Works in Functional & Integrative Genomics, 2025, Vol 25, Issue 1

Results: 136

Transcriptome analysis reveals no obvious unintended effects in the spleen of CRISPR/Cas9-mediated CD163 and pAPN double-knockout pigs.

Published in:

Functional & Integrative Genomics, 2025, v. 25, n. 1, p. 1, doi. 10.1007/s10142-025-01639-5

By:

Liu, Zhi-Guo;
Wang, Nan;
Wang, Wan-Jie;
Huang, Lei;
Chi, Shun-Shun;
Nie, Yu-Xin;
Yuan, Mao-Sha;
Sun, Ya-Ru;
Mu, Yu-Lian;
Li, Kui

Publication type:

Article

Thermotolerance for yield and quality in rice: a novel NF-Ys-QT12 gene system.

Published in:

2025

By:

Waqas, Muhammad Abu Bakar

Publication type:

Letter

LRRC8A/PKC/FLNA pathway activation is detrimental to colon cancer patients.

Published in:

Functional & Integrative Genomics, 2025, v. 25, n. 1, p. 1, doi. 10.1007/s10142-025-01650-w

By:

Liu, Rong;
Zhao, Lijuan;
Cui, Shiyu;
Pouranfard, Masoud;
Jing, Zhenghui;
Ren, Yuhua;
Zhao, Wenbao;
Zhou, Dangxia;
Zhang, Haifeng

Publication type:

Article

Breaking the palatability trade-off: idealizing resistant starch in rice.

Published in:

2025

By:

Chandra, Tilak;
Jaiswal, Sarika;
Iquebal, Mir Asif;
Kumar, Dinesh

Publication type:

Letter

Exploring the m<sup>5</sup>C epitranscriptome of mRNAs in breast cancer cells through genome engineering and long-read sequencing approaches.

Published in:

Functional & Integrative Genomics, 2025, v. 25, n. 1, p. 1, doi. 10.1007/s10142-025-01648-4

By:

Athanasopoulou, Konstantina;
Adamopoulos, Panagiotis G.;
Tsiakanikas, Panagiotis;
Scorilas, Andreas

Publication type:

Article

Integrated multi-omics analysis of UL16-binding protein 2 as a prognostic and immunotherapy biomarker for colorectal cancer.

Published in:

Functional & Integrative Genomics, 2025, v. 25, n. 1, p. 1, doi. 10.1007/s10142-025-01646-6

By:

Qu, Xin-Yang;
Xu, Yong;
Wu, Rui-Min;
Xiao, Gao-Chun;
Wang, Ping-Feng;
Xie, Jin;
Liu, Xu-Sheng

Publication type:

Article

Comprehensive multi-omics analysis of nucleotide metabolism: elucidating the role and prognostic significance of UCK2 in bladder cancer.

Published in:

Functional & Integrative Genomics, 2025, v. 25, n. 1, p. 1, doi. 10.1007/s10142-025-01642-w

By:

Guo, Yadong;
Lin, Ziyou;
Zhang, Wentao;
Chen, Haotian;
Chen, Yuxin;
Liu, Yongqiang;
Shan, Zezhi;
Mao, Shiyu;
Yao, Xudong

Publication type:

Article

Multi-omics approaches: transforming the landscape of natural product isolation.

Published in:

Functional & Integrative Genomics, 2025, v. 25, n. 1, p. 1, doi. 10.1007/s10142-025-01645-7

By:

Sahana, Soumitra;
Sarkar, Jyotirmay;
Mandal, Sourav;
Chatterjee, Indranil;
Dhar, Susmita;
Datta, Samaresh;
Mondal, Sumanta

Publication type:

Article

WISP2/CCN5 revealed as a potential diagnostic biomarker for endometriosis based on machine learning and single-cell transcriptomic analysis.

Published in:

Functional & Integrative Genomics, 2025, v. 25, n. 1, p. 1, doi. 10.1007/s10142-025-01631-z

By:

Dou, Sheng;
Ling, Shaohua;
Nong, Weihua;
Wei, Bixiao;
Huang, Yuehua;
Li, Guangjing;
Wang, Rong;
Qin, Haimei

Publication type:

Article

Genome-wide analysis of AHP genes in soybean and the role of GmAHP10 in improving salt stress tolerance.

