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Frontiers in Genetics

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Editors See all (11,175) enrico domenici Department of Cellular, Computational and Integrated Biology, University of Trento Povo, Italy Field Chief Editor

Frontiers in Genetics

josé a g agúndez Institute of Molecular Pathology Biomarkers, University of Extremadura Cáceres, Spain Specialty Chief Editor

Pharmacogenetics and Pharmacogenomics

atsushi asakura University of Minnesota Twin Cities St. Paul, United States Specialty Chief Editor

Stem Cell Research

michael baudis University of Zurich Zürich, Switzerland Specialty Chief Editor

Cancer Genetics and Oncogenomics

Articles See all (14,564) Original Research

Published on 08 Mar 2024

Neurodevelopmental disorders as a risk factor for temporomandibular disorder: evidence from Mendelian randomization studies

in Behavioral and Psychiatric Genetics Xueqiang WuZefang LiYiping CuiZhaojun YanTingting LuSong Cui Frontiers in Genetics doi 10.3389/fgene.2024.1365596 Review

Published on 08 Mar 2024

Fibroblast heterogeneity and functions: insights from single-cell sequencing in wound healing, breast cancer, ovarian cancer and melanoma

in Cancer Genetics and Oncogenomics Omar Lujano OlazabaJeffrey FarrowTeresa Monkkonen Frontiers in Genetics doi 10.3389/fgene.2024.1304853 Original Research

Published on 08 Mar 2024

Impact of persistent barrier to gene flow and catastrophic events on red algae evolutionary history along the Chilean coast

in Evolutionary and Population Genetics Oscar R. HuanelAlejandro E. MontecinosFrancisco Sepúlveda-EspinozaMarie-Laure Guillemin Frontiers in Genetics doi 10.3389/fgene.2024.1336427 Original Research

Published on 08 Mar 2024

Dual-transgenic BiFC vector systems for protein-protein interaction analysis in plants

in Genomics of Plants and the Phytoecosystem Piaojuan ChenMeiling YeYadi ChenQin WangQiongli WangMing Zhong Frontiers in Genetics doi 10.3389/fgene.2024.1355568 Volumes See all (15)

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Volume 11 - 2020

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Elucidating the Role of Environmental Factors in Neurodevelopmental Disorders: Implications for Diagnosis and Treatments Jorge ManzoMircea NicoaraCiobica Alin

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Advancements in Hematopoietic Stem Cell Proliferation and Self-Renewal Maintenance Dr. Pawan Kumar RaghavGurudutta GangenahalliTakahiko Hara 143

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Immune System Renewal: Stem Cell Technologies, Artificial Intelligence, and Machine Learning Mariastefania AnticaFATMA VISAL OKURValentin P. ShichkinEnrico Velardi

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GetToolImpactFactorCommentsPageRequest(projectId=1, impactFactorId=13175, id=901d13175, selectType=1, sortType=1, contributeIds=null, level=null, parentIds=[])

