1. Singh A, Del-Valle-Anton L, de Juan Romero C, Zhang Z, Ortuño EF, Mahesh A, Espinós A, Soler R, Cárdenas A, Fernández V, Lusby R, Tiwari VK, Borrell V. Gene regulatory landscape of cerebral cortex folding. Sci Adv. 2024 Jun 7;10(23):eadn1640. doi: 10.1126/sciadv.adn1640. Epub 2024 Jun 5. PMID: 38838158; PMCID: PMC11152136.
2. Inayatullah M, Mahesh A, Turnbull AK, Dixon JM, Natrajan R, Tiwari VK. Basal-epithelial subpopulations underlie and predict chemotherapy resistance in triple-negative breast cancer. EMBO Mol Med. 2024 Apr;16(4):823-853. doi: 10.1038/s44321-024-00050-0. Epub 2024 Mar 13. PMID: 38480932; PMCID: PMC11018633
3. Lusby R, Zhang Z, Mahesh A, Tiwari VK. Decoding gene regulatory circuitry underlying TNBC chemoresistance reveals biomarkers for therapy response and therapeutic targets. NPJ Precis Oncol. 2024 Mar 12;8(1):64. doi: 10.1038/s41698-024-00529-6. PMID: 38472332; PMCID: PMC10933292.
4. de la Fuente AG, Dittmer M, Heesbeen EJ, de la Vega Gallardo N, White JA, Young A, McColgan T, Dashwood A, Mayne K, Cabeza-Fernández S, Falconer J, Rodriguez-Baena FJ, McMurran CE, Inayatullah M, Rawji KS, Franklin RJM, Dooley J, Liston A, Ingram RJ, Tiwari VK, Penalva R, Dombrowski Y, Fitzgerald DC. Ageing impairs the regenerative capacity of regulatory T cells in mouse central nervous system remyelination. Nat Commun. 2024 Mar 11;15(1):1870. doi: 10.1038/s41467-024-45742-w. PMID: 38467607; PMCID: PMC10928230.
5. Singh A, Tiwari VK. Transcriptional networks of transient cell states during human prefrontal cortex development. Front Mol Neurosci. 2023 Apr 17;16:1126438. doi: 10.3389/fnmol.2023.1126438. PMID: 37138706; PMCID: PMC10150774.
6. Little K, Singh A, Del Marco A, Llorián-Salvador M, Vargas-Soria M, Turch-Anguera M, Solé M, Bakker N, Scullion S, Comella JX, Klaassen I, Simó R, Garcia-Alloza M, Tiwari VK, Stitt AW; RECOGNISED consortium. Disruption of cortical cell type composition and function underlies diabetes-associated cognitive decline. Diabetologia. 2023 Aug;66(8):1557-1575. doi: 10.1007/s00125-023-05935-2. Epub 2023 Jun 23. PMID: 37351595; PMCID: PMC10317904.
7. Heiland M, Connolly NMC, Mamad O, Nguyen NT, Kesavan JC, Langa E, Fanning K, Sanfeliu A, Yan Y, Su J, Venø MT, Costard LS, Neubert V, Engel T, Hill TDM, Freiman TM, Mahesh A, Tiwari VK, Rosenow F, Bauer S, Kjems J, Morris G, Henshall DC. MicroRNA-335-5p suppresses voltage-gated sodium channel expression and may be a target for seizure control. Proc Natl Acad Sci U S A. 2023 Jul 25;120(30):e2216658120. doi: 10.1073/pnas.2216658120. Epub 2023 Jul 18. PMID: 37463203; PMCID: PMC10372546.
8. Sahu SK, Agirre E, Inayatullah M, Mahesh A, Tiwari N, Lavin DP, Singh A, Strand S, Diken M, Luco RF, Belmonte JCI, Tiwari VK. A complex epigenome-splicing crosstalk governs epithelial-to-mesenchymal transition in metastasis and brain development. Nat Cell Biol. 2022 Aug;24(8):1265-1277. doi: 10.1038/s41556-022-00971-3. Epub 2022 Aug 8. PMID: 35941369.
9. Singh A, Mahesh A, Noack F, Cardoso de Toledo B, Calegari F, Tiwari VK. Tcf12 and NeuroD1 cooperatively drive neuronal migration during cortical development. Development. 2022 Feb 1;149(3):dev200250. doi: 10.1242/dev.200250. Epub 2022 Feb 11. PMID: 35147187; PMCID: PMC8918803.
10. Lavin DP, Abassi L, Inayatullah M, Tiwari VK. Mnt Represses Epithelial Identity To Promote Epithelial-to-Mesenchymal Transition. Mol Cell Biol. 2021 Oct 26;41(11):e0018321. doi: 10.1128/MCB.00183-21. Epub 2021 Aug 30. PMID: 34460331; PMCID: PMC8547447.