Published in:

Functional & Integrative Genomics, 2025, v. 25, n. 1, p. 1, doi. 10.1007/s10142-025-01636-8

By:

Cao, Lingfang;
Cao, Jinlong;
Wang, Li;
Wang, Jianjun;
Che, Zhijun

Publication type:

Article

Genome-wide identification and functional analysis of TCX gene family and the critical role of GhTCX17 in response to drought and salt stress in cotton.

Published in:

Functional & Integrative Genomics, 2025, v. 25, n. 1, p. 1, doi. 10.1007/s10142-025-01632-y

By:

Wei, Yangyang;
Zhai, Jingjing;
Geng, Shuaikang;
Zhang, Shaoliang;
Zhao, Yongqing;
Cui, Bingkai;
Shan, Huiyun;
Li, Yanhua;
Wang, Cong;
Li, Pengtao;
Liu, Yuling;
Lu, Quanwei;
Zhang, Baohong;
Peng, Renhai

Publication type:

Article

QBEmax redefines the precise base editing in crop plants.

Published in:

Functional & Integrative Genomics, 2025, v. 25, n. 1, p. 1, doi. 10.1007/s10142-025-01638-6

By:

Sajjad, Muhammad Waseem;
Muzamil, Fatima;
Naqvi, Rubab Zahra;
Amin, Imran

Publication type:

Article

Doubling the grain: Harnessing the power of DG1 promoter inversion in sorghum.

Published in:

2025

By:

Chandra, Tilak

Publication type:

Letter

Unveiling the Therapeutic Potential of Targeting RRM2 in Hepatocellular Carcinoma: An Integrated In Silico and In Vitro Study.

Published in:

Functional & Integrative Genomics, 2025, v. 25, n. 1, p. 1, doi. 10.1007/s10142-025-01630-0

By:

Ibrahim, Lobna;
Mohamed, Rania Hassan;
Tolba, Mahmoud M.;
Radwan, Sara M.;
Hamdy, Nadia M.;
Elhefnawi, Mahmoud

Publication type:

Article

Genome-resolved metagenomics from short-read sequencing data in the era of artificial intelligence.

Published in:

Functional & Integrative Genomics, 2025, v. 25, n. 1, p. 1, doi. 10.1007/s10142-025-01625-x

By:

Qayyum, Hajra;
Ishaq, Zaara;
Ali, Amjad;
Kayani, Masood Ur Rehman;
Huang, Lisu

Publication type:

Article

CRISPR/Cas9-mediated editing of jasmonic acid pathways to enhance biotic & abiotic stress tolerance: An overview & prospects.

Published in:

Functional & Integrative Genomics, 2025, v. 25, n. 1, p. 1, doi. 10.1007/s10142-025-01623-z

By:

Kaur, Jaspreet;
Viswanathan P, Ananthu;
Bari, Vinay Kumar

Publication type:

Article

Integrated muti-omics data and machine learning reveal CD151 as a key biomarker inducing chemoresistance in metabolic syndrome-related early-onset left-sided colorectal cancer.

Published in:

Functional & Integrative Genomics, 2025, v. 25, n. 1, p. 1, doi. 10.1007/s10142-025-01634-w

By:

Hou, Yingdong;
Xia, Hubin;
Xu, Chenshan;
Yu, Yuhua;
Ji, Chenghao;
Ruan, Wenli;
Kong, Wencheng;
Zhou, Yifeng;
Zhang, Xiaofeng

Publication type:

Article

PIN1 serves as a prognostic and therapeutic biomarker in lung adenocarcinoma.

Published in:

Functional & Integrative Genomics, 2025, v. 25, n. 1, p. 1, doi. 10.1007/s10142-025-01629-7

By:

Yu, Juncheng;
Lu, Xiao;
Zhou, Dong;
Zhang, Jiao;
Deng, Xufeng;
Liu, Xiaobing;
Wang, Kai;
Liao, Shuangqing;
Zheng, Hong;
Dai, Jigang

Publication type:

Article

An efficient hairy root system for validation of CRISPR/Cas system activities in cotton.