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[GetPortalCommentsPageByObjectIdResponse(id=2145809, encodeId=544b214580929, content=审稿速度:6.0
经验分享：太无耻了，开始找的第一个审稿人建议大修，返回已经后是同意录用，后面一直在找别的审稿人，到投稿6个月的时候才找到第二个审稿人。但是奇葩操作来了，在最后一个审稿人没回复的情况下，编辑直接拒稿，我是想问这个杂志社是不是有毛病？拒稿为什么不早点拒稿，耽误别人半年时间，我想请问能不能发邮件喷这个SB编辑，再也不投这个fronter系列杂志了，白白延误别人时间又莫名其妙的拒稿。, beContent=null, objectType=tool_impact_factor, channel=null, level=null, likeNumber=45, replyNumber=3, topicName=null, topicId=null, topicList=[], attachment=null, authenticateStatus=null, createdAvatar=null, createdBy=024e2688919, createdName=287119938, createdTime=Sat Jul 01 12:35:51 CST 2023, time=2023-07-01, status=1, ipAttribution=贵州省), GetPortalCommentsPageByObjectIdResponse(id=2179183, encodeId=9b4221e9183e1, content=审稿速度:2.0
经验分享：经验分享：11月03日投稿，11月06日审稿人1 建议拒稿，11月27日审稿人2 建议Minor revision，11月28日审稿人3建议Major revision，给了2周返修时间，12月10日所有意见返修过去， 12月27日审稿人3 建议拒稿，12月28日，审稿人2 同意发表。各位帮忙分析一下我的文章还有戏吗? 焦虑中......., beContent=null, objectType=tool_impact_factor, channel=null, level=null, likeNumber=142, replyNumber=1, topicName=null, topicId=null, topicList=[], attachment=null, authenticateStatus=null, createdAvatar=/v1.0.0/img/user_icon.png, createdBy=80c66157856, createdName=ms3000000029380120, createdTime=Thu Jan 04 10:11:21 CST 2024, time=2024-01-04, status=1, ipAttribution=江苏省), GetPortalCommentsPageByObjectIdResponse(id=2143081, encodeId=03f3214308163, content=审稿速度:2.0 | 投稿命中率:50.0
偏重的研究方向：点突变
经验分享：麻烦问下，从接收到正式发表，需要多长时间呀, beContent=null, objectType=tool_impact_factor, channel=null, level=null, likeNumber=36, replyNumber=2, topicName=null, topicId=null, topicList=[], attachment=null, authenticateStatus=null, createdAvatar=null, createdBy=fceb6442587, createdName=ms9000001727788658, createdTime=Fri Jun 16 09:24:12 CST 2023, time=2023-06-16, status=1, ipAttribution=北京), GetPortalCommentsPageByObjectIdResponse(id=1242528, encodeId=2c241242528ae, content=偏重的研究方向：肿瘤;基因;生信
经验分享：合伙搞了篇生信，投稿时需要原始数据，今天上传了，希望编辑和审稿人给过吧。, beContent=null, objectType=tool_impact_factor, channel=null, level=null, likeNumber=72, replyNumber=20, topicName=null, topicId=null, topicList=[], attachment=null, authenticateStatus=null, createdAvatar=/v1.0.0/img/user_icon.png, createdBy=7c696163486, createdName=ms8000000941284145, createdTime=Thu Sep 01 18:13:31 CST 2022, time=2022-09-01, status=1, ipAttribution=), GetPortalCommentsPageByObjectIdResponse(id=2100097, encodeId=5140210009e8e, content=偏重的研究方向：纯生信;生信;生物信息
经验分享：请问一下纯生信的只给原始数据不上传代码可以吗？, beContent=null, objectType=tool_impact_factor, channel=null, level=null, likeNumber=33, replyNumber=1, topicName=null, topicId=null, topicList=[], attachment=null, authenticateStatus=null, createdAvatar=null, createdBy=8e795651310, createdName=ms9000000913432311, createdTime=Sat Nov 12 16:13:48 CST 2022, time=2022-11-12, status=1, ipAttribution=), GetPortalCommentsPageByObjectIdResponse(id=966740, encodeId=3f85966e40d3, content=第一次见到这种杂志哦，已经accepted for publication了，而且版面费都交了，结果突然来了一封信说拒稿退钱，这是什么操作啊？, beContent=null, objectType=tool_impact_factor, channel=null, level=null, likeNumber=75, replyNumber=10, topicName=null, topicId=null, topicList=[], attachment=null, authenticateStatus=null, createdAvatar=http://cdnapi.center.medsci.cn/medsci/head/2019/07/19/fe015ad718825715f9776074575b45f8.jpg, createdBy=85a02541803, createdName=哈哈小猪, createdTime=Wed May 19 07:41:33 CST 2021, time=2021-05-19, status=1, ipAttribution=), GetPortalCommentsPageByObjectIdResponse(id=2119119, encodeId=27f4211911946, content=审稿速度:3.0 | 投稿命中率:75.0
经验分享：4个审稿人，纯生信文章，2个半月, beContent=null, objectType=tool_impact_factor, channel=null, level=null, likeNumber=42, replyNumber=5, topicName=null, topicId=null, topicList=[], attachment=null, authenticateStatus=null, createdAvatar=https://img.medsci.cn/20220704/1acf1fcc54b540239da4b101eb02ebc4/379539e2ee554698a231b4f45583be89.jpg, createdBy=62942283774, createdName=董柏, createdTime=Sun Mar 12 20:33:55 CST 2023, time=2023-03-12, status=1, ipAttribution=浙江省), GetPortalCommentsPageByObjectIdResponse(id=2097565, encodeId=f1eb209e5654c, content=审稿速度:2.0 | 投稿命中率:50.0
经验分享：投了一篇纯生信的文章，今年研三了，刚好完成了自己的毕业指标。总体来说是属于比较幸运的类型。从投稿到接收快两个月，下面分享一下自己的时间线希望对大家有所帮助。
2022.8.31 投稿
2022.9.9 送审
2022.9.14 第一个审稿人初审结束（小修）
2022.9.28 第二个审稿人初审结束（大修）
2022.10.1 交互评审开放，给了半个月时间修改，提示截止2022.10.15提交自己修改后的稿件
2022.10.14 提交修改后的手稿
2022.10.15 第一个审稿人二审结束，finalized (endorsed the publication)
2022.10.19 第二个审稿人二审结束，finalized (没看到是什么意见，但是根据第一个推测也是endorsed)
两个审稿人都结束以后直接就进入了review finalized 阶段，这个过程持续了9天
2022.10.27 进入final validation 阶段
2022.10.29 接收
总体来说很快，我感觉整个投稿过程除了第二个审稿人在一审的时候花费了比较久的时间，其他的都很给力。
, beContent=null, objectType=tool_impact_factor, channel=null, level=null, likeNumber=60, replyNumber=7, topicName=null, topicId=null, topicList=[], attachment=null, authenticateStatus=null, createdAvatar=null, createdBy=f6be8230020, createdName=ms2000001036693367, createdTime=Mon Oct 31 10:26:01 CST 2022, time=2022-10-31, status=1, ipAttribution=), GetPortalCommentsPageByObjectIdResponse(id=2167189, encodeId=aba8216e1895d, content=偏重的研究方向：肿瘤免疫
经验分享：投了一篇，秒拒。理由：This manuscript does not fulfill the standards established for the journal to be considered for publication, and according to Frontiers policies”This decision applies across all Frontiers journals and is final.
这到底是啥情况啊？发邮件问原因，也不回复。而且还说这个决定适用于frontiers系列所有期刊。我们的研究都有原始数据。这到底是是为啥呢？, beContent=null, objectType=tool_impact_factor, channel=null, level=null, likeNumber=22, replyNumber=2, topicName=null, topicId=null, topicList=[], attachment=null, authenticateStatus=null, createdAvatar=/v1.0.0/img/user_icon.png, createdBy=c6351657413, createdName=海边的雪儿, createdTime=Tue Nov 07 10:50:39 CST 2023, time=2023-11-07, status=1, ipAttribution=山东省), GetPortalCommentsPageByObjectIdResponse(id=2167225, encodeId=3c0f216e22511, content=请问肿瘤纯生信还收吗？, beContent=null, objectType=tool_impact_factor, channel=null, level=null, likeNumber=33, replyNumber=1, topicName=null, topicId=null, topicList=[], attachment=null, authenticateStatus=null, createdAvatar=, createdBy=96c15321357, createdName=148ac126m95暂无昵称, createdTime=Tue Nov 07 14:52:16 CST 2023, time=2023-11-07, status=1, ipAttribution=浙江省)]

2023-07-01

287119938

来自贵州省

审稿速度:6.0经验分享：太无耻了，开始找的第一个审稿人建议大修，返回已经后是同意录用，后面一直在找别的审稿人，到投稿6个月的时候才找到第二个审稿人。但是奇葩操作来了，在最后一个审稿人没回复的情况下，编辑直接拒稿，我是想问这个杂志社是不是有毛病？拒稿为什么不早点拒稿，耽误别人半年时间，我想请问能不能发邮件喷这个SB编辑，再也不投这个fronter系列杂志了，白白延误别人时间又莫名其妙的拒稿。

展开3条回复

2024-01-04

ms3000000029380120

来自江苏省

审稿速度:2.0经验分享：经验分享：11月03日投稿，11月06日审稿人1 建议拒稿，11月27日审稿人2 建议Minor revision，11月28日审稿人3建议Major revision，给了2周返修时间，12月10日所有意见返修过去， 12月27日审稿人3 建议拒稿，12月28日，审稿人2 同意发表。各位帮忙分析一下我的文章还有戏吗? 焦虑中.......

