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Rescue of deficits by Brwd1 copy number restoration in the Ts65Dn mouse model of Down syndrome.
Published in:
Nature Communications, 2022, v. 13, n. 1, p. 1, doi. 10.1038/s41467-022-34200-0
By:
- Fulton, Sasha L.;
- Wenderski, Wendy;
- Lepack, Ashley E.;
- Eagle, Andrew L.;
- Fanutza, Tomas;
- Bastle, Ryan M.;
- Ramakrishnan, Aarthi;
- Hays, Emma C.;
- Neal, Arianna;
- Bendl, Jaroslav;
- Farrelly, Lorna A.;
- Al-Kachak, Amni;
- Lyu, Yang;
- Cetin, Bulent;
- Chan, Jennifer C.;
- Tran, Tina N.;
- Neve, Rachael L.;
- Roper, Randall J.;
- Brennand, Kristen J.;
- Roussos, Panos
Publication type:
Article
Transcriptomic profiling of prefrontal cortex reveals shared mechanisms underlying Alzheimer's and Parkinson's Diseases.
Published in:
Alzheimer's & Dementia: The Journal of the Alzheimer's Association, 2023, v. 19, p. 1, doi. 10.1002/alz.075092
By:
- Bendl, Jaroslav;
- Hoffman, Gabriel E;
- Lee, Donghoon;
- M, Prashant N;
- Bennett, David A. A;
- Davis, David A.;
- Scott, William K.;
- Berretta, Sabina;
- Haroutunian, Vahram;
- Fullard, John F;
- Roussos, Panos
Publication type:
Article
Unraveling the transcriptomic landscape of healthy aging.
Published in:
Alzheimer's & Dementia: The Journal of the Alzheimer's Association, 2023, v. 19, p. 1, doi. 10.1002/alz.075833
By:
- Girdhar, Kiran;
- Bendl, Jaroslav;
- Hoffman, Gabriel E;
- Lee, Donghoon;
- M, Prashant N;
- Bennett, David A. A;
- Haroutunian, Vahram;
- Fullard, John F;
- Roussos, Panos
Publication type:
Article
Unraveling the transcriptomic landscape of healthy aging.
Published in:
Alzheimer's & Dementia: The Journal of the Alzheimer's Association, 2023, v. 19, p. 1, doi. 10.1002/alz.075833
By:
- Girdhar, Kiran;
- Bendl, Jaroslav;
- Hoffman, Gabriel E;
- Lee, Donghoon;
- M, Prashant N;
- Bennett, David A. A;
- Haroutunian, Vahram;
- Fullard, John F;
- Roussos, Panos
Publication type:
Article
Genome‐wide methylomic regulation of multiscale gene networks in Alzheimer's disease.
Published in:
Alzheimer's & Dementia: The Journal of the Alzheimer's Association, 2023, v. 19, n. 8, p. 3472, doi. 10.1002/alz.12969
By:
- Wang, Erming;
- Wang, Minghui;
- Guo, Lei;
- Fullard, John F.;
- Micallef, Courtney;
- Bendl, Jaroslav;
- Song, Won‐min;
- Ming, Chen;
- Huang, Yong;
- Li, Yuxin;
- Yu, Kaiwen;
- Peng, Junmin;
- Bennett, David A.;
- De Jager, Philip L.;
- Roussos, Panos;
- Haroutunian, Vahram;
- Zhang, Bin
Publication type:
Article
Neuronal, glial and microglial maps of epigenetic and transcriptomics dysregulations in Alzheimer's disease.
Published in:
Alzheimer's & Dementia: The Journal of the Alzheimer's Association, 2023, v. 19, p. 1, doi. 10.1002/alz.060964
By:
- Bendl, Jaroslav;
- Girdhar, Kiran;
- Hauberg, Mads E;
- Zeng, Biao;
- Kosoy, Roman;
- Dong, Pengfei;
- Rahman, Samir;
- Kleopoulos, Steven P;
- Voloudakis, Georgios;
- Hoffman, Gabriel E;
- Fullard, John F;
- Roussos, Panos
Publication type:
Article
Integration of Alzheimer's disease genetics and myeloid genomics reveals novel disease risk mechanisms: Functionalizing genetic variants in Alzheimer's disease.
Published in:
Alzheimer's & Dementia: The Journal of the Alzheimer's Association, 2020, v. 16, n. 11, p. 1, doi. 10.1002/alz.043897
By:
- Novikova, Gloriia;
- Marcora, Edoardo;
- Kapoor, Manav;
- TCW, Julia;
- Renton, Alan E.;
- Efthymiou, Anastasia M.;
- Abud, Edsel M.;
- Bendl, Jaroslav M.;
- Cheng, Haoxiang M.;
- Fullard, John F.;
- Roussos, Panos;
- Poon, Wayne W.;
- Hao, Ke;
- Goate, Alison M.