Published in:

Functional & Integrative Genomics, 2025, v. 25, n. 1, p. 1, doi. 10.1007/s10142-025-01627-9

By:

Zhang, Manyu;
Zhou, Lili;
Afridi, Mahideen;
Guo, Huiming;
Cheng, Hongmei

Publication type:

Article

LSINCT5: a pivotal oncogenic long non-coding RNA in cancers.

Published in:

Functional & Integrative Genomics, 2025, v. 25, n. 1, p. 1, doi. 10.1007/s10142-025-01610-4

By:

Sritharan, Sharanya K;
Arifin, Amar Harris;
Salvamani, Shamala;
Koh, Rhun Yian;
Gunasekaran, Baskaran

Publication type:

Article

BIRC5 as a master regulator in HCC: unraveling its role in tumor survival and therapeutic potential.

Published in:

Functional & Integrative Genomics, 2025, v. 25, n. 1, p. 1, doi. 10.1007/s10142-025-01615-z

By:

Ayoub, Aya M.;
Mahmoud, Elham Abdel-Badiea;
Mohamed, Rania Hassan;
Tolba, Mahmoud M.;
Hassan, Nahla S.;
Ghazy, Mohamed;
ElHefnawi, Mahmoud

Publication type:

Article

Identification of a NEK7-related pyroptosis gene signature against pancreatic cancer and evaluation of its potential in tumor microenvironment remodeling via regulating inflammasome complex.

Published in:

Functional & Integrative Genomics, 2025, v. 25, n. 1, p. 1, doi. 10.1007/s10142-025-01597-y

By:

Liu, Jia;
Yan, Zilong;
Zhong, Tongning;
Qu, Jianhua;
Lei, Defeng;
Lai, Jinglin;
Zhang, Citing;
Lai, Zhengquan;
Ai, Weipeng;
Liu, Xueqing

Publication type:

Article

Analyzing the potential targets and mechanism of per- and polyfluoroalkyl substances (PFAS) on breast cancer by integrating network toxicology, single-cell sequencing, spatial transcriptomics, and molecular simulation.

Published in:

Functional & Integrative Genomics, 2025, v. 25, n. 1, p. 1, doi. 10.1007/s10142-025-01616-y

By:

Li, Jiajun;
Wang, Deqi;
Song, Sihan;
Wang, Yi;
Wu, Xinlei;
Du, Zhuoyi;
Hong, Yanggang

Publication type:

Article

A novel oncogene, leucine-rich repeat protein 1, mediates hypoxia-induced hepatocellular carcinoma progression.

Published in:

Functional & Integrative Genomics, 2025, v. 25, n. 1, p. 1, doi. 10.1007/s10142-025-01626-w

By:

Tao, Li;
Guo, Yixian;
Liu, Runkun;
Lv, Meng;
Wang, Yufeng

Publication type:

Article

Selenium deficiency is functionally linked with the molecular etiopathogenesis of necrotizing enterocolitis (NEC).

Published in:

Functional & Integrative Genomics, 2025, v. 25, n. 1, p. 1, doi. 10.1007/s10142-025-01628-8

By:

Gürünlüoğlu, Kubilay;
Dündar, Muhammed;
Ünver, Turgay;
Turgut, Hatice;
Gürünlüoğlu, Semra;
Akpınar, Necmettin;
Ateş, Hasan;
Özdemir, Ramazan;
Yıldız, Turan;
Demircan, Mehmet;
Aslan, Mehmet;
Koç, Ahmet

Publication type:

Article

Functional genomics reveals adipose-kidney crosstalk as a contributor to kidney fibrosis via the OSM-OSMR pathway.