142

展开1条回复

2023-06-16

ms9000001727788658

来自北京

审稿速度:2.0 | 投稿命中率:50.0偏重的研究方向：点突变经验分享：麻烦问下，从接收到正式发表，需要多长时间呀

展开2条回复

2022-09-01

ms8000000941284145

偏重的研究方向：肿瘤;基因;生信经验分享：合伙搞了篇生信，投稿时需要原始数据，今天上传了，希望编辑和审稿人给过吧。

展开20条回复

2022-11-12

ms9000000913432311

偏重的研究方向：纯生信;生信;生物信息经验分享：请问一下纯生信的只给原始数据不上传代码可以吗？

展开1条回复

2021-05-19

哈哈小猪

第一次见到这种杂志哦，已经accepted for publication了，而且版面费都交了，结果突然来了一封信说拒稿退钱，这是什么操作啊？

展开10条回复

2023-03-12

董柏

来自浙江省

审稿速度:3.0 | 投稿命中率:75.0经验分享：4个审稿人，纯生信文章，2个半月

展开5条回复

2022-10-31

ms2000001036693367

审稿速度:2.0 | 投稿命中率:50.0经验分享：投了一篇纯生信的文章，今年研三了，刚好完成了自己的毕业指标。总体来说是属于比较幸运的类型。从投稿到接收快两个月，下面分享一下自己的时间线希望对大家有所帮助。2022.8.31 投稿2022.9.9 送审2022.9.14 第一个审稿人初审结束（小修）2022.9.28 第二个审稿人初审结束（大修）2022.10.1 交互评审开放，给了半个月时间修改，提示截止2022.10.15提交自己修改后的稿件2022.10.14 提交修改后的手稿2022.10.15 第一个审稿人二审结束，finalized (endorsed the publication)2022.10.19 第二个审稿人二审结束，finalized (没看到是什么意见，但是根据第一个推测也是endorsed)两个审稿人都结束以后直接就进入了review finalized 阶段，这个过程持续了9天2022.10.27 进入final validation 阶段2022.10.29 接收总体来说很快，我感觉整个投稿过程除了第二个审稿人在一审的时候花费了比较久的时间，其他的都很给力。

展开7条回复

2023-11-07

海边的雪儿

来自山东省

偏重的研究方向：肿瘤免疫经验分享：投了一篇，秒拒。理由：This manuscript does not fulfill the standards established for the journal to be considered for publication, and according to Frontiers policies”This decision applies across all Frontiers journals and is final. 这到底是啥情况啊？发邮件问原因，也不回复。而且还说这个决定适用于frontiers系列所有期刊。我们的研究都有原始数据。这到底是是为啥呢？

展开2条回复

2023-11-07

148ac126m95暂无昵称

来自浙江省

请问肿瘤纯生信还收吗？

展开1条回复

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可接收生信，影响因子3.7，平均3个月可接收！中科院2区，发文量较大 - 知乎

可接收生信，影响因子3.7，平均3个月可接收！中科院2区，发文量较大 - 知乎切换模式写文章登录/注册可接收生信，影响因子3.7，平均3个月可接收！中科院2区，发文量较大知乎用户fhRdNIFrontiers in Genetics由FRONTIERS MEDIA SA出版商出版出版周期1 issue/year该刊是发文范围涵盖遗传学等领域的综合期刊该刊已被SCI、SCIE数据库收录在中科院JCR最新升级版分区表中该刊分区信息为大类学科生物3区2022年影响因子为3.7基本信息瑞士医学期刊Frontiers in Genetics，于2010年创刊，是一份在线开放获取（OA）期刊，没有印刷版。所有发表在该期刊上的文章都可以免费在线获取，并且可以在Frontiers网站上找到。e-ISSN号：1664-8021。其Pubmed的检索名为Frontiers in Geneticsi。官网主页：http://www.frontiersin.org/journals/genetics影响因子Frontiers in Genetics的最新SCI影响因子较去年有些许下跌，但依旧稳定在3分以上。2022年的最新影响因子为3.7分。接收领域该期刊的主题包括但不限于：基因组结构和功能、基因表达调控、遗传变异和进化、遗传学与疾病、遗传学与环境、计算遗传学等。该期刊还特别关注系统生物学、表观遗传学、单细胞基因组学和合成生物学等新兴领域的研究。从它的官网来看有很多文章值得新手阅读和学习。JCR和中科院分区JCR分区：Frontiers in Genetics位于基因和遗传组学Q2区，且排名在相关领域分类中都比较靠前。中科院分区：在2022年12月最新升级版中，大类为医学2区，小类为基因和遗传组学2区，TOP期刊，综述期刊。截至目前，Web of Science核心合集已收录了2023年11月20日发布的文章，更新及时。发文量最近十几年，该刊的年刊文量有一定波动，2017年最低，仅210篇。后逐渐扩刊，2022年收录3834篇，但今年刊文量又明显下降，2023年降至1708篇。国人发文占比根据Web of Science核心合集统计，刊文量排名前十的国家或地区，国人学者刊文量超越美国，位居第一，5099篇，占比60.94 %。美国学者排名第二，1393篇，占比16.65% 。审稿速度通过对Frontiers in Genetic近期已发表文章审稿速度的抽样统计，大部分文章的审稿周期都是在3个月左右便可接受，相对符合官网给出的周期，最快竟然3天即可接收，最慢也仅仅需要4个多月，虽审稿差异有点大，不过整体算是比较快。版面费Frontiers in Genetics是一份开放获取期刊，因此不收取任何订阅费或版面费。然而，作者需要支付文章处理费用（APC），用于编辑、审稿和出版文章的成本。自引率近几年，Frontiers in Genetics杂志的自引率均在6%以下，2022年度最新自引率为5.2%，无自引风险。大家可以放心冲！总结Frontiers in Genetics创办于2010年。该刊SCI影响因子常年在3.2~4.7之间稳定波动，虽然今年因影响因子算法变动有所下跌，但未来望涨到5分还是现实的。同时，它还具备国人友好、不收费、审稿快速等优点，且又成为了TOP 2区的期刊。因此，对于时间要求比较紧急、缺少经费报销的朋友，这本期刊可以说是相当不错的选择之一了。本文来自“大碗学术”公众号原创，转载请注明出处。发布于 2023-12-21 15:37・IP 属地重庆生长因子生物信息学高影响因子赞同1 条评论分享喜欢收藏申请

