensive multi-omics analysis reveals mitochondrial stress as a central biological hub for spaceflight impact","volume":"183","author":"Silveira","year":"2020","journal-title":"Cell"},{"key":"2022112111121037100_ref58","doi-asserted-by":"crossref","first-page":"aad9780","DOI":"10.1126\/science.aad9780","article-title":"Epigenetic balance of gene expression by Polycomb and COMPASS families","volume":"352","author":"Piunti","year":"2016","journal-title":"Science"},{"key":"2022112111121037100_ref59","doi-asserted-by":"crossref","first-page":"801","DOI":"10.1016\/j.molcel.2005.10.003","article-title":"Gamma-H2AX dephosphorylation by protein phosphatase 2A facilitates DNA double-strand break repair","volume":"20","author":"Chowdhury","year":"2005","journal-title":"Mol Cell"},{"key":"2022112111121037100_ref60","doi-asserted-by":"crossref","first-page":"959","DOI":"10.1016\/j.dnarep.2004.03.024","article-title":"H2AX: the histone guardian of the genome","volume":"3","author":"Fernandez-Capetillo","year":"2004","journal-title":"DNA Repair"},{"key":"2022112111121037100_ref61","doi-asserted-by":"crossref","first-page":"5858","DOI":"10.1074\/jbc.273.10.5858","article-title":"DNA double-stranded breaks induce histone H2AX phosphorylation on serine 139","volume":"273","author":"Rogakou","year":"1998","journal-title":"J Biol Chem"},{"key":"2022112111121037100_ref62","doi-asserted-by":"crossref","first-page":"489","DOI":"10.1038\/nature12752","article-title":"The nexus of chromatin regulation and intermediary metabolism","volume":"502","author":"Gut","year":"2013","journal-title":"Nature"},{"key":"2022112111121037100_ref63","doi-asserted-by":"crossref","first-page":"317","DOI":"10.1038\/nature14248","article-title":"Integrative analysis of 111 reference human epigenomes","volume":"518","author":"Roadmap Epigenomics","year":"2015","journal-title":"Nature"},{"key":"2022112111121037100_ref64","first-page":"57","article-title":"An integrated encyclopedia of DNA elements in the human genome","volume-title":"Nature","author":"Nature","year":"2012"},{"key":"2022112111121037100_ref65","doi-asserted-by":"crossref","first-page":"151","DOI":"10.1038\/nrendo.2014.229","article-title":"Long non-coding RNAs as regulators of the endocrine system","volume":"11","author":"Knoll","year":"2015","journal-title":"Nat Rev Endocrinol"},{"key":"2022112111121037100_ref66","doi-asserted-by":"crossref","first-page":"764","DOI":"10.1016\/j.cmet.2015.04.003","article-title":"De novo reconstruction of adipose tissue transcriptomes reveals long non-coding RNA regulators of brown adipocyte development","volume":"21","author":"Alvarez-Dominguez","year":"2015","journal-title":"Cell Metab"},{"key":"2022112111121037100_ref67","doi-asserted-by":"crossref","first-page":"E190","DOI":"10.1038\/35087138","article-title":"Navigating gene expression using microarrays--a technology review","volume":"3","author":"Schulze","year":"2001","journal-title":"Nat Cell Biol"},{"key":"2022112111121037100_ref68","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1038\/4434","article-title":"Expression profiling using cDNA microarrays","volume":"21","author":"Duggan","year":"1999","journal-title":"Nat Genet"},{"key":"2022112111121037100_ref69","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1038\/nrg2484","article-title":"RNA-Seq: a revolutionary tool for transcriptomics","volume":"10","author":"Wang","year":"2009","journal-title":"Nat Rev Genet"},{"key":"2022112111121037100_ref70","doi-asserted-by":"crossref","first-page":"87","DOI":"10.1038\/nrg2934","article-title":"RNA sequencing: advances, challenges and opportunities","volume":"12","author":"Ozsolak","year":"2011","journal-title":"Nat Rev Genet"},{"key":"2022112111121037100_ref71","doi-asserted-by":"crossref","first-page":"1348","DOI":"10.1038\/s41587-021-01108-x","article-title":"Nanopore sequencing technology, bioinformatics and applications","volume":"39","author":"Wang","year":"2021","journal-title":"Nat