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  1. 1.   Duplicate entries in the Protein Data Bank: how to detect and handle them
  2. Wlodawer,Alexander; Dauter, Zbigniew; Rubach, Pawel; Minor, Wladek; Jaskolski, Mariusz; Jiang, Ziqiu; Jeffcott, William; Anosova, Olga; Kurlin, Vitaliy
  3. Acta Crystallographica. Section D, Structural Biology. 2025, Apr 01;
  1. 2.   Prior SARS-Cov-2 infection affects adaptive immune responses to Omicron BA.4/BA.5 mRNA booster
  2. Wachter, Brianna T; Xu, Qin; Shi, Lihong; Burbelo, Peter D; Myint-Hpu, Kathy; Schwartzberg, Pamela L; Rehman,Tauseef; Dewar,Robin; Boswell, Kristin L; Koup, Richard A; Oguz, Cihan; Imberti, Luisa; Bellusci, Lorenza; Pourhashemi, Sara; Khurana, Surender; Manthiram, Kalpana; Notarangelo, Luigi D; Delmonte, Ottavia M
  3. The journal of Allergy and Clinical Immunology. . 2025, Mar 03;
  1. 3.   Adjuvants to the S1-subunit of the SARS-CoV-2 spike protein vaccine improve antibody and T cell responses and surrogate neutralization in mice
  2. Becker, William; Rebbani, Khadija; Duan, Zhijian; Valkov,Eugene; Bryant, Shawn; Ho, Mitchell; Berzofsky, Jay A; Olkhanud, Purevdorj B
  3. Scientific Reports. 2024, Nov 28; 14(1): 29609.
  1. 4.   Neutralizing Antibody Immune Correlates for a Recombinant Protein Vaccine in the COVAIL Trial
  2. Fong, Youyi; Dang, Lauren; Zhang, Bo; Fintzi, Jonathan; Chen, Shiyu; Wang, Jing; Rouphael, Nadine G; Branche, Angela R; Diemert, David J; Falsey, Ann R; Losada, Cecilia; Baden, Lindsey R; Frey, Sharon E; Whitaker, Jennifer A; Little, Susan J; Kamidani, Satoshi; Walter, Emmanuel B; Novak, Richard M; Rupp, Richard; Jackson, Lisa A; Yu, Chenchen; Magaret, Craig A; Molitor, Cindy; Borate, Bhavesh; Babu, Tara M; Kottkamp, Angelica C; Luetkemeyer, Anne F; Immergluck, Lilly C; Presti, Rachel M; Bäcker, Martín; Winokur, Patricia L; Mahgoub, Siham M; Goepfert, Paul A; Fusco, Dahlene N; Atmar, Robert L; Posavad, Christine M; Mu, Jinjian; Makowski, Mat; Makhene, Mamodikoe K; Nayak, Seema U; Roberts, Paul C; Follmann, Dean; Gilbert, Peter B
  3. Clinical Infectious Diseases : an official publication of the Infectious Diseases Society of America. 2024, Sep 26;
  1. 5.   African ancestry-derived APOL1 risk genotypes show proximal epigenetic associations
  2. Breeze, Charles E; Lin, Bridget M; Winkler,Cheryl; Franceschini, Nora
  3. BMC Genomics. 2024, May 08; 25(1): 452.
  1. 6.   Germline pathogenic variants associated with triple-negative breast cancer in US Hispanic and Guatemalan women using hospital and community-based recruitment strategies
  2. Godinez Paredes, Jesica M; Rodriguez, Isabel; Ren, Megan; Orozco, Anali; Ortiz, Jeremy; Albanez, Anaseidy; Jones, Catherine; Nahleh, Zeina; Barreda, Lilian; Garland,Lisa; Torres-Gonzalez, Edmundo; Wu,Dongjing; Luo,Wen; Liu,Jia; Argueta, Victor; Orozco, Roberto; Gharzouzi, Eduardo; Dean, Michael
  3. Breast Cancer Research and Treatment. 2024, Mar 23;
  1. 7.   Natural history of Ebola virus disease in rhesus monkeys shows viral variant emergence dynamics and tissue-specific host responses
  2. Normandin, Erica; Triana, Sergio; Raju, Siddharth S; Lan, Tammy C T; Lagerborg, Kim; Rudy, Melissa; Adams, Gordon C; DeRuff, Katherine C; Logue, James; Liu, David; Strebinger, Daniel; Rao, Arya; Messer, Katelyn S; Sacks, Molly; Adams, Ricky D; Janosko, Krisztina; Kotliar, Dylan; Shah, Rickey; Crozier,Ian; Rinn, John L; Melé, Marta; Honko, Anna N; Zhang, Feng; Babadi, Mehrtash; Luban, Jeremy; Bennett, Richard S; Shalek, Alex K; Barkas, Nikolaos; Lin, Aaron E; Hensley, Lisa E; Sabeti, Pardis C; Siddle, Katherine J