Frontiers in Genetics | Articles

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All sections Applied Genetic EpidemiologyBehavioral and Psychiatric GeneticsCancer Genetics and OncogenomicsComputational GenomicsELSI in Science and GeneticsEpigenomics and EpigeneticsEvolutionary and Population GeneticsGenetics of AgingGenetics of Common and Rare DiseasesGenomic Assay TechnologyGenomics of Plants and the PhytoecosystemHuman and Medical GenomicsImmunogeneticsLivestock GenomicsMolecular CytogeneticsNeurogenomicsNutritional GenomicsPharmacogenetics and PharmacogenomicsRNAStatistical Genetics and MethodologyStem Cell ResearchToxicogenomics Part of Research Topics null Part of Research Topics

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All sections Applied Genetic Epidemiology Behavioral and Psychiatric Genetics Cancer Genetics and Oncogenomics Computational Genomics ELSI in Science and Genetics Epigenomics and Epigenetics Evolutionary and Population Genetics Genetics of Aging Genetics of Common and Rare Diseases Genomic Assay Technology Genomics of Plants and the Phytoecosystem Human and Medical Genomics Immunogenetics Livestock Genomics Molecular Cytogenetics Neurogenomics Nutritional Genomics Pharmacogenetics and Pharmacogenomics RNA Statistical Genetics and Methodology Stem Cell Research Toxicogenomics

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Articles Original Research

Published on 08 Mar 2024

Neurodevelopmental disorders as a risk factor for temporomandibular disorder: evidence from Mendelian randomization studies

in Behavioral and Psychiatric Genetics Xueqiang WuZefang LiYiping CuiZhaojun YanTingting LuSong Cui Frontiers in Genetics doi 10.3389/fgene.2024.1365596 Review

Published on 08 Mar 2024

Fibroblast heterogeneity and functions: insights from single-cell sequencing in wound healing, breast cancer, ovarian cancer and melanoma

in Cancer Genetics and Oncogenomics Omar Lujano OlazabaJeffrey FarrowTeresa Monkkonen Frontiers in Genetics doi 10.3389/fgene.2024.1304853 Original Research

Published on 08 Mar 2024

Impact of persistent barrier to gene flow and catastrophic events on red algae evolutionary history along the Chilean coast

in Evolutionary and Population Genetics Oscar R. HuanelAlejandro E. MontecinosFrancisco Sepúlveda-EspinozaMarie-Laure Guillemin Frontiers in Genetics doi 10.3389/fgene.2024.1336427 Original Research

Published on 08 Mar 2024

Dual-transgenic BiFC vector systems for protein-protein interaction analysis in plants

in Genomics of Plants and the Phytoecosystem Piaojuan ChenMeiling YeYadi ChenQin WangQiongli WangMing Zhong Frontiers in Genetics doi 10.3389/fgene.2024.1355568 Original Research

Accepted on 07 Mar 2024

A comprehensive analysis of the prognostic characteristics of microRNAs in Breast Cancer

in RNA Lingying WangGui WangJiahong SongDi YaoTianyou ChenYong Wang Frontiers in Genetics doi 10.3389/fgene.2024.1293824 Original Research

Accepted on 07 Mar 2024

iDNA-OpenPrompt: OpenPrompt learning for identifying DNA methylation

in Computational Genomics Xia YuJia RenHaixia LongRao ZengGuoqiang ZhangYani Cui Frontiers in Genetics doi 10.3389/fgene.2024.1377285 Original Research

Published on 07 Mar 2024

High-resolution genomic profiling and locus-specific FISH in subcutaneous and visceral adipose tissue of obese patients

in Molecular Cytogenetics Vivian-Pascal BrandtHeidrun HollandMatthias BlüherNora Klöting Frontiers in Genetics doi 10.3389/fgene.2023.1323052 148

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Review

Published on 07 Mar 2024

tRNA engineering strategies for genetic code expansion

in RNA YouJin KimSuho ChoJoo-Chan KimHee-Sung Park Frontiers in Genetics doi 10.3389/fgene.2024.1373250 163

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Original Research

Published on 07 Mar 2024

Searching for gene-gene interactions through variance quantitative trait loci of 29 continuous Taiwan Biobank phenotypes

in Applied Genetic Epidemiology Wan-Yu Lin Frontiers in Genetics doi 10.3389/fgene.2024.1357238 Original Research

Published on 07 Mar 2024

Uganda chicken genetic resources: II. genetic diversity and population demographic history inferred from mitochondrial DNA D-loop sequences

in Livestock Genomics Illyass YussifDonald Rugira KugonzaCharles Masembe Frontiers in Genetics doi 10.3389/fgene.2024.1325569 135

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Original Research

Published on 07 Mar 2024

Mendelian randomization study shows no causal relationship between psychiatric disorders and glaucoma in European and East Asian populations

in Applied Genetic Epidemiology Yan ZhangLonghui FuFang FengBo LiuYing LeiQianyan Kang Frontiers in Genetics doi 10.3389/fgene.2024.1349860 102

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Original Research

Accepted on 06 Mar 2024

Transcriptome profiling and analysis of patients with esophageal squamous cell carcinoma from Kazakhstan

in Computational Genomics Aigul SharipSaule RakhimovaAskhat MolkenovAinur AshenovaUlan KozhamkulovIlyas AkhmetollayevAndrei ZinovyevYuri ZhukovMarat OmarovMukhtar Tuleutaev Frontiers in Genetics doi 10.3389/fgene.2024.1249751 Methods

Accepted on 06 Mar 2024

Automated recognition of chromosome fusion using an alignment-free natural vector method

in Computational Genomics Hongyu YuStephen S.-T. Yau Frontiers in Genetics doi 10.3389/fgene.2024.1364951 Original Research