Publication type:
Article
Genetic studies of Alzheimer's disease risk implicate clearance of lipid rich debris in myeloid cells: Lipids in AD and FTD: From genes to interventions.
Published in:
Alzheimer's & Dementia: The Journal of the Alzheimer's Association, 2020, v. 16, n. 11, p. 1, doi. 10.1002/alz.040601
By:
- Novikova, Gloriia;
- T.C.W., Julia;
- Marcora, Edoardo;
- Kapoor, Manav;
- Renton, Alan E.;
- Efthymiou, Anastasia M.;
- Abud, Edsel M.;
- Bendl, Jaroslav M.;
- Cheng, Haoxiang M.;
- Fullard, John F.;
- Roussos, Panos;
- Poon, Wayne W.;
- Hao, Ke;
- Goate, Alison M.
Publication type:
Article
Large eQTL meta-analysis reveals differing patterns between cerebral cortical and cerebellar brain regions.
Published in:
Scientific Data, 2020, v. 7, n. 1, p. N.PAG, doi. 10.1038/s41597-020-00642-8
By:
- Sieberts, Solveig K.;
- Perumal, Thanneer M.;
- Carrasquillo, Minerva M.;
- Allen, Mariet;
- Reddy, Joseph S.;
- Hoffman, Gabriel E.;
- Dang, Kristen K.;
- Calley, John;
- Ebert, Philip J.;
- Eddy, James;
- Wang, Xue;
- Greenwood, Anna K.;
- Mostafavi, Sara;
- The CommonMind Consortium (CMC);
- Akbarian, Schahram;
- Bendl, Jaroslav;
- Breen, Michael S.;
- Brennand, Kristen;
- Brown, Leanne;
- Browne, Andrew
Publication type:
Article
CommonMind Consortium provides transcriptomic and epigenomic data for Schizophrenia and Bipolar Disorder.
Published in:
Scientific Data, 2019, v. 6, n. 1, p. N.PAG, doi. 10.1038/s41597-019-0183-6
By:
- Hoffman, Gabriel E.;
- Bendl, Jaroslav;
- Voloudakis, Georgios;
- Montgomery, Kelsey S.;
- Sloofman, Laura;
- Wang, Ying-Chih;
- Shah, Hardik R.;
- Hauberg, Mads E.;
- Johnson, Jessica S.;
- Girdhar, Kiran;
- Song, Lingyun;
- Fullard, John F.;
- Kramer, Robin;
- Hahn, Chang-Gyu;
- Gur, Raquel;
- Marenco, Stefano;
- Lipska, Barbara K.;
- Lewis, David A.;
- Haroutunian, Vahram;
- Hemby, Scott
Publication type:
Article
FireProt: web server for automated design of thermostable proteins.
Published in:
Nucleic Acids Research, 2017, v. 45, n. W1, p. W393, doi. 10.1093/nar/gkx285
By:
- Musil, Milos;
- Stourac, Jan;
- Bendl, Jaroslav;
- Brezovsky, Jan;
- Prokop, Zbynek;
- Zendulka, Jaroslav;
- Martinek, Tomas;
- Bednar, David;
- Damborsky, Jiri
Publication type:
Article
HotSpot Wizard 2.0: automated design of site-specific mutations and smart libraries in protein engineering.
Published in:
Nucleic Acids Research, 2016, v. 44, n. W1, p. W479, doi. 10.1093/nar/gkw416
By:
- Bendl, Jaroslav;
- Stourac, Jan;
- Sebestova, Eva;
- Vavra, Ondrej;
- Musil, Milos;
- Brezovsky, Jan;
- Damborsky, Jiri
Publication type:
Article
Integration of Alzheimer's disease genetics and myeloid genomics identifies disease risk regulatory elements and genes.
Published in:
Nature Communications, 2021, v. 12, n. 1, p. 1, doi. 10.1038/s41467-021-21823-y
By:
- Novikova, Gloriia;
- Kapoor, Manav;
- TCW, Julia;
- Abud, Edsel M.;
- Efthymiou, Anastasia G.;
- Chen, Steven X.;
- Cheng, Haoxiang;
- Fullard, John F.;
- Bendl, Jaroslav;
- Liu, Yiyuan;
- Roussos, Panos;
- Björkegren, Johan LM;
- Liu, Yunlong;
- Poon, Wayne W.;
- Hao, Ke;
- Marcora, Edoardo;
- Goate, Alison M.
Publication type:
Article
DeepGAMI: deep biologically guided auxiliary learning for multimodal integration and imputation to improve genotype–phenotype prediction.