11. Lusby R, Dunne P, Tiwari VK. Tumour invasion and dissemination. Biochem Soc Trans. 2022 Jun 30;50(3):1245-1257. doi: 10.1042/BST20220452. PMID: 35713387; PMCID: PMC9246329.
12. Larivière S, Royer J, Rodríguez-Cruces R, Paquola C, Caligiuri ME, Gambardella A, Concha L, Keller SS, Cendes F, Yasuda CL, Bonilha L, Gleichgerrcht E, Focke NK, Domin M, von Podewills F, Langner S, Rummel C, Wiest R, Martin P, Kotikalapudi R, O’Brien TJ, Sinclair B, Vivash L, Desmond PM, Lui E, Vaudano AE, Meletti S, Tondelli M, Alhusaini S, Doherty CP, Cavalleri GL, Delanty N, Kälviäinen R, Jackson GD, Kowalczyk M, Mascalchi M, Semmelroch M, Thomas RH, Soltanian-Zadeh H, Davoodi-Bojd E, Zhang J, Winston GP, Griffin A, Singh A, Tiwari VK, Kreilkamp BAK, Lenge M, Guerrini R, Hamandi K, Foley S, Rüber T, Weber B, Depondt C, Absil J, Carr SJA, Abela E, Richardson MP, Devinsky O, Severino M, Striano P, Tortora D, Kaestner E, Hatton SN, Vos SB, Caciagli L, Duncan JS, Whelan CD, Thompson PM, Sisodiya SM, Bernasconi A, Labate A, McDonald CR, Bernasconi N, Bernhardt BC. Structural network alterations in focal and generalized epilepsy assessed in a worldwide ENIGMA study follow axes of epilepsy risk gene expression. Nat Commun. 2022 Jul 27;13(1):4320. doi: 10.1038/s41467-022-31730-5. PMID: 35896547; PMCID: PMC9329287.
13. Griffin A, Mahesh A, Tiwari VK. Disruption of the gene regulatory programme in neurodevelopmental disorders. Biochim Biophys Acta Gene Regul Mech. 2022 Oct;1865(7):194860. doi: 10.1016/j.bbagrm.2022.194860. Epub 2022 Aug 23. PMID: 36007842.
14. Basu A, Tiwari VK. Epigenetic reprogramming of cell identity: lessons from development for regenerative medicine. Clin Epigenetics. 2021 Jul 23;13(1):144. doi: 10.1186/s13148-021-01131-4. PMID: 34301318; PMCID: PMC8305869.
15. Roussel M, Ferrant J, Reizine F, Le Gallou S, Dulong J, Carl S, Lesouhaitier M, Gregoire M, Bescher N, Verdy C, Latour M, Bézier I, Cornic M, Vinit A, Monvoisin C, Sawitzki B, Leonard S, Paul S, Feuillard J, Jeannet R, Daix T, Tiwari VK,Tadié JM, Cogné M, Tarte K. Comparative immune profiling of acute respiratory distress syndrome patients with or without SARS-CoV-2 infection. Cell Rep Med. 2021 Jun 15;2(6):100291. doi: 10.1016/j.xcrm.2021.100291. Epub 2021 May 6. PMID: 33977279; PMCID: PMC8101789.
16. Herzog DP, Pascual Cuadrado D, Treccani G, Jene T, Opitz V, Hasch A, Lutz B, Lieb K, Sillaber I, van der Kooij MA, Tiwari VK, Müller MB. A distinct transcriptional signature of antidepressant response in hippocampal dentate gyrus granule cells. Transl Psychiatry. 2021 Jan 5;11(1):4. doi: 10.1038/s41398-020-01136-2. PMID: 33414410; PMCID: PMC7791134.
17. Lavin DP, Tiwari VK. Unresolved Complexity in the Gene Regulatory Network Underlying EMT. Front Oncol. 2020 May 12;10:554.
18. Basu, Amitava, Iván Mestres, Sanjeeb Kumar Sahu, Neha Tiwari, Bimola Khongwir, Jan Baumgart, Aditi Singh, Federico Calegari, and Vijay K. Tiwari. "Phf21b imprints the spatiotemporal epigenetic switch essential for neural stem cell differentiation." Genes & Development 34, no. 17-18 (2020): 1190-1209.
19. Pataskar A, Vanderlinden W, Emmerich J, Singh A, Lipfert J, Tiwari VK*(*co-corresponding author). Deciphering the gene regulatory landscape encoded in DNA biophysical features. iScience, 2019, Nov; S2589-0042(19)30436-5.