Published on 06 Mar 2024

Hybrid de novo and haplotype-resolved genome assembly of Vechur cattle — elucidating genetic variation

in Livestock Genomics Poorvishaa V. MuthusamyRajesh Vakayil ManiShivani KumariManpreet KaurBalu BhaskarRajeev Raghavan PillaiThankappan Sajeev KumarThapasimuthu Vijayamma AnilkumarNongmaithem Sadananda Singh Frontiers in Genetics doi 10.3389/fgene.2024.1338224 294

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Review

Published on 06 Mar 2024

Long read sequencing on its way to the routine diagnostics of genetic diseases

in Human and Medical Genomics Giulia OlivucciEmanuela IovinoGiovanni InnellaDaniela TurchettiTommaso PippucciPamela Magini Frontiers in Genetics doi 10.3389/fgene.2024.1374860 337

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Original Research

Published on 06 Mar 2024

Comparative stigmatic transcriptomics reveals self and cross pollination responses to heteromorphic incompatibility in Plumbago auriculata Lam.

in Genomics of Plants and the Phytoecosystem Di HuDi LinShouli YiSuping GaoTing LeiWenji LiTingdan Xu Frontiers in Genetics doi 10.3389/fgene.2024.1372644 206

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Frontiers in Genetics | About

Navigation group Top bar navigation Frontiers in Genetics

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Field chief editor

enrico domenici Department of Cellular, Computational and Integrated Biology, University of Trento Povo, Italy Field Chief Editor

Frontiers in Genetics

Mission & scope Frontiers in Genetics publishes research on genes and genomes relating to all the domains of life, from humans to livestock, and plants to other model organisms.

Led by Field Chief Editor Enrico Domenici (Department of Cellular, Computational and Integrated Biology, University of Trento, Italy) Frontiers in Genetics is indexed in PubMed Central (PMC) and Scopus, among others, and explores the full spectrum of genetic and genomic research, encompassing fundamental studies and their clinical applications, while also embracing methodological advancements and exploring their applications and implications. Topics of interest include, but are not limited to:

• how genes or genomes relate to traits and human pathophysiology

• advances in genomic data technology and analysis

• gene flow among species and populations

• livestock genome research Interactions between organisms, their environment, and xenobiotics

• molecular and cellular genetics

• societal implications of genetic research.

Submissions that emphasize advancement in the understanding of the function and variability of the genome, the use of genetic and genomic tools, and the analysis of the genetic underpinnings of biological processes are of particular interest to this journal.

Furthermore, the journal actively welcomes submissions which support and advance the UN’s Sustainable Development Goals (SDGs), notably SDG 3: good health and well-being.

Manuscripts that focus solely on clinical outcomes, patient management, or therapeutic interventions without a clear genetic or genomic component are not suitable for publication in this journal. Studies that are purely epidemiological or observational, without a foundation in genetic or genomic mechanisms, are also not within the scope of this journal. Manuscripts consisting solely of bioinformatics, computational analyses of public data which are not accompanied by validation (independent clinical or patient cohort, or biological validation in vitro or in vivo) or are not highly innovative are not suitable for publication in this journal.

Frontiers in Genetics is committed to advancing developments in the field of genetics and genomics by allowing unrestricted access to articles, and communicating scientific knowledge to both researchers and the public, to enable the scientific breakthroughs of the future.

Frontiers in Genetics is member of the Committee on Publication Ethics.

Facts Short name Front. Genet. Abbreviation fgene Electronic ISSN 1664-8021 PMCID All published articles receive a PMCID Impact 3.7 Impact Factor 5.2 CiteScore Indexed in

PubMed, PubMed Central (PMC), Scopus, Google Scholar, DOAJ, CrossRef, Chemical Abstracts Service (CAS), Embase, AGRICOLA, Semantic Scholar, Ulrich's Periodicals Directory, BIOSIS Citation Index, Biological Abstracts, CLOCKSS, EBSCO, OpenAIRE, Zetoc, Mastermind

Journal sections

Frontiers in Genetics is composed of the following Specialty

sections:

Applied Genetic Epidemiology

Behavioral and Psychiatric Genetics

Cancer Genetics and Oncogenomics

Computational Genomics

ELSI in Science and Genetics

Epigenomics and Epigenetics

Evolutionary and Population Genetics

Genetics of Aging

Genetics of Common and Rare Diseases

Genomic Assay Technology

Genomics of Plants and the Phytoecosystem

Human and Medical Genomics

Immunogenetics

Livestock Genomics

Molecular Cytogenetics

Neurogenomics

Nutritional Genomics

Pharmacogenetics and Pharmacogenomics

RNA

Statistical Genetics and Methodology

Stem Cell Research

Toxicogenomics

The specialty sections of

Frontiers in Genetics welcome submission of the following

article types:

Addendum, Brief Research Report, Case Report, Classification, Clinical Trial, Community Case Study, Correction, Data Report, Editorial, General Commentary, Hypothesis & Theory, Methods, Mini Review, Opinion, Original Research, Perspective, Policy Brief, Policy and Practice Reviews, Registered Report, Review, Study Protocol, Systematic Review, Technology and Code.

When submitting a manuscript to Frontiers in Genetics, authors must

submit the material directly to one of the specialty

sections. Manuscripts are peer-reviewed by the

Associate and Review Editors of the respective specialty section.