Published in:
Genome Medicine, 2023, v. 15, n. 1, p. 1, doi. 10.1186/s13073-023-01248-6
By:
- Chandrashekar, Pramod Bharadwaj;
- Alatkar, Sayali;
- Wang, Jiebiao;
- Hoffman, Gabriel E.;
- He, Chenfeng;
- Jin, Ting;
- Khullar, Saniya;
- Bendl, Jaroslav;
- Fullard, John F.;
- Roussos, Panos;
- Wang, Daifeng
Publication type:
Article
Unbiased identification of novel transcription factors in striatal compartmentation and striosome maturation.
Published in:
eLife, 2021, p. 1, doi. 10.7554/eLife.65979
By:
- Cirnaru, Maria-Daniela;
- Sicheng Song;
- Tshilenge, Kizito-Tshitoko;
- Chuhyon Corwin;
- Mleczko, Justyna;
- Aguirre, Carlos Galicia;
- Benlhabib, Houda;
- Bendl, Jaroslav;
- Apontes, Pasha;
- Fullard, John;
- Creus-Muncunill, Jordi;
- Reyahi, Azadeh;
- Nik, Ali M.;
- Carlsson, Peter;
- Roussos, Panos;
- Mooney, Sean D.;
- Ellerby, Lisa M.;
- Ehrlich, Michelle E.
Publication type:
Article
Maximizing the Efficiency of Multienzyme Process by Stoichiometry Optimization.
Published in:
ChemBioChem, 2014, v. 15, n. 13, p. 1891, doi. 10.1002/cbic.201402265
By:
- Dvorak, Pavel;
- Kurumbang, Nagendra P.;
- Bendl, Jaroslav;
- Brezovsky, Jan;
- Prokop, Zbynek;
- Damborsky, Jiri
Publication type:
Article
FireProt: Energy- and Evolution-Based Computational Design of Thermostable Multiple-Point Mutants.
Published in:
2015
By:
- Bednar, David;
- Beerens, Koen;
- Sebestova, Eva;
- Bendl, Jaroslav;
- Khare, Sagar;
- Chaloupkova, Radka;
- Prokop, Zbynek;
- Brezovsky, Jan;
- Baker, David;
- Damborsky, Jiri
Publication type:
Product Review
PredictSNP: Robust and Accurate Consensus Classifier for Prediction of Disease-Related Mutations.
Published in:
PLoS Computational Biology, 2014, v. 10, n. 1, p. 1, doi. 10.1371/journal.pcbi.1003440
By:
- Bendl, Jaroslav;
- Stourac, Jan;
- Salanda, Ondrej;
- Pavelka, Antonin;
- Wieben, Eric D.;
- Zendulka, Jaroslav;
- Brezovsky, Jan;
- Damborsky, Jiri
Publication type:
Article
Multi-omic atlas of the parahippocampal gyrus in Alzheimer's disease.
Published in:
Scientific Data, 2023, v. 10, n. 1, p. 1, doi. 10.1038/s41597-023-02507-2
By:
- Coleman, Claire;
- Wang, Minghui;
- Wang, Erming;
- Micallef, Courtney;
- Shao, Zhiping;
- Vicari, James M.;
- Li, Yuxin;
- Yu, Kaiwen;
- Cai, Dongming;
- Peng, Junmin;
- Haroutunian, Vahram;
- Fullard, John F.;
- Bendl, Jaroslav;
- Zhang, Bin;
- Roussos, Panos
Publication type:
Article
NewProt - a protein engineering portal.
Published in:
PEDS: Protein Engineering, Design & Selection, 2017, v. 30, n. 6, p. 441, doi. 10.1093/protein/gzx024
By:
- Schwarte, Andreas;
- Genz, Maika;
- Skalden, Lilly;
- Nobili, Alberto;
- Vickers, Clare;
- Melse, Okke;
- Kuipers, Remko;
- Joosten, Henk-Jan;
- Stourac, Jan;
- Bendl, Jaroslav;
- Black, Jon;
- Haase, Peter;
- Baakman, Coos;
- Damborsky, Jiri;
- Bornscheuer, Uwe;
- Vriend, Gert;
- Venselaar, Hanka
Publication type:
Article
PredictSNP2: A Unified Platform for Accurately Evaluating SNP Effects by Exploiting the Different Characteristics of Variants in Distinct Genomic Regions.
Published in:
PLoS Computational Biology, 2016, v. 12, n. 5, p. 1, doi. 10.1371/journal.pcbi.1004962
By:
- Bendl, Jaroslav;
- Musil, Miloš;
- Štourač, Jan;
- Zendulka, Jaroslav;
- Damborský, Jiří;
- Brezovský, Jan
Publication type:
Article
Lineage specific 3D genome structure in the adult human brain and neurodevelopmental changes in the chromatin interactome.