  3. Cell Genomics. 2023, Dec 13; 3(12): 100440.
  1. 8.   Sequencing-based functional assays for classification of BRCA2 variants in mouse ESCs
  2. Biswas,Kajal; Mitrophanov,Alex; Sahu,Sounak; Sullivan,Teresa; Southon,Eileen; Nousome,Darryl; Reid, Susan; Narula, Sakshi; Smolen, Julia; Sengupta, Trisha; Riedel-Topper, Maximilian; Kapoor, Medha; Babbar, Anav; Stauffer,Stacey; Cleveland, Linda; Tandon, Mayank; Malys,Tyler; Sharan,Shyam
  3. Cell Reports Methods. 2023, Nov 20; 3(11): 100628.
  1. 9.   Joint associations between established genetic susceptibility loci, pesticide exposures, and risk of prostate cancer
  2. Hurwitz, Lauren M; Beane Freeman, Laura E; Andreotti, Gabriella; Hofmann, Jonathan N; Parks, Christine G; Sandler, Dale P; Lubin, Jay H; Liu,Jia; Jones,Kristine; Berndt, Sonja I; Koutros, Stella
  3. Environmental Research. 2023, Nov 15; 237(Pt 2): 117063.
  1. 10.   Tumor-associated macrophages trigger MAIT cell dysfunction at the HCC invasive margin
  2. Ruf, Benjamin; Bruhns, Matthias; Babaei, Sepideh; Kedei, Noemi; Ma, Lichun; Revsine, Mahler; Benmebarek, Mohamed-Reda; Ma, Chi; Heinrich, Bernd; Subramanyam, Varun; Qi, Jonathan; Wabitsch, Simon; Green, Benjamin L; Bauer, Kylynda C; Myojin, Yuta; Greten, Layla T; McCallen, Justin D; Huang, Patrick; Trehan, Rajiv; Wang, Xin; Nur, Amran; Murphy Soika, Dana Qiang; Pouzolles, Marie; Evans, Christine N; Chari,Raj; Kleiner, David E; Telford, William; Dadkhah, Kimia; Ruchinskas, Allison; Stovroff, Merrill K; Kang, Jiman; Oza, Kesha; Ruchirawat, Mathuros; Kroemer, Alexander; Wang, Xin Wei; Claassen, Manfred; Korangy, Firouzeh; Greten, Tim F
  3. Cell. 2023, Aug 17; 186(17): 3686-3705.e32.
  1. 11.   Rare disease variant curation from literature: assessing gaps with creatine transport deficiency in focus
  2. Lyons,Erica; Watson,Daniel; Alodadi,Mohammad; Haugabook, Sharie J; Tawa, Gregory J; Hannah-Shmouni, Fady; Porter, Forbes D; Collins, Jack R; Ottinger, Elizabeth A; Mudunuri,Uma
  3. BMC Genomics. 2023, Aug 16; 24(1): 460.
  1. 12.   Structural variant analysis of a cancer reference cell line sample using multiple sequencing technologies
  2. Talsania,Keyur; Shen,Tsai-Wei; Chen, Xiongfong; Jaeger, Erich; Li, Zhipan; Chen, Zhong; Chen, Wanqiu; Tran,Bao; Kusko, Rebecca; Wang, Limin; Pang, Andy Wing Chun; Yang, Zhaowei; Choudhari, Sulbha; Colgan, Michael; Fang, Li Tai; Carroll, Andrew; Shetty,Jyoti; Kriga,Yuliya; German,Oksana; Smirnova,Tatyana; Liu, Tiantain; Li, Jing; Kellman, Ben; Hong, Karl; Hastie, Alex R; Natarajan, Aparna; Moshrefi, Ali; Granat, Anastasiya; Truong, Tiffany; Bombardi, Robin; Mankinen, Veronnica; Meerzaman, Daoud; Mason, Christopher E; Collins, Jack; Stahlberg, Eric; Xiao, Chunlin; Wang, Charles; Xiao, Wenming; Zhao,Yongmei