Open access statement Frontiers' philosophy is that all research is for the benefit of humankind. Research is the product of an investment by society and therefore its fruits should be returned to all people without borders or discrimination, serving society universally and in a transparent fashion. That is why Frontiers provides online free and open access to all of its research publications. For more information on open access click here. Open access funder and institutional mandatesFrontiers is fully compliant with open access mandates, by publishing its articles under the Creative Commons Attribution licence (CC-BY). Funder mandates such as those by the Wellcome Trust (UK), National Institutes of Health (USA) and the Australian Research Council (Australia) are fully compatible with publishing in Frontiers. Authors retain copyright of their work and can deposit their publication in any repository. The work can be freely shared and adapted provided that appropriate credit is given and any changes specified.Copyright statement Under the Frontiers Conditions for Website Use and the Frontiers General Conditions for Authors, authors of articles published in Frontiers journals retain copyright on their articles, except for any third-party images and other materials added by Frontiers, which are subject to copyright of their respective owners. Authors are therefore free to disseminate and re-publish their articles, subject to any requirements of third-party copyright owners and subject to the original publication being fully cited. The ability to copy, download, forward or otherwise distribute any materials is always subject to any copyright notices displayed. Copyright notices must be displayed prominently and may not be obliterated, deleted or hidden, totally or partially.Quality Each Frontiers article strives for the highest quality, thanks to genuinely collaborative interactions between authors, editors and reviewers, who include many of the world's best scientists and scholars. Frontiers is well aware of the potential impact of published research both on future research and on society and, hence, does not support superficial review, light review or no-review publishing models.Frontiers uses the single anonymized peer review model, where the reviewer identity is not made visible to the author, while the author identity is visible to the reviewer, and reviewer and the authors’ identities are visible to the decision-making editor. Reviewers interact with the handling editor and the authors. Editor and reviewer names and affiliations are published on all Frontiers articles.Research must be certified by peers before entering a stream of knowledge that may eventually reach the public - and shape society. Therefore, Frontiers only applies the most rigorous and unbiased reviews, established in the high standards of the Frontiers Review System. Furthermore, only the top certified research, evaluated objectively through quantitative online article level metrics, is disseminated to increasingly wider communities as it gradually climbs the tiers of the Frontiers Tiering System from specialized expert readership towards public understanding.Frontiers has a number of procedures in place to support and ensure the quality of the research articles that are published: 2023

Editorial Board Quality

Only leading experts and established members of the research community are appointed to the Frontiers Editorial Boards. Chief Editors, Associate Editors and Review Editors are all listed with their names and affiliations on the Journal pages and are encouraged to publicly list their publication credentials.

Associate Editor Assignment Quality

Associate Editors oversee the peer-review and take the final acceptance decision on manuscripts. Editorial decision power is distributed in Frontiers, because we believe that many experts within a community should be able to shape the direction of science for the benefit of society.

Submitting authors can choose a preferred Associate Editor to handle their manuscript, because they can judge well who would be an appropriate expert in editing their manuscript. There is no guarantee for this preference of choice, Associate Editors can decline invitations any time, and the handling Associate Editor can also be over-ridden by the Chief Editor before she/he is invited to edit the article or at any other stage.

Associate Editors are mandated to only accept to edit a manuscript if they have no conflicts of interest (as stated here and in their review invitation and assignment emails).

Should it become clear that the Associate Editor has a conflict of interest or is unable to perform the peer-review timely and adequately, a new Associate Editor can be assigned to the manuscript by the Chief Editor, who has full control to intervene in the peer-review process at any time.

The Associate Editor initially checks that the article meets basic quality standards and has no obvious objective errors.

Reviewer Assignment Quality

The Associate Editor can then personally choose and invite the most appropriate reviewers to handle the peer-review of the manuscript, including Review Editors from the board or external reviewers.

The Associate Editor is aided in this by the Frontiers Collaborative Review Forum software and interface, which suggests the most relevant Review Editors based on a match between their expertise and the topic of the manuscript. Associate Editors can however choose any reviewer they deem adequate.

After a certain time frame and if no reviewers have in the meantime been assigned to the manuscript, the Frontiers platform and algorithmic safety-net steps in and invites the most appropriate Review Editors based on constantly updated and improved algorithms that match reviewer expertise with the submitted manuscript.

Review Editors and reviewers are mandated to only accept to review a manuscript if they have no conflicts of interest (as stated here and in their review invitation and assignment emails).

Frontiers algorithms are constantly fine-tuned to better match Review Editors with manuscripts, and additional checks are being coded into the platform, for example regarding conflicts of interest.

Should it become clear that a particular reviewer has a conflict of interest or is unable to perform the peer-review timely and adequately, he or she shall be replaced with an alternative reviewer by the Associate Editor or the Chief Editor, who will be alerted and has full control to intervene into the peer-review at any time.

Independent Review Stage Quality

In the Independent Review Stage the assigned reviewers perform an in-depth review of the article independently of each other to safeguard complete freedom of opinion.

The reviewers are aided by an online standardized review questionnaire – adopted to article types – with the goal to facilitate rigorous evaluation according to objective criteria and the Frontiers Review Guidelines.

Interactive Review Stage Quality

The Associate Editor assesses the reviews and activates the “Interactive Review” – informing the authors of the extent of revisions that are required to address the reviewers’ comments, and starting the Interactive Discussion Forum where authors and also the reviewers get full access to all review reports.

Manuscript and review quality at this stage are enhanced by allowing authors and reviewers to discuss directly with each other in real-time until they reach consensus and a final version of the manuscript is endorsed by the reviewers.

Reviewer identity is protected at this stage to safeguard complete freedom of opinion.

Reviewers can recommend rejection at this stage if their requests to correct objective errors are not being met by the authors or if they deem the article overall of insufficient quality.

Should a dispute arise, authors or reviewers can trigger an arbitration and will alert the Associate Editor, who can assign more reviewers and/or bring the dispute to the attention of the Chief Editor. The Associate Editor can also weigh in on the discussion and is asked to mediate the process to ensure a constructive revision stage.

Decision Stage Quality

The decision to accept an article needs to be unanimous amongst all reviewers and the handling Associate Editor.

The names of the Associate Editor and reviewers are disclosed on published articles to encourage in depth and rigorous reviews, acknowledge work well done on the article and to bring transparency and accountability into peer-review.

Associate Editors can recommend the rejection of an article to the Chief Editor, who needs to check that the authors’ rights have been upheld during the peer-review process, and who can then ultimately reject the article if it is of insufficient quality, has objective errors or if the authors were unreasonably unwilling to address the points raised during the review.

Chief Editors can at any stage of the peer-review step in to comment on the review process, change assigned editors, assign themselves as a reviewer and even as the handling editor for the manuscript, and therefore have full authority and all the mechanisms to act independently in their online editorial office to ensure quality.

Safeguards against Financial Conflicts of Interest

Only leading researchers acting as Associate Editors, who are not part of Frontiers staff, can make acceptance decisions based on reviews performed by external experts acting as Review Editors or reviewers. None have a financial incentive to accept articles, i.e. they are not paid for their role to act as Associate or Review Editors, and any award scheme is not linked to acceptances of manuscripts.

Chief Editors receive an honorarium if their specialty section or field reaches certain submission levels. However, this honorarium is based on the total number of submitted articles during a calendar year, and not the number of accepted articles. Therefore they also have no financial incentive to accept manuscripts.