20. Tiwari N, Pataskar A, Péron S, Thakurela S, Sahu SK, Figueres-Oñate M, Marichal N, López-Mascaraque L, Tiwari VK*, Berninger B* (*co-corresponding authors).Stage-Specific Transcription Factors Drive Astrogliogenesis by Remodeling Gene Regulatory Landscapes. Cell Stem Cell, 2018, Oct 4; 23(4):557.
21. Sahu S, Tiwari N, Pataskar A, Borisova M, Diken M, Strand S, Beli P, Tiwari VK*(*corresponding author). FBXO32 promotes microenvironment underlying Epithelial-Mesenchymal Transition via CtBP1 during tumor metastasis and brain development Nature Communications, 2017, Nov 15;8(1):1523
22. Pataskar A, Jung J, Smialowski P, Calegari F, Straub T, Tiwari VK* (*corresponding author). NeuroD1 reprograms chromatin and transcription factor landscapes to induce the neuronal program. The EMBO Journal, 2016 Jan 4;35(1):24-45 (Featured article, see news & views by Glahs & Zinzen: The EMBO Journal, 2016 Jan 4;35(1):1-3) (Rated “Exceptional” by Faculty of 1000)
23. Thakurela S, Sahu SK, Garding A, Tiwari VK* (*corresponding author). Dynamics and function of distal regulatory elements during neurogenesis and neuroplasticity. Genome Research, 2015 Sep;25(9):1309-24
24. Sahu SK, Garding A, Berninger B, Nitsch R, Schmidt M, Tiwari VK* (*corresponding author). JNK-dependent gene regulatory circuitry governs mesenchymal fate. The EMBO Journal, 2015 Aug 13;34(16):2162-81.
25. Thakurela S, Garding A, Jung, Schübeler D, Burger L, Tiwari VK* (*corresponding author). Gene Regulation and Priming by Topoisomerase IIα in embryonic stem cells. Nature Communications, 2013, Sep 27; 4:2478
26. Tiwari VK*, Burger L, Nikoletopoulou V, Deogracious R, Thakurela S, Wirbelauer C, Hoerner L, Mielke C, Boege F, Murr R, Peters A, Barde YA, Schübeler D* (*co-corresponding authors). Target genes of Topoisomerase IIbeta regulate neuronal survival and are defined by their chromatin state. PNAS,2012 Apr 17;109(16):E934-43
27. Tiwari VK, Stadler M, Wirbelauer C, Paro R, Beisel C, Schübeler D. A Chromatin-modifying Function of JNK during Stem Cell Differentiation. Nature Genetics, 2012 Jan 18;44(1):94-100. (Featured in Faculty of 1000, medical express and bioportfolio)
28. Stadler MB, Murr R, Burger L, Ivanek R, Lienert F, Schöler A, Nimwegen E, Wirebeluer C, Oakeley EJ, Gaidatzis D, Tiwari VK, Schübeler D. DNA-binding factors shape the mouse methylome at distal regulatory regions. Nature,2011 Dec 14;480(7378):490-5
29. Tiwari VK, McGarvey KM, Licchesi J, Ohm JE, Herman JG, Schübeler D, Baylin SB. PcG Proteins, DNA methylation and gene repression by chromatin looping. PLoS Biology, 2008 Dec 2; 6(12):2911-27
30. (“Editor’s choice”, see: PLoS Biol. 2008 December; 6(12): e313, by Mary Hoff)
31. Tiwari VK, Cope L, McGarvey KM, Ohm JE, Baylin SB.A Novel 6C assay uncovers polycomb-mediated higher order chromatin conformations. Genome Research,2008 Jul; 18(7): 1171-9.
1. Noack F, Pataskar A, Schneider M, Buchholz F, Tiwari VK, Calegari F. Direct Assessment and site-specific manipulation of DNA (hydroxy-)methylation during mouse corticogenesis. Life Sci Alliance. 2019 Feb 27;2(2). pii: e201900331.
2. Camargo Ortega G, Falk S, Johansson PA, Peyre E, Broix L, Sahu SK, Hirst W, Schlichthaerle T, De Juan Romero C, Draganova K, Vinopal S, Chinnappa K, Gavranovic A, Karakaya T, Steininger T, Merl-Pham J, Feederle R, Shao W, Shi SH, Hauck SM, Jungmann R, Bradke F, Borrell V, Geerlof A, Reber S, Tiwari VK, Huttner WB, Wilsch-Bräuninger M, Nguyen L, Götz M. The centrosome protein AKNA regulates neurogenesis via microtubule organization. Nature, 2019 Mar; 567(7746):113-117.