Biotechnol"},{"key":"2022112111121037100_ref72","doi-asserted-by":"crossref","DOI":"10.3390\/bios11070214","article-title":"Nanopore technology and its applications in gene sequencing","volume":"11","author":"Lin","year":"2021","journal-title":"Biosensors"},{"key":"2022112111121037100_ref73","doi-asserted-by":"crossref","first-page":"16035","DOI":"10.1038\/npjmgrav.2016.35","article-title":"Nanopore sequencing in microgravity","volume":"2","author":"McIntyre","year":"2016","journal-title":"Microgravity"},{"key":"2022112111121037100_ref74","doi-asserted-by":"crossref","first-page":"739","DOI":"10.1074\/mcp.M113.035550","article-title":"Reproducible and consistent quantification of the Saccharomyces cerevisiae proteome by SWATH-mass spectrometry","volume":"14","author":"Selevsek","year":"2015","journal-title":"Mol Cell Proteomics"},{"key":"2022112111121037100_ref75","doi-asserted-by":"crossref","first-page":"1314","DOI":"10.1074\/mcp.M600007-MCP200","article-title":"Quantitative proteomic analysis of post-translational modifications of human histones","volume":"5","author":"Beck","year":"2006","journal-title":"Mol Cell Proteomics"},{"key":"2022112111121037100_ref76","doi-asserted-by":"crossref","first-page":"255","DOI":"10.1038\/nbt0303-255","article-title":"Proteomic analysis of post-translational modifications","volume":"21","author":"Mann","year":"2003","journal-title":"Nat Biotechnol"},{"key":"2022112111121037100_ref77","doi-asserted-by":"crossref","first-page":"677","DOI":"10.1038\/nmeth.1636","article-title":"A large-scale method to measure absolute protein phosphorylation stoichiometries","volume":"8","author":"Wu","year":"2011","journal-title":"Nat Methods"},{"key":"2022112111121037100_ref78","doi-asserted-by":"crossref","first-page":"427","DOI":"10.1038\/nrm2900","article-title":"Decoding signalling networks by mass spectrometry-based proteomics","volume":"11","author":"Choudhary","year":"2010","journal-title":"Nat Rev Mol Cell Biol"},{"key":"2022112111121037100_ref79","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1002\/mas.20108","article-title":"Mass spectrometry-based metabolomics","volume":"26","author":"Dettmer","year":"2007","journal-title":"Mass Spectrom Rev"},{"key":"2022112111121037100_ref80","doi-asserted-by":"crossref","first-page":"263","DOI":"10.1038\/nrm3314","article-title":"Innovation: metabolomics: the apogee of the omics trilogy","volume":"13","author":"Patti","year":"2012","journal-title":"Nat Rev Mol Cell Biol"},{"key":"2022112111121037100_ref81","doi-asserted-by":"crossref","first-page":"151","DOI":"10.1093\/bib\/bbl009","article-title":"Review: on the analysis and interpretation of correlations in metabolomic data","volume":"7","author":"Steuer","year":"2006","journal-title":"Brief Bioinform"},{"key":"2022112111121037100_ref82","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1016\/j.aca.2009.11.042","article-title":"Chemometrics in metabolomics--a review in human disease diagnosis","volume":"659","author":"Madsen","year":"2010","journal-title":"Anal Chim Acta"},{"key":"2022112111121037100_ref83","doi-asserted-by":"crossref","first-page":"e7762","DOI":"10.7717\/peerj.7762","article-title":"Simulated manned Mars exploration: effects of dietary and diurnal cycle variations on the gut microbiome of crew members in a controlled ecological life support system","volume":"7","author":"Dong","year":"2019","journal-title":"PeerJ"},{"key":"2022112111121037100_ref84","doi-asserted-by":"crossref","first-page":"831","DOI":"10.2217\/fmb-2017-0251","article-title":"Effect of microgravity & space radiation on microbes","volume":"13","author":"Senatore","year":"2018","journal-title":"Future Microbiol"},{"key":"2022112111121037100_ref85","doi-asserted-by":"crossref","first-page":"923","DOI":"10.3389\/fmicb.2020.00923","article-title":"Molecular mechanisms of microbial survivability in outer space: a systems biology approach","volume":"11","author":"Milojevic","year":"2020","journal-title":"Front Microbiol"},{"key":"2022112111121037100_ref86","doi-asserted-by":"crossref","first-page":"152","DOI":"10.1186\/s40168-021-01070-5","article-title":"Defining