Post-Publication Stage Quality

The Frontiers platform enables post-publication commenting and discussions on papers and hence the possibility to critically evaluate articles even after the peer-review process.

Frontiers has a community retraction protocol in place to retract papers where serious concerns have been raised and validated by the community that warrant retraction, including ethical concerns, honest errors or scientific misconduct.

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Frontiers in Genetics | Research Topics

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All sections Applied Genetic Epidemiology Behavioral and Psychiatric Genetics Cancer Genetics and Oncogenomics Computational Genomics ELSI in Science and Genetics Epigenomics and Epigenetics Evolutionary and Population Genetics Genetics of Aging Genetics of Common and Rare Diseases Genomic Assay Technology Genomics of Plants and the Phytoecosystem Human and Medical Genomics Immunogenetics Livestock Genomics Molecular Cytogenetics Neurogenomics Nutritional Genomics Pharmacogenetics and Pharmacogenomics RNA Statistical Genetics and Methodology Stem Cell Research Toxicogenomics

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Elucidating the Role of Environmental Factors in Neurodevelopmental Disorders: Implications for Diagnosis and Treatments Jorge ManzoMircea NicoaraCiobica Alin

Submission open

Advancements in Hematopoietic Stem Cell Proliferation and Self-Renewal Maintenance Dr. Pawan Kumar RaghavGurudutta GangenahalliTakahiko Hara 143

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Submission open

Immune System Renewal: Stem Cell Technologies, Artificial Intelligence, and Machine Learning Mariastefania AnticaFATMA VISAL OKURValentin P. ShichkinEnrico Velardi

Submission open

Recent Advancements in Musculoskeletal Regenerative Medicine Elizabeth VinodCsaba MattaBoopalan Ramasamy

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Sequence transfers in plant organelle genomes Chengwen GaoShuo WangKhalid Rehman Hakeem

Submission open

A Year in Review: Discussions in Genomic Assay Technology Jiannis (Ioannis) RagoussisKin ChanEugenia Poliakov

Submission open

A Year in Review: Discussions in Computational Genomics Richard D EmesQuan Zou

Submission open

Non-Mouse Models of Genetic Diseases Andrew NelsonTodd SchoborgArturo López Castel 107

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Pluripotent Stem Cells: Maintenance, Differentiation, and Applications Vahideh AssadollahiYuling HanShaji R Velayudhan 178

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Submission open

Single Cell Landscapes in Gastrointestinal Cancer Rick JansenRoberta BardiniElena Grassi 128

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Cell Apoptosis in Tumor Immune Microenvironment and Its Therapeutic Potential Ronghua YangLei YangLibing ShenXusheng Wang 258

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Submission open

The Physiological, pathological or pathophysiological characters for VRAC and its related genes. Haifeng ZhangWenbo Ma 419

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Frontiers | Automated recognition of chromosome fusion using an alignment-free natural vector method

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Sec. Computational Genomics

Volume 15 - 2024 |

doi: 10.3389/fgene.2024.1364951

Automated recognition of chromosome fusion using an alignment-free natural vector method Provisionally accepted

Hongyu Yu

Stephen S. Yau

1,2* 1

Tsinghua University, Beijing, Beijing, China

Yanqi Lake Beijing Institute of Mathematical and Applications, Beijing, China

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Chromosomal fusion is a significant form of structural variation, but research into algorithms for its identification has been limited. Most existing methods rely on synteny analysis, which necessitates manual annotations and always involves inefficient sequence alignments. In this paper, we present a novel alignment-free algorithm for chromosomal fusion recognition. Our method transforms the problem into a series of assignment problems using natural vectors and efficiently solves them with the Kuhn-Munkres algorithm. When applied to the human/gorilla and swamp buffalo/river buffalo datasets, our algorithm successfully and efficiently identifies chromosomal fusion events. Notably, our approach offers several advantages, including higher processing speeds by eliminating time-consuming alignments and removing the need for manual annotations. By an alignment-free perspective, our algorithm initially considers entire chromosomes instead of fragments to identify chromosomal structural variations, offering substantial potential to advance research in this field. Keywords:

Chromosomal fusion, alignment-free, Natural vector, Kuhn-Munkres algorithm, Automated recognition

Received:

03 Jan 2024;

Accepted:

06 Mar 2024.

open-access article distributed under the terms of the

Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted,

provided the original author(s) or licensor are credited and that the

original publication in this journal is cited, in accordance with accepted

academic practice. No use, distribution or reproduction is permitted which

does not comply with these terms.

* Correspondence:

Stephen S. Yau, Tsinghua University, Beijing, 100084, Beijing, China Disclaimer:

All claims expressed in this article are solely those of the authors and

do not necessarily represent those of their affiliated organizations, or

those of the publisher, the editors and the reviewers. Any product that

may be evaluated in this article or claim that may be made by its

manufacturer is not guaranteed or endorsed by the publisher.

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Editors See all (660) erica e. davis Stanley Manne Children’s Research Institute, Ann & Robert H. Lurie Children's Hospital of Chicago Chicago, United States Specialty Chief Editor