  3. Genome Biology. 2022, Dec 13; 23(1): 255.
  1. 13.   Massively parallel reporter assays and variant scoring identified functional variants and target genes for melanoma loci and highlighted cell-type specificity
  2. Long, Erping; Yin, Jinhu; Funderburk, Karen M; Xu, Mai; Feng, James; Kane, Alexander; Zhang, Tongwu; Myers, Timothy; Golden, Alyxandra; Thakur, Rohit; Kong, Hyunkyung; Jessop, Lea; Kim, Eun Young; Jones, Kristine; Chari,Raj; Machiela, Mitchell J; Yu, Kai; Iles, Mark M; Landi, Maria Teresa; Law, Matthew H; Chanock, Stephen J; Brown, Kevin M; Choi, Jiyeon
  3. American Journal of Human Genetics. 2022, Nov 18;
  1. 14.   HPV16 E7 Nucleotide Variants Found in Cancer-Free Subjects Affect E7 Protein Expression and Transformation
  2. Lou,Hong; Boland, Joseph F; Li,Hongchuan; Burk, Robert; Yeager, Meredith; Anderson,Steve; Wentzensen, Nicolas; Schiffman, Mark; Mirabello, Lisa; Dean, Michael
  3. Cancers. 2022, Oct 06; 14(19):
  1. 15.   Potent monoclonal antibodies neutralize Omicron sublineages and other SARS-CoV-2 variants
  2. Chen, Zhaochun; Zhang, Peng; Matsuoka, Yumiko; Tsybovsky,Yaroslav; West, Kamille; Santos, Celia; Boyd, Lisa F; Nguyen, Hanh; Pomerenke, Anna; Stephens,Tyler; Olia, Adam S; Zhang, Baoshan; De Giorgi, Valeria; Holbrook, Michael R; Gross, Robin; Postnikova, Elena; Garza, Nicole L; Johnson, Reed F; Margulies, David H; Kwong, Peter D; Alter, Harvey J; Buchholz, Ursula J; Lusso, Paolo; Farci, Patrizia
  3. Cell Reports. 2022, Sep 30; 41(5): 111528.
  1. 16.   An intranasally administrated SARS-CoV-2 beta variant subunit booster vaccine prevents beta variant replication in rhesus macaques
  2. Sui, Yongjun; Li, Jianping; Andersen, Hanne; Zhang, Roushu; Prabhu, Sunaina K; Hoang, Tanya; Venzon, David; Cook, Anthony; Brown, Renita; Teow, Elyse; Velasco, Jason; Pessaint, Laurent; Moore, Ian N; Lagenaur, Laurel; Talton, Jim; Breed,Matthew; Kramer,Josh; Bock, Kevin W; Minai, Mahnaz; Nagata, Bianca M; Choo-Wosoba, Hyoyoung; Lewis, Mark G; Wang, Lai-Xi; Berzofsky, Jay A
  3. PNAS Nexus. 2022, Jul; 1(3): pgac091.
  1. 17.   Rare germline variants in PALB2 and BRCA2 in familial and sporadic chordoma
  2. Xia, Bing; Biswas,Kajal; Foo, Tzeh Keong; Torres, Thiago; Riedel-Topper, Maximilian; Southon,Eileen; Kang, Zhihua; Huo, Yanying; Reid,Susan; Stauffer,Stacey; Zhou,Weiyin; Zhu, Bin; Koka, Hela; Yepes, Sally; Brodie, Seth A; Jones,Kristine; Vogt,Aurelie; Zhu,Bin; Cater, Brian; Freedman, Neal D; Hicks,Belynda; Yeager, Meredith; Chanock, Stephen J; Couch, Fergus; Parry, Dilys M; Monteiro, Alvaro N; Goldstein, Alisa M; Carvalho, Marcelo A; Sharan,Shyam; Yang, Xiaohong R
  3. Human Mutation. 2022, Jun 28;
  1. 18.   Duplex One-Step RT-qPCR Assays for Simultaneous Detection of Genomic and Subgenomic RNAs of SARS-CoV-2 Variants
  2. Bhosle, Sushma M; Tran, Julie P; Yu, Shuiqing; Geiger, Jillian; Jackson, Jennifer D; Crozier,Ian; Crane, Anya; Wada, Jiro; Warren, Travis K; Kuhn, Jens H; Worwa, Gabriella
  3. Viruses. 2022, May 17; 14(5):
  1. 19.   CpG Site-Specific Methylation-Modulated Divergent Expression of PRSS3 Transcript Variants Facilitates Nongenetic Intratumor Heterogeneity in Human Hepatocellular Carcinoma
  2. Lin, Shuye; Xu, Hanli; Pang, Mengdi; Zhou, Xiaomeng; Pan, Yuanming; Zhang, Lishu; Guan, Xin; Wang, Xiaoyue; Lin, Bonan; Tian, Rongmeng; Chen,Keqiang; Zhang, Xiaochen; Yang, Zijiang; Ji, Fengmin; Huang, Yingying; Wei, Wu; Gong,Wang; Ren, Jianke; Wang,Jiming; Guo, Mingzhou; Huang, Jiaqiang