the resilience of the human salivary microbiota by a 520-day longitudinal study in a confined environment: the Mars500 mission","volume":"9","author":"Bacci","year":"2021","journal-title":"Microbiome"},{"key":"2022112111121037100_ref87","doi-asserted-by":"crossref","first-page":"335","DOI":"10.1038\/nmeth.f.303","article-title":"QIIME allows analysis of high-throughput community sequencing data","volume":"7","author":"Caporaso","year":"2010","journal-title":"Nat Methods"},{"key":"2022112111121037100_ref88","doi-asserted-by":"crossref","first-page":"387","DOI":"10.1016\/j.atherosclerosis.2015.05.035","article-title":"Unraveling the environmental and genetic interactions in atherosclerosis: central role of the gut microbiota","volume":"241","author":"Org","year":"2015","journal-title":"Atherosclerosis"},{"key":"2022112111121037100_ref89","doi-asserted-by":"crossref","first-page":"855","DOI":"10.1038\/nrg2897","article-title":"Phenomics: the next challenge","volume":"11","author":"Houle","year":"2010","journal-title":"Nat Rev Genet"},{"key":"2022112111121037100_ref90","doi-asserted-by":"crossref","first-page":"1060","DOI":"10.3357\/AMHP.5007.2018","article-title":"Fracture risk in spaceflight and potential treatment options","volume":"89","author":"Swaffield","year":"2018","journal-title":"Aerosp Med Hum Perform"},{"key":"2022112111121037100_ref91","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1016\/j.pathophys.2015.10.001","article-title":"Electromyographic evaluation of countermeasures during the terrestrial simulation of interplanetary spaceflight in Mars500 project","volume":"23","author":"Meigal","year":"2016","journal-title":"Pathophysiology"},{"key":"2022112111121037100_ref92","doi-asserted-by":"crossref","first-page":"575","DOI":"10.3389\/fphys.2019.00575","article-title":"Multi-system adaptation to confinement during the 180-day Controlled Ecological Life Support System (CELSS) experiment","volume":"10","author":"Yuan","year":"2019","journal-title":"Front Physiol"},{"key":"2022112111121037100_ref93","doi-asserted-by":"crossref","first-page":"1023","DOI":"10.3357\/ASEM.3612.2013","article-title":"Circadian rhythm of autonomic cardiovascular control during Mars500 simulated mission to Mars","volume":"84","author":"Vigo","year":"2013","journal-title":"Aviat Space Environ Med"},{"key":"2022112111121037100_ref94","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1038\/s41526-021-00133-z","article-title":"A review of alterations to the brain during spaceflight and the potential relevance to crew in long-duration space exploration","volume":"7","author":"Roy-O\u2019Reilly","year":"2021","journal-title":"NPJ Microgravity"},{"key":"2022112111121037100_ref95","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.bbr.2012.08.022","article-title":"The influence of exercise on prefrontal cortex activity and cognitive performance during a simulated space flight to Mars (MARS500)","volume":"236","author":"Schneider","year":"2013","journal-title":"Behav Brain Res"},{"key":"2022112111121037100_ref96","doi-asserted-by":"crossref","first-page":"83","DOI":"10.1016\/j.lssr.2019.09.004","article-title":"Changes of brain DTI in healthy human subjects after 520 days isolation and confinement on a simulated mission to Mars","volume":"24","author":"Brem","year":"2020","journal-title":"Life Sci Space Res"},{"key":"2022112111121037100_ref97","doi-asserted-by":"crossref","first-page":"211","DOI":"10.1016\/j.ijpsycho.2014.04.008","article-title":"How stressful are 105 days of isolation? Sleep EEG patterns and tonic cortisol in healthy volunteers simulating manned flight to Mars","volume":"93","author":"Gemignani","year":"2014","journal-title":"Int J Psychophysiol"},{"key":"2022112111121037100_ref98","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1080\/10803548.2021.1994750","article-title":"The effects of emotional trait factors on simulated flight performance under an acute psychological stress