Published in:
Nucleic Acids Research, 2023, v. 51, n. 20, p. 11142, doi. 10.1093/nar/gkad798
By:
- Rahman, Samir;
- Dong, Pengfei;
- Apontes, Pasha;
- Fernando, Michael B;
- Kosoy, Roman;
- Townsley, Kayla G;
- Girdhar, Kiran;
- Bendl, Jaroslav;
- Shao, Zhiping;
- Misir, Ruth;
- Tsankova, Nadia;
- Kleopoulos, Steven P;
- Brennand, Kristen J;
- Fullard, John F;
- Roussos, Panos
Publication type:
Article
Functional interpretation of genetic variants using deep learning predicts impact on chromatin accessibility and histone modification.
Published in:
Nucleic Acids Research, 2019, v. 47, n. 20, p. 10597, doi. 10.1093/nar/gkz808
By:
- Hoffman, Gabriel E;
- Bendl, Jaroslav;
- Girdhar, Kiran;
- Schadt, Eric E;
- Roussos, Panos
Publication type:
Article
Single cell transcriptomes and multiscale networks from persons with and without Alzheimer's disease.
Published in:
Nature Communications, 2024, v. 15, n. 1, p. 1, doi. 10.1038/s41467-024-49790-0
By:
- Wang, Qi;
- Antone, Jerry;
- Alsop, Eric;
- Reiman, Rebecca;
- Funk, Cory;
- Bendl, Jaroslav;
- Dudley, Joel T.;
- Liang, Winnie S.;
- Karr, Timothy L.;
- Roussos, Panos;
- Bennett, David A.;
- De Jager, Philip L.;
- Serrano, Geidy E.;
- Beach, Thomas G.;
- Van Keuren-Jensen, Kendall;
- Mastroeni, Diego;
- Reiman, Eric M.;
- Readhead, Benjamin P.
Publication type:
Article
decorate: differential epigenetic correlation test.
Published in:
Bioinformatics, 2020, v. 36, n. 9, p. 2856, doi. 10.1093/bioinformatics/btaa067
By:
- Hoffman, Gabriel E;
- Bendl, Jaroslav;
- Girdhar, Kiran;
- Roussos, Panos
Publication type:
Article
Common schizophrenia risk variants are enriched in open chromatin regions of human glutamatergic neurons.
Published in:
Nature Communications, 2020, v. 11, n. 1, p. N.PAG, doi. 10.1038/s41467-020-19319-2
By:
- Hauberg, Mads E.;
- Creus-Muncunill, Jordi;
- Bendl, Jaroslav;
- Kozlenkov, Alexey;
- Zeng, Biao;
- Corwin, Chuhyon;
- Chowdhury, Sarah;
- Kranz, Harald;
- Hurd, Yasmin L.;
- Wegner, Michael;
- Børglum, Anders D.;
- Dracheva, Stella;
- Ehrlich, Michelle E.;
- Fullard, John F.;
- Roussos, Panos
Publication type:
Article
Functional annotation of rare structural variation in the human brain.
Published in:
Nature Communications, 2020, v. 11, n. 1, p. 1, doi. 10.1038/s41467-020-16736-1
By:
- Han, Lide;
- Zhao, Xuefang;
- Benton, Mary Lauren;
- Perumal, Thaneer;
- Collins, Ryan L.;
- Hoffman, Gabriel E.;
- Johnson, Jessica S.;
- Sloofman, Laura;
- Wang, Harold Z.;
- Stone, Matthew R.;
- CommonMind Consortium;
- Akbarian, Schahram;
- Bendl, Jaroslav;
- Breen, Michael;
- Brennand, Kristen J.;
- Brown, Leanne;
- Browne, Andrew;
- Buxbaum, Joseph D.;
- Charney, Alexander;
- Chess, Andrew
Publication type:
Article
A chromosomal connectome for psychiatric and metabolic risk variants in adult dopaminergic neurons.
Published in:
Genome Medicine, 2020, v. 12, n. 1, p. 1, doi. 10.1186/s13073-020-0715-x
By:
- Espeso-Gil, Sergio;
- Halene, Tobias;
- Bendl, Jaroslav;
- Kassim, Bibi;
- Ben Hutta, Gabriella;
- Iskhakova, Marina;
- Shokrian, Neda;
- Auluck, Pavan;
- Javidfar, Behnam;
- Rajarajan, Prashanth;
- Chandrasekaran, Sandhya;
- Peter, Cyril J.;
- Cote, Alanna;
- Birnbaum, Rebecca;
- Liao, Will;
- Borrman, Tyler;
- Wiseman, Jennifer;
- Bell, Aaron;
- Bannon, Michael J.;
- Roussos, Panagiotis
Publication type:
Article

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