Published in:

Functional & Integrative Genomics, 2025, v. 25, n. 1, p. 1, doi. 10.1007/s10142-025-01624-y

By:

Zhang, Jing;
Liu, Zhaojun;
Dong, Shihui;
Xu, Kun;
Wang, Kangchun;
Gong, Luyu;
Liu, Qiaoqiao;
Guo, Yue;
Zhu, Yeping;
She, Jingrong;
Jiang, Song;
Shi, Shaolin;
Liu, Zhihong;
Yang, Jingping

Publication type:

Article

Genome-wide characterization of GRF-GIF transcriptional modules in kenaf (Hibiscus cannabinus L.) reveals their roles in plant development and multi-stress adaptation.

Published in:

Functional & Integrative Genomics, 2025, v. 25, n. 1, p. 1, doi. 10.1007/s10142-025-01622-0

By:

Yue, Jiao;
Wu, Qijing;
Tan, Yuqi;
Wang, Qiuping;
Wei, Rujian;
Wang, Xu;
Chen, Tao;
Luo, Dengjie;
Chen, Peng

Publication type:

Article

The CRISPR-Cas revolution in head and neck cancer: a new era of targeted therapy.

Published in:

Functional & Integrative Genomics, 2025, v. 25, n. 1, p. 1, doi. 10.1007/s10142-025-01612-2

By:

Hashemi, Mohsen;
Khanaghah, Xaniar Mohmmadi;
Nahand, Javid Sadri

Publication type:

Article

Decoding fungal communication networks: molecular signaling, genetic regulation, and ecological implications.

Published in:

Functional & Integrative Genomics, 2025, v. 25, n. 1, p. 1, doi. 10.1007/s10142-025-01620-2

By:

Ishfaq, Shumila;
Anum, Hadiqa;
Shaheen, Tayyaba;
Zulfiqar, Sana;
Ishfaq, Anila;
Anjum, Arslan;
Ramzan, Umera;
Rafiq, Amna;
Mehboob-ur-Rahman;
Guo, Wei

Publication type:

Article

N4-acetylcytidine modification of LncRNA GFOD1-AS1 promotes high glucose-induced dysfunction in human dermal microvascular endothelial cells through stabilization of DNMT1 protein.

Published in:

Functional & Integrative Genomics, 2025, v. 25, n. 1, p. 1, doi. 10.1007/s10142-025-01617-x

By:

Yuan, Jingjing;
Li, Lusha;
Lv, Yang;
Yang, Wenjun

Publication type:

Article

New hope and promise with CRISPR-Cas9 technology for the treatment of HIV.

Published in:

Functional & Integrative Genomics, 2025, v. 25, n. 1, p. 1, doi. 10.1007/s10142-025-01613-1

By:

Hassan, Hesham M.;
Zubair, Akmal;
Helal, Mohamed H.;
Almagharbeh, Wesam Taher;
Elmagzoub, Ranya Mohammed

Publication type:

Article

The ferroptosis-related gene GGTLC2 is identified as a novel biomarker for gastric cancer within the GGT family, with associations to immune infiltration and liver metastasis.

Published in:

Functional & Integrative Genomics, 2025, v. 25, n. 1, p. 1, doi. 10.1007/s10142-025-01614-0

By:

Yan, Nan;
Liu, Jianhong;
Li, Gaofu;
Zhao, Linglin;
Yang, Jie;
Guo, Qijing;
Zhou, Wei;
Luo, Yushuang;
Gao, Yue

Publication type:

Article

mlstverse-web: advancing real-time identification of mycobacteria from sputum using targeted sequencing NALC-Seq.

Published in:

Functional & Integrative Genomics, 2025, v. 25, n. 1, p. 1, doi. 10.1007/s10142-025-01609-x

By:

Matsumoto, Yuki;
Fukushima, Kiyoharu;
Zhang, Shunran;
Fauzyah, Yuzy;
Motooka, Daisuke;
Saito, Haruko;
Yamauchi, June;
Nitta, Tadayoshi;
Nii, Takuro;
Matsuki, Takanori;
Tsujino, Kazuyuki;
Miki, Keisuke;
Kida, Hiroshi;
Nakamura, Shota

Publication type:

Article

Comprehensive profiling of Bcl-2-associated athanogene (BAG) genes and their genetic potential role under cold stress in Cotton.