situation","volume":"12","author":"Dai","year":"2021","journal-title":"Int J Occup Saf Ergon"},{"key":"2022112111121037100_ref99","doi-asserted-by":"crossref","first-page":"e93298","DOI":"10.1371\/journal.pone.0093298","article-title":"Psychological and behavioral changes during confinement in a 520-day simulated interplanetary mission to mars","volume":"9","author":"Basner","year":"2014","journal-title":"PLoS One"},{"key":"2022112111121037100_ref100","first-page":"4","article-title":"Needs and challenges of space medicine in China's follow-up manned space missions","volume-title":"Manned Spaceflight","author":"Li","year":"2007"},{"key":"2022112111121037100_ref101","doi-asserted-by":"crossref","first-page":"214","DOI":"10.1016\/j.bbi.2010.09.005","article-title":"Developmental origins of the metabolic syndrome: body clocks and stress responses","volume":"25","author":"Cagampang","year":"2011","journal-title":"Brain Behav Immun"},{"key":"2022112111121037100_ref102","first-page":"141","article-title":"Principal variance components analysis: estimating batch effects in microarray gene expression data","volume-title":"Sources and Solutions","author":"Li","year":"2009"},{"key":"2022112111121037100_ref103","article-title":"Umap: uniform manifold approximation and projection for dimension reduction","author":"McInnes","year":"2018"},{"key":"2022112111121037100_ref104","doi-asserted-by":"crossref","first-page":"118","DOI":"10.1093\/biostatistics\/kxj037","article-title":"Adjusting batch effects in microarray expression data using empirical Bayes methods","volume":"8","author":"Johnson","year":"2006","journal-title":"Biostatistics"},{"key":"2022112111121037100_ref105","doi-asserted-by":"crossref","first-page":"e0156594","DOI":"10.1371\/journal.pone.0156594","article-title":"Removing batch effects from longitudinal gene expression - quantile normalization plus ComBat as best approach for microarray transcriptome data","volume":"11","author":"M\u00fcller","year":"2016","journal-title":"PLoS One"},{"key":"2022112111121037100_ref106","doi-asserted-by":"crossref","first-page":"882","DOI":"10.1093\/bioinformatics\/bts034","article-title":"The sva package for removing batch effects and other unwanted variation in high-throughput experiments","volume":"28","author":"Leek","year":"2012","journal-title":"Bioinformatics"},{"key":"2022112111121037100_ref107","first-page":"3","article-title":"RUV for normalization of expression array data","volume-title":"Bioconductor","author":"Jacob","year":"2014"},{"key":"2022112111121037100_ref108","first-page":"1079","article-title":"BatchServer: a web server for batch effect evaluation, visualization, and correction","volume-title":"J Proteome Res","author":"Zhu","year":"2020"},{"key":"2022112111121037100_ref109","volume-title":"Proceedings of the sixth annual international conference on Computational biology","author":"Bar-Joseph"},{"key":"2022112111121037100_ref110","doi-asserted-by":"crossref","first-page":"100","DOI":"10.1007\/978-3-540-92273-5_6","volume-title":"Transactions on Computational Systems Biology X. Springer","author":"Rueda","year":"2008"},{"key":"2022112111121037100_ref111","doi-asserted-by":"crossref","first-page":"367","DOI":"10.1016\/S0165-0114(01)00047-1","article-title":"A fuzzy seasonal ARIMA model for forecasting","volume":"126","author":"Tseng","year":"2002","journal-title":"Fuzzy Sets Syst"},{"key":"2022112111121037100_ref112","first-page":"1","article-title":"Time series forecasting using holt-winters exponential smoothing","volume-title":"Kanwal Rekhi school of information Technology","author":"Kalekar PSJKRsoiT","year":"2004"},{"key":"2022112111121037100_ref113","first-page":"1","article-title":"GluonTS: probabilistic and neural time series modeling in Python","volume-title":"J Mach Learn Res","author":"Alexandrov","year":"2020"},{"key":"2022112111121037100_ref114","doi-asserted-by":"crossref","first-page":"e0241686","DOI":"10.1371\/journal.pone.0241686","article-title":"Evaluation of classification and forecasting methods on time series