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Elements with complex information like charts and graphs can be hard to read when only color is used to distinguish the data. Try to use other visual aspects to communicate information, such as shape, labels, and size. Incorporating patterns into the shape fills also make differences clearer; for an example please see below:Supplementary materialData that are not of primary importance to the text, or which cannot be included in the article because they are too large or the current format does not permit it (such as videos, raw data traces, PowerPoint presentations, etc.), can be uploaded as supplementary material during the submission procedure and will be displayed along with the published article. All supplementary files are deposited to Figshare for permanent storage and receive a DOI.Supplementary material is not typeset, so please ensure that all information is clearly presented without tracked changes/highlighted text/line numbers, and the appropriate caption is included in the file. To avoid discrepancies between the published article and the supplementary material, please do not add the title, author list, affiliations or correspondence in the supplementary files.The supplementary material can be uploaded as:data sheet (Word, Excel, CSV, CDX, FASTA, PDF or Zip files)presentation (PowerPoint, PDF or Zip files)image (CDX, EPS, JPEG, PDF, PNG or TIF/TIFF),table (Word, Excel, CSV or PDF)audio (MP3, WAV or WMA)video (AVI, DIVX, FLV, MOV, MP4, MPEG, MPG or WMV).Technical requirements for supplementary images:300 DPIsRGB color mode.For supplementary material templates (LaTeX and Word), see our supplementary material templates.ReferencesFrontiers' journals use one of two reference styles, either Harvard (author-date) or Vancouver (numbered). Please check our help center to find the correct style for the journal to which you are submitting.All citations in the text, figures or tables must be in the reference list and vice-versaThe names of the first six authors followed by et al. and the DOI (when available) should be providedGiven names of authors should be abbreviated to initials (e.g., Smith, J., Lewis, C.S., etc.)The reference list should only include articles that are published or acceptedUnpublished data, submitted manuscripts, or personal communications should be cited within the text only, for article types that allow such inclusionsFor accepted but unpublished works use 'in press' instead of page numbersData sets that have been deposited to an online repository should be included in the reference list. Include the version and unique identifier when availablePersonal communications should be documented by a letter of permissionWebsite URLs should be included as footnotesAny inclusion of verbatim text must be contained in quotation marks and clearly reference the original sourcePreprints can be cited as long as a DOI or archive URL is available, and the citation clearly mentions that the contribution is a preprint. If a peer-reviewed journal publication for the same preprint exists, the official journal publication is the preferred source. See the preprints section for each reference style below for more information.Harvard reference style (author-date)Many Frontiers journals use the Harvard referencing system; to find the correct reference style and resources for the journal you are submitting to, please visit our help center. Reference examples are found below, for more examples of citing other documents and general questions regarding the Harvard reference style, please refer to the Chicago Manual of Style.In-text citationsFor works by a single author, include the surname, followed by the yearFor works by two authors, include both surnames, followed by the yearFor works by more than two authors, include only the surname of the first author followed by et al., followed by the yearFor humanities and social sciences articles, include the page numbers.Reference examplesArticle in a print journal

Sondheimer, N., and Lindquist, S. (2000). Rnq1: an epigenetic modifier of protein function in yeast. Mol. Cell. 5, 163-172.Article in an online journal

Tahimic, C.G.T., Wang, Y., Bikle, D.D. (2013). Anabolic effects of IGF-1 signaling on the skeleton. Front. Endocrinol. 4:6. doi: 10.3389/fendo.2013.00006Article or chapter in a book

Sorenson, P. W., and Caprio, J. C. (1998). "Chemoreception," in The Physiology of Fishes, ed. D. H. Evans (Boca Raton, FL: CRC Press), 375-405.Book

Cowan, W. M., Jessell, T. M., and Zipursky, S. L. (1997). Molecular and Cellular Approaches to Neural Development. New York: Oxford University Press.Abstract

Hendricks, J., Applebaum, R., and Kunkel, S. (2010). A world apart? Bridging the gap between theory and applied social gerontology. Gerontologist 50, 284-293. Abstract retrieved from Abstracts in Social Gerontology database. (Accession No. 50360869)Website

World Health Organization. (2018). E. coli. https://www.who.int/news-room/fact-sheets/detail/e-coli [Accessed March 15, 2018].Patent

Marshall, S. P. (2000). Method and apparatus for eye tracking and monitoring pupil dilation to evaluate cognitive activity. U.S. Patent No 6,090,051. Washington, DC: U.S. Patent and Trademark Office.Data

Smith, J. (2008) Post-structuralist discourse relative to phenomological pursuits in the deconstructivist arena. [dissertation/master’s thesis]. [Chicago (IL)]: University of ChicagoPreprint

Smith, J. (2008). Title of the document. Preprint repository name [Preprint]. Available at: https://persistent-url (Accessed March 15, 2018).Vancouver reference style (numbered)Many Frontiers journals use the numbered referencing system; to find the correct reference style and resources for the journal you are submitting to, please visit our help center. Reference examples are found below, for more examples of citing other documents and general questions regarding the Vancouver reference style, please refer to Citing Medicine.In-text citationsPlease apply the Vancouver system for in-text citationsIn-text citations should be numbered consecutively in order of appearance in the text – identified by Arabic numerals in the parenthesis (use square brackets for physics and mathematics articles).Reference examplesArticle in a print journal

Sondheimer N, Lindquist S. Rnq1: an epigenetic modifier of protein function in yeast. Mol Cell (2000) 5:163-72.Article in an online journal

Tahimic CGT, Wang Y, Bikle DD. Anabolic effects of IGF-1 signaling on the skeleton. Front Endocrinol (2013) 4:6. doi: 10.3389/fendo.2013.00006Article or chapter in a book

Sorenson PW, Caprio JC. "Chemoreception". In: Evans DH, editor. The Physiology of Fishes. Boca Raton, FL: CRC Press (1998). p. 375-405.Book

Cowan WM, Jessell TM, Zipursky SL. Molecular and Cellular Approaches to Neural Development. New York: Oxford University Press (1997). 345 p.Abstract

Christensen S, Oppacher F. An analysis of Koza's computational effort statistic for genetic programming. In: Foster JA, editor. Genetic Programming. EuroGP 2002: Proceedings of the 5th European Conference on Genetic Programming; 2002 Apr 3–5; Kinsdale, Ireland. Berlin: Springer (2002). p. 182–91.Website

World Health Organization. E. coli (2018). https://www.who.int/news-room/fact-sheets/detail/e-coli [Accessed March 15, 2018].Patent

Pagedas AC, inventor; Ancel Surgical R&D Inc., assignee. Flexible Endoscopic Grasping and Cutting Device and Positioning Tool Assembly. United States patent US 20020103498 (2002).Data

Perdiguero P, Venturas M, Cervera MT, Gil L, Collada C. Data from: Massive sequencing of Ulms minor's transcriptome provides new molecular tools for a genus under the constant threat of Dutch elm disease. Dryad Digital Repository. (2015) http://dx.doi.org/10.5061/dryad.ps837Theses and dissertationsSmith, J. (2008) Post-structuralist discourse relative to phenomological pursuits in the deconstructivist arena. [dissertation/master’s thesis]. [Chicago (IL)]: University of ChicagoPreprint

Smith, J. Title of the document. Preprint repository name [Preprint] (2008). Available at: https://persistent-url (Accessed March 15, 2018). Aside Side menu navigation

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