Published in:

Functional & Integrative Genomics, 2025, v. 25, n. 1, p. 1, doi. 10.1007/s10142-025-01618-w

By:

Abro, Aamir Ali;
Sun, Cong;
Abbas, Mubashir;
Liu, Qiankun;
Jie, Zheng;
Xu, Yanchao;
Hou, Yuqing;
Zhou, Zhongli;
Iqbal, Rashid;
Liu, Fang;
Cai, Xiaoyan

Publication type:

Article

Zebrafish metabolomics: a comprehensive approach to understanding health and disease.

Published in:

Functional & Integrative Genomics, 2025, v. 25, n. 1, p. 1, doi. 10.1007/s10142-025-01621-1

By:

Vivekaa, A;
Nellore, Jayshree;
Sunkar, Swetha

Publication type:

Article

Precise genome editing process and its applications in plants driven by AI.

Published in:

Functional & Integrative Genomics, 2025, v. 25, n. 1, p. 1, doi. 10.1007/s10142-025-01619-9

By:

Jiang, Bo;
An, Zeyu;
Niu, Linlin;
Qin, Debin

Publication type:

Article

3'UTR RNA editing driven by ADAR1 modulates MDM2 expression in breast cancer cells.

Published in:

Functional & Integrative Genomics, 2025, v. 25, n. 1, p. 1, doi. 10.1007/s10142-025-01611-3

By:

Almeric, Elanur;
Karagozoglu, Deniz;
Cicek, Mustafa;
Dioken, Didem Naz;
Tac, Huseyin Avni;
Cicek, Esra;
Kirim, Busra Aytul;
Gurcuoglu, Irmak;
Sezerman, Osman Ugur;
Ozlu, Nurhan;
Erson-Bensan, Ayse Elif

Publication type:

Article

Durum wheat nuclear factor Y (NF-Y) a subfamily: structure, phylogeny, and expression analysis in response to hormones and abiotic stresses.

Published in:

Functional & Integrative Genomics, 2025, v. 25, n. 1, p. 1, doi. 10.1007/s10142-025-01607-z

By:

Chouaibi, Yosra;
Taieb Bouteraa, Mohamed;
Ben Romdhane, Walid;
Baazaoui, Narjes;
Y. Alfaifi, Mohammad;
Kačániová, Miroslava;
Čmiková, Natália;
Ben Hsouna, Anis;
Garzoli, Stefania;
Wiszniewska, Alina;
Saad, Rania Ben

Publication type:

Article

sc-MULTI-omics approach in nano-rare diseases: understanding the pathophysiological mechanism of Mulvihill-Smith Syndrome.

Published in:

Functional & Integrative Genomics, 2025, v. 25, n. 1, p. 1, doi. 10.1007/s10142-025-01608-y

By:

Riess, Angelika;
Roggia, Cristiana;
Selting, Antje Schulze;
Lysenkov, Vladislav;
Ossowski, Stephan;
Casadei, Nicolas;
Riess, Olaf;
Singh, Yogesh

Publication type:

Article

Establishment of a rapid RAA-CRISPR/Cas12a system targeting the recN gene for on-site detection of Streptococcus suis in livestock and fresh pork meat.

Published in:

Functional & Integrative Genomics, 2025, v. 25, n. 1, p. 1, doi. 10.1007/s10142-025-01605-1

By:

Yang, Jian;
Li, Wenjing;
Hu, Yulian;
Han, Yun;
Lei, Changwei;
Wang, Hongning

Publication type:

Article

Twenty-five years of WWOX insight in cancer: a treasure trove of knowledge.

Published in:

Functional & Integrative Genomics, 2025, v. 25, n. 1, p. 1, doi. 10.1007/s10142-025-01601-5

By:

Hammouz, Raneem Y.;
Baryła, Izabela;
Styczeń-Binkowska, Ewa;
Bednarek, Andrzej K.

Publication type:

Article

Genomic dissection of terminal heat tolerance in synthetic hexaploid derived nested introgression libraries of wheat (Triticum aestivum L.).