gene expression data","volume":"15","author":"Tripto","year":"2020","journal-title":"PLoS One"},{"key":"2022112111121037100_ref115","first-page":"1096","article-title":"maSigPro: a method to identify significantly differential expression profiles in time-course microarray experiments","volume-title":"Bioinformatics","author":"Conesa","year":"2006"},{"key":"2022112111121037100_ref116","first-page":"e119","article-title":"Impulse model-based differential expression analysis of time course sequencing data","volume-title":"Nucleic Acids Res","author":"Fischer","year":"2018"},{"key":"2022112111121037100_ref117","first-page":"288","article-title":"Comparative analysis of differential gene expression tools for RNA sequencing time course data","author":"Spies","year":"2019"},{"key":"2022112111121037100_ref118","first-page":"e47","article-title":"Limma powers differential expression analyses for RNA-sequencing and microarray studies","volume-title":"Nucleic Acids Res","author":"Ritchie","year":"2015"},{"key":"2022112111121037100_ref119","doi-asserted-by":"crossref","first-page":"453","DOI":"10.1038\/nmeth.3337","article-title":"Robust enumeration of cell subsets from tissue expression profiles","volume":"12","author":"Newman","year":"2015","journal-title":"Nat Methods"},{"key":"2022112111121037100_ref120","doi-asserted-by":"crossref","first-page":"5","DOI":"10.6026\/97320630002005","article-title":"Mfuzz: a software package for soft clustering of microarray data","volume":"2","author":"Kumar","year":"2007","journal-title":"Bioinformation"},{"key":"2022112111121037100_ref121","doi-asserted-by":"crossref","first-page":"191","DOI":"10.1186\/1471-2105-7-191","article-title":"STEM: a tool for the analysis of short time series gene expression data","volume":"7","author":"Ernst","year":"2006","journal-title":"BMC Bioinformatics"},{"issue":"Suppl 1","key":"2022112111121037100_ref122","doi-asserted-by":"crossref","first-page":"i159","DOI":"10.1093\/bioinformatics\/bti1022","article-title":"Clustering short time series gene expression data","volume":"21","author":"Ernst","year":"2005","journal-title":"Bioinformatics"},{"key":"2022112111121037100_ref123","article-title":"Torchmeta: a meta-learning library for pytorch","volume-title":"arXiv preprint","author":"Deleu"},{"key":"2022112111121037100_ref124","volume-title":"Int J Comput Math","author":"He"},{"key":"2022112111121037100_ref125","doi-asserted-by":"crossref","DOI":"10.1109\/TPAMI.2023.3312125","article-title":"LibFewShot: a comprehensive library for few-shot learning","volume-title":"arXiv preprint","author":"Li"},{"key":"2022112111121037100_ref126","doi-asserted-by":"crossref","first-page":"1367","DOI":"10.1109\/BigData.2018.8621990","volume-title":"2018 IEEE international conference on big data (Big Data)","author":"Fawaz","year":"2018"},{"key":"2022112111121037100_ref127","first-page":"162432","article-title":"Deep learning applied for histological diagnosis of breast cancer","volume-title":"IEEE Access","author":"Yari","year":"2020"},{"key":"2022112111121037100_ref128","first-page":"7381","article-title":"Transfer learning approaches to improve drug sensitivity prediction in multiple myeloma patients","volume-title":"IEEE Access","author":"Turki","year":"2017"},{"key":"2022112111121037100_ref129","first-page":"561","article-title":"Tridirectional transfer learning for predicting gastric cancer morbidity","volume-title":"IEEE Trans Neural Netw Learn Syst","author":"Song","year":"2020"},{"key":"2022112111121037100_ref130","first-page":"83","article-title":"Imbalanced breast cancer classification using transfer learning","volume-title":"IEEE\/ACM Trans Comput Biol Bioinform","author":"Singh","year":"2020"},{"key":"2022112111121037100_ref131","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1186\/1471-2105-14-7","article-title":"GSVA: gene set variation analysis for microarray and RNA-Seq data","volume":"14","author":"H\u00e4nzelmann","year":"2013","journal-title":"BMC