3. Camp JG, Falk S, Gerber T, Pataskar A, Gac-Santel M, Kageyama J, Brazovskaja A, Garding A, Fan W, Riedemann T, Casamassa A, Smiyakin A, Schichor C, Götz M, Tiwari VK, Treutlein B, Berninger B. Direct pericyte-to-neuron reprogramming via unfolding of a neural stem cell-like program Karow M, Nature Neurosci. 2018 Jun 18. doi: 10.1038/s41593-018-0168-3.
4. Jeong H, Tiwari VK*(*corresponding author). Exploring the Complexity of Cortical Development Using Single-Cell Transcriptomics. Front Neurosci., 2018 Feb 2;12:31.
5. Navandar M, Garding A, Sahu SK, Pataskar A, Schick S, Tiwari VK*. (*corresponding author). ERK signalling modulates epigenome to drive epithelial to mesenchymal transition. Oncotarget, 2017 Apr 25;8(17):29269-29281.
6. Gezelius H, Moreno-Juan V, Mezzera C, Pistolic J, Benes B, Tiwari VK, López-Bendito G. Genetic labelling of nuclei-specific thalamocortical neurons reveals putative sensory-modality specific genes. Cerebral Cortex, 2017 Nov 1;27(11):5054-5069.
7. Thakurela S, Garding A, Jung RB, Müller C, Goebbels S, White R, Werner H*, Tiwari VK* (*co-corresponding authors). The transcriptome of mouse central nervous system myelin. Nature Scientific Reports, 2016 May 13;6:25828.
8. Sahu SK, Fritz A, Tiwari N, Kovacs Z, Pouya A, Wüllner V, Bora P, Schacht T, Baumgart J, Peron S, Berninger B, Tiwari VK*, Methner A* (*co-corresponding authors). TOX3 regulates neural progenitor identity. BBA Gene Regulatory Mechanisms, 2016 Apr 11;1859(7):833-840.
9. Pataskar A, Tiwari VK*. (*corresponding author). Computational challenges in modeling gene regulatory networks. Transcription, 2016
10. Pataskar A, Jung J, Tiwari VK*. (*corresponding author). Deciphering the epigenetic code of embryonic neurogenesis. Encyclopedia of Molecular Cell Biology and Molecular Medicine (Wiley), 2016·
11. Thakurela S, Tiwari N, Schick S, Garding A, Berninger B and Tiwari VK* (*corresponding author). Mapping gene regulatory circuitry of Pax6 during neurogenesis. Cell Discovery, 2016 2, 15045.
12. Wagner M, Jung J, Koslowski M, Türeci Ö, Tiwari VK*, Sahin U*. (*co-corresponding authors). Chromatin Immunoprecipitation Assay to Identify Genomic Binding Sites of Regulatory Factors. Methods Mol Biol. 2016;1366:53-65. doi: 10.1007/978-1-4939-3127-9_6.
13. Schick S*, Becker K*, Thakurela S, Fournier D, Hampel MH, Legewie S*, Tiwari VK* (*co-corresponding authors). Identifying Novel Transcriptional Regulators with Circadian Expression. Mol Cell Biol, 2016 36, 545-58.
14. Stanzel S, Stubbusch J, Pataskar A, Ernsberger U, Tiwari VK, Rohrer H, Tsarovina K. Distinct roles of Hand2 in developing and adult autonomic neurons. Developmental Neurobiology, 2016 Jan 28. doi: 10.1002/dneu.22378.
15. Schick S, Fournier D, Thakurela S, Sahu SK, Garding A, Tiwari VK* (*corresponding author). Dynamics of chromatin accessibility and epigenetic state in response to UV damage. Journal of Cell Science, 2015: doi: 10.1242/jcs.173633.
16. Prakash K, Fournier D, Redl S, Best G, Borsos M, Tiwari VK, Ketting R, Tachibana-Konwalski K, Cremer C and Birk U (2015). Super-resolution imaging reveals structurally distinct periodic patterns of chromatin along pachytene chromosomes. PNAS, 2015 112, 14635-14640
17. von der Lippen C, Sahu SK, Seifermann M, Tiwari VK and Epe B. The repair of oxidized purines in the DNA of human lymphocytes requires an activation involving NF-YA-mediated upregulation of OGG1. DNA Repair, 2015 25, 1-8.