Published in:

Functional & Integrative Genomics, 2025, v. 25, n. 1, p. 1, doi. 10.1007/s10142-025-01604-2

By:

Kaur, Amandeep;
Dhillon, Guriqbal Singh;
Dhaliwal, Sandeep Kaur;
Kaur, Balihar;
Garg, Monika;
Chhuneja, Parveen;
Singh, Kuldeep;
Srivastava, Puja;
Sharma, Achla;
Kaur, Satinder

Publication type:

Article

Integration of metabolite and transcriptome profiles of cultivated and wild rice to unveil gene regulatory networks and key genes determining rice source and sink strength.

Published in:

Functional & Integrative Genomics, 2025, v. 25, n. 1, p. 1, doi. 10.1007/s10142-025-01606-0

By:

Singh, Anuradha;
Mathan, Jyotirmaya;
Dwivedi, Aditi;
Rani, Ruchi;
Ranjan, Aashish

Publication type:

Article

Mitochondrial genome evolution in the orchid subfamily Cypripedioideae (Orchidaceae).

Published in:

Functional & Integrative Genomics, 2025, v. 25, n. 1, p. 1, doi. 10.1007/s10142-025-01596-z

By:

Qin, Shiyu;
Wang, Hanchen;
Wang, Miaomiao;
Shao, Bingyi;
Ma, Chongbo;
Yang, Boyun;
Jin, Xiaohua

Publication type:

Article

RNA-binding protein HuR interacts with UFM1 mRNA to ameliorate chondrocyte inflammation, apoptosis and extracellular matrix degradation.

Published in:

Functional & Integrative Genomics, 2025, v. 25, n. 1, p. 1, doi. 10.1007/s10142-025-01591-4

By:

Li, LeXiang;
Zhou, Rong;
Yue, ZhiPeng;
Li, HaoBo;
Han, YaGuang;
Zhang, Lei;
Zhu, Jun

Publication type:

Article

EXO1 as a potential biomarker for prognosis, immune infiltration, and immunotherapy in pan-cancer analysis.

Published in:

Functional & Integrative Genomics, 2025, v. 25, n. 1, p. 1, doi. 10.1007/s10142-025-01586-1

By:

Wang, Jikang;
Wang, Fubo;
Huang, Haoxuan

Publication type:

Article

Multi-omics integration reveals YWHAE as a key mediator of ferroptosis in ARDS.

Published in:

Functional & Integrative Genomics, 2025, v. 25, n. 1, p. 1, doi. 10.1007/s10142-025-01603-3

By:

Cui, Honghui;
Huang, Xia

Publication type:

Article

Can the molecular and transgenic breeding of crops be an alternative and sustainable technology to meet food demand?

Published in:

Functional & Integrative Genomics, 2025, v. 25, n. 1, p. 1, doi. 10.1007/s10142-025-01594-1

By:

Gracia-Rodriguez, Celeste;
Martínez-Medina, Angela Elena;
Torres-Cosio, Liliana;
Lopez-Ortiz, Carlos;
Nimmakayala, Padma;
Luévanos-Escareño, Miriam Paulina;
Hernández-Almanza, Ayerim Yedid;
Castro-Alonso, María José;
Sosa-Martínez, Jazel Doménica;
Reddy, Umesh K.;
Balagurusamy, Nagamani

Publication type:

Article

A Multi-omics approach to identify and validate shared genetic architecture in rheumatoid arthritis, multiple sclerosis, and type 1 diabetes: integrating GWAS, GEO, MSigDB, and scRNA-seq data.

Published in:

Functional & Integrative Genomics, 2025, v. 25, n. 1, p. 1, doi. 10.1007/s10142-025-01598-x

By:

Wang, Tailin;
He, Qian;
Chan, Kei Hang Katie

Publication type:

Article

Multi-omic profiling identifies KRT1 as a predictor of immune infiltration and prognosis in gastroesophageal junction cancer.

Published in:

Functional & Integrative Genomics, 2025, v. 25, n. 1, p. 1, doi. 10.1007/s10142-025-01595-0

By:

Song, Tongkun;
Chen, Jiangbo;
Xing, Pu;
Hao, Hao;
Yang, Xinying;
Chen, Bo;
Xu, Kai;
Xing, Jiadi;
Su, Xiangqian

Publication type:

Article