Bioinformatics"},{"key":"2022112111121037100_ref132","doi-asserted-by":"crossref","first-page":"225","DOI":"10.1186\/1471-2105-6-225","article-title":"Pathway level analysis of gene expression using singular value decomposition","volume":"6","author":"Tomfohr","year":"2005","journal-title":"BMC Bioinformatics"},{"key":"2022112111121037100_ref133","doi-asserted-by":"crossref","first-page":"108","DOI":"10.1038\/nature08460","article-title":"Systematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1","volume":"462","author":"Barbie","year":"2009","journal-title":"Nature"},{"key":"2022112111121037100_ref134","doi-asserted-by":"crossref","first-page":"e1000217","DOI":"10.1371\/journal.pcbi.1000217","article-title":"Inferring pathway activity toward precise disease classification","volume":"4","author":"Lee","year":"2008","journal-title":"PLoS Comput Biol"},{"key":"2022112111121037100_ref135","first-page":"764","article-title":"LEAP: constructing gene co-expression networks for single-cell RNA-sequencing data using pseudotime ordering","volume-title":"Bioinformatics","author":"Specht","year":"2017"},{"key":"2022112111121037100_ref136","first-page":"1","article-title":"dynGENIE3: dynamical GENIE3 for the inference of gene networks from time series expression data","volume-title":"Sci Rep","author":"Huynh-Thu","year":"2018"},{"key":"2022112111121037100_ref137","first-page":"i197","article-title":"Integrative random forest for gene regulatory network inference","volume-title":"Bioinformatics","author":"Petralia","year":"2015"},{"key":"2022112111121037100_ref138","first-page":"1","article-title":"The Inferelator: an algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo","volume-title":"Genome Biol","author":"Bonneau","year":"2006"},{"key":"2022112111121037100_ref139","first-page":"2252","article-title":"Windowed Granger causal inference strategy improves discovery of gene regulatory networks","volume-title":"Proc Natl Acad Sci U S A","author":"Finkle","year":"2018"},{"key":"2022112111121037100_ref140","first-page":"1","article-title":"DREM 2.0: improved reconstruction of dynamic regulatory networks from time-series expression data","volume-title":"BMC Syst Biol","author":"Schulz","year":"2012"},{"key":"2022112111121037100_ref141","first-page":"e164","article-title":"Personalized characterization of diseases using sample-specific networks","volume-title":"Nucleic Acids Res","author":"Liu","year":"2016"},{"key":"2022112111121037100_ref142","first-page":"851","article-title":"Deep learning in bioinformatics","volume":"18","author":"Min","year":"2017","journal-title":"Brief Bioinform"},{"key":"2022112111121037100_ref143","first-page":"483","volume-title":"International conference on machine learning","author":"Lee","year":"2015"},{"key":"2022112111121037100_ref144","first-page":"1","volume-title":"2015 IEEE Biomedical Circuits and Systems Conference","author":"Lee","year":"2015"},{"key":"2022112111121037100_ref145","doi-asserted-by":"crossref","first-page":"434","DOI":"10.1016\/j.arr.2006.06.002","article-title":"Systems approaches to the networks of aging","volume":"5","author":"Kriete","year":"2006","journal-title":"Ageing Res Rev"}],"container-title":["Briefings in Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/23\/6\/bbac415\/47143890\/bbac415.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/23\/6\/bbac415\/47143890\/bbac415.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,11,26]],"date-time":"2023-11-26T22:12:57Z","timestamp":1701036777000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bib\/article\/doi\/10.1093\/bib\/bbac415\/6748488"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,10,5]]},"references-count":145,"journal-issue":{"issue":"6","published-print":{"date-parts":[[2022,11,19]]}},"URL":"https:\/\/doi.org\/10.1093\/bib\/bbac415","relation":{},"ISSN":["1467-5463","1477-4054"],"issn-type":[{"value":"1467-5463","type":"print"},{"value":"1477-4054","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2022,11]]},"published":{"date-parts":[[2022,10,5]]},"article-number":"bbac415"}}