18. Garding A, Bhattacharya N, Claus R, Ruppel M, Tschuch C, Filarsky K, Idler I, Zucknick M, Caudron-Herger M, Oakes C, Serra L, Thakurela S, Tiwari VK, Weichenhan D, Benner A, Radlwimmer B, Zentgraf H, Wiemann S, Rippe K, Plass C, Döhner H, Lichter P, Stilgenbauer S and Mertens D (2013). Epigenetic upregulation of lncRNAs at 13q14.3 in leukemia is linked to the In Cis downregulation of a gene cluster that targets NF-kB. PLoS Genet, 9, e1003373.
19. Tiwari N, Tiwari VK, Waldmeier L, Balwierz P, Arnold P, Pachkov M, Meyer-Schaller N, Schübeler D, van Nimwegen E and Christofori G (2013). Sox4 Is a Master Regulator of Epithelial-Mesenchymal Transition by Controlling Ezh2 Expression and Epigenetic Reprogramming. Cancer Cell, 2013 23, 768-783
20. Bell O, Tiwari VK, Thomä NH and Schübeler D. Dynamics and determinants of DNA accessibility. Nature Reviews Genetics 2011, 12, 554-564.
21. Lienert F, Mohn F, Tiwari VK, Baubec T, Roloff TC, Gaidatzis D, Stadler MB and Schubeler D.Genomic Prevalence of Heterochromatic H3K9me2 and Transcription Do Not Discriminate Pluripotent from Terminally Differentiated Cells. PLOS Genet, 2011 7, e1002090.
22. Licchesi JD, Van Neste L, Tiwari VK, Cope L, Lin X, Baylin SB and Herman JG. Transcriptional regulation of Wnt inhibitory factor-1 by Miz-1/c-Myc. Oncogene, 2011 29, 5923-5934.
23. Tiwari VK* and Baylin SB*. (*co-corresponding authors). Mapping networks of protein-mediated physical interactions between chromatin elements. Curr Protoc Mol Biol, 2010 Chapter 21, Unit 21 16 1-13.
24. Sandhu KS, Shi C, Sjölinder M, Liu L, Tiwari VK, Guibert S, Emilsson L, Imreh MP and Ohlsson R. Nonallelic transvection of multiple imprinted loci is organized by the H19 imprinting control region during germline development. Genes Dev, 2009 23, 2598-2603.
25. Tiwari VK* and Baylin SB*. (*co-corresponding authors). Combined 3C-ChIP-cloning (6C) assay: a tool to unravel protein-mediated genome architecture. Cold Spring Harb Protoc, 2009 pdb prot5168.
26. Tiwari VK and Baylin SB. Breaching the boundaries that safeguard against repression. Mol Cell, 2009 34, 395-397.
27. Nemeth A, Guibert S, Tiwari VK, Ohlsson R and Langst G. Epigenetic regulation of TTF-I-mediated promoter-terminator interactions of rRNA genes. EMBO J, 2008 27, 1255-1265.
28. Tiwari VK*, Kurukuti S*, Tavoosidana G *, Pugacheva E, Murrell A, Zhao Z, Lobanenkov V, Reik W and Ohlsson R. (* indicates equal contribution). CTCF binding at the H19 imprinting control region mediates maternally inherited higher-order chromatin conformation to restrict enhancer access to Igf2. PNAS, 2006 103, 10684-10689.
29. Zhao Z, Tavoosidana G, Sjolinder M, Gondor A, Mariano P, Wang S, Kanduri C, Lezcano M, Singh Sandhu K, Singh U, Pant V, Tiwari VK, Kurukuti S and Ohlsson R (2006). Circular chromosome conformation capture (4C) uncovers extensive networks of epigenetically regulated intra- and interchromosomal interactions.
Nat Genet, 2006 38, 1341-1347.
30. Burke LJ*, Zhang R*, Bartkuhn M*, Tiwari VK, Tavoosidana G, KurukutiS, Weth C, Leers J, Galjart N, Ohlsson R and Renkawitz R (2005). CTCF binding and higher order structure of Igf2-H19 locus is conserved through mitosis. (* indicates equal contribution).EMBO J, 2005 24, 3291-3300.
31. Pugacheva EM, Tiwari VK, Abdullaev Z, Vostrov AA, Flanagan PT, Quitschke WW, Loukinov DI, Ohlsson R and Lobanenkov VV (2005). Familial cases of point mutations in the XIST promoter reveal a correlation between CTCF binding and pre-emptive choices of X chromosome inactivation.
Hum Mol Genet, 2005 14, 953-65.
32. Tiwari VK*, Thakur N*, Thomassin H, Pandey RR, Kanduri M, Gondor A, Grange T, Ohlsson R and Kanduri C (2004). (* indicates equal contribution). An antisense RNA regulates the bidirectional silencing property of the Kcnq1 imprinting control region. Mol Cell Biol, 2004 24, 7855-62.