  3. Frontiers in Oncology. 2022, Apr 11; 12: 831268.
  1. 20.   Associations between APOL1 genetic variants and blood pressure in African American mothers and children from a U.S. pregnancy cohort: Modification by air pollution exposures
  2. Ni, Yu; Simpson, Claire L; Davis, Robert L; Szpiro, Adam A; Karr, Catherine J; Kovesdy, Csaba P; Hjorten, Rebecca C; Tylavsky, Frances A; Bush, Nicole R; LeWinn, Kaja Z; Winkler,Cheryl; Kopp, Jeffrey B; Obi, Yoshitsugu
  3. Environmental Research. 2022, Mar 28; 212
  1. 21.   Genetic variation within the human papillomavirus type 16 genome is associated with oropharyngeal cancer prognosis
  2. Lang Kuhs, K A; Faden, D L; Chen, L; Smith, D K; Pinheiro, M; Wood, C B; Davis, S; Yeager,Meredith; Boland, J F; Cullen, M; Steinberg, M; Bass, S; Wang, X; Liu, P; Mehrad, M; Tucker, T; Lewis, J S; Ferris, R L; Mirabello, L
  3. Annals of Oncology : official journal of the European Society for Medical Oncology. 2022, Mar 16; 33(6): 638-648.
  1. 22.   T cell reactivity to the SARS-CoV-2 Omicron variant is preserved in most but not all individuals
  2. Naranbhai, Vivek; Nathan, Anusha; Kaseke, Clarety; Berrios, Cristhian; Khatri, Ashok; Choi, Shawn; Getz, Matthew A; Tano-Menka, Rhoda; Ofoman, Onosereme; Gayton, Alton; Senjobe, Fernando; Zhao, Zezhou; St Denis, Kerri J; Lam, Evan C; Carrington,Mary; Garcia-Beltran, Wilfredo F; Balazs, Alejandro B; Walker, Bruce D; Iafrate, A John; Gaiha, Gaurav D
  3. Cell. 2022, Feb 03; 185
  1. 23.   Standards for the classification of pathogenicity of somatic variants in cancer (oncogenicity): Joint recommendations of Clinical Genome Resource (ClinGen), Cancer Genomics Consortium (CGC), and Variant Interpretation for Cancer Consortium (VICC)
  2. Horak, Peter; Griffith, Malachi; Danos, Arpad M; Pitel, Beth A; Madhavan, Subha; Liu, Xuelu; Chow, Cynthia; Williams, Heather; Carmody, Leigh; Barrow-Laing, Lisa; Rieke, Damian; Kreutzfeldt, Simon; Stenzinger, Albrecht; Tamborero, David; Benary, Manuela; Rajagopal, Padma Sheila; Ida, Cristiane M; Lesmana, Harry; Satgunaseelan, Laveniya; Merker, Jason D; Tolstorukov, Michael Y; Campregher, Paulo Vidal; Warner, Jeremy L; Rao, Shruti; Natesan, Maya; Shen, Haolin; Venstrom, Jeffrey; Roy, Somak; Tao, Kayoko; Kanagal-Shamanna, Rashmi; Xu, Xinjie; Ritter, Deborah I; Pagel, Kym; Krysiak, Kilannin; Dubuc, Adrian; Akkari, Yassmine M; Li, Xuan Shirley; Lee, Jennifer; King, Ian; Raca, Gordana; Wagner, Alex H; Li, Marylin M; Plon, Sharon E; Kulkarni, Shashikant; Griffith, Obi L; Chakravarty, Debyani; Sonkin, Dmitriy
  3. Genetics in Medicine : Official Journal of the American College of Medical Genetics. 2022, Jan 28;
  1. 24.   A Pre-Vaccination Baseline of SARS-CoV-2 Genetic Surveillance and Diversity in the United States
  2. Capoferri,Adam; Shao,Wei; Spindler,Jon; Coffin, John M.; Rausch,Jason; Kearney,Mary
  3. Viruses-Basel. 2022, Jan 7; 14(1):
  1. 25.   Identification of a dysfunctional exon-skipping splice variant in GLUT9/SLC2A9 causal for renal hypouricemia type 2
  2. Toyoda, Yu; Cho, Sung Kweon; Tasic, Velibor; Pavelcová, Katerina; Bohatá, Jana; Suzuki, Hiroshi; David, Victor A; Yoon,Jaeho; Pallaiova, Anna; Šaligová, Jana; Nousome,Darryl; Cachau, Raul; Winkler,Cheryl; Takada, Tappei; Stiburková, Blanka
  3. Frontiers in Genetics. 2022 13: 1048330.
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